1. Aug 2025
    1. julgamento
      • Informativo 1142
      • ADI 7496 MC-Ref / GO
      • Órgão julgador: Tribunal Pleno
      • Relator(a): Min. DIAS TOFFOLI
      • Julgamento: 21/06/2024 (Virtual)
      • Ramo do Direito: Processual Penal, Constitucional Matéria: Foro por prerrogativa de função; medidas cautelares; autorização prévia para investigação criminal/ Repartição de competências; direito penal e processual penal; direitos e garantias fundamentais

      Tribunal de justiça e foro por prerrogativa de função: apreciação de medidas cautelares de natureza criminal

      Resumo

      • É inconstitucional — por violar a competência privativa da União para legislar sobre direito penal e processual penal (CF/1988, art. 22, I), o sistema acusatório e o princípio da isonomia (CF/1988, art. 5º, caput e LIII) — norma de Constituição estadual que condiciona à prévia autorização judicial, mediante decisão fundamentada da maioria absoluta do órgão especial do respectivo tribunal de justiça, o pedido de medida cautelar para fins de investigação criminal ou instrução processual penal em desfavor de autoridades com foro por prerrogativa de função.

      • A norma impugnada, ao regular o foro por prerrogativa de função, não poderia dispor diversamente ou desbordar dos limites estabelecidos no modelo federal que, no caso, estão contidos no próprio Regimento Interno do STF (art. 21, XV). Conforme disposto na referida norma, que possui status de lei ordinária, a competência para supervisão judicial dos atos investigatórios de autoridades com prerrogativa de foro deve ser conferida ao relator, não havendo, portanto, necessidade de deliberação colegiada (1).

      • A razão jurídica que justifica a necessidade de supervisão judicial dos atos investigatórios de autoridades com prerrogativa de foro no STF aplica-se, por simetria, às autoridades com prerrogativa de foro nos tribunais de segundo grau de jurisdição. Ademais, conforme jurisprudência desta Corte, a competência do respectivo tribunal para a supervisão judicial nesses casos não torna obrigatória a deliberação do respectivo órgão colegiado, sendo <u>suficiente</u> decisão do ministro ou desembargador relator (2).

      • Nesse contexto, a exigência de controle judicial prévio por deliberação de órgão colegiado do tribunal de justiça local, além de conferir tratamento diferenciado aos seus detentores de foro por prerrogativa de função, destoa da lógica estabelecida por outras importantes disposições do RISTF (art. 21, IV e V, §§ 5º e 8º, e art. 230-C, § 2º).

      • Com base nesses e em outros entendimentos, o Plenário, por unanimidade, converteu o referendo da medida cautelar em julgamento definitivo de mérito e, confirmando-a, julgou a ação parcialmente procedente para (i) declarar a inconstitucionalidade da expressão “mediante decisão fundamentada tomada pela maioria absoluta do órgão especial previsto no inciso VI do art. 93 da Constituição da República”, contida na alínea “p” do inciso VIII do art. 46 da Constituição do Estado de Goiás, com redação dada pela EC estadual nº 77/2023 (3); e (ii) dar à parte remanescente do referido dispositivo interpretação conforme a Constituição, a fim de esclarecer que “o Desembargador Relator pode apreciar monocraticamente as medidas cautelares penais requeridas durante a fase de investigação ou no decorrer da instrução processual nos casos de urgência e, ainda, quando a sigilosidade se mostrar necessária para assegurar a efetivação da diligência pretendida, ressalvada a obrigatoriedade de referendo pelo órgão colegiado competente, em momento oportuno, sobretudo quando resultar em prisão cautelar, mas sempre sem comprometer ou lhe frustrar a execução”.

      (1) Regimento Interno do STF/1980: “Art.21. São atribuições do Relator: (...) XV – determinar a instauração de inquérito a pedido do Procurador-Geral da República, da autoridade policial ou do ofendido, bem como o seu arquivamento, quando o requerer o Procurador-Geral da República, ou quando verificar: (...)”

      (2) Precedentes citados: ADI 6.732, ADI 7.083 e ADI 5.331.

      (3) Constituição do Estado de Goiás: “Art. 46. Compete privativamente ao Tribunal de Justiça: (...) VIII - processar e julgar originariamente: (...) p) o pedido de medida cautelar para fins de investigação criminal ou instrução processual penal, quando o investigado ou o processado for autoridade cujos atos estejam sujeitos diretamente à sua jurisdição, mediante decisão tomada pelo voto da maioria absoluta do órgão especial previsto no inciso XI do art. 93 da Constituição da República;”

    1. será proposta
      • Informativo nº 859
      • 26 de agosto de 2025.
      • PRIMEIRA TURMA Processo: Processo em segredo de justiça, Rel. Ministro Gurgel de Faria, Primeira Turma, por maioria, julgado em 19/8/2025.

      Ramo do Direito DIREITO ADMINISTRATIVO, DIREITO PROCESSUAL CIVIL

      TemaPaz, Justiça e Instituições Eficazes <br /> Ação de Improbidade administrativa. Defensoria pública. Ilegitimidade ativa.

      Destaque - A Defensoria Pública não possui legitimidade para propor a ação de improbidade administrativa.

      Informações do Inteiro Teor - A controvérsia volta-se ao debate acerca da legitimidade ativa da Defensoria Pública para a ação de improbidade administrativa.

      • A Lei n. 11.448/2007 alterou o art. 5º da Lei n. 7.347/1985 para incluir a Defensoria Pública como legitimada ativa para a propositura da ação civil pública em sentido largo; mas, podendo, não alterou a legitimidade para a propositura de ação civil pública regida pela Lei n. 8.429/1992 (Lei de Improbidade Administrativa - LIA), cujo objeto específico é a condenação pela prática de atos ímprobos.

      • Isto é, a escolha do legislador operou-se mediante "silêncio eloquente", excluindo da Defensoria Pública a legitimidade para propor ação civil pública cujo pedido seja de aplicar as sanções previstas no art. 12 da Lei n. 8.429/1992.

      • Note-se que, embora ambas as ações civis públicas (a geral da Lei n. 7.347/1985 e a de improbidade administrativa da Lei n. 8.429/1992) tenham algum ponto de aproximação, notadamente por serem instrumentos de proteção a direito transindividual, pelo que integram, em caráter global, o microssistema da tutela coletiva, elas diferenciam-se bastante no aspecto ontológico. É que as ações de improbidade são revestidas de caráter punitivo/sancionador próprio, sem equivalente na ação civil pública geral, e, por isso, aquela é regida por regras especiais, inclusive no que concerne à legitimidade ativa.

      • Compreende-se que essa distinção entre a ação civil pública geral e a ação voltada a condenação por atos ímprobos também se extrai da opção do legislador ordinário, que resolveu concentrar exclusivamente no Ministério Público a legitimidade para propor esta última (art. 17, caput, da LIA, com a redação atual).

      • Não se desconhece que o STF, após a ADI 7042, declarou a inconstitucionalidade parcial, com interpretação conforme sem redução de texto, do caput e dos §§ 6º-A e 10-C do art. 17 da Lei n. 8.429/1992, na redação dada pela Lei n. 14.230/2021, de modo a restabelecer a existência de legitimidade ativa concorrente e disjuntiva entre o Ministério Público e as pessoas jurídicas interessadas para a propositura da ação por ato de improbidade administrativa e para a celebração de acordos de não persecução civil.

      • Contudo, no que se refere à ação de improbidade, esse julgamento somente admitiu a legitimidade ativa concorrente entre o Ministério Público e a pessoa jurídica supostamente lesada pelo ato ímprobo, sem que tenha sido estendida a ampliação da legitimidade à Defensoria Pública.

      • Destarte, a legitimidade para propor a ação civil com fundamento na Lei n. 7.347/1985 não confere, em absoluto, a mesma legitimidade para propor a ação de improbidade da Lei n. 8.429/1992, sendo, portanto, a Defensoria Pública parte ilegítima para propor a ação de improbidade administrativa.

    1. eLife Assessment

      This useful study develops an individual-based model to investigate the evolution of division of labor in vertebrates, comparing the contributions of group augmentation and kin selection. The model incorporates several biologically relevant features, including age-dependent task switching and separate manipulation of relatedness and group-size benefits. However, the evidence remains inadequate to support the authors' central claim that group augmentation is the primary driver of vertebrate division of labor. Key modelling assumptions-such as floater dominance advantages, the absence of task synergy, and the narrow parameter space explored-restrict the potential for kin selection to produce division of labor, thereby limiting the generality of the conclusions.

    2. Reviewer #1 (Public review):

      This paper presents a computational model of the evolution of two different kinds of helping ("work," presumably denoting provisioning, and defense tasks) in a model inspired by cooperatively breeding vertebrates. The helpers in this model are a mix of previous offspring of the breeder and floaters that might have joined the group, and can either transition between the tasks as they age or not. The two types of help have differential costs: "work" reduces "dominance value," (DV), a measure of competitiveness for breeding spots, which otherwise goes up linearly with age, but defense reduces survival probability. Both eventually might preclude the helper from becoming a breeder and reproducing. How much the helpers help, and which tasks (and whether they transition or not), as well as their propensity to disperse, are all evolving quantities. The authors consider three main scenarios: one where relatedness emerges from the model, but there is no benefit to living in groups, one where there is no relatedness, but living in larger groups gives a survival benefit (group augmentation, GA), and one where both effects operate. The main claim is that evolving defensive help or division of labor requires the group augmentation; it doesn't evolve through kin selection alone in the authors' simulations.

      This is an interesting model, and there is much to like about the complexity that is built in. Individual-based simulations like this can be a valuable tool to explore the complex interaction of life history and social traits. Yet, models like this also have to take care of both being very clear on their construction and exploring how some of the ancillary but potentially consequential assumptions affect the results, including robust exploration of the parameter space. I think the current manuscript falls short in these areas, and therefore, I am not yet convinced of the results.

      In this round, the authors provided some clarity, but some questions still remain, and I remain unconvinced by a main assumption that was not addressed.

      Based on the authors' response, if I understand the life history correctly, dispersers either immediately join another group (with 1-the probability of dispersing), or remain floaters until they successfully compete for a breeder spot or die? Is that correct? I honestly cannot decide because this seems implicit in the first response but the response to my second point raises the possibility of not working while floating but can work if they later join a group as a subordinate. If it is the case that floaters can have multiple opportunities to join groups as subordinates (not as breeders; I assume that this is the case for breeding competition), this should be stated, and more details about how.

      So there is still some clarification to be done, and more to the point, the clarification that happened only happened in the response. The authors should add these details to the main text. Currently, the main text only says vaguely that joining a group after dispersing " is also controlled by the same genetic dispersal predisposition" without saying how.

      In response to my query about the reasonableness of the assumption that floaters are in better condition (in the KS treatment) because they don't do any work, the authors have done some additional modeling but I fail to see how that addresses my point. The additional simulations do not touch the feature I was commenting on, and arguably make it stronger (since assuming a positive beta_r -which btw is listed as 0 in Table 1- would make floaters on average be even more stronger than subordinates). It also again confuses me with regard to the previous point, since it implies that now dispersal is also potentially a lifetime event. Is that true?

      Meanwhile, the simplest and most convincing robustness check, which I had suggested last round, is not done: simply reduce the increase in the R of the floater by age relative to subordinates. I suspect this will actually change the results. It seems fairly transparent to me that an average floater in the KS scenario will have R about 15-20% higher than the subordinates (given no defense evolves, y_h=0.1 and H_work evolves to be around 5, and the average lifespan for both floaters and subordinates are in the range of 3.7-2.5 roughly, depending on m). That could be a substantial advantage in competition for breeding spots, depending on how that scramble competition actually works. I asked about this function in the last round (how non-linear is it?) but the authors seem to have neglected to answer.

      More generally, I find that the assumption (and it is an assumption) floaters are better off than subordinates in a territory to be still questionable. There is no attempt to justify this with any data, and any data I can find points the other way (though typically they compare breeders and floaters, e.g.: https://bioone.org/journals/ardeola/volume-63/issue-1/arla.63.1.2016.rp3/The-Unknown-Life-of-Floaters--The-Hidden-Face-of/10.13157/arla.63.1.2016.rp3.full concludes "the current preliminary consensus is that floaters are 'making the best of a bad job'."). I think if the authors really want to assume that floaters have higher dominance than subordinates, they should justify it. This is driving at least one and possibly most of the key results, since it affects the reproductive value of subordinates (and therefore the costs of helping).

      Regarding division of labor, I think I was not clear so will try again. The authors assume that the group reproduction is 1+H_total/(1+H_total), where H_total is the sum of all the defense and work help, but with the proviso that if one of the totals is higher than "H_max", the average of the two totals (plus k_m, but that's set to a low value, so we can ignore it), it is replaced by that. That means, for example, if total "work" help is 10 and "defense" help is 0, total help is given by 5 (well, 5.1 but will ignore k_m). That's what I meant by "marginal benefit of help is only reduced by a half" last round, since in this scenario, adding 1 to work help would make total help go to 5.5 vs. adding 1 to defense help which would make it go to 6. That is a pretty weak form of modeling "both types of tasks are necessary to successfully produce offspring" as the newly added passage says (which I agree with), since if you were getting no defense by a lot of food, adding more food should plausibly have no effect on your production whatsoever (not just half of adding a little defense). This probably explains why often the "division of labor" condition isn't that different than the no DoL condition.

    3. Reviewer #2 (Public review):

      Summary:

      This paper formulates an individual-based model to understand the evolution of division of labor in vertebrates. The model considers a population subdivided in groups, each group has a single asexually-reproducing breeder, other group members (subordinates) can perform two types of tasks called "work" or "defense", individuals have different ages, individuals can disperse between groups, each individual has a dominance rank that increases with age, and upon death of the breeder a new breeder is chosen among group members depending on their dominance. "Workers" pay a reproduction cost by having their dominance decreased, and "defenders" pay a survival cost. Every group member receives a survival benefit with increasing group size. There are 6 genetic traits, each controlled by a single locus, that control propensities to help and disperse, and how task choice and dispersal relate to dominance. To study the effect of group augmentation without kin selection, the authors cross-foster individuals to eliminate relatedness. The paper allows for the evolution of the 6 genetic traits under some different parameter values to study the conditions under which division of labour evolves, defined as the occurrence of different subordinates performing "work" and "defense" tasks. The authors envision the model as one of vertebrate division of labor.

      The main conclusion of the paper is that group augmentation is the primary factor causing the evolution of vertebrate division of labor, rather than kin selection. This conclusion is drawn because, for the parameter values considered, when the benefit of group augmentation is set to zero, no division of labor evolves and all subordinates perform "work" tasks but no "defense" tasks.

      Strengths:

      The model incorporates various biologically realistic details, including the possibility to evolve age polytheism where individuals switch from "work" to "defence" tasks as they age or vice versa, as well as the possibility of comparing the action of group augmentation alone with that of kin selection alone.

      Weaknesses:

      The model and its analysis is limited, which makes the results insufficient to reach the main conclusion that group augmentation and not kin selection is the primary cause of the evolution of vertebrate division of labor. There are several reasons.

      First, the model strongly restricts the possibility that kin selection is relevant. The two tasks considered essentially differ only by whether they are costly for reproduction or survival. "Work" tasks are those costly for reproduction and "defense" tasks are those costly for survival. The two tasks provide the same benefits for reproduction (eqs. 4, 5) and survival (through group augmentation, eq. 3.1). So, whether one, the other, or both tasks evolve presumably only depends on which task is less costly, not really on which benefits it provides. As the two tasks give the same benefits, there is no possibility that the two tasks act synergistically, where performing one task increases a benefit (e.g., increasing someone's survival) that is going to be compounded by someone else performing the other task (e.g., increasing that someone's reproduction). So, there is very little scope for kin selection to cause the evolution of labour in this model. Note synergy between tasks is not something unusual in division of labour models, but is in fact a basic element in them, so excluding it from the start in the model and then making general claims about division of labour is unwarranted. I made this same point in my first review, although phrased differently, but it was left unaddressed.

      Second, the parameter space is very little explored. This is generally an issue when trying to make general claims from an individual-based model where only a very narrow parameter region has been explored of a necessarily particular model. However, in this paper, the issue is more evident. As in this model the two tasks ultimately only differ by their costs, the parameter values specifying their costs should be varied to determine their effects. Instead, the model sets a very low survival cost for work (yh=0.1) and a very high survival cost for defense (xh=3), the latter of which can be compensated by the benefit of group augmentation (xn=3). Some very limited variation of xh and xn is explored, always for very high values, effectively making defense unevolvable except if there is group augmentation. Hence, as I stated in my previous review, a more extensive parameter exploration addressing this should be included, but this has not been done. Consequently, the main conclusion that "division of labor" needs group augmentation is essentially enforced by the limited parameter exploration, in addition to the first reason above.

      Third, what is called "division of labor" here is an overinterpretation. When the two tasks evolve, what exists in the model is some individuals that do reproduction-costly tasks (so-called "work") and survival-costly tasks (so-called "defense"). However, there are really no two tasks that are being completed, in the sense that completing both tasks (e.g., work and defense) is not necessary to achieve a goal (e.g., reproduction). In this model there is only one task (reproduction, equation 4,5) to which both "tasks" contribute equally and so one task doesn't need to be completed if the other task compensates for it. So, this model does not actually consider division of labor.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      This paper presents a computational model of the evolution of two different kinds of helping ("work," presumably denoting provisioning, and defense tasks) in a model inspired by cooperatively breeding vertebrates. The helpers in this model are a mix of previous offspring of the breeder and floaters that might have joined the group, and can either transition between the tasks as they age or not. The two types of help have differential costs: "work" reduces "dominance value," (DV), a measure of competitiveness for breeding spots, which otherwise goes up linearly with age, but defense reduces survival probability. Both eventually might preclude the helper from becoming a breeder and reproducing. How much the helpers help, and which tasks (and whether they transition or not), as well as their propensity to disperse, are all evolving quantities. The authors consider three main scenarios: one where relatedness emerges from the model, but there is no benefit to living in groups, one where there is no relatedness, but living in larger groups gives a survival benefit (group augmentation, GA), and one where both effects operate. The main claim is that evolving defensive help or division of labor requires the group augmentation; it doesn't evolve through kin selection alone in the authors' simulations.

      This is an interesting model, and there is much to like about the complexity that is built in. Individual-based simulations like this can be a valuable tool to explore the complex interaction of life history and social traits. Yet, models like this also have to take care of both being very clear on their construction and exploring how some of the ancillary but potentially consequential assumptions affect the results, including robust exploration of the parameter space. I think the current manuscript falls short in these areas, and therefore, I am not yet convinced of the results. Much of this is a matter of clearer and more complete writing: the Materials and Methods section in particular is incomplete or vague in some important junctions. However, there are also some issues with the assumptions that are described clearly.

      Below, I describe my main issues, mostly having to do with model features that are unclear, poorly motivated (as they stand), or potentially unrealistic or underexplored.

      We would like to thank the reviewer for the thoughtful comments that helped us to greatly improve the clarity of our paper.  

      One of the main issues I have is that there is almost no information on what happens to dispersers in the model. Line 369-67 states dispersers might join another group or remain as floaters, but gives no further information on how this is determined. Poring through the notation table also comes up empty as there is no apparent parameter affecting this consequential life history event. At some point, I convinced myself that dispersers remain floaters until they die or become breeders, but several points in the text contradict this directly (e.g., l 107). Clearly this is a hugely important model feature since it determines fitness cost and benefits of dispersal and group size (which also affects relatedness and/or fitness depending on the model). There just isn't enough information to understand this crucial component of the model, and without it, it is hard to make sense of the model output.

      We use the same dispersal gene β to represent the likelihood an individual will either leave or join a group, thereby quantifying both dispersal and immigration using the same parameter. Specifically, individuals with higher β are more likely to remain as floaters (i.e., disperse from their natal group to become a breeder elsewhere), whereas those with lower β are either more likely to remain in their natal group as subordinates (i.e., queue in a group for the breeding position) or join another group if they dispersed.  

      We added in the text “Dispersers may migrate to another group to become subordinates or remain as floaters waiting for breeding opportunities, which is also controlled by the same genetic dispersal propensity as subordinates” to clarify this issue. We also added in Table 1 that β is the “genetic predisposition to disperse versus remain in a group”, and to Figure 1 that “subordinates in the group (natal and immigrants) […]” after we already clarified that “Dispersers/floaters may join a random group to become subordinates.”

      Related to that, it seems to be implied (but never stated explicitly) that floaters do not work, and therefore their DV increases linearly with age (H_work in eq.2 is zero). That means any floaters that manage to stick around long enough would have higher success in competition for breeding spots relative to existing group members. How realistic is this? I think this might be driving the kin selection-only results that defense doesn't evolve without group augmentation (one of the two main ways). Any subordinates (which are mainly zero in the no GA, according to the SI tables; this assumes N=breeder+subordinates, but this isn't explicit anywhere) would be outcompeted by floaters after a short time (since they evolve high H and floaters don't), which in turn increases the benefit of dispersal, explaining why it is so high. Is this parameter regime reasonable? My understanding is that floaters often aren't usually high resource holding potential individuals (either b/c high RHP ones would get selected out of the floater population by establishing territories or b/c floating isn't typically a thriving strategy, given that many resources are tied to territories). In this case, the assumption seems to bias things towards the floaters and against subordinates to inherit territories. This should be explored either with a higher mortality rate for floaters and/or a lower DV increase, or both.

      When it comes to floaters replacing dead breeders, the authors say a bit more, but again, the actual equation for the scramble competition (which only appears as "scramble context" in the notation table) is not given. Is it simply proportional to R_i/\sum_j R_j ? Or is there some other function used? What are the actual numbers of floaters per breeding territory that emerge under different parameter values? These are all very important quantities that have to be described clearly.

      Although it is true that dispersers do not work when they are floaters, they may later help if they immigrate into a group as a subordinate. Consequently, immigrant subordinates have no inherent competitive advantage over natal subordinates (as step 2.2. “Join a group” is followed by step 3. “Help”, which occurs before step 5. “Become a breeder”). Nevertheless, floaters can potentially outcompete subordinates of the same age if they attempt to breed without first queuing as a subordinate (step 5) when subordinates are engaged in work tasks. We believe that this assumption is realistic and constitutes part of the costs associated with work tasks. However, floaters are at a disadvantage for becoming a breeder because: (1) floaters incur higher mortality than individuals within groups (Eq. 3); and (2) floaters may only attempt to become breeders in some breeding cycles (versus subordinate groups members, who are automatically candidates for an open breeding position in the group in each cycle). Therefore, due to their higher mortality, floaters are rarely older than individuals within groups, which heavily influences their dominance value and competitiveness. Additionally, any competitive advantage that floaters might have over other subordinate group members is unlikely to drive the kin selection-only results because subordinates would preferably choose defense tasks instead of work tasks so as not to be at a competitive disadvantage compared to floaters.  

      Regarding whether floaters aren't usually high resource holding potential (RHP) individuals and, therefore, our assumptions might be unrealistic; empirical work in a number of species has shown that dispersers are not necessarily those of lower RHP or of lower quality. In fact, according to the ecological constraints hypothesis, one might predict that high quality individuals are the ones that disperse because only individuals in good condition (e.g., larger body size, better energy reserves) can afford the costs associated with dispersal (Cote et al., 2022). To allow differences in dispersal propensity depending on RHP, we extended our model in the Supplemental Materials by incorporating a reaction norm of dispersal based on their rank (D = 1 / (1 + exp (β<sub>R</sub> * Rβ<sub>0</sub>)) under the section “Dominance-dependent dispersal propensities” and now referenced in L195. This approach allows individuals to adjust their dispersal strategy to their competitiveness and to avoid kin competition by remaining as a subordinate in another group. Results show that the addition of the reaction norm of dispersal to rank did not qualitatively influence the results described in the main text.  

      We also added “number of floaters” present in the whole population to the summary tables as requested.  

      As a side note, the “scramble context” we mention was an additional implementation in which we made rank independent of age. However, since the main conclusions remained unchanged, we decided to remove it for simplicity from the final manuscript, but we forgot to remove it from Table 1 before submission.  

      I also think the asexual reproduction with small mutations assumption is a fairly strong one that also seems to bias the model outcomes in a particular way. I appreciate that the authors actually measured relatedness within groups (though if most groups under KS have no subordinates, that relatedness becomes a bit moot), and also eliminated it with their ingenious swapping-out-subordinates procedure. The fact remains that unless they eliminate relatedness completely, average relatedness, by design, will be very high. (Again, this is also affected by how the fate of the dispersers is determined, but clearly there isn't a lot of joining happening, just judging from mean group sizes under KS only.) This is, of course, why there is so much helping evolving (even if it's not defensive) unless they completely cut out relatedness.

      As we showed in the Supplementary Tables and the section on relatedness in the SI (“Kin selection and the evolution of division of labor"), high relatedness does not appear to explain our results. In evolutionary biology generally and in game theory specifically (with the exception of models on sexual selection or sex-specific traits), asexual reproduction is often modelled because it reduces unnecessary complexity. To further study the effect of relatedness on kin structures more closely resembling those of vertebrates, however, we created an additional “relatedness structure level”, where we shuffled half of the philopatric offspring using the same method used to remove relatedness completely, effectively reducing withingroup relatedness structure by half. As shown in the new Figure S3, the conclusions of the model remain unchanged.  

      Finally, the "need for division of labor" section is also unclear, and its construction also would seem to bias things against division of labor evolving. For starters, I don't understand the rationale for the convoluted way the authors create an incentive for division of labor. Why not implement something much simpler, like a law of minimum (i.e., the total effect of helping is whatever the help amount for the lowest value task is) or more intuitively: the fecundity is simply a function of "work" help (draw Poisson number of offspring) and survival of offspring (draw binomial from the fecundity) is a function of the "defense" help. As it is, even though the authors say they require division of labor, in fact, they only make a single type of help marginally less beneficial (basically by half) if it is done more than the other. That's a fairly weak selection for division of labor, and to me it seems hard to justify. I suspect either of the alternative assumptions above would actually impose enough selection to make division of labor evolve even without group augmentation.

      In nature, multiple tasks are often necessary to successfully rear offspring. We simplify this principle in the model by maximizing reproductive output when both tasks are carried out to a similar extent, allowing for some flexibility from the mean. We added to the manuscript “For example, in many cooperatively breeding birds, the primary reasons that individuals fail to produce offspring are (1) starvation, which is mitigated by the feeding of offspring, and (2) nest depredation, which is countered by defensive behavior. Consequently, both types of tasks are necessary to successfully produce offspring, and focusing solely on one while neglecting the other is likely to result in lower reproductive success than if both tasks are performed by individuals within the group.”

      Regarding making fecundity a function of work tasks and offspring survival as a function of defensive tasks, these are actually equivalent in model terms, as it’s the same whether breeders produce three offspring and two die, or if they only produce one. This represents, of course, an oversimplification of the natural context, where breeding unsuccessfully is more costly (in terms of time and energy investment) than not breeding at all.

      Overall, this is an interesting model, but the simulation is not adequately described or explored to have confidence in the main conclusions yet. Better exposition and more exploration of alternative assumptions and parameter space are needed.

      We hope that our clarifications and extension of the model satisfy your concerns.  

      Reviewer #2 (Public review):

      Summary:

      This paper formulates an individual-based model to understand the evolution of division of labor in vertebrates. A main conclusion of the paper is that direct fitness benefits are the primary factor causing the evolution of vertebrate division of labor, rather than indirect fitness benefits.

      Strengths:

      The paper formulates an individual-based model that is inspired by vertebrate life history. The model incorporates numerous biologically realistic details, including the possibility to evolve age polytheism where individuals switch from work to defence tasks as they age or vice versa, as well as the possibility of comparing the action of group augmentation alone with that of kin selection alone.

      Weaknesses:

      The model makes assumptions that restrict the possibility that kin selection leads to the evolution of helping. In particular, the model assumes that in the absence of group augmentation, subordinates can only help breeders but cannot help non-breeders or increase the survival of breeders, whereas with group augmentation, subordinates can help both breeders and non-breeders and increase the survival of breeders. This is unrealistic as subordinates in real organisms can help other subordinates and increase the survival of non-breeders, even in the absence of group augmentation, for instance, with targeted helping to dominants or allies. This restriction artificially limits the ability of kin selection alone to lead to the evolution of helping, and potentially to division of labor. Hence, the conclusion that group augmentation is the primary driving factor driving vertebrate division of labor appears forced by the imposed restrictions on kin selection. The model used is also quite particular, and so the claimed generality across vertebrates is not warranted.

      We would like to thank the reviewer for the in-depth review. We respond to these and other comments below.  

      I describe some suggestions for improving the paper below, more or less in the paper's order.

      First, the introduction goes to great lengths trying to convince the reader that this model is the first in this or another way, particularly in being only for vertebrates, as illustrated in the abstract where it is stated that "we lack a theoretical framework to explore the conditions under which division of labor is likely to evolve" (line 13). However, this is a risky and unnecessary motivation. There are many models of division of labor and some of them are likely to be abstract enough to apply to vertebrates even if they are not tailored to vertebrates, so the claims for being first are not only likely to be wrong but will put many readers in an antagonistic position right from the start, which will make it harder to communicate the results. Instead of claiming to be the first or that there is a lack of theoretical frameworks for vertebrate division of labor, I think it is enough and sufficiently interesting to say that the paper formulates an individual-based model motivated by the life history of vertebrates to understand the evolution of vertebrate division of labor. You could then describe the life history properties that the model incorporates (subordinates can become reproductive, low relatedness, age polyethism, etc.) without saying this has never been done or that it is exclusive to vertebrates; indeed, the paper states that these features do not occur in eusocial insects, which is surprising as some "primitively" eusocial insects show them. So, in short, I think the introduction should be extensively revised to avoid claims of being the first and to make it focused on the question being addressed and how it is addressed. I think this could be done in 2-3 paragraphs without the rather extensive review of the literature in the current introduction.

      We have revised the novelty statements in the Introduction by more clearly emphasizing how our model addresses gaps in the existing literature. More details are provided in the comments below.

      Second, the description of the model and results should be clarified substantially. I will give specific suggestions later, but for now, I will just say that it is unclear what the figures show. First, it is unclear what the axes in Figure 2 show, particularly for the vertical one. According to the text in the figure axis, it presumably refers to T, but T is a function of age t, so it is unclear what is being plotted. The legend explaining the triangle and circle symbols is unintelligible (lines 227-230), so again it is unclear what is being plotted; part of the reason for this unintelligibility is that the procedure that presumably underlies it (section starting on line 493) is poorly explained and not understandable (I detail why below). Second, the axes in Figure 3 are similarly unclear. The text in the vertical axis in panel A suggests this is T, however, T is a function of t and gamma_t, so something else must be being done to plot this. Similarly, in panel B, the horizontal axis is presumably R, but R is a function of t and of the helping genotype, so again some explanation is lacking. In all figures, the symbol of what is being plotted should be included.

      We added the symbols of the variables to the Figure axes to increase clarity. In Figure 3A, we corrected the subindex t in the x-axis; it should be subindex R (reaction norm to dominance rank instead of age). As described in Table 1, all values of T, H and R are phenotypically expressed values. For instance, T values are the phenotypically expressed values from the individuals in the population according to their genetic gamma values and their current dominance rank at a given time point.  

      Third, the conclusions sound stronger than the results are. A main conclusion of the paper is that "kin selection alone is unlikely to select for the evolution of defensive tasks and division of labor in vertebrates" (lines 194-195). This conclusion is drawn from the left column in Figure 2, where only kin selection is at play, and the helping that evolves only involves work rather than defense tasks. This conclusion follows because the model assumes that without group augmentation (i.e., xn=0, the kin selection scenario), subordinates can only help breeders to reproduce but cannot help breeders or other subordinates to survive, so the only form of help that evolves is the least costly, not the most beneficial as there is no difference in the benefits given among forms of helping. This assumption is unrealistic, particularly for vertebrates where subordinates can help other group members survive even in the absence of group augmentation (e.g., with targeted help to certain group members, because of dominance hierarchies where the helping would go to the breeder, or because of alliances where the helping would go to other subordinates). I go into further details below, but in short, the model forces a narrow scope for the kin selection scenario, and then the paper concludes that kin selection alone is unlikely to be of relevance for the evolution of vertebrate division of labor. This conclusion is particular to the model used, and it is misleading to suggest that this is a general feature of such a particular model.

      The scope of this paper was to study division of labor in cooperatively breeding species with fertile workers (i.e., primarily vertebrates), in which help is exclusively directed towards breeders to enhance offspring production (i.e., alloparental care). Our focus is in line with previous work in most other social animals, including eusocial insects and humans, which emphasizes how division of labor maximizes group productivity. Other forms of “general” help are not considered in the paper, and such forms of help are rarely considered in cooperatively breeding vertebrates or in the division of labor literature, as they do not result in task partitioning to enhance productivity.

      Overall, I think the paper should be revised extensively to clarify its aims, model, results, and scope of its conclusions.

      Recommendations for the authors: 

      Reviewer #1 (Recommendations for the authors):

      I reserved this section for more minor comments, relating to clarity and a general admonition to give us more detail and exploration of some basic population genetic quantities.

      Another minor point, although depending on whether I assume right or wrong, it could be major: I am not entirely sure that dispersers help in the groups they join as helpers, because of line 399, which states specifically that individuals who do remain in natal territories do. But I assume dispersers help (elsewhere, the authors state helping is not conditional on relatedness to the breeder). Otherwise, this model becomes even weirder for me. Either way, please clarify.

      Apologies if this was not clear. Immigrants that join a group (so dispersers from another group) as a subordinate help and queue for a breeding position, as does any natal subordinate born into the group. We rephased the sentence to “Subordinate group members, either natal or immigrants to the group, […]”  

      More generally, in simulation studies like this, there can be interactions between the strength of selection (which affects overall genetic variation maintained in the population), population size, and mutation rate/size, which can affect, for example, relatedness values. None of these quantities is explored here (and their interactions are not quantified), so it is not possible to evaluate the robustness of any of these results.

      Thank you for your comments about the parameter landscape. It is important to point out that variations in the mutation rate do not qualitatively affect our results, as this is something we explored in previous versions of the model (not shown). Briefly, we find that variations in the mutation rates only alter the time required to reach equilibrium. Increasing the step size of mutation diminishes the strength of selection by adding stochasticity and reducing the genetic correlation between offspring and their parents. Population size could, in theory, affect our results, as small populations are more prone to extinction. Since this was not something we planned to explore in the paper directly, we specifically chose a large population size, or better said, a large number of territories (i.e. 5000) that can potentially host a large population.  

      The authors also never say how it is actually determined. There is the evolved helping variable, and there is also the evolved reaction norm. I assume that the actual amount of help of each type is given by the product of T (equation 1) and H (for defense) and (1-T) and H (for work), but this should be stated explicitly.  

      Help provided is an interaction between H (total effort) and T (proportion of total effort invested in each type of task). To clarify the distinction between these two processes, we have now added “Hence, the gene α regulates the amount of help expressed, while the genes γ determine which specific helping tasks are performed at different time points in the breeding cycle”.  

      It is also weird that after introducing the T variable as a function of age, Figure 3 actually depicts it as a function of dominance value.

      Thank you for pointing out an error in Eq. 1. This inequality was indeed written incorrectly in the paper (but is correct in the model code); it is dominance rank instead of age (see code in Individual.cpp lines 99-119). We corrected this mistake throughout the manuscript.

      What is "scramble context"?

      “Scramble context” was an additional implementation that we decided to remove from the final manuscript, but we forgot to remove from Table 1 before submission. We have now removed it from the table.

      Reviewer #2 (Recommendations for the authors):

      Some specific comments:

      (1) L 31: "All theoretical..." These absolute statements are risky and unnecessary.

      Rephrased to “To date, most theoretical and empirical work…”

      (2) L 46: I believe Tom Wenseleers has published on the evolution of division of labor with reproductive workers and high within-colony conflict.

      Tom Wenseleers has indeed produced some models on the evolution of cooperation in social insects where some workers may reproduce. However, these models focus on the relevance of relatedness and policing selecting for a reduction in within-group conflict and the evolution of reproductive division of labor. Our model focuses instead on division of labor among workers (helpers). We have rephased this section to “task specialization is linked to sterility and where conflict of interest is generally low” to account for species of social insect in which variation in relatedness between group members and higher levels of reproductive conflict may arise. We also cited one of his papers.  

      (3) L 57: Again, unnecessary categorical statements.

      Rephrased to “Although a great deal of recent empirical work highlights the importance of direct benefits in the evolution of cooperative breeding behavior in vertebrates [21–24], we lack understanding on the joint influence of direct and indirect fitness benefits in the evolution of division of labor.”

      (4) L 67: This is said to be a key distinction, but in the paper, such a key role is not clearly shown. This and other tangential points are unnecessary to keep the introduction to the point.

      The different fitness costs of different tasks is the basis of our model on division of labor. Therefore, this is a key distinction and basis from which to describe different tasks in the model. We have left this sentence unchanged.

      (5) L 61-73: "In vertebrates, however, helpers may obtain fitness benefits directly via reproduction..." Some social insects may do so as well. It seems unnecessary and incorrect to say that vertebrate sociality is fundamentally different from invertebrate one. I think it is sufficiently interesting to say this work aims to understand vertebrate division of labor, by explicitly modeling aspects of its life history, without saying this can't happen in invertebrates or that no other model has ever done anything like it.

      Our point is not that, in some social insects, workers cannot obtain direct fitness benefits, but that previous models where the focus is on the colony reproductive outcome are only a good approximation to eusocial insect with sterile workers. However, to make this clearer we have added “In vertebrates and social insect with fertile workers, however, helpers may obtain fitness benefits directly via […]”.  

      (6) L 74-86: By this point, the introduction reads like a series of disconnected comments without a clear point.

      In L60 we added: “Understanding how direct and indirect benefits interact is particularly important in systems where individuals may differentially bear the fitness costs of cooperation”. By adding this sentence, we emphasize our focus on the largely unexplored direct fitness benefits and costs, as well as their interaction with indirect fitness. We then proceed to explain why it is crucial to consider that tasks have varying direct fitness costs and how the fitness benefits derived from cooperation change with age and resource-holding potential. These elements are essential for studying the division of labour in species with totipotent workers.

      (7) L 87: This sentence gives a clear aim. It would be clearer if the introduction focused on this aim.

      With the new sentence added in L60 (see previous comment), we bring the focus to the main question that we are trying to address in this paper earlier in the Introduction.  

      (8) L 88: "stochastic model" should be changed to "individual-based model".

      Done.

      (9) L 104: "limited number" is unclear. Say a fixed finite number, or something specific.

      Done.

      (10) L 105: "unspecified number" is unclear. Say the number of subordinates emerges from the population dynamics.

      Changed to “variable number of subordinate helpers, the number of which is shaped by population dynamics, with all group members capable of reproducing during their lifetime”.

      (11) L 112: "Dispersers" is used, but in the previous lines 107-109, the three categories introduced used different terms. Those three terms introduced should be used consistently throughout the paper, without using two or more terms for one thing.

      We use the term “disperser” to describe individuals that disperse from their natal group.

      Dispersers can assume one of three roles: (1) they can join another group as "subordinates"; (2) they can join another group as "breeders" if they successfully outcompete others; or (3) they can remain as "floaters" if they fail to join a group. "Floaters" are individuals who persist in a transient state without access to a breeding territory, waiting for opportunities to join a group in an established territory. We rephased the sentence to “Dispersers cannot reproduce without acquiring a territory (denoted here as floaters)”. This was also clarified in other instances where the term “dispersers” was used (e.g. L407). Other instances where this might not have been so clear, we replace “dispersers” with “floaters”.  

      (12) L 112: "(floaters)" Unclear parenthesis.

      See previous comment.  

      (13) L 115: There should be a reference to Methods around here.

      Added a reference to Figure 1.

      (14) L 117: To be clearer, say instead that dominance value is a linearly increasing function of age as a proxy of RHP and a linearly decreasing function of help provided due to the costs of working tasks. And refer to equation 2.

      Rephrased to “We use the term dominance value to designate the competitiveness of an individual compared to other candidates in becoming a breeder, regardless of group membership, that increases as a function of age, serving as a proxy for resource holding potential (RHP), and decreases as a function of help provided, reflecting costs to body condition from performing working tasks (Eq. 2).” We did not include “linearly” to keep it simpler, since it is clear from Eq. 2, which is now referenced here.  

      (15) L 119: "Subordinate helpers". As all subordinates are helpers, the helper qualifier is confusing.

      Subordinates are not necessarily helpers, as they can evolve help values of 0, hence, why we make it explicit here.

      (16) L 119: "choose". This terminology may be misleading. The way things are implemented in the model is that individuals are assigned a task depending on their genetic traits gamma. Perhaps it would be better to use a less intentional term, like perform one of two tasks.

      We changed “choose between two” to “engage in one of two”, which has less connotations of intentionality.

      (17) L 124: "Subordinates can [...] exhibit task specialization that [...] varies with their dominance value". It should be that it varies with age.

      Apologies. The equation was wrong; it does vary with dominance value. We corrected it accordingly.

      (18) L 133: "maximised" This is apparently important for the modelling procedure, but it is completely unclear what it means. Equation 4 comes out of nowhere, and it is said that such an equation is the maximum amount of help that can affect fecundity. Why? What does this mean? If there is something that is maximised, this should be proven. This value is then used for something (line 507), but it is unclear why or what it is used for (it says "we use the value of Hmax instead" without saying what for, no justification for the listed inequalities are given, and the claimed maximisation of an unspecified variable at those H values is not proven). Moreover, the notation in this section is also unclear: what are the sums over? Also, Hdefence and Hwork should vary over the index that is summed over, but the notation suggests that those quantities don't vary.

      We changed “maximized” to “greatest”, and we added a clarification to the rationality behind the maximization of the impact of help in the breeder’s productivity: “For example, in many cooperatively breeding birds, the primary reasons that breeders fail to produce offspring are (1) starvation, which is mitigated by the feeding of offspring, here considered as a work task, and (2) nest depredation, which is countered by defensive behavior. Consequently, both types of tasks are often necessary for successful reproduction, and focusing solely on one while neglecting the other is likely to result in lower reproductive success than if both tasks are performed by helpers within the group.”

      We now also clarify that the sums are for help given within a group (L 507), and added indexes to the equations.

      (19) L 152: "habitat saturation" How is this implemented? How is density dependence implemented? Or can the population size keep increasing indefinitely? It would be good to plot the population size over time, the group size over time, and the variance in group size over time. This could substantiate later statements about enhancing group productivity and could all be shown in the SI.

      Habitat saturation emerges from population dynamics due to the limited availability of territories and the fluctuating number of individuals, leading highly productive environments to experience habitat saturation. Although the number of group members is not restricted in our model, the population could theoretically increase indefinitely. However, this is not observed in the results presented here, as we selected parameter landscapes that stabilize population numbers. We confined our parameters to those where the population neither increased indefinitely (nor collapsed), as we did not incorporate density-dependent mortality traits for simplification. Consequently, the group size in the SI, where the standard deviation is already included, closely represents group size at any other given time during equilibrium.

      L 336: we changed “environments with habitat saturation” to “environments that lead to habitat saturation”, to increase clarity.

      (20) L 152: "lifecycle". Rather than the lifecycle, the figure describes the cycle of events in a single time step. The lifecycle (birth to death) goes over multiple time steps (as individuals live over multiple steps). So this figure shouldn't be called a life cycle.

      We changed “lifecycle” to “breeding cycle”.

      (21) L 156: "generation". This is not a generation but a time step.

      We changed “generation” to “breeding cycle”.

      (22) L 157: "previous life cycle" would mean that the productivity of a breeder depends on the number of helpers that its parents had, which is not what is meant.

      We changed “lifecycle” to “breeding cycle”.

      (23) L 158: "Maximum productivity is achieved when different helping tasks are performed to a similar extent." Again, unclear why that is the case.

      We added a clarification on this, see response to comment 18.  

      (24) L 160: "Dispersers/floaters". Use just one term for a single thing.

      See response to comment 11.   

      (25) L 162: "dispersal costs". I don't recall these being described in Methods.

      Individuals that disperse do not enjoy the protection of living in a territory and within a group of other individuals, so they have a higher mortality risk, described in Eq. 3.3. (negative values in the exponential part of the equation increase survival). The cost of dispersal is the same as individuals that remain as floaters at a given time step.

      (26) L 164: "generation" -> time step.

      We changed this to “breeding cycle”.  

      (27) L 170: "Our results show that division of labor initially emerges because of direct fitness benefits..." This is a general statement, but the results are only particular to the model. So this statement and others in the manuscript should be particular to the model. Also, Figure 2 doesn't say anything about what evolves "initially" as it only plots evolutionary equilibria.

      We rephrased this statement to “Our results suggest that voluntary division of labor involving tasks with different fitness costs is more likely to emerge initially because of direct fitness benefits”, to more accurately represent the conditions under which we modeled the division of labor.  

      Our reference to “initially” is regarding group formation (family groups versus aggregations of unrelated individuals or a mix). This is shown in the comparison between the different graphs at equilibrium. The initial state of the simulation is that all individuals disperse and do not cooperate.  

      (28) L 171: "but a combination of direct and indirect fitness benefits leads to higher rates and more stable forms of division of labor". What do you mean by "higher rates and more stable forms of division of labor"? Say how division of labor is shown in the figure (with intermediate T?).

      Yes, intermediate values of T show division of labor if γR ≠ 0. This is described under the section “The role of dominance in task specialization”. We added “with intermediate values suggesting a division of labor” to the Figure 2 legend.  

      (29) L173-175: "as depicted in Figure 2, intermediate values of task specialization indicate in all cases age/dominance-mediated task specialization (γt ≠ 0; Table 1) and never a lack of specialization (γt = 0; Table 1)". This sentence is unclear and imprecise. Does this sentence want to say that in Figure 2, all plots with intermediate values of T involve gamma t different from zero? If so, just say that.

      Rephrased to: “In Figure 2, all plots depicting intermediate values of T exhibit non-zero γR values and, hence, division of labor”.

      (30) L179-180: "forms of help that impact survival never evolve under any environmental condition when only kin selection occurs". This is misleading because under the KS scenario, help cannot positively impact survival in this model, so they never evolve.

      Help cannot affect survival but could potentially affect group persistence. If helpers increase breeder productivity and offspring remain philopatric and queue for the breeding position, then they will receive help from related individuals.   

      (31) L 210: "initially". What do you mean by that?

      Help only evolves in our model in family groups, which may then open the door for the evolution of help in mixed-kin groups. Therefore, we use “initially” to refer to the ancestral group structure that likely led to cooperation under benign environmental conditions. We rephased this section to “in more benign (and often highly productive) environments that lead to habitat saturation, help likely evolved initially in family groups, and defensive tasks are favored because competition for the breeding position is lower under kin selection.”

      (32) L 212: "kin selection is achieved". What does that mean?

      Rephased to “kin selection acts not only by selecting subordinates in their natal group to increase the productivity of a related breeder […]”

      (33) L 216: "division of labor seems to be more likely to evolve in increasingly harsh environments". Say in parentheses where this is shown.

      Added.  

      (34) L 218: "help evolves in benign environments". I don't see where this is shown. Figure 2 doesn't show that H is higher with lower m (e.g., in KS+GA column).

      Help does not evolve in benign environments under only direct fitness benefits derived from group augmentation (shown in Figure 2).  

      (35) L 225: "y-axis" should be "vertical axis", as y has another meaning in the model.

      Done.

      (36) L 226: "likelihood". Here and throughout, "likelihood" should be changed to probability. Likelihood means something else.

      Thank you for the advice, we have corrected this through the manuscript.  

      (37) L 236: "the slope of the reaction norm for the dominance value in task specialization".

      Unclear. Clearer to say: the rate at which individuals to shift from defense to work as they age.

      The important part is not so much the rate but the direction, that is, from work task to defense (or vice versa) as their rank increases. Changed to “the direction and rate of change in task specialization with dominance”.

      (38) L 257: "(task = 0; cost to dominance value)," This seems out of place.

      This aims to clarify that work tasks have a cost to dominance, while defense tasks have a cost to survival. This is particularly relevant in this model since different helping tasks are defined by their fitness costs.

      (39) L 258: "increase"-> "increase with age".

      Added “with dominance”.

      (40) L 262: "division of labor equilibria" What is that?

      Changed to “at equilibrium when division of labor evolves”

      (41) L 268: "Our findings suggest that direct benefits of group living play a driving role in the evolution of division of labor via task specialization in species with totipotent workers". This is a very general statement, but the results are much more circumscribed. First, the model is quite specific by assuming that, in the absence of group augmentation (xn=0), indirect fitness benefits can only be given to breeders (Equation 5) but not to other subordinates (Equations 2, 3.1). This is unrealistic, particularly for vertebrates, and reduces the possibility that indirect fitness benefits play a role.  

      As previously discussed, the scope of this paper was to study division of labor in cooperatively breeding species with fertile workers in which help is exclusively directed towards breeders to enhance offspring production through alloparental care. Other forms of “general” help do not result in task partitioning to enhance productivity.

      Second, the difference in costs of work and defense are what drive the evolution of "division of labor" (understood as intermediate T in case this is what the authors mean) in the KS scenario, but the functional forms of those two costs are quite specific and not of the same form, so these functions may bias the results found. Specifically, R is an unbounded linear function of work and the effect of this function becomes weaker as the individual ages due to the weakening force of selection with age (Equation 2) whereas Sh is a particular bounded nonlinear function of defense (Equation 3.1). These differences may tend to make the effect of Sh stronger due to the particular functions chosen.  

      The difference in costs is inherent to the nature of the different tasks (work versus defense): while survival is naturally bounded, with death as the lower bound, dominance costs are potentially unbounded, as they are influenced by dynamic social contexts and potential competitors. Therefore, we believe that the model’s cost structure is not too different from that in nature.  

      Third, no parameter sweep is given to see to what extent these results hold across the many parameters involved. So, in summary, the discussion should at least reflect that the results are of a restricted nature rather than giving the impression that they are of the suggested level of generality.

      During the exploratory phase of the model development, various parameters and values were assessed. However, the manuscript only details the ranges of values and parameters where changes in the behaviors of interest were observed, enhancing clarity and conciseness. For instance, variation in yh (the cost of help on dominance when performing “work tasks”) led to behavioral changes similar to those caused by changes in xh (the cost of help in survival when performing “defensive tasks”), as both are proportional to each other. Specifically, since an increase in defense costs raises the proportion of work relative to defense tasks, while an increase in the costs of work task has the opposite effect, only results for the variation of xh were included in the manuscript to avoid redundancy. Added to Table 1: “To maintain conciseness, further exploration of the parameter landscape was not included in the manuscript”.

      (42) L 270: "in eusocial insects often characterized by high relatedness and reproductive inhibition, sterile workers acquire fitness benefits only indirectly". This is misleading. Sterile workers of any taxa, be it insects or vertebrates, can only acquire fitness benefits indirectly as they are sterile, but eusocial insects involve not only sterile workers.

      Rephased to “In contrast, in eusocial species characterized by high relatedness and permanent worker sterility, such as most eusocial insects, workers acquire fitness benefits only indirectly”. In any case, permanent sterility only occurs in eusocial invertebrates; in vertebrates with reproductive inhibition sterility is only temporal and context dependent. Therefore, in vertebrates, sterile workers may potentially obtain direct fitness benefits if the social context changes, as is the case in naked mole-rats.  

      (43) L 273: "Group members in eusocial species are therefore predicted to maximize colony fitness due to the associated lower within-group conflict". Again, this is incorrect. Primitively eusocial insects have high conflict.

      We added “Group members in such eusocial species” to clarify that we are not referring here to primitively eusocial species but those with permanent sterile workers.  

      (44) L 277: "when the benefits of cooperation are evenly distributed among group members". In this model, the benefits of cooperation are not evenly distributed among group members: breeders reproduce, but subordinates don't.

      Subordinates may reproduce if they become breeders later in life. However, subordinates also benefit from cooperation as subordinates directly (greater survival in larger groups), and indirectly if they are related to the breeder. Here we refer to the first one, and we expand on that in the following sentence.  

      (45) L 280: "survival fitness benefits derived from living in larger groups seem to be key for the evolution of cooperative behavior in vertebrates [22, 63], and may also translate into low within-group conflict. This suggests that selection for division of labor in vertebrates is stronger in smaller groups". I don't see how the previous sentence suggests this. The paper does not present results to support this statement (i.e., no selection gradients in smaller vs larger groups are shown).

      The benefits of living in a larger group entail diminishing returns, so those living in smaller groups benefit greater by an increase in productivity and group size than those in a larger group.  

      (46) L 284: "Our model demonstrates that vertebrates evolve a more stable division of labor". Where is that shown? How is "more stable" measured?

      Rephrased to “vertebrates are more likely to evolve division of labor”. This is shown in Figure 2, that exemplifies that division of labor evolves in a wider range of environmental condition and to a higher degree (intermediate values of T).  

      (47) L 287: "direct fitness benefits in the form of group augmentation select more strongly for defensive tasks". Where is that shown? Establishing this would entail comparing selection gradients with direct fitness benefits of group augmentation and without them.

      In Figure 2, when we compare the GA column to KS+GA column, we see that at equilibrium, more helpers choose defense tasks, specially when they are free to choose their preferred task (circles).  

      (48) L 288: "kin selection alone seems to select only for work tasks." Again, this may be an artifact of the model assuming that helpers cannot increase non-breeders' fitness components except via group augmentation, and that defense tasks are inherently more costly than work tasks.

      As stated previously, we are studying task specialization in cooperative breeders where help is in the form of alloparental care (from allofeeding and egg care to defense from predators). We also assume that the costs are different, but whether one or the other is more costly depends on the relative context (e.g., a task can be more costly if it affects competitiveness in a very competitive environment). It is important to note that we name these tasks “work” and “defense” for practical reasons, but the focus of the paper is on tasks with different fitness costs that for their characteristics may not fit so well in under this terminology. While we acknowledge that most tasks have both kinds of fitness costs to a degree, here we focus on the main fitness costs of each kind of task (L430-436).  

      (49) L 290: "are comparatively large". This sounds as if the tasks are large, which is presumably not what is meant.

      Rephrased to “costs to dominance value and to the probability of attaining a breeding position are comparatively larger than survival costs.”

      (50) L 298: "helpers are predicted to increase defensive tasks with age or rank, whereas in harsh environments, work tasks are predicted to increase with age or rank." Add parentheses referring to where this is shown.

      This is shown in Figure 3, but since this is described in the discussion, we did not add a reference to the figure. If the editor would like us to refer to figures here, we can (see also comments below relating to the same issue).

      (51) L 308: "the role of age and environmental harshness on the evolution of division of labor". What is the prediction? Simply, the role of age is an assumption, not a prediction.

      Rephrased to “the role of environmental harshness on the evolution of division of labor via age-dependent task specialization”.

      (52) L 315: "individuals shifting from work tasks such as foraging for food, digging, and maintaining the burrow system, to defensive tasks such as guarding and patrolling as individuals grow older and larger". Say in parentheses where this is predicted.

      This prediction comes from Figure 3, we do not reference it here since we are in the Discussion section.  

      (53) L 320: "Under these conditions, our model predicts the highest levels of task partitioning and division of labor." Where is this predicted? Add parentheses referring to where this is shown. As it is, it is not possible to check the validity of the statement.

      This prediction comes from Figure 2 column KS+GA, we do not reference it here since we are in the Discussion section. The results with references to the figures are found under the Results section. In the discussion, we reiterate the results already described and add some examples from real data that seem to confirm our predictions.  

      (54) L 322: "In line with our model predictions, larger and older helpers of this species invest relatively more in territory maintenance, whereas younger/smaller helpers defend the breeding shelter of the dominant pair to a greater extent against experimentally exposed egg predators". These predictions are neat, but are now very difficult to understand from the figures. Maybe at the bottom of 3A, you could add a diagram work->defense for negative gamma_t and defense>work for positive gamma_t (or whatever order it is).

      Done.

      (55) L 325: "Territory maintenance has been shown to greatly affect routine metabolic rates and, hence, growth rates [80], which directly translates into a decrease in the likelihood of becoming dominant and attaining breeding status, as predicted by our model." This seems to be an assumption, not a prediction.

      That is true. We removed: “as predicted by our model”.  

      (56) L 352: "controlled". This means something else.

      Changed to “addressed”.

      (57) L 356: "summary, our study represents the first theoretical model aimed at elucidating the potential mechanisms underlying division of labor between temporal non-reproductives via task specialization in taxa beyond eusocial organisms". Again, claiming to be the first is risky and unnecessary.

      Rephrased to “our study helps to elucidate”.

      (58) L 358: "Harsh environments, where individuals can obtain direct fitness benefits from group living, favor division of labor, thereby enhancing group productivity and, consequently, group size." I'm not sure about this conclusion as harsh environments (large m in Figure 2) also involve the evolution of no division of labor (from the triangles and circles that are zero in the right bottom panel) and perhaps more so than with less harsh environments (intermediate m). Incidentally, in the bottom right panel of Figure 2, do the two separate clusters of triangles and circles mean that there is some sort of evolutionary branching?

      Yes, there are two different equilibria for the same set of conditions. Although it is true that for m=0.3 less division of labor evolves when kin selection and group augmentation act together, it is not the case when only group augmentation takes place. In addition, we qualify m=0.2 as harsh as opposed to benign in which we observe the rise of habitat saturation (m=0.1). m=0.3 is then an extreme harsh environment, in which in several instances different parameter landscape causes population collapse (see figures in the Supplemental Material).  

      (59) L 360: "Variation in the relative fitness costs of different helping tasks with age favors temporal polyethism". I don't see that this has been shown. Temporal polyethism evolves here whenever gamma_t evolves non-zero values. Figure 3A shows that non-zero gamma_t evolves with harsher environments, but I don't see what the "variation in relative fitness costs of different helping tasks" refers to.

      The evolved reaction norms of the model are towards different fitness costs depending on the task performed, since this is how we define the different types of tasks in the model.  

      (60) L 382: "undefined". Say variable. Undefined is something else.

      Undefined is more accurate, since we did not define how many subordinates there were per group, while “variable” could have been defined within a range, which was not the case in this model.  

      (61) L 390: "each genetic locus". Say earlier that each genetic trait is controlled by a single locus.

      Added.  

      (62) L 395: "complete" and "consistent" -> "certain".

      We changed one to “certain” and another to “absolute” to avoid using the same adjective twice in a sentence.  

      (63) L 396: What determines whether dispersers become subordinates or floaters? A trait? Or a fixed probability?

      We added “which is also controlled by the same genetic dispersal predisposition as for subordinates”.

      (64) L 412-413: "cycle". This should be a breeding step.

      Changed to “season” instead.

      (65) L 418: Say negatively impacts (it could also be positively impacts, which I guess is not what you mean).

      Done.

      (66) L 425: "a sample of floaters". Chosen how?

      Added “randomly drawn”.

      (67) L 426-428. But the equation in Table 1 indicates that all floaters compete for breeding spots, not a sample of floaters. This is not clear.

      The number of floaters sampled to try to breed at a given group is N<sub>f,b</sub> = 𝑓∗𝑁<sub>𝑓</sub>/𝑁<sub>𝑏</sub> (Table 1).

      Therefore, N<sub>f,b</sub> is the sample size of floaters for a given open breeding position, and f is how many groups on average a floater attempts to access in each time step.  

      (68) L 432. In the figure, the breeding cycle is called a step, but here it is called a cycle. There should be a single term used throughout. Breeding is not really a cycle here (it doesn't involve multiple steps that are repeated cyclically), so it seems more appropriate to call this breeding steps or breeding seasons.

      Taken into account previous comments, we changed the terms “generation” and “life cycle” to “breeding cycle”. We added “or seasons”.  

      (69) L 439: "generations". What are generations here, as generations are overlapping? You probably mean time steps or something else.

      Changed to “breeding cycles”.

      (70) L 439: "equilibrium was reached". Presumably, equilibrium is reached only asymptotically, so some cutoff is implemented in practice. So maybe say explicitly what cutoff was implemented.

      As mentioned, we run the model for 200’000 time steps, and if equilibrium was not reached for the phenotypic values, then we run the model for longer, with 400’000 time steps being the maximum at which all simulation reached equilibrium. In some cases, genetic values did not reach equilibrium at ranges at which there was no impact on phenotypic values, so these were disregarded to assess whether equilibrium was reached.  

      (71) L 452: "Even though individuals are likely to change the total amount of help given throughout their lives". Do you mean in real organisms or in the model? Say which. If it is in the model, it is not clear how.

      We added “in nature” to clarify that this was not the case in the model.  

      (72) L 455: "For more details on how individuals may adapt their level of help with age and social and environmental conditions, see [63]." Do you mean real individuals or in the model? Again, if it is in the model, it is unclear how this is possible and should be explained in this paper at least briefly rather than citing another one.

      We rephrased it to “How individuals in the model may adapt their level of help with age and social and environmental conditions has been described elsewhere.” We do not go into detail here because it is not within the scope of the paper, and those results have been described elsewhere.  

      (73) L 475: "helpers". Make terminology consistent throughout.

      All helpers are subordinates, but not all subordinates are helpers, as they may evolve no help. Since here we are describing those subordinates that do help, we use that terminology. We added “subordinate helpers” to clarify this further.  

      (74) L 476: "proportional". The dependence in Equation 1 is not "proportional to". Say something like "a survival probability (not rate) that decreases with the amount of help provided".

      Done.

      (75) L 482: "environmental"-> baseline, as defined first.

      Done.

      (76) L 486: "benefits". Can you briefly say in parentheses what those benefits are in real organisms? As in line 475, where you reminded the reader of survival costs due to predator defense.

      Added “such as those offered by safety in numbers or increased resource defense potential”.

      (77) L 494. "we first outline a basic model in which individuals". It is not clear what this sentence says, and the remainder of this section does not clarify it.

      We made two models for comparison, one where individuals can choose freely which task they prefer to perform, and another in which there is an increase in productivity when both kinds of tasks are performed to a similar extent at group level. In the latter model, individuals may choose an unpreferred task at certain times during their lived to increase the effect of the help provided in the breeder’s (and group’s) productivity.  

      We rephrased this section to “we first outline a basic model where individuals evolve their preferred helping task. Then we compare this to another model in which the breeder’s reproductive outcome is maximized when the group’s helping effort in each kind of tasks is performed to a roughly equal degree.”

      (78) L 496: "by performing both tasks". Sounds as if the breeder performs both tasks, not helpers.

      We changed to “when the group’s helping effort in each kind of tasks”.

      (79) L 497: "the maximum amount of cumulative help of each type (sigma Hmax) that can affect fecundity is given by Eq. 4:" This statement is imprecise. Presumably, what is meant is that this level of help maximises breeder productivity, as stated earlier in the paper. However, there is no proof that this level of help maximises breeder productivity, so this expression seems unjustified and it is unclear how it is used.

      This is a description of the model set up. As described later in the same section, the cumulative help of each time that will influence the breeder’s fecundity if maximum Hmax. Therefore, it does represent the maximum amount of cumulative help of each type that can affect the breeder’s fecundity.

      (80) L 500: "reproduced" -> "reproduce".

      Done.  

      (81) L 503. Say here what K is so that the reader knows what equation 5 is showing.

      Added “K” to the “The quantity of offspring produced (K)”.

      (82) L 503: "diminishing returns" -> "diminishing returns as help increases".

      Done.  

      (83) L 507: Why these inequalities?

      These inequalities explain the use of Hmax (response to comment 79). We rephased it to “the cumulative defense effort is larger than or the cumulative work effort is larger than ”.  

      (84) L 526: "removing the influence of relatedness from the model". It would be helpful to plot relatedness in this and the other scenario to check that it is indeed low here and high in the other.

      The actual values of relatedness are provided in the Supplemental Material Table S1. We added this reference to Figure 2.  

      (85) L 528: "It is possible that direct and indirect fitness benefits could have an additive effect on the evolution of alloparental care". This is technically incorrect. It is also unclear what the point of this sentence is.

      We have removed this sentence.  

      (86) Table 1: Say what are the allowed values for these genotypic traits (can they take negative values, be greater than one, are they continuous or discrete?): e.g., alpha \in [0,1] or alpha \in (-infinity, infinity). For phenotypic traits, it would be helpful if the third column lists the equation where the trait is defined. As the variables in the first column are scalars, they should not be bold face. Survival "rate" should be survival "probability" throughout.

      All genetic traits can take any real number (-infinity, infinity), but the phenotypic values are either constrained by the equation like for logistic formulas, or manually constrained like for dispersal propensity or help (only positive numbers allowed). We added “Each genetic trait is controlled by a single locus, and may take any real number” (L403), and added the boundaries for help and dominance value in Table 1. We decided against including the equations in the table due to space constraints. We removed the bold face as suggested. We changed all instances of “survival rate” to “survival probability”.

      (87) Figures S1, S2: I don't recall seeing references to these figures in the main text, but there should be, as well as for Tables S1-S3.

      Table S1 is now referenced in Figure 2. The other figures are now referenced in the main text when we reference the different sections in the Supplemental Materials (L190 and L198). Other Tables are referenced in their respective Figures in the SI.

    1. eLife Assessment

      This study introduces a novel and potentially valuable metric-phenological lag-to quantify the gap between observed and expected phenological shifts under climate warming. While the dataset is extensive and the framework is clearly defined, key assumptions (e.g., base temperature, linear forcing response) are not empirically tested, and the analysis underexplores key spatial and climatic gradients. The strength of evidence is mostly solid but would benefit from further validation and deeper analysis.

    2. Reviewer #1 (Public review):

      Jiang et al. present a measure of phenological lag by quantifying the effects of abiotic constraints on the differences between observed and expected phenological changes, using a combination of previously published phenology change data for 980 species, and associated climate data for study sites. They found that, across all samples, observed phenological responses to climate warming were smaller than expected responses for both leafing and flowering spring events. They also show that data from experimental studies included in their analysis exhibited increased phenological lag compared to observational studies, possibly as a result of reduced sensitivity to climatic changes. Furthermore, the authors present evidence that spatial trends in phenological responses to warming may differ than what would be expected from phenological sensitivity, due to the seasonal timing of when warming occurs. Thus, climate change may not result in geographic convergences of phenological responses. This study presents an interesting way to separate the individual effects of climate change and other abiotic changes on the phenological responses across sites and species.

      Strengths:

      A straightforward mathematical definition of phenological lag allows for this method to potentially be applied in different geographic contexts. Where data exists, other researchers can partition the effects of various abiotic forcings on phenological responses that differ from those expected from warming sensitivity alone.

      Identifying phenological lag, and associated contributing factors, provides a method by which more nuanced predictions of phenological responses to climate change can be made. Thus, this study could improve ecological forecasting models.

      Weaknesses:

      The analysis here could be more robust. A more thorough examination of phenological lag would provide stronger evidence that the framework presented has utility. The differences in phenologica lag by study approach, species origin, region, and growth form are interesting, and could be expanded. For example, the authors have the data to explore the relationships between phenological lag and the quantitative variables included in the final model (altitude, latitude, mean annual temperature) and other spatial or temporal variables. This would also provide stronger evidence for the author's claims about potential mechanisms that contribute to phenological lag.

      The authors include very little data visualizations, and instead report results and model statistics in tables. This is difficult to interpret and may obscure underlying patterns in the data. Including visual representations of variable distributions and between-variable relationships, in addition to model statistics, provides stronger evidence than model statistics alone.

    3. Reviewer #3 (Public review):

      Summary:

      The authors developed a new phenological lag metric and applied this analytical framework to a global dataset to synthesize shifts in spring phenology and assess how abiotic constraints influence spring phenology.

      Strengths:

      The dataset developed in this study is extensive, and the phenological lag metric is valuable.

      Weaknesses:

      The stability of the method used in this study needs improvement, particularly in the calculation of forcing requirements. In addition, the visualization of the results (such as Table 1) should be enhanced.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Jiang et al. present a measure of phenological lag by quantifying the effects of abiotic constraints on the differences between observed and expected phenological changes, using a combination of previously published phenology change data for 980 species, and associated climate data for study sites. They found that, across all samples, observed phenological responses to climate warming were smaller than expected responses for both leafing and flowering spring events. They also show that data from experimental studies included in their analysis exhibited increased phenological lag compared to observational studies, possibly as a result of reduced sensitivity to climatic changes. Furthermore, the authors present compelling evidence that spatial trends in phenological responses to warming may differ from what would be expected from phenological sensitivity, due to the seasonal timing of when warming occurs. Thus, climate change may not result in geographic convergences of phenological responses. This study presents an interesting way to separate the individual effects of climate change and other abiotic changes on the phenological responses across sites and species.

      Greater phenological lag with experimental studies results in reduced sensitivity to climatic changes, not other way around.

      Strengths:

      A clearly defined and straightforward mathematical definition of phenological lag allows for this method to be applied in different scientific contexts. Where data exists, other researchers can partition the effects of various abiotic forcings on phenological responses that differ from those expected from warming sensitivity alone.

      Sensitivity does not tell the magnitude of phenological changes, nor does it provide indications of mechanisms responsible for changes in spring phenology. Because of uneven warming, the same average temperature change (annual or spring temperatures) can have greater (greater warming prior to budburst) or smaller (smaller warming prior to budburst) phenological change than that with even warming. When average temperature change is close to zero, uneven warming can lead to infinite sensitivity values, either advanced (warmer temperatures prior to budburst) or delayed (cooler temperatures prior to budburst) spring phenology.

      It is not clear why sensitivity is so popularly used in phenological research.

      Identifying phenological lag and associated contributing factors provides a method by which more nuanced predictions of phenological responses to climate change can be made. Thus, this study could improve ecological forecasting models.

      Weaknesses:

      The authors include very few data visualizations, and instead report results and model statistics in tables. This is difficult to interpret and may obscure underlying patterns in the data. Including visual representations of variable distributions and between-variable relationships, in addition to model statistics, provides stronger evidence than model statistics alone.

      The use of stepwise, automated regression may be less suitable than a hypothesis-driven approach to model selection, combined with expanded data visualization. The use of stepwise regression may produce inappropriate models based on factors of the sample data that may preclude or require different variable selection.

      We used two statistical methods, variance analysis to examine differential phenological responses (Figure 2) and regression analysis to determine the relative importance of forcing change, budburst temperature, and physiological lag, the drivers of changes in spring phenology (Table 2). Our objective was to understand why plants show differential responses by research approach, species origin, climatic region, and growth form identified in previous research. Variable selection may affect minor (altitude, latitude, MAT, and average spring temperature change) or insignificant (photoperiod and long-term precipitation) variables, but not those related to drivers of spring phenology. We are not sure how hypothesis-driven approach can help with our objective.

      Reviewer #2 (Public review):

      Summary:

      This is a meta-analysis of the relative contributions of spring forcing temperature, winter chilling, photoperiod and environmental variables in explaining plant flowering and leafing phenology. The authors develop a new summary variable called phenology lag to describe why species might have different responses than predicted by spring temperature.

      Strengths:

      The summary statistic is used to make a variety of comparisons, such as between observational studies and experimental studies.

      Weaknesses:

      By combining winter chilling effects, photoperiod effects, and environmental stresses that might affect phenology, the authors create a new variable that is hard to interpret. The authors do not provide information in the abstract about new insights that this variable provides.

      Phenological lag contains effects of all constraints that may include chilling effects, photoperiod effects, and environmental stresses and is, indeed, hard to interpret without investigation of individual constraints. In our synthesis, spring phenology (or photoperiod effect) is not significant across all studies complied. It is also unlikely that lack of winter chilling causes the systemic differences in phenological lag between observational and experimental studies or between native and exotic species (see discussion at lines 335-339). At individual study level, the contribution of different constraints to the overall lag effect can be specifically determined if moisture stresses, species chilling and photoperiod effects, or cold hardiness are known from on-site monitoring or previous research.

      The meaning of phenological lag is described at lines 34-38 in the abstract.

      Comments:

      It would be useful to have a map showing the sites of the studies.

      A map showing the sites of the studies was added as supplementary Figure S1.

      The authors should provide a section in which the strengths and weaknesses of the approach are discussed. Is it possible that mixing different types of data, studies, sample sizes, number of years, experimental set-ups, and growth habits results in artifacts that influence the results?

      Both strengths and weaknesses are discussed at various places throughout the paper. The weakness of our method, as indicated by the reviewer, is the inclusion of different constraints in the phenological lag and has been described at lines 34-38 in the abstract and lines 80-86 in the introduction of the concept. We have also expanded Conclusion section to discuss possible caveats at lines 369-393.

      As in all data analyses, the results can change with addition of more/different data, especially when sample size is relatively small. Ideally, comparisons are made among levels of fixed effects while controlling variations of other conditions. In phenological studies, however, climatic, phenological, and biological conditions all vary. For example, observational and experimental studies differ not only in the nature of warming (natural climate change vs artificial warming), but also in levels of warming (greater warming with experimental studies) and climatic, phenological, and biological conditions (Table 1). All phenological syntheses (or meta-analyses) have to make do with this uncontrolled nature of phenological data.

      Now that the authors have created this new variable, phenological lag, which of the components that contribute to it has the most influence on it? Or which components are most influential in which circumstances? For example, what are some examples where photoperiod causes a phenological lag?

      Any of the phenological constraints identified can contribute alone or in combination with others to the overall effect of phenological lag. Across all studies with this synthesis, the lack of significance with spring phenology rules out photoperiod effect, while the association of longer phenological lags with longer accumulation of winter chilling does not suggest general chilling shortage with the current extent of climate change.

      Although spring phenology is not significant across all studies, photoperiod effect can be influential at individual studies where changes in spring phenology are large. However, reported photoperiod effects in the literature are mostly confounding effects with temperatures, i.e., longer photoperiods are associated with longer hours of high daytime temperatures (see Chu et al., 2021). Other than European beech under an unlikely scenario of climate change (growth resumes at beginning of winter), there has been not clear evidence showing the effect of photoperiod in constraining spring phenology.

      Another confounding effect with photoperiod is extra heating effect with artificial light sources in warming experiments. Some early studies have shown that leaf temperature can be several degrees above the ambient air, due to long-wave radiation with artificial light sources. It is hard to believe the constraining effect of photoperiod on spring phenology if phenological changes are within inter-annual variations (can be a few weeks), although photoperiod effect has been increasingly discussed recently.

      Recommendations for the authors:

      Reviewing Editor:

      A key methodological concern is the inconsistent definition of growth temperature across observations. It is calculated over the interval between the baseline phenological date and the expected date under warming - a window that varies by species, site, and treatment. This variability limits comparability across observations and may introduce circularity, as growth temperature is derived from the same modelled expectation (i.e., the expected phenological advance) that it is later used to explain.

      The term “growth temperature” has been replaced with “budburst temperature” to indicate temperatures at species events. Budburst temperature is the average temperature within the window of expected response with the warmer climate and, as indicated by the editor, varies by species, sites, and treatments. This species-specific temperature provides an opportunity to compare among species, sites, and treatments and helps explain differences in observed responses, as demonstrated in the discussion of results in this synthesis.

      Forcing change, budburst temperature, and expected response are related. High budburst temperatures are associated with smaller expected responses, which helps explain smaller observed responses with late season species and areas of warm climates that have been often attributed to chilling or photoperiod effect.

      Additionally, the use of degree days above 0 {degree sign}C as a universal metric for spring forcing oversimplifies species' temperature responses. This approach assumes not only a fixed base temperature but also a linear response to temperature accumulation, which overlooks well-established nonlinear or species-specific thermal response curves. To improve the robustness and interpretability of the phenological lag framework, we encourage the authors to consider these limitations and explore ways to test or justify these modelling assumptions more explicitly.

      The use of 0 degree base temperature may not be the best choice for some species. Except for some early work, there has been few experimental research on physiological aspects of chilling and forcing processes. A popular alternative is modelling using assumed temperature response models. As variables influencing chilling and forcing processes are not controlled, the determined base temperatures and temperature response models may be OK with the species studied under particular conditions but would be inappropriate for applications beyond. It is hard to believe that species, in a study, all have different base temperature for accumulation of spring forcing and optimum temperature for winter chilling. Apparently, this is the result of model fitting, not actual dynamics of chilling and forcing processes.

      Two base temperatures are commonly used, 0 and 5 oC, although choice is not generally justified. It is known for long time that temperatures above 0oC contribute to spring forcing. My personal experience at tree nursery suggests that seedlings will flush after winter cold storage, even at forcing temperatures ≤ 5 oC in the dark. The use of 5 oC is rather the choice of tradition (5 oC is commonly used to define growing season) than scientific justification. The use of high base temperatures may not make much difference at high temperatures due to short forcing duration but will underestimate forcing at low temperatures due to long forcing duration and large proportions of forcing between 0 and base temperatures. We are not aware of any experimental studies that demonstrate non-zero base temperatures.

      Within the dominant range of spring temperatures (e.g., between 5 and 25 oC), the forcing responses to temperatures can be approximated with linear models. Again, we are not aware of any non-linear forcing models that can be safely applied beyond the species studied under particular conditions.

      Regardless, the uses of different base temperatures or forcing models would not affect the partitioning of phenological changes, simply because temperature response models reflect physiological aspects of chilling and forcing processes and would not change with climate warming.

      The authors introduce a new metric, phenological lag, to assess how phenological constraints influence spring phenology, offering new insights into phenological research. However, there are several concerns. First, the research question and the study's aim are not clearly presented. The authors primarily analyzed phenological lag and simply compared it across different groups, but additional analyses are needed to adequately address the research question. In addition, the broader importance of this study is not clearly explained - why this research is necessary and what it contributes to the field should be explicitly stated.

      The research question is outlined at lines 92-108. We added “Our objective was to determine how phenological responses differ among different groups and how differential responses are related to drivers of spring phenology, i.e., forcing change, budburst temperature, and phenological lag” at lines 106-108.

      (1) Abstract: The methodological improvements and more key results should be included.

      Growth temperature has been replaced with “budburst temperature” to indicate temperatures at time of budburst. More results are added at lines 40-48.

      (2) Line 32: Terms such as "sensitivity analysis" and "phenological lag" need clearer definitions.

      We added at lines 32-33 to define sensitivity analysis “that is based on rates of phenological changes, not on drivers of spring phenology”. Phenological lag is defined at lines 34-38.

      (3) Lines 38-47: Further results and the urgency or importance of the study should be conveyed.

      More results are added at lines 40-48. The importance of this study is described at lines 48-50.

      (4) Line 57-58: This sentence is unclear - please clarify.

      The sentence is modified to “difficult using sensitivity analysis that is based on rates of phenological changes, not on drivers of spring phenology".

      (5) Line 60: break "endodormancy".

      Breaking dormancy would mean endodormancy.

      (6) Line 67: What does "growth temperature" refer to?

      Growth temperature has been replaced with “budburst temperature” to indicate temperatures at time of budburst. It is calculated as the average temperature within the window of expected response with the warmer climate.

      (7) Lines 87-94: The specific purpose of the study is vague. Why is this method needed, and how will it serve future research?

      We have modified the paragraph at lines 92-108 to provide justification and objective of the study.

      (8) Lines 163-164: The rationale for exploring differences in observed responses and phenological lag needs to be better justified.

      We added explanations at lines 179-182 why observed responses and phenological lag were chosen in the analysis.

      (9) Lines 178-183: Tables and figures should be properly cited within the text.

      Table S3 was added at line 197.

      (10) Lines 195-198: Clarify whether variables were scaled before model analysis.

      We clarified at line 192 “variables were not standardized prior to regression analysis”.

      (11) Line 206-207: The observed response is presented as the number of advanced days, while temperature sensitivity refers to the response of spring phenology to temperature - these are different variables and should not be conflated.

      The two variables are related but show different aspects of phenological changes. Observed response divided by average temperature change gives temperature sensitivity. Observed response is the total changes in number of days observed, while temperature sensitivity is the change in number of days per unit change in average temperature (oC). Sensitivity may reflects rates of phenological change with temperature (see responses to reviewer 1).

      (12) In the discussion section, the authors compared phenological responses among different groups separately. This section requires substantial improvement to more clearly answer the research question.

      These discussions are related to our objective “how phenological responses differ among different groups identified in previous research (i.e., research approach, species origin, climatic region, and growth form) and how these differential responses are related to drivers of spring phenology, i.e., forcing change, budburst temperature, and phenological lag”.

    1. Figure 3.4: Human uncertainty (CI width) vs |LLM − Human|. Spearman correlation reported.

      This one is rather intricate, it might need some more analysis and talking through.

    2. Table 3.3: CI coverage: does one interval contain the other’s point estimate?

      I think DHK also looked at 'human in human' -- Might as well add this as a comparator?

    3. Table 3.1: Agreement metrics by metric (Pearson, Spearman, mean/median bias, κ unweighted/weighted).

      I assume this is referring to the correlation of (the average of?) the human ratings and the LLM ratings?

      Because we could also look at the agreement between humans (something David HJ was working on ... Might be useful to share this with him for his thoughts if he's interested at all.)

    4. As another indicator of agreement

      Exactly. It's sort of a measure of agreement, although I'm not sure quite how to interpret it. It's not a measure of calibration per se because we were asking them to rate these things, not to predict them.

      Although we could ask the LLM to do this as a prediction exercise, with or without training data, that might be interesting, And then, of course, the calibration would be meaningful.

    5. he horizontal radius covers the union of all human evidence for that paper — combining individual raters’ point scores and their CIs

      It's not fully clear to me what this does. I guess you center it (horizontally) at the midpoints of the human ratings.

      Are you using the outer bounds of both raters' CIs?

      Probably the best thing to do ultimately would be to impute a distribution over each individual ratings and CI these and then do some sort of belief aggregation. -- Horizontal linear aggregation actually feels the most intuitive to me from what I've read. ... And then give the implied CIs for that

    6. For each paper (selected metric), the ellipse is centered at the pair of midpoints (Human, LLM).

      This is pretty clear but it took me a second to get this, so maybe mention human = horizontal, LLM = vertical in the text.

  2. www.planalto.gov.br www.planalto.gov.br
    1. § 3º
      • Informativo nº 859
      • 26 de agosto de 2025.
      • RECURSOS REPETITIVOS
      • Processo: REsp 2.148.059-MA, Rel. Ministro Luis Felipe Salomão, Corte Especial, por unanimidade, julgado em 20/8/2025. (Tema 1306).

      REsp 2.148.580-MA, Rel. Ministro Luis Felipe Salomão, Corte Especial, por unanimidade, julgado em 20/8/2025 (Tema 1306).

      REsp 2.150.218-MA, Rel. Ministro Luis Felipe Salomão, Corte Especial, por unanimidade, julgado em 20/8/2025 (Tema 1306).

      Ramo do Direito DIREITO PROCESSUAL CIVIL

      TemaPaz, Justiça e Instituições Eficazes <br /> Fundamentação por referência (per relationem ou por remissão). Ato decisório. Técnica de fundamentação. Cabimento. Tema 1306.

      Destaque - 1) A técnica da fundamentação por referência (per relationem) é permitida desde que o julgador, ao reproduzir trechos de decisão anterior, documento e/ou parecer como razões de decidir, enfrente, ainda que de forma sucinta, as novas questões relevantes para o julgamento do processo, dispensada a análise pormenorizada de cada uma das alegações ou provas.

      • 2) O § 3º do artigo 1.021, do CPC não impede a reprodução dos fundamentos da decisão agravada como razões de decidir pela negativa de provimento de agravo interno quando a parte deixa de apresentar argumento novo para ser apreciado pelo colegiado.

      Informações do Inteiro Teor - Cinge-se a controvérsia a definir se a fundamentação por referência (per relationem ou por remissão) - na qual são reproduzidas as motivações contidas em decisão judicial anterior como razões de decidir - resulta na nulidade do ato decisório, à luz do disposto nos artigos 489, § 1º, e 1.022, parágrafo único, inciso II, do Código de Processo Civil de 2015.

      • Segundo a doutrina, a obrigatoriedade da fundamentação das decisões judiciais, sob pena de nulidade, consubstancia, "a um só tempo, princípio processual, dever do juiz, direito individual da parte e garantia da Administração Pública".

      • Tal obrigatoriedade - de justificação da convicção do magistrado em decisões judiciais - encontra-se prevista na Constituição Federal de 1988 (art. 93, inciso IX), tendo relação intrínseca com a definição da República Federativa do Brasil como Estado Democrático de Direito.

      • Cuida-se de direito fundamental do jurisdicionado - consectário da garantia do devido processo legal - que subordina todos os integrantes do Poder Judiciário, aos quais é vedado proferir decisões arbitrárias, ou seja, pronunciamentos jurisdicionais que não se coadunem com o conceito democrático do exercício do poder, que exige a justificação - dialógica, racional e inteligível - do ato decisório de modo a viabilizar o seu "controle interno" pela parte e pelas instâncias judiciais subsequentes, bem como o seu "controle externo e difuso" pela sociedade, o que revela uma dupla função dessa obrigatoriedade.

      • O Código de Processo Civil de 2015 inseriu o dever de fundamentação das decisões judiciais entre as "normas fundamentais do processo civil" (artigo 11), determinando ainda que: (i) em regra, "não se proferirá decisão contra uma das partes sem que ela seja previamente ouvida" (artigo 9º, caput); e (ii) "o juiz não pode decidir, em grau algum de jurisdição, com base em fundamento a respeito do qual não se tenha dado às partes oportunidade de se manifestar, ainda que se trate de matéria sobre a qual deva decidir de ofício" (artigo 10).

      • No capítulo que versa sobre a "sentença" (lato sensu), o artigo 489 do CPC enumera os elementos essenciais do ato decisório, bem como hipóteses - exemplificativas - de "decisões não fundamentadas". Do referido dispositivo se extrai que o dever de fundamentação da decisão judicial considera-se adequadamente atendido quando o magistrado explicita as razões fáticas e jurídicas consideradas determinantes para a resposta oferecida no processo dentre outras conclusões possíveis.

      • Ademais, nos termos do rol previsto no § 1º do artigo 489 do CPC, a fundamentação da decisão judicial deve ainda conter: a) explicação sobre o vínculo entre a norma jurídica - considerada aplicável à espécie - e a causa ou a questão decidida nos autos (inciso I); b) especificação do motivo concreto para o emprego de conceito jurídico indeterminado (inciso II); c) exame da situação concreta submetida ao crivo do Judiciário, revelando-se insuficiente a invocação de motivos que se prestariam a justificar qualquer outra decisão (inciso III); d) enfrentamento de "todos os argumentos deduzidos no processo capazes de, em tese, infirmar a conclusão adotada pelo julgador" (inciso IV); e) juízo de conformação entre a ratio decidendi de precedente - ou de enunciado de súmula - aplicado na decisão e o caso concreto (inciso V); f) indicação das diferenças fáticas que justificam a não aplicação de precedente obrigatório ao caso concreto (inciso VI, primeira parte); e g) informação sobre a superação de precedente obrigatório invocado nos autos (inciso VI, parte final).

      • Assim, à luz do disposto no parágrafo único do artigo 1.022 do CPC, considera-se omissa - e, portanto, impugnável por embargos de declaração - a decisão que: (i) deixa de se manifestar sobre tese firmada em julgamento de casos repetitivos ou em incidente de assunção de competência aplicável à espécie; ou (ii) incorre em qualquer das hipóteses de ausência de fundamentação descritas no § 1º do artigo 489.

      • Com as alterações promovidas em 2010 no Decreto-Lei n. 4.657/1942 (Lei de Introdução às Normas do Direito Brasileiro - LINDB), também passou a ser exigido que as consequências práticas - postas no debate judicial e que tenham lastro probatório nos autos - constem da fundamentação da decisão que, nas esferas administrativa, controladora ou judicial, decretar a invalidação de ato, contrato, ajuste, processo ou norma administrativa (artigos 20 e 21).

      • Diante desse cenário normativo, discute-se se a utilização da técnica da fundamentação por referência - por remissão ou per relationem - é compatível com o dever de fundamentação imposto a todos os órgãos do Poder Judiciário, cuja inobservância resulta na nulidade do ato decisório. Trata-se de técnica discursiva na qual são reproduzidas as motivações contidas em decisão judicial anterior - ou em documento outro, a exemplo de parecer do Ministério Público - como razões de decidir.

      • De acordo com a doutrina, a fundamentação por referência apresenta duas formas habituais: (i) a exclusiva (ou pura); e (ii) a integrativa (ou moderada). A utilização da "fundamentação por referência exclusiva ou pura" - ou seja, aquela consubstanciada na mera remissão ou transcrição integral dos fundamentos de outra peça processual sem análise específica dos argumentos trazidos pela parte - <u>implica violação ao direito fundamental ao contraditório</u> e vai de encontro às disposições contidas no § 1º do artigo 489 do CPC. Por outro lado, é válida a "fundamentação por referência integrativa ou moderada", na qual a transcrição de decisão ou parecer anterior é acompanhada de análise própria (do julgador) que dialoga com os argumentos levantados pela parte em sua impugnação.

      • Ao tratar da matéria (sob o enfoque constitucional), o Supremo Tribunal Federal reconheceu a validade da fundamentação por referência - como técnica de motivação da decisão judicial - quando verificada "a compatibilidade entre o que alegado e o entendimento fixado pelo órgão julgador", ficando dispensado "o exame detalhado de cada argumento suscitado" (RE 1.397.056 ED-AgR/MA, Ministra Rosa Weber, Tribunal Pleno, DJe de 28/3/2023).

      • Essa mesma exegese encontra-se retratada na jurisprudência do Superior Tribunal de Justiça (inclusive das Turmas de Direito Penal).

      • Revela-se importante destacar, outrossim, que, em relação à norma inserta no § 3º do artigo 1.021 do CPC - segundo a qual "é vedado ao relator limitar-se à reprodução dos fundamentos da decisão agravada para julgar improcedente o agravo interno" - a jurisprudência do STJ firmou-se no sentido da necessidade de interpretação do referido comando em conjunto com a regra do inciso IV do § 1º do artigo 489, que somente reputa nula a decisão judicial que deixa de "enfrentar todos os argumentos deduzidos no processo capazes de, em tese, infirmar a conclusão adotada pelo julgador".

      • Não obstante, é certo que já foram constatadas, por esta Corte, hipóteses de utilização da técnica de fundamentação por referência com flagrante violação dos artigos 489, § 1º, 1.021, § 3º, e 1.022, parágrafo único, inciso II, do CPC. Nesses casos, em virtude do uso inadequado da referida técnica discursiva, determinou-se o retorno dos autos à origem para rejulgamento de embargos de declaração das partes.

      • Nesse contexto doutrinário e jurisprudencial, sendo pacífica a possibilidade de utilização da técnica de fundamentação da decisão por remissão, mas com cautela para garantir o contraditório e o direito à defesa, fixam-se as seguintes teses para fins dos artigos 1.036 a 1.041 do CPC:

      • 1) A técnica da fundamentação por referência (per relationem) é permitida desde que o julgador, ao reproduzir trechos de decisão anterior, documento e/ou parecer como razões de decidir, enfrente, ainda que de forma sucinta, as novas questões relevantes para o julgamento do processo, dispensada a análise pormenorizada de cada uma das alegações ou provas.

      • 2) O § 3º do artigo 1.021, do CPC não impede a reprodução dos fundamentos da decisão agravada como razões de decidir pela negativa de provimento de agravo interno quando a parte deixa de apresentar argumento novo para ser apreciado pelo colegiado.

    2. modificar
      • Informativo nº 806
      • CORTE ESPECIAL
      • Processo: EAREsp 1.766.665-RS, Rel. Ministro Francisco Falcão, Rel. para acórdão Ministro Ricardo Villas Bôas Cueva, Corte Especial, por maioria, julgado em 3/4/2024.

      Ramo do Direito DIREITO PROCESSUAL CIVIL

      TemaPaz, Justiça e Instituições Eficazes <br /> Multa cominatória. Valor exorbitante. Desproporcionalidade. Valor acumulado. Possiblidade de revisão. Exigência de postura ativa do devedor. Sucessivas revisões. Impossibilidade. Preclusão consumativa.

      DESTAQUE - Incide a preclusão consumativa sobre o montante acumulado da multa cominatória, de forma que, já tendo havido modificação, não é possível nova alteração, preservando-se as situações já consolidadas.

      INFORMAÇÕES DO INTEIRO TEOR - A controvérsia diz respeito à ocorrência de preclusão sobre decisão que revisa o valor de astreintes. Sobre tema, a Corte Especial, no julgamento do EAREsp n. 650.536-RJ, firmou o entendimento de ser possível a redução quando o valor for exorbitante, levando-se em conta a razoabilidade e a proporcionalidade, e a fim de evitar o enriquecimento sem causa do credor.

      • No entanto, a questão demanda reflexões mais aprofundadas, especialmente porque essa decisão, muito embora tenha sido proferida sob a égide do CPC atual, baseou-se especialmente em jurisprudência majoritária construída à época em que vigia o CPC/1973, com destaque para o Tema Repetitivo n. 706: "A decisão que comina astreintes não preclui, não fazendo tampouco coisa julgada" (REsp n. 1.333.988/SP, Segunda Seção, Rel. Ministro Paulo de Tarso Sanseverino, DJe 11/4/2014).

      • Além disso, não se levou em consideração que o CPC/2015 alterou substancial e expressamente o regime jurídico das astreintes no tocante à possibilidade de modificação. Com efeito, de acordo com a premissa estabelecida no julgamento do EAREsp n. 650.536-RJ, a regra que permite ao magistrado alterar a multa cominatória estaria prevista no art. 461, § 6°, do CPC/1973 e no seu correspondente, art. 537, § 1°, do CPC/2015. Todavia, há uma diferença substancial entre essas duas regras, em particular no que diz respeito a quais valores podem ser modificados.

      • A partir da análise dessas regras supracitadas, percebe-se a nítida intenção do legislador de autorizar a revisão ou a exclusão apenas da "multa vincenda", ou seja, a decisão não pode ter eficácia retroativa para atingir o montante acumulado da multa. Por outro lado, há quem sustente a possibilidade de decisão com efeitos retroativos no caso de redução do montante da multa que já incidiu, pois a expressão "vincendas" diria respeito apenas à multa que está incidindo.

      • Contudo, não há motivo para submeter a modificação e a exclusão a regimes jurídicos diversos. A regra do art. 537, § 1°, do CPC deixa claro que o legislador optou por preservar as situações já consolidadas, independentemente de se tratar da multa que está incidindo ou do montante oriundo da sua incidência. Analisando a questão com mais profundidade, tem-se que a pendência de discussão acerca do montante da multa não guarda relação com o seu vencimento, mas, sim, com a sua definitividade.

      • Dessa forma, se a incidência da multa durante o período de inadimplência alcança valores exorbitantes, seja porque o devedor permaneceu inerte e não requereu a revisão ou exclusão, seja porque o magistrado não agiu de ofício, qualquer decisão que venha a ser proferida somente poderia provocar, em regra, efeitos prospectivos.

      • Percebe-se que o legislador do CPC/2015 optou por levar em consideração a postura do devedor, a fim de premiar aquele que, muito embora inadimplente num primeiro momento, acaba por cumprir a obrigação, ainda que parcialmente, ou que demonstra a impossibilidade de cumprimento. Significa dizer que somente tem direito à redução da multa aquele que abandona a recalcitrância.

      • Desse modo, a partir da regra expressa do art. 537, §1°, do CPC, somente seria possível alterar o valor acumulado das multas vincendas e, consoante disposto no inciso II, a redução exige postura ativa do devedor, consubstanciada no cumprimento parcial da obrigação ou na demonstração de sua impossibilidade.

      • De qualquer sorte, na hipótese, há outro óbice para a revisão pretendida, qual seja a preclusão pro judicato consumativa, pois já havia sido revisado o valor da multa diária.

      • O STJ sedimentou, por meio de recurso especial julgado na sistemática dos repetitivos, que "a decisão que comina astreintes não preclui, não fazendo tampouco coisa julgada" (Tema 706), conforme já anotado. Trata-se, no entanto, de não incidência de preclusão temporal, de forma que o valor da multa pode ser modificado a qualquer tempo. Não se trata de ausência de preclusão consumativa, sob pena de grave violação da segurança jurídica.

      • Dessa forma, uma vez fixada a multa, é possível alterá-la ou excluí-la a qualquer momento. No entanto, uma vez reduzido o valor, não serão lícitas sucessivas revisões, a bel prazer do inadimplente recalcitrante, sob pena de estimular e premiar a renitência sem justa causa. Em outras palavras, é possível modificar a decisão que comina a multa, mas não é lícito modificar o que já foi modificado.

      • Considerando que a multa cominatória é um importantíssimo instrumento para garantir a efetividade das decisões judiciais e pode ser fixada de ofício, trata-se de matéria de ordem pública. No caso, a multa fixada em sentença transitada em julgado pode ser alterada na fase de execução porque tem natureza de técnica processual, de modo que não é acobertada pela coisa julgada material. Uma vez fixada ou alterada no início da execução, mantém tal natureza e, portanto, pode ser modificada a qualquer momento, inclusive de ofício.

      • Todavia, o valor acumulado da multa deixa de ser técnica processual e passa a integrar o patrimônio do exequente como crédito de valor, perdendo a natureza de matéria de ordem pública. Com efeito, nos termos do art. 537, § 2°, do CPC, "o valor [acumulado] da multa será devido ao exequente".

      • Além disso, mesmo se considerada também a multa acumulada como matéria de ordem pública, deve incidir a preclusão pro judicato consumativa, de forma que, tendo havido modificação, não é possível nova alteração, preservando-se as situações já consolidadas, como deixa claro o art. 537, § 1°, do CPC ao se referir a "multa vincenda". Isso porque há preclusão consumativa em relação às questões de ordem pública, inclusive àquelas que estão fora da esfera de disponibilidade das partes, tais como os pressupostos processuais e as condições da ação, conforme entendimento sedimentado no STJ.

      • Assim sendo, e com maior razão, há preclusão consumativa no tocante ao montante acumulado da multa cominatória, pois ostenta natureza patrimonial e disponível.

    3. obrigação de fazer ou de não fazer
      • Informativo nº 859
      • 26 de agosto de 2025.
      • SEGUNDA TURMA
      • Processo: REsp 2.218.969-SP, Rel. Ministro Afrânio Vilela, Segunda Turma, por unanimidade, julgado em 19/8/2025.

      Ramo do Direito DIREITO ADMINISTRATIVO, DIREITO PROCESSUAL CIVIL

      Tutela do patrimônio histórico-cultural. Imóvel tombado. Restauração. Meras intenções e atos administrativos convergentes com a pretensão judicial. Perda de objeto. Inocorrência. Necessidade de atendimento integral do pedido. Condução estrutural da fase executória.

      Destaque - A mera intenção ou mesmo o início das obras de restauração de bem tombado não caracteriza por si só a perda de interesse processual, uma vez que o cumprimento integral da obrigação judicial é necessário para a extinção do processo por perda do objeto.

      Informações do Inteiro Teor - A questão em discussão consiste em saber se o início das obras de restauração do bem tombado pelo município caracteriza perda de interesse processual, tornando desnecessária a continuidade da demanda.

      • No caso, trata-se de ação civil pública ajuizada pelo Ministério Público contra um município, visando à restauração do Galpão da Oficina de Locomotivas, patrimônio tombado por Lei Municipal. A sentença condenou o ente federativo a executar as obras no prazo de seis meses, sob pena de multa e a apelação foi desprovida.

      • A deterioração do bem é registrada desde a década de 1980, o tombamento ocorreu nos anos 1990, o imóvel está interditado desde 2009 e a municipalidade manifesta reiteradamente, ao longo de décadas, suas melhores intenções de devolver o bem à coletividade, sem efetivá-lo.

      • No que tange ao interesse de agir do Ministério Público, o município recorrente defende sua inexistência porque teria conduzido a matéria administrativa de maneira adequada, com licitação e início das obras para restaurar o bem tombado.

      • A pretensão de que seja reconhecida a perda de objeto dita unilateral depende de que a parte ré entregue ao autor o bem da vida integralmente demandado em juízo. No caso, a parte apenas manifesta a intenção de entregar parte do bem da vida demandado.

      • Nas situações envolvendo o Poder Público, essa pretensão de reconhecimento da perda de objeto deve ser tratada com ainda maior critério. Isso porque, nos termos da doutrina, "Atores governamentais com frequência usam a perda de objeto para evadirem-se de precedentes desfavoráveis.".

      • Por isso, a mera intenção ou mesmo início das obras de restauração não caracteriza perda de objeto, pois o cumprimento <u>integral</u> da obrigação judicial é necessário para a extinção do interesse processual.

      • O cumprimento da obrigação disposta na sentença, portanto, somente poderá ser verificado na fase executória do provimento. É o juízo da execução que poderá considerar de modo efetivo os atos e esforços concretos da municipalidade que atendem de forma mais eficiente ao provimento judicial, inclusive com eventual modulação de prazos e multas, que não devem ser afastados de plano.

      • Além disso, do cenário descrito, depreende-se a <u>natureza estrutural da demanda</u>. Assim, a abordagem da causa, ainda que tardiamente, já em sua fase executória, pode e deve ser feita pela lente dos processos estruturais.

      • É certo que o caso trata de uma "nanoinstitucionalidade", uma situação de violação sistemática dos direitos da coletividade à cultura e à memória bastante delimitada, com um provimento jurisdicional bem específico, condição que nem sempre é entendida como matéria estrutural, dado seu limitado alcance.

      • Mas isso não impede que, no momento da execução da sentença, práticas, métodos e princípios típicos do processo estrutural sejam adotados pelo juízo exequente, conforme necessários e adequados. Nesse sentido, recentemente o Conselho Nacional de Justiça - CNJ aprovou a Recomendação n. 163 de 16/6/2025, norma incentivadora da condução estrutural de processos judiciais.

      • Ademais, considerando que se trata de patrimônio histórico e cultural de uma municipalidade, a adoção de técnicas estruturais de condução do feito atende, ainda, à concretização do princípio da participação comunitária, conforme reconhecido desde 1967 pelos Estados membros da Organização dos Estados Americanos - OEA,

      • Nessa linha, e conforme disposto pelo Fórum Permanente de Processualistas Civis, como boa prática na condução do feito estrutural em instância recursal, afigura-se adequado dar indicações concretas ao juízo de execução sobre os parâmetros de atuação nessa circunstância (Boa Prática n. 22/FPPC), nos termos já adotados, inclusive como paradigmas desse agir, por esta Corte (REsp n. 1.854.842/CE, relatora Ministra Nancy Andrighi, Terceira Turma, julgado em 2/6/2020, DJe de 4/6/2020).

      • Assim, recomenda-se ao magistrado encarregado da execução, resguardada sua independência funcional, a adoção de, entre outras, de medidas de natureza estruturante, tais como: i) estabelecimento de comitê de condução e monitoramento do projeto de restauração, inclusive com a participação de entidades da sociedade civil representantes do setor de cultura e memória, órgãos especializados de suporte, como o CREA, e representantes do Legislativo, além das partes e representante do juízo; ii) a eventual dilação do prazo de conclusão das obras, inclusive com suspensão temporária das multas condicionada ao cumprimento de eventual cronograma acordado pelas partes; iii) determinação de publicação no portal do Poder Executivo Municipal de relatórios periódicos, em intervalos de não mais que 45 dias, de execução do projeto de restauração, com os itens mínimos que entender necessários; e iv) realização de audiência pública prévia ao encerramento da obra, na sua iminência, para coleta de manifestações da sociedade sobre o alcance dos objetivos da sentença de conhecimento e prestação de contas pelos réus.

      • Recomenda-se, ainda, ao Tribunal respectivo que providencie o apoio institucional necessário ao magistrado singular na implementação dessas medidas, tudo orientado pelo princípio maior de cooperação.

      • Por fim, ao contrário do que alega a municipalidade, se a sentença confirma sua intenção administrativa, a imposição judicial pode destravar as diversas amarras burocráticas e políticas impostas a seus próprios gestores.

      • A sentença não será vazia, mas catalisadora dos efeitos concretos da política pública de proteção ao patrimônio histórico-cultural que a própria Administração não só é obrigada por lei a implementar, como assim também o deseja há tantas décadas.

      • Será, ainda, obrigação específica, decorrente de título judicial executivo, que vinculará não só a gestão atual como as futuras, de forma impessoal e para além de voluntarismos, como exige a situação degradante enfrentada pelo bem municipal tombado.

      • Por isso, o provimento judicial resguardará tanto a pretensão do autor como as intenções do réu, de modo a concretizá-las a ambas as partes. Desse modo, o objeto jurídico, que deve ser entendido como a devolução à coletividade do bem histórico-cultural que verdadeiramente lhe pertence, permanece íntegro.

    1. Art. 113
      • Informativo nº 859
      • 26 de agosto de 2025.
      • TERCEIRA TURMA
      • Processo: * Processo em segredo de justiça, Rel. Ministra Nancy Andrighi, Terceira Turma, por unanimidade, julgado em 17/6/2025, DJEN 27/6/2025.

      Ação de exoneração de alimentos. Alimentos entre ex-cônjuges. Pagamento de pensão alimentícia por mais de duas décadas após o termo final da obrigação. Liberalidade. Expectativa legítima de continuidade da prestação. Supressio configurada.

      Destaque - É possível a manutenção do pagamento de pensão alimentícia por prazo indeterminado, na hipótese em que o ex-marido, mesmo exonerado, optou voluntariamente por continuar realizando o pagamento de alimentos por duas décadas, em razão da configuração dos institutos da supressio para o alimentante, que deixou de exercer seu direito de cessar os pagamentos, e da surrectio para a alimentanda diante da expectativa de que o direito de exoneração dos alimentos não mais seria reivindicado pelo ex-cônjuge.

      Informações do Inteiro Teor - Cinge-se a controvérsia em decidir se o pagamento de pensão alimentícia pelo ex-marido, por mais de duas décadas após o termo final da obrigação, configura a incidência do instituto da supressio, fazendo nascer para a ex-esposa a expectativa legítima de continuidade da prestação, em homenagem à boa-fé objetiva.

      • A confiança, no contexto das relações privadas, desempenha papel fundamental ao assegurar proteção qualificada ao comportamento humano, sendo expressão concreta da solidariedade social constitucionalmente albergada. Essa confiança impõe a todos o dever jurídico de não frustrar, injustificadamente, as legítimas expectativas de terceiros. No âmbito das relações familiares, a noção de confiança deve ser especialmente protegida, de forma que as condutas contrárias à confiança serão, em regra, também contrárias à boa-fé objetiva.

      • A tutela da confiança assume relevância ética nas relações privadas ao proibir comportamentos contraditórios (venire contra factum proprium) e ao reconhecer efeitos decorrentes da inércia prolongada (supressio) ou da prática constante (surrectio). Tais figuras jurídicas operam como mecanismos de estabilização das expectativas, impedindo mudanças abruptas de conduta que contrariem a confiança anteriormente depositada.

      • Identifica-se a supressio como a perda de determinada faculdade jurídica em razão do não exercício prolongado desse direito, o que leva ao seu esvaziamento. Em contrapartida, a surrectio consiste no surgimento de uma vantagem para determinada pessoa, justamente porque a outra parte deixou de exercer o direito ao qual faria jus, criando, assim, a expectativa de que esse direito não mais seria reivindicado futuramente.

      • A supressio aproxima-se, sem dúvida, do venire contra factum proprium, pois ambas as figuras atuam como fatores de preservação da confiança alheia. Mas dele se diferencia primordialmente pois, enquanto no venire, a expectativa do outro decorre de uma conduta ativa anterior, que não pode ser desmentida posteriormente; na supressio, a expectativa nasce da omissão prolongada do titular do direito, cuja inércia, associada a elementos objetivos que indiquem o desuso, conduz à convicção de que tal direito não será mais exercido.

      • Assim, a inércia prolongada do credor de alimentos em promover a execução da pensão em débito pode gerar, no devedor, a legítima expectativa de que a prestação não é mais necessária, conduzindo à estabilização da situação de inadimplemento. Em sentido inverso, o alimentante que, mesmo exonerado, opta voluntariamente por continuar realizando os pagamentos, conduz ao alimentando a expectativa de continuidade da prestação, a qual pode tornar-se juridicamente relevante, especialmente diante da reiterada e sistemática manifestação de vontade.

      • A aplicação da boa-fé no âmbito do Direito de Família reforça a dimensão ética e funcional da confiança, reafirmando seu papel como vetor interpretativo e integrativo. A eventual violação de justa expectativa deverá ser verificada na situação em concreto, devendo o julgador buscar a melhor forma de concretização das expectativas e esperanças criadas no ambiente familiar.

      • O caráter de transitoriedade dos alimentos entre ex-cônjuges parece traduzir o conteúdo da boa-fé objetiva, uma vez que deve a obrigação alimentar garantir o fornecimento de auxílio material ao cônjuge depreciado em razão de sua vulnerabilidade social e econômica, até que possa retomar sua autonomia financeira.

      • Os alimentos transitórios não serão cabíveis, entretanto, quando as necessidades são permanentes, em decorrência da incapacidade perene do alimentando de promover seu próprio sustento.

      • A jurisprudência do Superior Tribunal de Justiça tem admitido a perenidade da obrigação de prestar alimentos entre ex-cônjuges em situações excepcionais, como na impossibilidade prática de reinserção do alimentando no mercado de trabalho; em hipótese de idade avançada do alimentando; ou de condição de saúde fragilizada.

      • Dessa forma, constatando-se, na espécie, a incapacidade laboral do alimentando, saúde fragilizada, idade avançada ou qualquer impossibilidade prática de inserção no mercado de trabalho, ou de adquirir autonomia financeira, a pensão alimentícia entre ex-cônjuges poderá ser fixada por prazo indeterminado.

      • No caso, é incontroverso que as partes se encontram divorciadas há mais de 30 (trinta anos), tendo firmado acordo para pagamento de pensão alimentícia pelo ex-marido à ex-esposa, correspondente a 5% dos seus rendimentos líquidos, além de pagamento de plano de saúde, pelo prazo de um ano. Referido acordo fora homologado judicialmente em 1993.

      • Dois anos depois, as partes peticionaram nos autos da ação de divórcio requerendo a alteração do acordo, para que o pagamento da pensão alimentícia fosse prorrogado por prazo indeterminado. Embora não tenha o juízo conhecido do pedido, em razão da necessidade de ajuizamento de ação própria, o ex-marido permaneceu alcançando a pensão alimentícia à ex-esposa por mais de 25 (vinte e cinco) anos, até o ajuizamento da ação de exoneração, em julho de 2018.

      • O fato de a ex-esposa ter recebido pensão alimentícia por mais de 25 (vinte e cinco) anos, no entanto, não demonstra sua inércia em retomar a independência financeira. Do contrário, a inércia do ex-marido em permanecer realizando os pagamentos mensais acordados por longo período, mesmo que exonerado, provocou na alimentanda a expectativa de que o direito de exoneração não seria mais por ele exercida.

      • Portanto, evidencia-se, da conduta do alimentante, o instituto da supressio, visto que deixou de exercer seu direito de cessar o pagamento dos alimentos por mais de duas décadas, conduzindo à estabilização da situação de fato. Lado outro, surge para a alimentanda a surrectio, diante da expectativa de que o direito de exoneração dos alimentos não mais seria reivindicado pelo ex-marido.

      • Com efeito, o alimentante que, mesmo exonerado, opta voluntariamente por continuar realizando os pagamentos, conduz ao alimentando a expectativa de continuidade da prestação, a qual pode tornar-se juridicamente relevante, especialmente diante da reiterada e sistemática manifestação de vontade.

      • Some-se a isso o fato de que a ex-esposa teve de abdicar de seu trabalho em razão de mudança da família para a cidade de Petrópolis, em função do emprego do ex-marido. A realidade vivenciada pelo casal ao tempo da constância da sociedade conjugal deve ser considerada quando da fixação da pensão alimentícia.

      • Ademais, tendo em vista que a alimentanda é pessoa idosa, possui doença grave e se encontra impossibilitada de se reinserir no mercado de trabalho; e o alimentante aufere renda suficiente para permanecer cumprindo a obrigação constituída; deve-se manter o pagamento da pensão alimentícia por prazo indeterminado.

    1. Should we add any further CNs from the shortlisting exercise of additional codes?

      to answer this, I think requires a bit of further analysis like you did with 0305 to check at least if they have similar weights?

    2. “Equipment that is specifically designed and installed as part of another type of equipment that is excluded from or does not fall within the scope of this Directive, and can fulfil its function only if it is part of that equipment.

      hmm wouldn't this also be the definition of the open scope, contracting to it?

    3. . A direct comparison between these needs to account for this.

      if few we can help compare, if many, I would stick to those that are present in year 2020, and remove the different ones that are not, since HS codes have been updated in 2022. It's interesting that this happens. Give two people the same job and they would create different correspondences, so I suspect this is what happened with the CN-CN and HS-HS not been equivalent when substringing. Alternatively, stick to the approach 1?

    4. 851761

      HS 851761: base stations. For me it should not be 0305. The way that 0310 is currently described, it should go there. However, like I said before not sure it is within scope. Seeing your analysis, I also think it is a category on its own.

    5. It may be something we can ask a specific question on at the consultation

      based on your analysis, I would say 0305 only 851711 and 851718, the rest goes to 0310. However,I don't think 851761 should be in 0310 since we want unu keys with similar weight, price.

      Regarding understanding HS codes, I contacted this guy once to understand some updates of HS codes for renewable energy and he actually replied. Might be worth contacting him:

      https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://nl.linkedin.com/in/izaak-wind-9432943b&ved=2ahUKEwi5-PuI_6qPAxVIU0EAHdWUO8cQFnoECCMQAQ&usg=AOvVaw3GqwGAAWScky-rBOtWKmfl

    1. eLife Assessment

      This paper presents a valuable software package, named "Virtual Brain Inference" (VBI), that enables faster and more efficient inference of parameters in dynamical system models of whole-brain activity, grounded in artificial network networks for Bayesian statistical inference. The authors have provided convincing evidence, across several case studies, for the utility and validity of the methods using simulated data from several commonly used models, but more thorough benchmarking could be used to demonstrate the practical utility of the toolkit. This work will be of interest to computational neuroscientists interested in modelling large-scale brain dynamics.

    2. Reviewer #1 (Public review):

      This work provides a new Python toolkit for combining generative modeling of neural dynamics and inversion methods to infer likely model parameters that explain empirical neuroimaging data. The authors provided tests to show the toolkit's broad applicability, accuracy, and robustness; hence, it will be very useful for people interested in using computational approaches to better understand the brain.

      Strengths:

      The work's primary strength is the tool's integrative nature, which seamlessly combines forward modelling with backward inference. This is important as available tools in the literature can only do one and not the other, which limits their accessibility to neuroscientists with limited computational expertise. Another strength of the paper is the demonstration of how the tool can be applied to a broad range of computational models popularly used in the field to interrogate diverse neuroimaging data, ensuring that the methodology is not optimal to only one model. Moreover, through extensive in-silico testing, the work provided evidence that the tool can accurately infer ground-truth parameters even in the presence of noise, which is important to ensure results from future hypothesis testing are meaningful.

      Weaknesses

      The paper still lacks appropriate quantitative benchmarking relative to non-Bayesian-based inference tools, especially with respect to performance accuracy and computational complexity and efficiency. Without this benchmarking, it is difficult to fully comprehend the power of the software or its ability to be extended to contexts beyond large-scale computational brain modelling.

    3. Reviewer #2 (Public review):

      Summary:

      Whole-brain network modeling is a common type of dynamical systems-based method to create individualized models of brain activity incorporating subject-specific structural connectome inferred from diffusion imaging data. This type of model has often been used to infer biophysical parameters of the individual brain that cannot be directly measured using neuroimaging but may be relevant to specific cognitive functions or diseases. Here, Ziaeemehr et al introduce a new toolkit, named "Virtual Brain Inference" (VBI), offering a new computational approach for estimating these parameters using Bayesian inference powered by artificial neural networks. The basic idea is to use simulated data, given known parameters, to train artificial neural networks to solve the inverse problem, namely, to infer the posterior distribution over the parameter space given data-derived features. The authors have demonstrated the utility of the toolkit using simulated data from several commonly used whole-brain network models in case studies.

      Strength:

      - Model inversion is an important problem in whole-brain network modeling. The toolkit presents a significant methodological step up from common practices, with the potential to broadly impact how the community infers model parameters.<br /> - Notably, the method allows the estimation of the posterior distribution of parameters instead of a point estimation, which provides information about the uncertainty of the estimation, which is generally lacking in existing methods.<br /> - The case studies were able to demonstrate the detection of degeneracy in the parameters, which is important. Degeneracy is quite common in this type of models. If not handled mindfully, they may lead to spurious or stable parameter estimation. Thus, the toolkit can potentially be used to improve feature selection or to simply indicate the uncertainty.<br /> - In principle, the posterior distribution can be directly computed given new data without doing any additional simulation, which could improve the efficiency of parameter inference on the artificial neural network is well-trained.

      Weaknesses:

      - The z-scores used to measure prediction error are generally between 1-3, which seems quite large to me. It would give readers a better sense of the utility of the method if comparisons to simpler methods, such as k-nearest neighbor methods, are provided in terms of accuracy.<br /> - A lot of simulations are required to train the posterior estimator, which is computationally more expensive than existing approaches. Inferring from Figure S1, at the required order of magnitudes of the number of simulations, the simulation time could range from days to years, depending on the hardware. The payoff is that once the estimator is well-trained, the parameter inversion will be very fast given new data. However, it is not clear to me how often such use cases would be encountered. It would be very helpful if the authors could provide a few more concrete examples of using trained models for hypothesis testing, e.g., in various disease conditions.

    4. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      This work provides a new Python toolkit for combining generative modeling of neural dynamics and inversion methods to infer likely model parameters that explain empirical neuroimaging data. The authors provided tests to show the toolkit's broad applicability and accuracy; hence, it will be very useful for people interested in using computational approaches to better understand the brain.

      Strengths:

      The work's primary strength is the tool's integrative nature, which seamlessly combines forward modelling with backward inference. This is important as available tools in the literature can only do one and not the other, which limits their accessibility to neuroscientists with limited computational expertise. Another strength of the paper is the demonstration of how the tool can be applied to a broad range of computational models popularly used in the field to interrogate diverse neuroimaging data, ensuring that the methodology is not optimal to only one model. Moreover, through extensive in-silico testing, the work provided evidence that the tool can accurately infer ground-truth parameters, which is important to ensure results from future hypothesis testing are meaningful.

      We are happy to hear the positive feedback on our effort to provide an open-source and widely accessible tool for both fast forward simulations and flexible model inversion, applicable across popular models of large-scale brain dynamics.

      Weaknesses:

      Although the tool itself is the main strength of the work, the paper lacked a thorough analysis of issues concerning robustness and benchmarking relative to existing tools.

      The first issue is the robustness to the choice of features to be included in the objective function. This choice significantly affects the training and changes the results, as the authors even acknowledged themselves multiple times (e.g., Page 17 last sentence of first paragraph or Page 19 first sentence of second paragraph). This brings the question of whether the accurate results found in the various demonstrations are due to the biased selection of features (possibly from priors on what worked in previous works). The robustness of the neural estimator and the inference method to noise was also not demonstrated. This is important as most neuroimaging measurements are inherently noisy to various degrees.

      The second issue is on benchmarking. Because the tool developed is, in principle, only a combination of existing tools specific to modeling or Bayesian inference, the work failed to provide a more compelling demonstration of its added value. This could have been demonstrated through appropriate benchmarking relative to existing methodologies, specifically in terms of accuracy and computational efficiency.

      We fully agree with the reviewer that the VBI estimation heavily depends on the choice of data features, and this is the core of the inference procedure, not its weakness. We have demonstrated different scenarios showing how the informativeness of features (commonly used in the literature) results in varying uncertainty quantification. For instance, using summary statistics of functional connectivity (FC) and functional connectivity dynamics (FCD) matrices to estimate global coupling parameter leads to fast convergence; however, it is not sufficient to accurately estimate the whole-brain heterogeneous excitability parameter, which requires features such as statistical moments of time series. VBI provides a taxonomy of data features that users can employ to test their hypotheses. It is important to note that one major advantage of VBI is its ability to make estimation using a battery of data features, rather than relying on a limited set (such as only FC or FCD) as is often the case in the literature. In the revised version, we will elaborate further by presenting additional scenarios to demonstrate the robustness of the estimation. We will also evaluate the robustness of the neural density estimators to (dynamical/additive) noise.

      More importantly, relative to benchmarking, we would like to draw attention to a key point regarding existing tools and methods. The literature often uses optimization for fitting whole-brain network models, and its limitations for reliable causal hypothesis testing have been pointed out in the Introduction/Discussion. As also noted by the reviewer under strengths, and to the best of our knowledge, there are no existing tools other than VBI that can scale and generalize to operate across whole-brain models for Bayesian model inversion. Previously, we developed Hamiltonian Monte Carlo (HMC) sampling for Epileptor model in epilepsy (Hashemi et al., 2020, Jha et al., 2022). This phenomenological model is very well-behaved in terms of numerical integration, gradient calculation, and dynamical system properties (Jirsa et al., 2014). However, this does not directly generalize to other models, particularly the Montbrió model for resting-state, which exhibits bistability with noise driving transitions between states. As shown in Baldy et al., 2024, even at the level of a single neural mass model (i.e., one brain region), gradient-based HMC failed to capture such switching behaviour, particularly when only one state variable (membrane potential) was observed while the other (firing rate) was missing. Our attempts to use other methods (e.g., the second-derivative-based Laplace approximation used in Dynamic Causal Modeling) also failed, due to divergence in gradient calculation. Nevertheless, reparameterization techniques (Baldy et al., 2024) and hybrid algorithms (Gabrié et al., 2022) could offer improvements, although this remains an open problem for these classes of computational models.

      In sum, for oscillatory systems, it has been shown previously that SBI approach used in VBI substantially outperforms both gradient-based and gradient-free alternative methods (Gonçalves et al., 2020, Hashemi et al., 2023, Baldy et al., 2024). Importantly, for bistable systems with switching dynamics, gradient-based methods fail to converge, while gradient-free methods do not scale to the whole-brain level (Hashemi et al., 2020). Hence, the generalizability of VBI relies on the fact that neither the model nor the data features need to be differentiable. We will clarify this point in the revised version. Moreover, we will provide better explanations for some terms mentioned by the reviewer in Recommendations.

      Hashemi, M., Vattikonda, A. N., Sip, V., Guye, M., Bartolomei, F., Woodman, M. M., & Jirsa, V. K. (2020). The Bayesian Virtual Epileptic Patient: A probabilistic framework designed to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread. NeuroImage, 217, 116839.

      Jha, J., Hashemi, M., Vattikonda, A. N., Wang, H., & Jirsa, V. (2022). Fully Bayesian estimation of virtual brain parameters with self-tuning Hamiltonian Monte Carlo. Machine Learning: Science and Technology, 3(3), 035016.

      Jirsa, V. K., Stacey, W. C., Quilichini, P. P., Ivanov, A. I., & Bernard, C. (2014). On the nature of seizure dynamics. Brain, 137(8), 2210-2230.

      Baldy, N., Breyton, M., Woodman, M. M., Jirsa, V. K., & Hashemi, M. (2024). Inference on the macroscopic dynamics of spiking neurons. Neural Computation, 36(10), 2030-2072.

      Baldy, N., Woodman, M., Jirsa, V., & Hashemi, M. (2024). Dynamic Causal Modeling in Probabilistic Programming Languages. bioRxiv, 2024-11.

      Gabrié, M., Rotskoff, G. M., & Vanden-Eijnden, E. (2022). Adaptive Monte Carlo augmented with normalizing flows. Proceedings of the National Academy of Sciences, 119(10), e2109420119.

      Gonçalves, P. J., Lueckmann, J. M., Deistler, M., Nonnenmacher, M., Öcal, K., Bassetto, G., ... & Macke, J. H. (2020). Training deep neural density estimators to identify mechanistic models of neural dynamics. elife, 9, e56261.

      Hashemi, M., Vattikonda, A. N., Jha, J., Sip, V., Woodman, M. M., Bartolomei, F., & Jirsa, V. K. (2023). Amortized Bayesian inference on generative dynamical network models of epilepsy using deep neural density estimators. Neural Networks, 163, 178-194.

      Reviewer #2 (Public review):

      Summary:

      Whole-brain network modeling is a common type of dynamical systems-based method to create individualized models of brain activity incorporating subject-specific structural connectome inferred from diffusion imaging data. This type of model has often been used to infer biophysical parameters of the individual brain that cannot be directly measured using neuroimaging but may be relevant to specific cognitive functions or diseases. Here, Ziaeemehr et al introduce a new toolkit, named "Virtual Brain Inference" (VBI), offering a new computational approach for estimating these parameters using Bayesian inference powered by artificial neural networks. The basic idea is to use simulated data, given known parameters, to train artificial neural networks to solve the inverse problem, namely, to infer the posterior distribution over the parameter space given data-derived features. The authors have demonstrated the utility of the toolkit using simulated data from several commonly used whole-brain network models in case studies.

      Strengths:

      (1) Model inversion is an important problem in whole-brain network modeling. The toolkit presents a significant methodological step up from common practices, with the potential to broadly impact how the community infers model parameters.

      (2) Notably, the method allows the estimation of the posterior distribution of parameters instead of a point estimation, which provides information about the uncertainty of the estimation, which is generally lacking in existing methods.

      (3) The case studies were able to demonstrate the detection of degeneracy in the parameters, which is important. Degeneracy is quite common in this type of model. If not handled mindfully, they may lead to spurious or stable parameter estimation. Thus, the toolkit can potentially be used to improve feature selection or to simply indicate the uncertainty.

      (4) In principle, the posterior distribution can be directly computed given new data without doing any additional simulation, which could improve the efficiency of parameter inference on the artificial neural network if well-trained.

      We thank the reviewer for the careful consideration of important aspects of the VBI tool, such as uncertainty quantification, degeneracy detection, parallelization, and amortization strategy.

      Weaknesses:

      (1) While the posterior estimator was trained with a large quantity of simulated data, the testing/validation is only demonstrated with a single case study (one point in parameter space) per model. This is not sufficient to demonstrate the method's accuracy and reliability, but only its feasibility. Demonstrating the accuracy and reliability of the posterior estimation in large test sets would inspire more confidence.

      (2) The authors have only demonstrated validation of the method using simulated data, but not features derived from actual EEG/MEG or fMRI data. So, it is unclear if the posterior estimator, when applied to real data, would produce results as sensible as using simulated data. Human data can often look quite different from the simulated data, which may be considered out of distribution. Thus, the authors should consider using simulated test data with out-of-distribution parameters to validate the method and using real human data to demonstrate, e.g., the reliability of the method across sessions.

      (3) The z-scores used to measure prediction error are generally between 1-3, which seems quite large to me. It would give readers a better sense of the utility of the method if comparisons to simpler methods, such as k-nearest neighbor methods, are provided in terms of accuracy.

      (4) A lot of simulations are required to train the posterior estimator, which seems much more than existing approaches. Inferring from Figure S1, at the required order of magnitudes of the number of simulations, the simulation time could range from days to years, depending on the hardware. Although once the estimator is well-trained, the parameter inverse given new data will be very fast, it is not clear to me how often such use cases would be encountered. Because the estimator is trained based on an individual connectome, it can only be used to do parameter inversion for the same subject. Typically, we only have one session of resting state data from each participant, while longitudinal resting state data where we can assume the structural connectome remains constant, is rare. Thus, the cost-efficiency and practical utility of training such a posterior estimator remains unclear.

      We agree with the reviewer that it is necessary to show results on larger synthetic test sets, and we will elaborate further by presenting additional scenarios to demonstrate the robustness of the estimation. However, there are some points raised by the reviewer that we need to clarify.

      The validation on empirical data was beyond the scope of this study, as it relates to model validation rather than the inversion algorithms. This is also because we aimed to avoid repetition, given that we have previously demonstrated model validation on empirical data using theses techniques, for invasive sEEG (Hashemi et al., 2023), MEG (Sorrentino et al., 2024), EEG (Angiolelli et al., 2025) and fMRI (Lavanga et al., 2024, Rabuffo et al., 2025). Note that if the features of the observed data are not included during training, VBI ignores them, as it requires an invertible mapping function between parameters and data features.

      We have used z-scores and posterior shrinkage to measure prediction performance, as these are Bayesian metrics that take into account the variance of both prior and posterior rather than only the mean value or thresholding for ranking of the prediction used in k-NN or confusion matrix methods. This helps avoid biased accuracy estimation, for instance, if the mean posterior is close to the true value but there is no posterior shrinkage. Although shrinkage is bounded between 0 and 1, we agree that z-scores have no upper bound for such diagnostics.

      Finally, the number of required simulations depends on the dimensionality of the parameter space and the informativeness of the data features. For instance, estimating a single global scaling parameter requires around 100 simulations, whereas estimating whole-brain heterogeneous parameters requires substantially more simulations. Nevertheless, we have provided fast simulations, and one key advantage of VBI is that simulations can be run in parallel (unlike MCMC sampling, which is more limited in this regard). Hence, with commonly accessible CPUs/GPUs, the fast simulations and parallelization capabilities of the VBI tool allow us to run on the order of 1 million simulations within 2–3 days on desktops, or in less than half a day on supercomputers at cohort level, rather than over several years! It has been previously shown that the SBI method used in VBI provides an order-of-magnitude faster inversion than HMC for whole-brain epilepsy spread (Hashemi et al., 2023). Moreover, after training, the amortized strategy is critical for enabling hypothesis testing within seconds to minutes. We agree that longitudinal resting-state data under the assumption of a constant structural connectome is rare; however, this strategy is essential in brain diseases such as epilepsy, where experimental hypothesis testing is prohibitive.

      We will clarify these points and better explain some terms mentioned by the reviewer in the revised manuscript.

      Hashemi, M., Vattikonda, A. N., Jha, J., Sip, V., Woodman, M. M., Bartolomei, F., & Jirsa, V. K. (2023). Amortized Bayesian inference on generative dynamical network models of epilepsy using deep neural density estimators. Neural Networks, 163, 178-194.

      Sorrentino, P., Pathak, A., Ziaeemehr, A., Lopez, E. T., Cipriano, L., Romano, A., ... & Hashemi, M. (2024). The virtual multiple sclerosis patient. IScience, 27(7).

      Angiolelli, M., Depannemaecker, D., Agouram, H., Regis, J., Carron, R., Woodman, M., ... & Sorrentino, P. (2025). The virtual parkinsonian patient. npj Systems Biology and Applications, 11(1), 40.

      Lavanga, M., Stumme, J., Yalcinkaya, B. H., Fousek, J., Jockwitz, C., Sheheitli, H., ... & Jirsa, V. (2023). The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging. NeuroImage, 283, 120403.

      Rabuffo, G., Lokossou, H. A., Li, Z., Ziaee-Mehr, A., Hashemi, M., Quilichini, P. P., ... & Bernard, C. (2025). Mapping global brain reconfigurations following local targeted manipulations. Proceedings of the National Academy of Sciences, 122(16), e2405706122.

      Recommendations for the authors:

      We appreciate the time and effort of the reviewers, and their insightful and constructive comments to improve the paper. We have now addressed the reviewers’ comments in our revised manuscript and provide here below detailed explanations of the changes.

      We have adapted the Wilson-Cowan model to follow the same brain network modeling notation as the other models (Fig. 3 in the main text and Figs. S2–S4 in the supplementary materials). Additionally, we have included multiple figures in the supplementary material presenting extensive in-silico testing to demonstrate the accuracy and reliability of the estimations across different configurations, as well as the sensitivity to both additive and dynamical noise.

      Reviewer #1 (Recommendations for the authors):

      (1) There were some inaccurate statements throughout the text that need to be corrected.

      a) In section 2.1, paragraph 1, the authors mentioned that they would describe network models corresponding to different types of neuroimaging recordings. This is inaccurate. The models were developed to approximate various aspects of the architecture of neural circuits. They were not developed per se to solely describe a specific neuroimaging modality.

      Thank you for pointing this out. We agree that our phrasing in Section 2.1, paragraph 1, was not clear that the network models were developed to generate neural activity at the source level, and that a projection needs to be established to transform the simulated neural activity into empirically measurable quantities, such as BOLD fMRI, EEG, or MEG. We have revised the wording in the revised manuscript to clarify this point accordingly.

      b) The use of the term "spatio-temporal data features" is misleading as there are no true spatial features extracted.

      We have clarified that:Following Hashemi et al., 2024, we use the term spatio-temporal data features to refer to both statistical and temporal features derived from time series. In contrast, we refer to the connectivity features extracted from FC/FCD matrices as functional data features. We would like to retain this term, as it is used consistently in the code.

      (2) The authors need to improve the model descriptions in Equations (1)-(10). Several variables/parameters were not explained, limiting the accessibility of the work to those without prior experience in computational modeling.

      Thank you for pointing this out. In the revised manuscript, we have improved the model descriptions, all variables and parameters used in these equations.

      (3) Various things need further clarification and/or explanation:

      a) There is a need to highlight that the models section only provides examples of one of the many possible variants of the models. For example, the Wilson-Cowan model described is not your typical and more popular cortico-cortical-based Wilson-Cowan model. This is important to ensure that the work reflects an accurate account of the literature, avoiding future references that the models presented are THE models.

      This is a very important point. We have now highlighted that each model represents one of many possible variants. Moreover, we adapted the Wilson-Cowan model as a whole-brain network modeling approach to harmonize with all other models.

      b) In Figure 1, it is unclear where the empirical data come into play. The neural density estimator also sounds like a black box and needs further explanation (e.g., its architecture).

      Thank you for the careful reading. This is correct. We have now clarified where the empirical data enters as input to the neural density estimator and have added further explanation in section 2.2.

      c) There is also a need to better explain what shrinkage means and what the z-score vs shrinkage implies.

      We have elaborated on the definition of posterior z-score and shrinkage.

      d) It is unclear how the authors decided on the number of training samples to use.

      There is no specific rule for determining the optimal number of simulations required for training. In general, the larger number of simulations, within the available computational budget, the better the posterior estimation is likely to be. In the case of synthetic data, we have monitored the z-score and posterior shrinkage to assess the quality and reliability of the inferred parameters.  This also critically depends on the parameter dimensionality. For instance, in estimating only global coupling parameter, a maximum of 300 simulations was used, demonstrating accurate estimation across models and different realizations (Fig S20), except for the Jansen-Rit model, where coupling did not induce a significant change in the intrinsic frequency of regional activity. We have now pointed this out in the discussion.

      e) In the Results section, paragraph 1, there is a need to clarify that "ground truth" is available because you simulate data using predefined parameters. In fact, these predefined parameters and how they were chosen to generate the observed data were never described in the text.

      The "ground truth" is often chosen randomly within biologically plausible ranges, typically with some level of heterogeneity, and this has now been highlighted.

      f) Can the authors comment on why the median of the posterior distributions (e.g., in Figure 4E) is actually far off from the ground truth parameters? This is probably understandable in the Jansen-Ritt model due to complexity, but not obvious in the very low-dimensional Stuart-Landau oscillator model.

      This can happen due to non-identifiability in high-dimensional settings. Figure 4E represents the posterior estimation using Jansen-Rit model with high-dimensional parameters. An accurate estimation close to the true values can be observed in the low-dimensional Stuart-Landau model, as shown in Figure 5.

      g) In Figure 7, the FC and FCD matrices look weird relative to those typically seen in other works.

      We have updated Figure 7. To do the our best, we have followed the code and the parameters from the following paper Kong et al., Nat Commun 12, 6373 (2021), and the following repo https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/fMRI_dynamics/Kong2021_pMFM/examples/scripts/CBIG_pMFM_parameter_estimation_example.py

      We considered 300 iterations for optimizing the parameters, using CMA-ES method, and with window length of 60 sec, and TR=0.72 sec, yielding a 1118 × 1118 FCD matrix for each run. Nevertheless, some discrepancy can happen with the shown FC/FCD, due to convergence of the optimization process and other model parameters.

      h) In Figure 8, results for the J parameter are missing. Also, the BOLD signal time series of some regions in Figure 8B looks very weird, with some having very large deflections.

      We have updated Figure 8. In this figure, the parameter J is not inferred; it is instead presented in the appendix (S18). Please note that the system is in a bistable regime. We have implemented the full Wong-Wang model (Deco, 2014, Journal of Neuroscience), by optimized external current and global coupling (using CMA-ES optimization) to maximize the fluidity of FCD, as those typically seen in other works:

      Author response image 1.

      i) On page 14, the authors mentioned that they perform a PCA on the FC/FCD matrices. Can the authors explain this step further and what it specifically gives out, as this is something unusual in the generative model fitting literature?

      Indeed, PCA is a widely used dimension reduction method in machine learning. Please note that in SBI, any dimensionality reduction technique, such as PCA, can be used, as long as it preserves information relevant to the target parameters.

      j) On page 3, what does ABC in ABC methods stand for?

      ABC stands for Approximate Bayesian Computation, which is now spelled out in the text.

      Reviewer #2 (Recommendations for the authors):

      Overall, I found the paper well-written. These are basically just minor comments:

      We appreciate your positive feedback.

      (1) P3:

      - Amortization requires more explanation for the neuroscience audience.

      - What does ABC stand for?

      We have elaborated on Amortization. ABC stands for Approximate Bayesian Computation, which is now spelled out in the text.

      (2) Section 2.1:

      Should clarify the parcellation used

      In section 2.1, we now mentioned that: “The structural connectome was built with TVB-specific reconstruction pipeline using generally available neuroimaging software (Schirner et al., Neuroimage 2015)”.

      (3) P20: The method for sensitivity analysis (Figure 5F) is not clearly described.

      We have now added a subsection in the Methods section to explain the sensitivity analysis.

      (4) P21: statement that 10k simulations took less than 1 min doesn't match info shown in Figure S1. Please clarify.

      This is correct, as for the Epileptor model, the total integration time is less than 100 ms. Due to the model’s stable behavior with a large time step and the use of 10 CPU cores, all simulations were completed in less than a minute. Previously (Hashemi et al., 2023) it has been reported that each VEP run to simulate 100sec of whole-brain epileptic patterns takes only 0.003 s using a JIT compiler. The other models require more computational cost due to longer integration durations and smaller time steps. We have clarified this point.

      (5) P23-24: the distribution of FCDs also doesn't match well even if we don't consider element-wise correspondence. Please clarify.

      This is correct, as we used summary statistics of the FCD, such as fluidity, and due to noise, each realization of the FCD matrix exhibits different element-wise correspondence. We have already mentioned this point.

    1. https://www.youtube.com/watch?v=9bR-bsvi0Nk

      Annotating on hypothesis as a resource for others in the Fellowship of the Sacred Commons

      Four Sessoins in September

      Gifting was way of life in Brehon Life Cumann was the original Commons Even in feudal times, the people had a Cumann Capitalism destroyed the Cumann - it is anti-commons The state regulates the market Commons as a social welfare system 1980's globalisation - nations can no longer regulate Restore the Cumann and use it to regulate the present into the future No place for Religion No place for Ideaology Local - Translocal - Cosmo-Local Web3 - Crypto as models

      SESSION 1 Macro History Review Patterns Cyclical Humanity COmmons arrises when Market and State become hegemonic Commons can also become hegenomic Transition now What kind of commons? Physical Commons Social Commons Digital Commons Phy-gital Commons An interesting time in humanity Who are the commoners? Thesis and Empirical Evidence of 20 years observation of Seed Forms Verifiable Data that something is happening Coherent Speculation

      Commons in Feudalism Commons in Capitalism

      Alan Paige Fisk - The structure of social life Communal Shareholding - Family Equality Matching - Gifting Authority Ranking - Protect & Reward The Market

      Humanity wants to create Mode A at a higher level of com-lexity - people, family, but we want it at civilisational scale

      Religion was the first attempot to civilise civilisation - to civilise warriors - Caim Aideain -

      Capitalism is mass ideaology

      Immination of the Eschaton Life is a vale of tears but we can go to heaven The age of the Father - The Age of the Son - The Age of the Spirit - live like monks, we do not need church

      Paradise is in the future Reformation Mass Utopia - past present future

      BUT THIS IS OVER!!! 1789 to 1989

      The Age of Cosmo-Local Networks

      Software Currencies Our Hopes are invested in Blockchain which is a form of Jesus

      Civilisations Spiral - there is always somethign left behind It bifurcates - a reaction against the failure of the previous cycle

      In Rome, work was slavery In Christianity - work is sacred to make heaven on earth

      Commonsres think translocally - cosmically We do nto need the nation state

      Fair BnB can replace Air BnB - it does not need the nation state

      The Spirit as modes of exchange

      Matter and Spirit are at the same level - the physical is sacred

      Ideaology and Materialism can be integrated

      Michel's very traumatic childhood

      Marxism explained his suffering HIs abandonment of Trotsky-ism Shifted to self change Looking at the world world his marxist glasses Joined a Reich commune Women compete for the Alpa Males - and Michel was not an alpa male

      People are confused when they have no methodology at all In order to be free, one has to know how one is determined

      A tourist sees a building, but a local sees the people who inhabited the building as a culture over time

      We learn from people that we disagree with

      Listenign to right wing people - I do nto agree with you, AND I get you

      3D is light and shadow - it is perspecival which also then creates a shadow

      Christian Atheism Conservative Communism

      Michel was cancelled in 2018 - it was his shock Universities used to be mostly men, now there are two women for every man in univesities

      Something has gone wrong with the Left and Masculinity

      The network state world is antithetical to family

      In a society that has to struggle, the male is dominant When that society becomes richer, the female becomes dominant (Dominus = Lord)

      Rich women have an advantage over poor women becase their kids will survive In an egqlitarian sopciety, all kids survive, so the rich women discourage other women to have children

      Being a mother, growing life has to have prestige

      when reproduction rates are low, society suicides itself

      Commons is a practice and an institution

      Network State Movement = collect money with crypto and then buy land - create a new corporate state - be a shareholder not a citizen

      Commons as cosmo local domain relevancies

      Crypto has the idea of contribution to the common good

      Michel started to read the Dark Masters when he was canceleld in 2018

      We can only want what oher peopel want - so we compete Then we need a scapegoat - we find a common enemy Religion is a way to sacreficie people Sacrifice is a potion regulated through religion - until Christ appears to end the sacrifice

      In feudal times, a merchant could not wear fur, it was only for royalty

      In egalitarisn societies, everyone can have everything, but the only way to solve the demand is mass production with mass consumption

      A rich woman can own an expensive bag yet in five years, everyoine can have it

      Capitalism regulates this through over-consumpotion

      Capitalism is now violent - billions of little cuts for thousands of years

      LEFT : Man is good instituions are bad RIGHT: Man is bad institutions are good

      We can be egalitarian by confronting our dark nature - we are envious - we are animalistic - we needed the ten commandments - but we were given 30 of them

      We began to go into thertapy in the 1970's to confront ourselves

      IN the 1980's we invited medication to suppporess the symptoms

      Generations have nto done their own inner work

      The Woke accuse old white men in the way they used to blame the Jews - scapegoating machineries

      Neo-Liberalals now medicate the psyche - medicalisation of symptoms

      We need to become somatic - we have to work it out in the body, thropugh the body - spirtituality arises in somatic experiences

      Michel then looked to the East - a supermarket of therapy

      Rashneesh Commune - preparign the world for neo-liberalism

      Forget guilt and shame - forget the others - follwo your own path - follow your own bliss - transcend yourself - become selfish - go fot it - have the life youw ant - INDIVIDUALLISTIC

      But if you did not have money - you cooudl not joiun that club

      People prostituted themselves to go to the Ashram for €75 a day - it was for upper middle class people

      How it becase a mastery of seduction - you want this

      Watch Wild Wild Country - OSHO

      Michel then looked at the traditions of the West - Templar - Rosicrucian -

      He had to reconcile hismelf with Western Civilisation

      Catholics were hostile to slavery - the church bought slaves from the ottomans - a low number of salves in Europe (it aboloshed slavery)

      Buddhists had slaves since the 1930's

      A Christian has to love their neighbour

      Keith Chandler - beyond civilisation - relationship between order and chaos

      Tribal people are not alienated, family is known as are enemies Civilisations are alienated - solider, slave, serf, religion

      Commons is not utopian New relationship with nature Social contracts Not paradise Not classless The transition is messy

      We can do better than destroying ourselves

      We are in a new phase of history

      Commons is a realistic hypothesis of cnage It's real already

      In the 14th century: we had purgatory so then we could lend money, we had the printing press to spead ideas and we had double entry book-keeping to create capitalism : THEY WERE SEED FORMS

      Social Change needs SEED FORMS - e,g, Commons

      P2P WIKI - 40,000 entries

      Ken Wilbur - Integral Studies

      Levels Schema Quadrants

      Golden Rosicrucians in Holland

      Gnostic Dialoistic New Christian - Saklas - Jehovah - Yeldabaoth - Pleroma - Monad - Barbelo - Aeon - Archon

      With Gnostics, MIchel could not accept a hateful world and decided to be creative - he was tired of introspection

      Transhumanism Documentary

      Head of Digital Strategy for a Telco 90's + Burnout

      William James - once born people - twice born people - we have to do a lot of work - crisis, we com eout of it - so many things - a richer integratveo capacity -dark night of the soul to be integrated 1998 (Age of 42)

      The world is tragic and I can do something without teh rage of being 18

      P2P Foundation - sabbatical

      Came back to his engagement - tremendous energy until 2018 - massive productivity

      10,000 academic references 4,000 google scholar references

      2018 - shared critical video of jordan petersen - fascist - disagreed with him, but Michelw as cancelled

      Michel is a librarian

      People reacted - where am I?? Its like Salma Rushdie beign attacked without reading him

      Nobody defended him from the extremists

      "You cannat talk becase youa re white" Deminised - defunded - debanked depaypalled - blacklisted - height of popularity to zero - unjust - questioning is thsi the left - am I still on the left?

      A good thing - he did not know anythign about the right

      From Trotsky to New Right and all in between - no labs

      He is a conservative communist - we need to improve and preserve - there are no contradictions

      In 2016 - counter culture switches to the right

      We lost the leftist opinion - it was a mourning

      Leftism used to be a brotherhood - now to go being a white person, we are sub-human

      Genital mutilation is not normal

      The woke right commits genocide and the jews cannot be criticised

      Identity is layered - over many years in a real life

      Life experiecne made him a compelx layered being

      In the USA, the Reds fear china, the blues fear the internet They are tribes - only 4% of blues marry reds In the USA, they are physically separating by relocaing to theri own states

      Ruling classs 1% Managers class with many factions

      After world war 2, one had to be Kenseyian - this was the faction supported

      In 1973, Oil Crisis - maybe Friedman??? the new neo-liberal elites that becase hegemonic

      Occupy 2014 - against the 1%

      6,000% increase in woke vocabularoty in press

      Elites decide to shift to anotehr faction - e.g Holland hegemonic abolished guilds - but then the peopel stopped fightign fot the elite

      We are in an accelerated disintegration of the western model

      Importance of Web3 and P2P

      Course on The Commons

      Michel's Higher Standpoint now

      Integrative Capacity Motivation (not rage and resentment) Activism is high on the dark triad Capacity to see relatvie truths of different human groups A new breed of people who are politically homeless Pragmatic - making sense

      MIchel's dream (web 3) social change if we have willing alliacnes from the top, the middle and the top

      Monasteries - Roman Elite - People

      Attract capital from sections of the elite who have the money

      There is huge capital flow

      if you are a parasite, they will come after you If you share, you will be welcome everywhere

      A SEED FORM dependent on our participation

      Event in Brussels - Commons Hob Brussels

      706 - cultural events in people's own houses

      Michel has something to say and wants to share it

      In timews like this, going deep is very important Too much action Deep Exchange Make time to step back NOT ACT ACTUALLY

      THINK DONT ACT!

    1. Discontent began a small rumble in the earthly mind. Then Doubt pushed through with its spiked head. And once Doubt ruptured the web, All manner of demon thoughts Jumped through— We destroyed the world we had been given

      us as people never appreciate what we have we want what others have and the world can be a bad place because we are never content with what we have

    1. lifetime_base <-10

      Considering the other type of HS codes wihin the proposed UNU KEy, and that base stations up to 20 years in the comment, it looks like base station should not be part of the new unu key.

    1. eLife Assessment

      This important study identifies and partially characterises two proteins optimised for coordinated peptidoglycan degradation during two spore morphogenesis programs in the bacterium Myxococcus xanthus. The evidence supporting the conclusions is solid, although the description of the data is somewhat overstated. After some editing, the paper will be of interest to those studying peptidoglycan synthesis and reorganisation, which is a central aspect of microbial cell biology.

    2. Reviewer #1 (Public review):

      Summary:

      Ramirez Carbo et al. use the powerful M. xanthus spore morphogenesis model to address fundamental mechanisms in coordinated peptidoglycan remodeling and degradation. As peptidoglycan is an essential macromolecule and difficult to study in vivo, the authors use indirect but important methodology. The authors first identify two lytic transglycosylase (Ltg) enzymes necessary for spore morphogenesis using mutant phenotypic studies. They characterize these mutants for their role in coordinating spore morphogenesis induced either in fruiting bodies (starvation-dependent) or in liquid-rich media conditions (chemical-dependent). They conclude from these phenotypic and epistatic analyses that LtgA is necessary for morphogenesis during chemical-induced sporulation, and LtgB appears to be necessary to coordinate LtgA activity by interfering with LtgA function. Under starvation-induced sporulation, the absence of LtgB interferes with the building of fruiting bodies. LtgA does not appear to play a primary role in promoting aggregation into fruiting bodies, nor in degradation of peptidoglycan as assayed by loss of signal in anti-PG immunofluorescence. The authors demonstrate that the purified periplasmic domain of LtgA is highly active in degrading purified PG sacculi in vitro, while that of LtgB is highly reduced (relative to LtgA or lysozyme). The authors use photoactivated mCherry Lyt fusions and PALM to track the fusion protein mobility, which they state correlates with activity as immobilization results from PG binding. They demonstrate that in vegetative cells, a greater proportion of LtgA-PAmCh is more immobile (more active) than LtgB-PAmCh, but that directly after chemical-induction of sporulation, LtgB-PAmCh becomes more immobile (active). These analyses in the partner mutant backgrounds suggest that LtgA-PAmCh is more immobile (less active) in the absence of LtgB, but the reverse is not observed. Finally, the authors demonstrate that overexpression of LtgA in vegetative conditions leads to cell rounding, likely because of uncontrolled PG degradation, while overexpression of LtgB displays no phenotype.

      Strengths:

      This paper capitalizes on a novel spore morphogenesis mechanism to define proteins and mechanisms involved in peptidoglycan reorganization. The authors use the powerful PALM microscopy technique to assess Ltg activity in vivo by assaying for immobility as a proxy for PG binding. The authors elucidate a novel mechanism by which two Ltg's function together- with one (LtgB) seeming to regulate the activity of the other (the primary Ltg).

      Despite some weaknesses, there is no question that this study provides important insight into mechanisms of peptidoglycan remodeling- a difficult but highly impactful area of study with implications for the development of novel therapeutics and the discovery of mechanisms of fundamental bacterial physiology.

      Weaknesses:

      In many places, the authors do not adequately justify interpretations of their assays, leading to some apparently unjustified conclusions. Many of these are minor and may just require citations to demonstrate that the interpretations are justified by previous studies (detailed in recommendations below), but two bigger concerns are as follows:

      (1) It is not clear how the muropeptides listed in Figure 1 were assigned, and it is missing in the methods. In the sporulating conditions, the spectra look like combinations of multiple peaks, and the data, as stated, is not convincing to the non-specialist eye.

      (2) The observation that the lytB mutant prevents appropriate aggregation into fruiting bodies does not allow the interpretation that the absence of LytB prevents PG morphogenesis in the starvation-induced sporulation pathway, per se. It is more likely that in the lytB mutant, the morphogenesis program is not even triggered. This is because signaling proteins and regulators (specifically, C-signal accumulation/activated FruA), which are dependent on increased cell-cell signaling in the fruiting body, do not accumulate appropriately in shallow aggregates. C-signal/FruA are necessary to trigger the sporulation program in FBs. BTW: A hypothesis to explain the indirect effect of ltgB absence on aggregation could be that UDP-precursors are not regulated appropriately (unregulated LtyA??), so polysaccharides necessary for motility are not properly produced.

      Along these lines, fruiting body formation does not equal sporulation, and even "darkened" fruiting bodies can be misleading, as some mutants form polysaccharide-rich fruiting bodies (that appear dark under certain light conditions in the stereomicroscope) but do not sporulate efficiently. The wording in the text suggests that the authors assume that sporulation levels are normal because fruiting bodies are produced (see specific comments for details).

      (3) The authors repeatedly state that production of spore coat polysaccharides likely affects the PG IP staining (see below), but this is not well justified. A citation is needed if this has already been directly shown, or the language needs to be softened.

      (4) Better justification for the immobility of Lyt proteins in vivo as an assay for activity may be required. If this is well known in the field, it should be explicitly stated. The authors address this better in the discussion - but still state it is a correlation.

    3. Reviewer #2 (Public review):

      Summary:

      The authors' initial goal was to demonstrate loss of PG during the slow sporulation process of Myxococcus xanthus, with examination of the PG degradation products in order to implicate possible enzymes involved. Upon finding a predominance of LGT products, they examined sporulation in strains lacking each of the 14 candidate LGTs encoded in the genome, leading to the identification of two sporulation-linked LGTs. An extensive characterization of the roles played by these LGTs. One LGT is responsible for the slow sporulation PG degradation, while another is required for the rapid sporulation process. Interestingly, the "slow" LGT seems to provide an important regulatory brake on the rapid enzyme. Single-molecule fluorescent tracking of these enzymes was used to develop a model for their interaction with PG that mimics their observed activity. The rate of PG synthesis activity was also shown to impact the rate of PG degradation, suggesting potential interplay between the synthetic and degradative enzymes.

      Strengths:

      The genetic analysis to identify sporulation-linked LGTs and their effects on growth, sporulation, and spore properties was well done and productive. The fluorescence microscopy to track LGT mobility, presumably tied to activity, produced a convincing argument about the mechanism of regulation of one LGT by another.

      Weaknesses:

      While the impact of LGTs on sporulation was clearly demonstrated, the PG analysis that resulted from the study of LGTs raised some important unanswered questions. The analyses suggest that the PG is degraded to quite small fragments, which would normally be lost during the purification of PG. How these small fragments were thus detected is unclear, and this suggests a more complex story concerning PG metabolism during sporulation. An anti-PG antibody is used to quantify PG in the spores, but it is not made clear what the specificity of this antibody is, and thus whether it would recognize the LGT-altered PG of the spore. The authors suggest a "new mechanism of sporulation" when they have actually simply identified an important factor (PG degradation by LGTs) within a complex "process of sporulation".

    1. eLife Assessment

      In this manuscript, Chen et al. used cryo-ET and in vitro reconstituted system to demonstrate that the autoinhibited form of LRRK2 can also assemble into filaments on the microtubule surface, with a new interface involving the N-terminal repeats that were disordered in the previous active-LRRK2 filament structure. The structure obtained in this study is the highest resolution of LRRK2 filaments done by subtomogram averaging, representing a major technical advance compared to the previous paper from the same group. This is an important study, especially considering the pharmacological implications of the effect of inhibitors of the protein. The strengths of the data are convincing, but the study would be considerably strengthened if the authors explored the physiological significance of the new interfaces and the incomplete decoration of microtubules described here.

    2. Reviewer #1 (Public review):

      Summary:

      In this manuscript, Chen et al. use cryo-electron tomography and an in vitro reconstitution system to demonstrate that the autoinhibited form of LRRK2 can assemble into filaments that wrap around microtubules. These filaments are generally shorter and less ordered than the previously characterized active-LRRK2 filaments. The structure reveals a novel interface involving the N-terminal repeats, which were disordered in the earlier active filament structure. Additionally, the autoinhibited filaments exhibit distinct helical parameters compared to the active form.

      Strengths:

      This study presents the highest-resolution structure of LRRK2 filaments obtained via subtomogram averaging, marking a significant technical advance over the authors' previous work published in Cell. The data are well presented, with high-quality visualizations, and the findings provide meaningful insights into the structural dynamics of LRRK2.

      Weaknesses and Suggestions:

      The revised manuscript by Chen et al. has fully addressed all of my previous suggestions regarding the rearrangement of the main figures.

    3. Reviewer #2 (Public review):

      The authors of this paper have done much pioneering work to decipher and understand LRRK2 structure and function and uncover the mechanism by which LRRK2 binds to microtubules and to study the roles that this may play in biology. Their previous data demonstrated that LRRK2 in the active conformation (pathogenic mutation or Type I inhibitor complex) bound to microtubule filaments in an ordered helical arrangement. This they showed induced a "roadblock" in the microtubule impacting vesicular trafficking. The authors have postulated that this is a potentially serious flaw with Type 1 inhibitors and that companies should consider generating Type 2 inhibitors in which the LRRK2 is trapped in the inactive conformation. Indeed the authors have published much data that LRRK2 complexed to Type 2 inhibitors does not seem to associate with microtubules and cause roadblocks in parallel experiments to those undertaken with type 1 inhibitors published above.

      In the current study the authors have undertaken an in vitro reconstitution of microtubule bound filaments of LRRK2 in the inactive conformation, which surprisingly revealed that inactive LRRK2 can also interact with microtubules in its auto-inhibited state. The authors' data shows that while the same interphases are seen with both the active LRRK2 and inactive microtubule bound forms of LRRK2, they identified a new interphase that involves the WD40-ARM-ANK- domains that reportedly contributes to the ability of the inactive form of LRRK2 to bind to microtubule filaments. The structures of the inactive LRRK2 complexed to microtubules are of medium resolution and do not allow visualisation of side chains.

      This study is extremely well written and the figures incredibly clear and well presented. The finding that LRRK2 in the inactive autoinhibited form can associate with microtubules is an important observation that merits further investigation. This new observation makes an important contribution to the literature and builds upon the pioneering research that this team of researchers has contributed to the LRRK2 fields.

      Comments on revised version:

      The authors have adequately addressed my questions and those of the other Reviewers in my opinion.

    4. Reviewer #3 (Public review):

      Summary:

      The manuscript by Chen et al examines the structure of the inactive LRRK2 bound to microtubules using cryo-EM tomography. Mutations in this protein have been shown to be linked to Parkinson's Disease. It is already shown that the active-like conformation of LRRK2 binds to the MT lattice, but this investigation shows that full-length LRRk2 can oligomerize on MTs in its autoinhibited state with different helical parameters than were observed with active-like state. The structural studies suggest that the autoinhibited state is less stable on MTs.

      Strengths:

      The protein of interest is very important biomedically and a novel conformational binding to microtubules in proposed

      The authors have addressed my original critique.

    5. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      In this manuscript, Chen et al. used cryo-ET and in vitro reconstituted system to demonstrate that the autoinhibited form of LRRK2 can also assemble into filaments that wrap around the microtubule, although the filaments are typically shorter and less regular compared to the previously reported active-LRRK2 filaments. The structure revealed a new interface involving the N-terminal repeats that were disordered in the previous active-LRRK2 filament structure. The autoinhibited-LRRK2 filament also has different helical parameters compared to the active form.

      Strengths:

      The structure obtained in this study is the highest resolution of LRRK2 filaments done by subtomogram averaging, representing a major technical advance compared to the previous Cell paper from the same group. Overall, I think the data are well presented with beautiful graphic rendering, and valuable insights can be gained from this structural study.

      Weaknesses:

      (1) There are only three main figures, together with 9 supplemental figures. The authors may consider breaking the currently overwhelming Figures 1 and 3 into smaller figures and moving some of the supplemental figures to the main figure, e.g., Figure S7.

      (2) The key analysis of this manuscript is to compare the current structure with the previous active-LRRK2 filament structure. Currently, such a comparison is buried in Figure 3H. It should be part of Figure 1.

      We thank the reviewer for this suggestion. As suggested, we have rearranged the figures, split Figure 1 and 3 into smaller Figures, and moved the comparison analysis in Figure 3H to the new Figure 1. Specifically, the old Figure 1 is separated into two figures, introducing the model-building process and describing the two symmetric axes. The old Figure 3 is also separated into two small figures, describing the geometric analysis and model comparison, respectively.

      Reviewer #2 (Public review):

      The authors of this paper have done much pioneering work to decipher and understand LRRK2 structure and function, to uncover the mechanism by which LRRK2 binds to microtubules, and to study the roles that this may play in biology. Their previous data demonstrated that LRRK2 in the active conformation (pathogenic mutation or Type I inhibitor complex) bound to microtubule filaments in an ordered helical arrangement. This they showed induced a "roadblock" in the microtubule impacting vesicular trafficking. The authors have postulated that this is a potentially serious flaw with Type 1 inhibitors and that companies should consider generating Type 2 inhibitors in which the LRRK2 is trapped in the inactive conformation. Indeed the authors have published much data that LRRK2 complexed to Type 2 inhibitors does not seem to associate with microtubules and cause roadblocks in parallel experiments to those undertaken with type 1 inhibitors published above.

      In the current study, the authors have undertaken an in vitro reconstitution of microtubule-bound filaments of LRRK2 in the inactive conformation, which surprisingly revealed that inactive LRRK2 can also interact with microtubules in its auto-inhibited state. The authors' data shows that while the same interphases are seen with both the active LRRK2 and inactive microtubule bound forms of LRRK2, they identified a new interphase that involves the WD40-ARM-ANK- domains that reportedly contributes to the ability of the inactive form of LRRK2 to bind to microtubule filaments. The structures of the inactive LRRK2 complexed to microtubules are of medium resolution and do not allow visualisation of side chains.

      This study is extremely well-written and the figures are incredibly clear and well-presented. The finding that LRRK2 in the inactive autoinhibited form can be associated with microtubules is an important observation that merits further investigation. This new observation makes an important contribution to the literature and builds upon the pioneering research that this team of researchers has contributed to the LRRK2 fields. However, in my opinion, there is still significant work that could be considered to further investigate this question and understand the physiological significance of this observation.

      We thank the reviewer for the positive comments and we agree that more work can be done next to understand the physiological significance of the autoinhibited LRRK2 in cellular environments. We are actively working on understanding how the stability of autoinhibited full-length LRRK2 is regulated, especially how the transfer between autoinhibited and active forms of LRRK2 can happen. Our in situ data (Watabane et al. 2020) indicates that overexpressed hyperactive PD-mutant LRRK2 mainly adopts its active-like conformation in cells. Thus, learning how the state transfer occurs will allow us to target autoinhibited LRRK2 specifically and efficiently in cells and study its structure and function in physiological conditions.

      Reviewer #3 (Public review):

      Summary:

      The manuscript by Chen et al examines the structure of the inactive LRRK2 bound to microtubules using cryo-EM tomography. Mutations in this protein have been shown to be linked to Parkinson's Disease. It is already shown that the active-like conformation of LRRK2 binds to the MT lattice, but this investigation shows that full-length LRRk2 can oligomerize on MTs in its autoinhibited state with different helical parameters than were observed with the active-like state. The structural studies suggest that the autoinhibited state is less stable on MTs.

      Strengths:

      The protein of interest is very important biomedically and a novel conformational binding to microtubules in the proposed.

      Weaknesses:

      (1) The structures are all low resolution.

      We thank the reviewer for the comments on both the strengths and weaknesses of the manuscript. We agree with the reviewer that higher resolution would provide more information about how LRRK2 interacts with microtubules and oligomerizes in its autoinhibited form. However, with the current resolution, our model-building benefited significantly from the published high-resolution models and the alpha-fold predictions. We used cryo-ET and subtomogram analysis to solve the structure because this filament is less regular than the right-handed active LRRK2 filament, preventing us from using conventional single-particle analysis. As highlighted by reviewer 1, being able to push the resolution to sub-nanometer is an important advance reflecting state-of-the-art subtomogram analysis, especially for a heterogeneous sample.  Notably, the microtubule reconstruction reached higher resolution, comparable to our previous single-particle studies on LRRK2-RCKW (Snead and Matyszewski et al.), confirming the data quality.

      (2) There are no measurements of the affinity of the various LRRK2 molecules (with and without inhibitors) to microtubules. This should be addressed through biochemical sedimentation assay.

      We thank the reviewer for the suggestion and we agree that learning the binding affinity between LRRK2 and microtubules would be informative. We attempted to purify the LRRK2 with mutants on the WD40:ARM/ANK interface we identified in the manuscript.. Unfortunately, either LRRK2 or LRRK2<sup>I2020T</sup> with N-terminal mutants (R521A/F573A/E854K), the yield and purity of the final samples are significantly worse than our routine LRRK2 prep. Our chromatography and gel electrophoresis results indicate that proteins are degrading during purification.

      Author response image 1.

      While we have attached the results here, and it would be interesting to investigate why N-terminal mutations destabilize LRRK2, we anticipate that significant efforts would be required for further experiments, which we respectfully consider outside of the scope of this manuscript. 

      Recommendations for the authors:

      Reviewer #1 (Recommendations for the authors):

      (1) In Figure S9, the graphic definition of "chain length" in panel A is misleading. The authors can simply note in the figure legend that "chain length is the number of asymmetric units in a continuous chain".

      We thank the reviewer for the suggestion. The updated figure and legend have incorporated the changes.

      (2) In Figure S7B, the conformation changes of the 'G-loop' and the 'DYG' motifs are not so convincing at the current resolution.

      We thank the reviewer for pointing it out. We agree that our model resolution is not high enough to support the unbiased observation of the conformation changes of the key kinase motifs. In the revised manuscript, we avoided emphasizing the comparison between the two models. Instead, we state that for both the MLi-2 bound map and the GZD-824 bound map, the corresponding published high-resolution models fit into each kinase map, but the MLi-2 bound model doesn’t fit as well in the GZD-824 bound map, with a correlation value dropped from 0.44 to 0.4, supporting our statement that “full-length LRRK2 bound to microtubules is in its autoinhibited state in our reconstituted system”.

      Reviewer #2 (Recommendations for the authors):

      (1) Are there any cellular experiments that could be done to demonstrate that inactive LRRK2 associates with microtubules in cells?

      We thank the reviewer for pointing out this direction for future studies. We are studying the physiological significance of the autoinhibited LRRK2 in cells, but haven’t yet been successful at demonstrating physiological binding to microtubules. Further, as noted in our response to reviewer #3, we are also actively working on understanding how the stability of autoinhibited full-length LRRK2 is regulated, especially how the transfer between autoinhibited and active forms of LRRK2 can happen. Our in situ data (Watabane et al. 2020) indicates that hyperactive PD-mutant overexpressed LRRK2 mainly adopts its active-like conformation in cells. Thus, learning how the state transfer occurs will allow us to target autoinhibited LRRK2 specifically and efficiently in cells and study its structure and function in physiological conditions.

      (2) Previous work that the authors and others have undertaken has suggested that only LRRK2 in its active conformation can associate with microtubule filaments and the authors have shown that this leads to a roadblock in vesicular transport only when LRRK2 is complexed with Type 1 but not Type 2 inhibitors. There seems to be some discrepancy here that is not addressed in the paper as based on the current results one would also expect LRRK2 bound to Type 2 inhibitors to induce roadblocks in microtubule filaments. How can this be explained?

      We thank the reviewer for raising this important question. Taking all of our published data together, we believe that LRRK2 can introduce roadblocks with Type 1 inhibitor bound in the active-like conformation, where N-terminus LRRK2 domains are flexible and don’t block the kinase active site. In other words, full-length LRRK2 can form roadblocks when it behaves more like the truncated LRRK2<sup>RCKW</sup> variant. The autoinhibited LRRK2 forms shorter and less stable oligomers on microtubules, making it harder to block transport. Consistent with this, our in situ LRRK2-microtubule structure was observed in cells where LRRK2 is in an active-like conformation, and the LRRK2 N-terminus appeared to be flexible and away from the microtubule when forming right-handed filaments.

      (3) Does the finding that inactive LRRK2 only binds to microtubules as a short filament, explain the differences between the inactive and active forms of LRRK2 binding to microtubules and causing roadblocks?

      We thank the reviewer for discussing this point with us and asking the question. As we replied in the previous comment, the reviewer’s conclusion explains how the roadblock phenomenon occurs only under certain circumstances. We expanded our discussion to add the following and address the question:

      “Notably, we previously demonstrated that active‐like LRRK2, when bound to a Type I inhibitor, can form roadblocks that impair vesicular transport. Since autoinhibited LRRK2 assembles into shorter, less stable oligomers on microtubules, we anticipate it will exert reduced road‐blocking effects in cells, regardless of the inhibitor bound.”

      (4) Could the authors undertake further characterization of the new WD40-ARM-ANK interphase that they have identified? Is this important for the binding of the autoinhibited mutant? Could mutants be made in this interphase to see if this prevents the autoinhibited but not the active conformation of LRRK2 binding to microtubules?

      We thank the reviewer for the comment. As mentioned in our response to Reviewer #2, public comment #2, we attempted to purify the LRRK2 with mutants on the WD40:ARM/ANK interface we identified in the manuscript multiple times. Unfortunately, either LRRK2 or LRRK2<sup>I2020T</sup> with N-terminal mutants (R521A/F573A/E854K), the yield and purity of the final samples are significantly worse than our routine LRRK2 prep. Our chromatography and gel electrophoresis results indicate that proteins are degrading during purification.

      (5) The authors identify several disease-relevant missense mutations that appear to lie within the novel interphase that the authors have characterised in this study. Although this is discussed in the Discussion, some experimental data demonstrating how these missense mutations impact the ability of inactive LRRK2 to bind to microtubule filaments in the presence or absence of Type 1 and Type 2 compounds could provide further experimental data that emphasises the physiological importance of the results presented in this study.

      We thank the reviewer for discussing this interesting direction. The disease-relevant missense mutations can have a direct or indirect impact on the binding of autoinhibited LRRK2 to microtubules, and we agree that it would be interesting to test it out in the future. However, we anticipate that significant effort would be required for further experiments. Alas, our funding for this project ended suddenly and we want to report our results to the community.

      (6) For the data that is shown in Figure 1, could the authors explain how this differs from results in previous papers of the authors showing that the active form of LRRK2 binds microtubules? How does the binding observed here differ from that observed in the previous studies? To a non-specialist reader, the data looks fairly like what has previously been reported.

      We thank the reviewer for asking the question. As mentioned in the response to the public review, the detailed comparison between the data and the previous papers is described in Figure 3, and we agree that it is helpful to incorporate this information in Figure 1. In the revised manuscript, we have incorporated the comparison panel in Figure 1.

      (7) The finding that the autoinhibited LRRK2 forms short and sparse oligomers on microtubules raises the question of how physiological this observation is. Having some data that suggests that this is physiologically relevant would boost the impact of this study.

      We agree with the reviewer on this comment. As discussed in the response to the first comment from the reviewer, we have not been able to assess the physiological relevance of LRRK2 binding to microtubules in either active or inactive state, but continue to pursue this line of research. We are aware and regret that this lessens the impact of this work.

      (8) For the more general reader the authors could potentially better highlight why the key finding in this paper is important.

      We thank the reviewer for the suggestion. To further address the significance of the key findings, especially how it can open up more possibilities for inhibitor-based drug development, we expand our discussion section to include the following:

      “Understanding how Type I and Type II inhibitors’ binding to LRRK2 affects its mechanism is vital to the design of inhibitor-based PD drug development strategies. Our findings revealed that different LRRK2 kinase inhibitors bind to autoinhibited LRRK2 similarly either in solution or on microtubules. Furthermore, the observation of autoinhibited LRRK2 forming short, less stable oligomers on microtubules opens new possibilities to inhibit LRRK2 activity in PD patients. A Type I inhibitor specifically targeting autoinhibited LRRK2 may alleviate the effect of LRRK2 roadblocks on microtubules. Alternatively, a promising strategy of LRRK2 inhibitor design can focus on the stabilization of allosteric N-terminus blocking on the kinase domain, which favors the formation of autoinhibited LRRK2 oligomers on microtubules and causes fewer side effects.”

      Reviewer #3 (Recommendations for the authors):

      In the third paragraph of the introduction, expand on whether type-1 inhibitors which "capture kinases in a closed, "active-like" conformation still inhibit the kinase activity.

      We thank the reviewer for the request to expand this paragraph. We added the following explanation for better understanding in the third paragraph:

      “Type-I inhibitors bind to the ATP binding site and target the kinase in its ‘active-like' conformation, inhibiting its kinase activity.”

    1. (seems to be differences)

      I have no explanation why the weights could be different per UNU key. Maybe if it is at category level, then it could be due to a mistake in the correspondence. I think 0501 or 0507 was allocated to lamps when it shouldn't in one of the folders.

    2. those figures from the trend analysis and Stichting Open

      based on the graphs on weight using regression, it seems to come more from Stichting Open, correct? Complication sounds a bit harsh for me haha. Just a consequence of using a different data source. I actually don't know how the original weights were determined, but I remember sending to Vincent some data that we collected within Panorama project at PCC level. Some were just the way you did with Comtrade weight then using correspondence to PCC, and some we just googled based on the description.

    3. We adopt the regression-based values

      it looks good, and it won't change much. Do we need to say something about weight post 2024? because then the regression stops making sense after.

    1. eLife Assessment

      This is an important study that demonstrates that blood pressure variability impairs myogenic tone and diminishes baroreceptor reflex. The study also provides evidence that blood pressure variability blunts functional hyperemia and contributes to cognitive decline. The evidence is compelling whereby the authors use appropriate and validated methodology in line with or more rigorous than the current state-of-the-art.

    2. Reviewer #1 (Public review):

      This study examined the effect of blood pressure variability on brain microvascular function and cognitive performance. By implementing a model of blood pressure variability using intermittent infusion of AngII for 25 days, the authors examined different cardiovascular variables, cerebral blood flow and cognitive function during midlife (12-15-month-old mice). Key findings from this study demonstrate that blood pressure variability impairs baroreceptor reflex and impairs myogenic tone in brain arterioles, particularly at higher blood pressure. They also provide evidence that blood pressure variability blunts functional hyperemia and impairs cognitive function and activity. Simultaneous monitoring of cardiovascular parameters, in vivo imaging recordings, and the combination of physiological and behavioral studies reflect rigor in addressing the hypothesis. The experiments are well designed, and data generated are clear.

      A number of issues raised earlier were addressed by the authors in the revised manuscript. The responses are convincing. These included circadian rhythm considerations, baroreflex findings, BP fluctuations driven by animal movement, and data presentation.

      Overall, this is a solid study with huge physiological implications. I believe that it will be of great benefit to the field.

    3. Author response:

      The following is the authors’ response to the original reviews

      Public Reviews:

      Reviewer #1 (Public review):

      This study examined the effect of blood pressure variability on brain microvascular function and cognitive performance. By implementing a model of blood pressure variability using an intermittent infusion of AngII for 25 days, the authors examined different cardiovascular variables, cerebral blood flow, and cognitive function during midlife (12-15-month-old mice). Key findings from this study demonstrate that blood pressure variability impairs baroreceptor reflex and impairs myogenic tone in brain arterioles, particularly at higher blood pressure. They also provide evidence that blood pressure variability blunts functional hyperemia and impairs cognitive function and activity. Simultaneous monitoring of cardiovascular parameters, in vivo imaging recordings, and the combination of physiological and behavioral studies reflect rigor in addressing the hypothesis. The experiments are well-designed, and the data generated are clear. I list below a number of suggestions to enhance this important work:

      (1) Figure 1B: It is surprising that the BP circadian rhythm is not distinguishable in either group. Figure 2, however, shows differences in circadian rhythm at different timepoints during infusion. Could the authors explain the lack of circadian effect in the 24-h traces?

      The circadian rhythm pattern is apparent in Figure 2 (Active BP higher than Inactive BP), where BP is presented as 12hour averages. When the BP data is expressed as one-hour averages (rather than minute-to-minute) over 24hours, now included in the revised manuscript as Supplemental Figure 3C-D, the circadian rhythm becomes noticeable. In addition, we have included one-hour average BP data for all mice in the control and BPV groups, Supplemental Figure 3A-B.

      Notably, the Ang-II induced pulsatile BP pattern remains evident in the one-hour averages for the BPV group, Supplemental Figure 3B. To minimize bias and validate variability, pump administrations start times were randomized for both control and BPV groups, Supplemental Figure 3A-B. Despite these adjustments, the circadian rhythm profile of BP is consistently maintained across individual mice and in the collective dataset, Supplemental Figure 3C-D.

      (2) While saline infusion does not result in elevation of BP when compared to Ang II, there is an evident "and huge" BP variability in the saline group, at least 40mmHg within 1 hour. This is a significant physiological effect to take into consideration, and therefore it warrants discussion.

      Thank you for this comment. The large variations in BP in the raw traces during saline infusion reflects transient BP changes induced by movement/activity, which is now included in Figure 1B (maroon trace). The revised manuscript now includes Line 222 “Note that dynamic activity-driven BP changes were apparent during both saline- and Ang II infusions, Figure 1B”.

      (3) The decrease in DBP in the BPV group is very interesting. It is known that chronic Ang II increases cardiac hypertrophy, are there any changes to heart morphology, mass, and/or function during BPV? Can the decrease in DBP in BPV be attributed to preload dysfunction? This observation should be discussed.

      The lower DBP in the BPV group was already present at baseline, while both groups were still infused with saline, and was a difference beyond our control. However, this is an important and valid consideration, particularly considering the minimal yet significant increase in SBP within the BPV group (Figure 1D). Our goal was to induce significant transient blood pressure responses (BPV) and investigate the impact on cardiovascular and neurovascular outcomes in the absence of hypertension. We did not anticipate any major cardiac remodeling at this early time point (considering the absence of overt hypertension) and thus cardiac remodeling was not assessed and this is now discussed in the revised manuscript (Line 443-453).

      (4) Examining the baroreceptor reflex during the early and late phases of BPV is quite compelling. Figures 3D and 3E clearly delineate the differences between the two phases. For clarity, I would recommend plotting the data as is shown in panels D and E, rather than showing the mathematical ratio. Alternatively, plotting the correlation of ∆HR to ∆SBP and analyzing the slopes might be more digestible to the reader. The impairment in baroreceptor reflex in the BPV during high BP is clear, is there any indication whether this response might be due to loss of sympathetic or gain of parasympathetic response based on the model used?

      We appreciate the reviewer’s suggestion and have accordingly generated new figures displaying scatter plots of SBP vs HR with linear regression analysis (Figure 3D-G). Our goal is to further investigate which branch of the autonomic nervous system is affected in this model. The loss of a bradycardic response suggests either an enhancement of sympathetic activity, a reduction in parasympathetic activity, or a combination of both. This is briefly discussed in the revised manuscript (Line 486-496).

      Heart rate variability (HRV) serves as an index of neurocardiac function and dynamic, non-linear autonomic nervous system processes, as described in Shaffer and Ginsber[1]. However, given that our data was limited to BP and HR readings collected at one-minute intervals, our primary assessment of autonomic function is limited to the bradycardic response. Further studies will be necessary to fully characterize the autonomic parameters influenced by chronic BPV.

      (5) Figure 3B shows a drop in HR when the pump is ON irrespective of treatment (i.e., independent of BP changes). What is the underlying mechanism?

      We apologize for any lack of clarity. These observed heart rate (HR) changes occurred during Ang II infusion, when blood pressure (BP) was actively increasing. In the control group, the pump solution was switched to Ang II during specific periods (days 3-5 and 21-25 of the treatment protocol) to induce BP elevations and a baroreceptor response, allowing direct comparisons between the control and BPV group.

      To clarify this point, we have revised Line 260-263 of the manuscript: “To compare pressure-induced bradycardic responses between BPV and control mice at both early and later treatment stages, a cohort of control mice received Ang II infusion on days 3-5 (early phase) (Supplemental Figure 4) and days 21-25 (late phase) thereby transiently increasing BP”.

      Additionally, a detailed description has been added to the Methods section (Line 96-101): “Controls receiving Ang II: To facilitate between-group comparisons (control vs BPV), a separate cohort of control mice were subjected to the same pump infusion parameters as BPV mice but for a brief period receiving Ang II infusions on days 3-5 and 21-25 for experiments assessing pressure-evoked responses, including bradycardic reflex, myogenic response, and functional hyperemia at high BP.”

      (6) The correlation of ∆diameter vs MAP during low and high BP is compelling, and the shift in the cerebral autoregulation curve is also a good observation. I would strongly recommend that the authors include a schematic showing the working hypothesis that depicts the shift of the curve during BPV.

      Thank you for this insightful comment. The increase in vessel reactivity to BP elevations in parenchymal arterioles of BPV mice suggests that chronic BPV induces a leftward shift and a potential narrowing of the cerebral autoregulation range (lower BP thresholds for both the upper and lower limits of autoregulation). This has been incorporated (and discussed) into the revised manuscript (see Figure 5N).

      One potential explanation for these changes is that the absence of sustained hypertension, a prominent feature in most rodent models of hypertension, limits adaptive processes that protect the cerebral microcirculation from large BP fluctuations (e.g., vascular remodeling). While this study does not specifically address arteriole remodeling, the lack of such adaptation may reduce pressure buffering by upstream arterioles, thereby rendering the microcirculation more vulnerable to significant BP fluctuations.

      The unique model allows for measurements of parenchymal arteriole reactivity to acute dynamic changes in BP (both an increase and decrease in MAP). Our findings indicate that chronic BPV enhances the reactivity of parenchymal arterioles to BP changes—both during an increase in BP and upon its return to baseline, Supplemental Figure 5C, F. The data suggest an increased myogenic response to pressure elevation, indicative of heightened contractility, a common adaptive process observed in rodent models of hypertension[2-4]. However, our model also reveals a notable tendency for greater dilation when the BP drops, Supplemental Figure 5F. This intriguing observation may suggest ischemia during the vasoconstriction phase (at higher BP), leading to enhanced release of dilatory signals, which subsequently manifest as a greater dilation upon BP reduction. This phenomenon bears similarities to chronic hypoperfusion models[5,6], where vasodilatory mechanisms become more pronounced in response to sustained ischemic conditions. Future studies investigating the effects of BPV on myogenic responses and brain perfusion will be a priority for our ongoing research.

      (7) Functional hyperemia impairment in the BPV group is clear and well-described. Pairing this response with the kinetics of the recovery phase is an interesting observation. I suggest elaborating on why BPV group exerts lower responses and how this links to the rapid decline during recovery.

      Based on the heightened reactivity of BPV parenchymal arterioles to intravascular pressure (Figure 5), we anticipate that the reduction of sensory-evoked dilations results from an increased vasoconstrictive activity and/or a decreased availability of vasodilatory signaling pathways (NO, EETs, COX-derived prostaglandins)[7,8]. Consequently, the magnitude of the FH response is blunted during periods of elevated BP in BPV mice.

      Additionally, upon termination of the stimulus-induced response−when vasodilatory signals would typically dominate−vasoconstrictive mechanisms are rapidly engaged (or unmasked), leading to quicker return to baseline. This shift in the balance between vasodilatory and vasoconstrictive forces favors vasoconstriction, contributing to the altered recovery kinetics observed in BPV mice. This has been included in the Discussion section of the revised manuscript.

      (8) The experimental design for the cognitive/behavioral assessment is clear and it is a reasonable experiment based on previous results. However, the discussion associated with these results falls short. I recommend that the authors describe the rationale to assess recognition memory, short-term spatial memory, and mice activity, and explain why these outcomes are relevant in the BPV context. Are there other studies that support these findings? The authors discussed that no changes in alternation might be due to the age of the mice, which could already exhibit cognitive deficits. In this line of thought, what is the primary contributor to behavioral impairment? I think that this sentence weakens the conclusion on BPV impairing cognitive function and might even imply that age per se might be the factor that modulates the various physiological outcomes observed here. I recommend clarifying this section in the discussion.

      We thank the reviewer for this comment. Clinical studies have demonstrated that patients with elevated BPV exhibit impairments across multiple cognitive domains, including declines in processing speed[9] and episodic memory[10]. To evaluate memory function, we utilized behavioral tests: the novel object recognition (NOR) task to assess episodic memory[11] and the spontaneous Y-maze to evaluate short-term spatial memory[12].

      Previous research indicates that older C57Bl6 mice (14-month-old) exhibit cognitive deficits compared to younger counterparts (4- and 9-month-old)[13]. To ensure rigorous selection for behavioral testing, we conducted preliminary NOR assessment, evaluating recognition memory at the one-hour delay but observing failures at the four-, and 24-hour delays, indicating age-related deficits. Based on these results, animals failing recognition criteria were excluded from subsequent behavioral assessment. However, because no baseline cognitive testing was conducted for the spontaneous Y-maze, it is possible that some mice with aged-related deficits were included in this test, which may have influenced data interpretation.

      Additionally, the absence of differences in the Y-maze performance may suggest that short-term spatial memory remains intact following 25 days of BPV, a point that is now discussed in the revised manuscript.

      (9) Why were only male mice used?

      We appreciate this comment and acknowledge the importance of conducting experiments in both male and female mice. Studies involving female mice are currently ongoing, with telemetry data collection approximately halfway completed and two-photon imaging studies on functional hyperemia also partially completed. However, using middleaged mice for these experiments has proven challenging due to high mortality rates following telemetry surgeries. As a result, we initially limited our first cohort to male mice.

      (10) In the results for Figure 3: "Ang II evoked significant increases in SBP in both control and BPV groups;...". Also, in the figure legend: "B. Five-minute average HR when the pump is OFF or ON (infusing Ang II) for control and BPV groups...." The authors should clarify this as the methods do not state a control group that receives Ang II.

      Please refer to response to comment 5.

      Reviewer #2 (Public review):

      Summary:

      Blood pressure variability has been identified as an important risk factor for dementia. However, there are no established animal models to study the molecular mechanisms of increased blood pressure variability. In this manuscript, the authors present a novel mouse model of elevated BPV produced by pulsatile infusions of high-dose angiotensin II (3.1ug/hour) in middle-aged male mice. Using elegant methodology, including direct blood pressure measurement by telemetry, programmable infusion pumps, in vivo two-photon microscopy, and neurobehavioral tests, the authors show that this BPV model resulted in a blunted bradycardic response and cognitive deficits, enhanced myogenic response in parenchymal arterioles, and a loss of the pressure-evoked increase in functional hyperemia to whisker stimulation.

      Strengths:

      As the presentation of the first model of increased blood pressure variability, this manuscript establishes a method for assessing molecular mechanisms. The state-of-the-art methodology and robust data analysis provide convincing evidence that increased blood pressure variability impacts brain health.

      Weaknesses:

      One major drawback is that there is no comparison with another pressor agent (such as phenylephrine); therefore, it is not possible to conclude whether the observed effects are a result of increased blood pressure variability or caused by direct actions of Ang II.

      We acknowledge this limitation and have attempted to address the concern by introducing an alternative vasopressor, norepinephrine (NE), Figure 4. A subcutaneous dose of 45 µg/kg/min was titrated to match Ang II-induced transient BP pulse (Systolic BP ~150-180 mmHg), Figure 4A. Similar to Ang II treated mice, NE-treated mice exhibited no significant changes in average mean arterial pressure (MAP) throughout the 20-day treatment period (Figure 4B). Although there was a trend (P=0.08) towards increased average real variability (ARV) (Figure 4C left), it did not reach statistical significance. The coefficient of variation (CV) (Figure 4C right) was significantly increased by day 3-4 of treatment (P=0.02).

      Notably, unlike the bradycardic response observed during Ang II-induced BP elevations, NE infusions elicited a tachycardic response (Figure 4A), likely due to β-1 adrenergic receptor activation. However, significant mortality was observed within the NE cohort: three of six mice died prematurely during the second week of treatment, and two additional mice required euthanasia on days 18 and 20 due to lethargy, impaired mobility, and tachypnea.

      While we recognize the importance of comparing results across vasopressors, further investigation using additional vasopressors would require a dedicated study, as each agent may induce distinct off-target effects, potentially generating unique animal models. Alternatively, a mechanical approach−such as implanting a tethered intra-aortic balloon[14] connected to a syringe pump−could be explored to modulate blood pressure variability without pharmacological intervention. However, such an approach falls beyond the scope of the present study.

      Ang II is known to have direct actions on cerebrovascular reactivity, neuronal function, and learning and memory. Given that Ang II is increased in only 15% of human hypertensive patients (and an even lower percentage of non-hypertensive), the clinical relevance is diminished. Nonetheless, this is an important study establishing the first mouse model of increased BPV.

      We agree that high Ang II levels are not a predominant cause of hypertension in humans, which is why it is critical that our pulsatile Ang II dosing did not cause overt hypertension, (no increase in 24-hour MAP). Ang II was solely a tool to produce controlled, transient increases in BP to yield a significant increase in BPV.

      Regarding BPV specifically, prior studies indicate that primary hypertensive patients with elevated urinary angiotensinogen-to-creatinine ratio exhibit significantly higher mean 24-hour systolic ARV compared to those with lower ratios[15]. However, the fundamental mechanisms driving these harmful increases in BPV remain poorly defined. A central theme across clinical BPV studies is impaired arterial stiffness, which has been proposed to contribute to BPV through reduced arterial compliance and diminished baroreflex sensitivity. Moreover, increased BPV can exert mechanical stress on arterial walls, leading to arterial remodeling and stiffness−ultimately perpetuating a detrimental feed-forward cycle[16].

      In our model, male BPV mice exhibited a minimal yet significant elevation in SBP without corresponding increases in DBP, potentially reflecting isolated systolic hypertension, which is strongly associated with arterial stiffness[17,18]. Our initial goal was to establish controlled rapid fluctuations in BP, and Ang II was selected as the pressor due to its potent vasoconstrictive properties and short half-life[19].

      We appreciate the reviewer’s insightful comment and acknowledge the necessity of exploring alternative mechanisms underlying BPV, and independent of Ang II. It is our long-term goal to investigate these factors in further studies.

      Recommendations for the authors:

      Reviewer #2 (Recommendations for the authors):

      (1) How was the dose of Ang II determined? It seems that this dose (3.1ug/hr) is quite high.

      The Ang II dose was titrated in a preliminary study to one that induced a significant and transient BP response without increasing 24-hour blood pressure (i.e. no hypertension).

      Ang II was delivered subcutaneously at 3.1 μg/hr, a concentration comparable to high-dose Ang II administration via mini-osmotic pumps (~1700 ng/kg/min)[20], with one-hour pulses occurring every 3-4 hours. With 6 pulses per day, the total daily dose equates to 18.6 µg/day in a ~30 gram mouse.

      For comparison, if the same 18.6 µg/day dose were administered continuously via a mini-osmotic pump (18.6 µg/0.03kg/1440min), the resulting dosage would be approximately 431 ng/kg/min[21,22], aligning with subpressor dose levels. Thus, while the total dose may appear high, it is not delivered in a constant manner but rather intermittently, allowing for controlled, rapid variations in blood pressure.

      (2) Were behavioral studies performed on the same mice that were individually housed? Individual housing causes significant stress in mice that can affect learning and memory tasks (PMC6709207). It's not a huge issue since the control mice would have been housed the same way, but it is something that could be mentioned in the discussion section.

      Behavioral studies were performed on mice that were individually housed following the telemetry surgery. The study was started once BP levels stabilized, as mice required several days to achieve hemodynamic stability post-surgery. Consequently, all mice were individually housed for several days before undergoing behavioral assessment.

      To account for potential cognitive variability, earlier novel object recognition (NOR) tests were conducted to established cognitive capacity, and mice that did not meet criteria were excluded from further behavioral testing. However, we acknowledge that individual housing induces stress, which can influence learning and memory, and this is a factor we were unable to fully control. Given that both experimental and control groups experienced the same housing conditions, this stress effect should be comparable across cohorts. A discussion on this limitation is now included in the text.

      (3) It looks like one control mouse that was included in both Figures 1 and 2 (control n=12) but was excluded in Table 1 (control n=11), this isn't mentioned in the text - please include the exclusion criteria in the manuscript.

      We apologize for the typo−12 control animals were consistently utilized across Figure 1-2, Table 1, Supplemental Table 1, Figure 6C, and Supplemental Figure 2B. Since the initial submission, one control mouse was completed and included into the telemetry control cohort. Thus, in the updated manuscript, we have corrected the control sample size to 13 mice across these figures ensuring consistency.

      Additionally, exclusion criteria have now been explicitly included in the manuscript (Line 173-175). Mice were excluded from the study if they died prematurely (died prior to treatment onset) or mice exhibited abnormally elevated pressure while receiving saline, likely due to complications from telemetry surgery.

      (4) Please include a statement on why female mice were not included in this study.

      As discussed in our response to Reviewer #1, our initial intention was to include both male and female mice in this study. However, high mortality rates following telemetry surgeries significantly constrained our ability to advance all aspects of the study. As a result, we limited our first cohort to males to establish the basics of the model. A statement is now included in the manuscript, Line 50-53: “Female mice were not included in the present study due to high post-surgery mortality observed in 12-14-month-old mice following complex procedures. To minimized confounding effects of differential survival and to establish foundational data for this model, we restricted the investigation to male mice.”

      Potential sex differences might be complex and warrants a separate future research to comprehensively assess sex as a biological variable, which are currently ongoing.

      (5) On page 14, "experiments from control vs experimental mice were not equally conducted in the same season raising the possibility for a seasonal effect" - does this mean that control experiments were not conducted at the same time as the Ang II infusions in BPV mice? This has huge implications on whether the effects observed are induced by treatment or just batch seasonal effects.

      We fully acknowledge the reviewer’s concern, and our statement aims to provide transparency regarding the study’s limitations. Several challenges contributed to this outcome, including high mortality rates following surgeries (primarily telemetry implantation) and technical issues related to instrumentation, particularly telemetry functionality.

      Differences between BPV and saline mice emerge primarily due to mortality or telemetry failures−some mice did not survive post-surgery, while others remain healthy but had non-functional telemeters. This issue was particularly pronounced in 14-month-old mice, as their fragile vasculature occasionally prevented proper BP readings.

      Each experiment required a minimum of two and a half months per mouse to complete, with a cost (also per mouse) exceeding $1500 USD ($300 pump, $175 mouse, $900 telemeters, per diem, drugs, reagents etc.). Despite our best effort to ensure comparable seasonal/batch data, these logistical and technical constraints prevented perfect synchronization.

      To evaluate whether seasonal differences influenced our results, we incorporated additional telemetry data into the control cohort. Of the seven included control mice, six underwent the same treatment but were allocated to a separate branch of the study, which endpoints did not require a chronic cranial window. We found no significant differences in 24-hour average MAP during the baseline period between control mice with or without a cranial window, Supplemental Figure 2A. Additionally, we grouped mice into seasonal categories based on Georgia’s climate: “Spring-Summer” (May-September) and “Fall-Winter” (October-April) but observed no BP differences between these periods, Supplemental Figure 2B.

      Given the absence of seasonal effects on BP and the fact that mice were sourced from two independent suppliers (Jackson Laboratory and NIA), we anticipate that the observed results are driven by treatment rather than seasonal or batch effects.

      (6) Methods, two-photon imaging: did the authors mean "retro-orbital" instead of "intra-orbital" injection of the Texas red dye? Also, is this a Texas red-dextran? If so, what molecular weight?

      Thank you for this comment. The correct terminology is “retro-orbital” rather than “intra-orbital” injection. Additionally, we utilized Texas Red-dextran (70 kDa, 5% [wt/vol] in saline) for the imaging experiments. These details have now been incorporated into the Methods section.

      (1) Shaffer F, Ginsberg JP. An Overview of Heart Rate Variability Metrics and Norms. Front Public Health. 2017;5:258. doi: 10.3389/fpubh.2017.00258

      (2) Pires PW, Jackson WF, Dorrance AM. Regulation of myogenic tone and structure of parenchymal arterioles by hypertension and the mineralocorticoid receptor. Am J Physiol Heart Circ Physiol. 2015;309:H127-136. doi: 10.1152/ajpheart.00168.2015

      (3) Iddings JA, Kim KJ, Zhou Y, Higashimori H, Filosa JA. Enhanced parenchymal arteriole tone and astrocyte signaling protect neurovascular coupling mediated parenchymal arteriole vasodilation in the spontaneously hypertensive rat. J Cereb Blood Flow Metab. 2015;35:1127-1136. doi: 10.1038/jcbfm.2015.31

      (4) Diaz JR, Kim KJ, Brands MW, Filosa JA. Augmented astrocyte microdomain Ca(2+) dynamics and parenchymal arteriole tone in angiotensin II-infused hypertensive mice. Glia. 2019;67:551-565. doi: 10.1002/glia.23564

      (5) Kim KJ, Diaz JR, Presa JL, Muller PR, Brands MW, Khan MB, Hess DC, Althammer F, Stern JE, Filosa JA. Decreased parenchymal arteriolar tone uncouples vessel-to-neuronal communication in a mouse model of vascular cognitive impairment. GeroScience. 2021. doi: 10.1007/s11357-020-00305-x

      (6) Chan SL, Nelson MT, Cipolla MJ. Transient receptor potential vanilloid-4 channels are involved in diminished myogenic tone in brain parenchymal arterioles in response to chronic hypoperfusion in mice. Acta Physiol (Oxf). 2019;225:e13181. doi: 10.1111/apha.13181

      (7) Tarantini S, Hertelendy P, Tucsek Z, Valcarcel-Ares MN, Smith N, Menyhart A, Farkas E, Hodges EL, Towner R, Deak F, et al. Pharmacologically-induced neurovascular uncoupling is associated with cognitive impairment in mice. J Cereb Blood Flow Metab. 2015;35:1871-1881. doi: 10.1038/jcbfm.2015.162

      (8) Ma J, Ayata C, Huang PL, Fishman MC, Moskowitz MA. Regional cerebral blood flow response to vibrissal stimulation in mice lacking type I NOS gene expression. Am J Physiol. 1996;270:H1085-1090. doi: 10.1152/ajpheart.1996.270.3.H1085

      (9) Sible IJ, Nation DA. Blood Pressure Variability and Cognitive Decline: A Post Hoc Analysis of the SPRINT MIND Trial. Am J Hypertens. 2023;36:168-175. doi: 10.1093/ajh/hpac128

      (10) Epstein NU, Lane KA, Farlow MR, Risacher SL, Saykin AJ, Gao S. Cognitive dysfunction and greater visit-to-visit systolic blood pressure variability. Journal of the American Geriatrics Society. 2013;61:2168-2173. doi: 10.1111/jgs.12542

      (11) Antunes M, Biala G. The novel object recognition memory: neurobiology, test procedure, and its modifications. Cognitive processing. 2012;13:93-110. doi: 10.1007/s10339-011-0430-z

      (12) Kraeuter AK, Guest PC, Sarnyai Z. The Y-Maze for Assessment of Spatial Working and Reference Memory in Mice. Methods Mol Biol. 2019;1916:105-111. doi: 10.1007/978-1-4939-8994-2_10

      (13) Singhal G, Morgan J, Jawahar MC, Corrigan F, Jaehne EJ, Toben C, Breen J, Pederson SM, Manavis J, Hannan AJ, et al. Effects of aging on the motor, cognitive and affective behaviors, neuroimmune responses and hippocampal gene expression. Behav Brain Res. 2020;383:112501. doi: 10.1016/j.bbr.2020.112501

      (14) Tediashvili G, Wang D, Reichenspurner H, Deuse T, Schrepfer S. Balloon-based Injury to Induce Myointimal Hyperplasia in the Mouse Abdominal Aorta. J Vis Exp. 2018. doi: 10.3791/56477

      (15) Ozkayar N, Dede F, Akyel F, Yildirim T, Ates I, Turhan T, Altun B. Relationship between blood pressure variability and renal activity of the renin-angiotensin system. J Hum Hypertens. 2016;30:297-302. doi: 10.1038/jhh.2015.71

      (16) Kajikawa M, Higashi Y. Blood pressure variability and arterial stiffness: the chicken or the egg? Hypertens Res. 2024;47:1223-1224. doi: 10.1038/s41440-024-01589-8

      (17) Laurent S, Boutouyrie P. Arterial Stiffness and Hypertension in the Elderly. Front Cardiovasc Med. 2020;7:544302. doi: 10.3389/fcvm.2020.544302

      (18) Wallace SM, Yasmin, McEniery CM, Maki-Petaja KM, Booth AD, Cockcroft JR, Wilkinson IB. Isolated systolic hypertension is characterized by increased aortic stiffness and endothelial dysfunction. Hypertension. 2007;50:228-233. doi: 10.1161/HYPERTENSIONAHA.107.089391

      (19) Al-Merani SA, Brooks DP, Chapman BJ, Munday KA. The half-lives of angiotensin II, angiotensin II-amide, angiotensin III, Sar1-Ala8-angiotensin II and renin in the circulatory system of the rat. J Physiol. 1978;278:471490. doi: 10.1113/jphysiol.1978.sp012318

      (20) Zimmerman MC, Lazartigues E, Sharma RV, Davisson RL. Hypertension caused by angiotensin II infusion involves increased superoxide production in the central nervous system. Circ Res. 2004;95:210-216. doi: 10.1161/01.RES.0000135483.12297.e4

      (21) Gonzalez-Villalobos RA, Seth DM, Satou R, Horton H, Ohashi N, Miyata K, Katsurada A, Tran DV, Kobori H, Navar LG. Intrarenal angiotensin II and angiotensinogen augmentation in chronic angiotensin II-infused mice. Am J Physiol Renal Physiol. 2008;295:F772-779. doi: 10.1152/ajprenal.00019.2008

      (22) Nakagawa P, Nair AR, Agbor LN, Gomez J, Wu J, Zhang SY, Lu KT, Morgan DA, Rahmouni K, Grobe JL, et al. Increased Susceptibility of Mice Lacking Renin-b to Angiotensin II-Induced Organ Damage. Hypertension. 2020;76:468-477. doi: 10.1161/HYPERTENSIONAHA.120.14972

  3. www.planalto.gov.br www.planalto.gov.br
    1. § 4º

      Trata-se de presunção relativa e não absoluta, cabendo à Administração executar as diligências previstas no § 2º, conforme acórdão do TCU:

      1. O critério definido no art. 59, § 4º, da Lei 14.133/2021 conduz a uma presunção <u>relativa</u> de inexequibilidade de preços, devendo a Administração, nos termos do art. 59, § 2º, da referida lei, dar à licitante a oportunidade de demonstrar a exequibilidade de sua proposta.

      (TCU, Acórdão 465/2024 Plenário, Representação, Relator Ministro-Substituto Augusto Sherman - Boletim nº 478)

    2. território
        1. O critério de desempate por localidade (art. 60, § 1º, inciso I, da Lei 14.133/2021) não se aplica a licitações realizadas no âmbito da Administração Pública Federal, por ausência de expressa previsão legal. A preferência por empresas estabelecidas no território do promotor do certame é restrita às licitações realizadas por órgãos e entidades dos entes subnacionais.

      (TCU, Acórdão 1733/2025, Plenário, Representação, Relator Ministro Benjamin Zymler)

      Obs.: Ou seja, propostas empatadas poderão ser decididas, se em igualdade de condições, por critério territorial. No entanto, observe que somente é aplicável tal critério aos entes subnacionais.

      Com isso, o TCU entendeu que é indevido o desempate por critérios territoriais em licitações federais por expressa falta de previsão legal, considerando a expressa delimitação da abrangência da norma. Ou seja, aplicar-se critérios territoriais em licitações federais viola o princípio da legalidade e da isonomia.

    1. "You will be free as soon as you are twenty-one, but I am a slave for life! Have not I as good a right to be free as you have?" These words used to trouble them; they would express for me the liveliest sympathy, and console me with the hope that something would occur by which I might be free.

      This means that in the text the men would be free as soon as they turned twenty-one, but the one person would rather be a slave for life, he was wondering if he will be ever free like the others and he needed to the hope that he will be free like the others from being a slave.

    2. Mr. Severe's place was filled by a Mr. Hopkins. He was a very different man. He was less cruel, less profane, and made less noise, than Mr. Severe. His course was characterized by no extraordinary demonstrations of cruelty. He whipped, but seemed to take no pleasure in it. He was called by the slaves a good overseer.

      I wonder if Douglass is showing how slavery made "ordinary" cruelty seem like “goodness” in comparison to others

    3. I shall never forget his first speech at the convention--the extraordinary emotion it excited in my own mind--the powerful impression it created upon a crowded auditory, completely taken by surprise--the applause which followed from the beginning to the end of his felicitous remarks

      the word choice in this sentence sets a scenery, makes me feel the emotion and I was able to see an image in my head while I was reading it

    4. IN the month of August, 1841, I attended an antislavery convention in Nantucket, at which it was my happiness to become acquainted with FREDERICK DOUGLAS

      I like how the beginning is a hook, makes the reading sound more interesting , wanting to more know.

    5. The master is frequently compelled to sell this class of his slaves, out of deference to the feelings of his white wife; and, cruel as the deed may strike any one to be, for a man to sell his own children to human flesh-mongers, it is often the dictate of humanity for him to do so;

      Often, the masters would have children with enslaved black women, resulting in mixed-race children, also known as "mulatto". Because they were his children (master), and mixed-race, they were harshly beaten. The wife/white-mistress hated them, the master wasn't allowed to openly protect them. So, they were sold, which was a better outcome as Frederick claimed.

    1. Synthèse (pas de phrases : listes) Innovation Apports larges/généraux spécifiques aux études aréales

      @noemie @caovy Quand on aura terminé de rédiger la partie précédente : quels sont nos besoins, quelles solutions veut-on explorer, quelles méthodes va-t-on tester, que va-t-on développer et partager, il faudra produire une synthèse par le biais de listes ou de schémas qui permettront d'imprimer dans la rétine du lecteur l'essentiel de notre discours.

    1. eLife Assessment

      This study offers a valuable contribution to our understanding of the role of layer 6b cortical neurons in sleep-wake regulation, providing new insight into how this understudied neural population may regulate cortical arousal via orexin signaling. The evidence supporting these findings is solid, although somewhat constrained by limitations in the specificity of the genetic targeting strategy. Nonetheless, the work introduces new avenues for uncovering how the classical wake-promoting peptide, orexin, exerts its effects on the cortex.

    2. Reviewer #1 (Public review):

      Summary:

      Meijer et al. sought to investigate the role of cortical layer 6b (L6b) neurons in modulating sleep-wake states and cortical oscillations under baseline and sleep deprived conditions and in response to orexin A and B. Using chronic EEG recordings in mice with silencing of Drd1a+ neurons (via constitutive Cre-dependent knockout of SNAP25), the authors report that while overall baseline sleep-wake architecture and response to sleep deprivation minimal/unchanged, "L6b silencing" leads to a slowing of theta activity during wakefulness and REM sleep, and a reduction in EEG power during NREM sleep. Additionally, orexin B-induced increases in theta activity were attenuated in L6b silenced mice, which the authors state suggests a modulatory role for L6b in orexin-mediated arousal regulation. The manuscript is generally well written with clarity and transparency. However, a major concern is the lack of specificity in the genetic manipulation, which targets Drd1a+ neurons not exclusive to L6b, undermining the attribution of observed effects solely to L6b. Verification of neuronal silencing is also unclear, and statistical inconsistencies between the main text and figures/tables make it difficult to effectively evaluate the text and stated outcomes.

      Strengths:

      (1) The text is well written.

      (2) The authors are transparent about methodological details.

      (3) The stated sleep, circadian, and orexin infusion experiments appear to be well designed, executed, and analyzed (with the exceptions of some statistical analyses detailed below).

      Weaknesses:

      (1) All outcomes are attributed specifically to L6b neurons, but the genetic manipulation is not specific to L6b neurons. The authors acknowledge this as a limitation, but in my view, this global manipulation is more than a limitation - it affects the overall interpretations of the data. The Hoerder-Suabedissen et al., 2018 paper shows sparse, but also dense, expression of Drd1a+ neurons in brain regions outside of the L6b. Given this issue, the results are largely overstated throughout the paper.

      (2) It is not clear to me that the "silencing" of Drd1a+ neurons was verified.

      (3) There were various discrepancies (and potentially misattributions) between the stated significant differences in Supplementary Table T1 data and Figure 3a & S2 spectral plots. This issue makes it difficult to effectively evaluate the main text and stated outcomes.

      Related, the authors stated that post hoc comparisons of EEG spectral frequency bins were not corrected for multiple testing. Instead, significance was only denoted if changes in at least two consecutive frequency bins were significant. However, there are multiple plots in which a single significance marker is placed over an isolated bin (i.e., 4c, 6, S5, S6). Unless each marker is equivalent to 2 consecutive frequency bins, these markers should be removed from the plots. Otherwise, please define the frequency and size of these markers in the main text.

      (4) A rainbow color scale, as in Figure 3, we've now learned, can be misleading and difficult to interpret. The viridis color scale or a different diverging color scale are good alternatives.

      (5) How much time elapsed between vehicle/orexin A & B infusions?

      (6) For Figure 6, there are statistical discrepancies between the main text and the plots (pg. 10):

      a) The text claims post hoc differences for relative ORXA frontal EEG, but there are no significance markers on the plot.<br /> b) The text states that there were no post hoc differences for the relative ORXA occipital EEG, but significance markers are on the plot.<br /> c) The main test for the relative ORXB frontal EEG was not significant, but there are post hoc significance markers on the plot.<br /> d) For relative ORXB occipital EEG, there are significant markers on the plot outside of the stated range in the text.

      (7) Some important details are only available in figure captions, making it difficult to understand the main text. For example, when describing Figure 3c in the main text on page 7, it is not clear what type of transitions are being discussed without reading the figure caption. Likewise, a "decrease," "shift," and "change" are mentioned, but relative to what? Similar comment for the EEG theta activity description on pages 7 - 8. Please add relevant details to the main text.

      (8) Statistical comparisons for data in Figure 3e, post hoc analyses for data in Figure S7a-b REM data, and post hoc analyses for Figure S7c (not b) occipital EEG should be included to support differences claims. Please denote these differences on the respective plots.

      (9) In the subsection titled "Layer 6b mediates effects of orexin on vigilance states (pg. 8)," there does not seem to be any stated differences between control and L6b silenced mice. A more accurate subtitle is needed.

    3. Reviewer #2 (Public review):

      Summary:

      In this manuscript, Meijer and colleagues investigated the effects of inactivation (conditional silencing) of cortical layer 6b neurons on sleep-wake states and EEG spectral power under the following three conditions: during natural sleep-wake states, after sleep deprivation, or after intracerebroventricular administration of orexin A and B. The authors report that silencing of L6b neurons did not have a significant effect on the total time spent in sleep-wake states, duration, or number of state epochs, or the response to sleep deprivation. However, silencing of L6b neurons did slow down theta-frequency (6-9 Hz) during wake and REM sleep, and reduced the total EEG power during NREM sleep. Infusion of orexin A in the mice in which cortical layer 6b neurons were inactivated produced an increase in wakefulness. A similar effect was observed after infusion of orexin A in the mice in which these neurons were not silenced, but the effect (i.e., increase in wakefulness) was of a smaller magnitude. Silencing of cortical layer 6b neurons attenuated the effect of orexin B in increasing theta activity, as was observed in the control mice. The authors conclude that the cortical neurons in layer 6b play an essential role in state-dependent dynamics of brain activity, vigilance state control, and sleep regulation.

      Strengths:

      (1) A focus on cortical layer 6b neurons, which are an understudied neuronal population, especially in the context of brain and behavioral state transitions.

      (2) The authors used a well-established mouse model to study the effect of inactivation of cortical layer 6b neurons.

      Weaknesses:

      (1) Although the authors used a highly selective approach to silence layer 6b neurons, the observed changes in EEG oscillations cannot be solely attributed to layer 6b neurons because of the ICV route for orexin administration.

      (2) The rationale for using only male rats is not provided.

    4. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      (1) All outcomes are attributed specifically to L6b neurons, but the genetic manipulation is not specific to L6b neurons. The authors acknowledge this as a limitation, but in my view, this global manipulation is more than a limitation - it affects the overall interpretations of the data. The Hoerder-Suabedissen et al., 2018 paper shows sparse, but also dense, expression of Drd1a+ neurons in brain regions outside of the L6b. Given this issue, the results are largely overstated throughout the paper.

      We appreciate the reviewer’s careful reading and concern that some of our statements may have overstated the implications of our data. The Drd1a Cre mouse model used (FK164) has a relatively selective expression of Drd1a Cre in cortex, especially in layer 6b, but indeed some expression is seen in layer 6a and subcortically. We will nuance our claims throughout the paper to ensure that the conclusions are supported by our findings, and further discuss the impact of this limitation on the overall interpretation of our results. Specifically, we will discuss the potential contribution of relevant subcortical areas and layer 6a in the effects we observed.

      (2) It is not clear to me that the "silencing" of Drd1a+ neurons was verified.

      In our previous publications, we showed confirmation of the loss of regulated synaptic vesicle release from the Cre positive neuronal population (Marques-Smith et al., 2016; Hoerder-Suabedissen et al., 2018; Messore et al., 2024), which validates our approach to “silence” cortical neurons. We will discuss this further in the revised manuscript.

      (3) There were various discrepancies (and potentially misattributions) between the stated significant differences in Supplementary Table T1 data and Figure 3a & S2 spectral plots. This issue makes it difficult to effectively evaluate the main text and stated outcomes.

      We thank the reviewer for spotting the inconsistencies in how the statistical comparisons were presented: indeed, in the text we described two-way ANOVAs with posthoc tests but in the figures significance markers were positioned based on multiple t-tests. We have revised Supplementary Table T1, Figure 3a and S2 to ensure that all statistics are presented consistently throughout the manuscript, i.e. with two-way ANOVAs and accompanying posthoc tests.

      Related, the authors stated that post hoc comparisons of EEG spectral frequency bins were not corrected for multiple testing. Instead, significance was only denoted if changes in at least two consecutive frequency bins were significant. However, there are multiple plots in which a single significance marker is placed over an isolated bin (i.e., 4c, 6, S5, S6). Unless each marker is equivalent to 2 consecutive frequency bins, these markers should be removed from the plots. Otherwise, please define the frequency and size of these markers in the main text.

      In line with the previous comment, we have adjusted markers to reflect the results from posthoc tests after two-way ANOVAs in Figures 6 and supplementary figures S5 and S6. 

      We thank the reviewer for pointing out that in our comparisons of EEG spectra, in some cases single isolated frequency bins, where p-value reached 0.05 were shown as significantly different, which indeed could have occurred by chance given that, in line with previous literature, we have not employed multiple testing comparison. In the revised manuscript we will use an unbiased approach by plotting actual p-values for all bins, and moderate our conclusions accordingly, while giving the readers the opportunity to evaluate the magnitude and extent of the differences directly, rather than relying on an arbitrary threshold for significance.

      (4) A rainbow color scale, as in Figure 3, we've now learned, can be misleading and difficult to interpret. The viridis color scale or a different diverging color scale are good alternatives.

      Thank you for pointing this out, we have adjusted the colour scale.

      (5) How much time elapsed between vehicle/orexin A & B infusions?

      There were 2-4 non-infusions days between infusions. We will add this information to methods when revising the manuscript.

      (6) For Figure 6, there are statistical discrepancies between the main text and the plots (pg. 10):

      a) The text claims post hoc differences for relative ORXA frontal EEG, but there are no significance markers on the plot.

      b) The text states that there were no post hoc differences for the relative ORXA occipital EEG, but significance markers are on the plot.

      c) The main test for the relative ORXB frontal EEG was not significant, but there are post hoc significance markers on the plot.

      d) For relative ORXB occipital EEG, there are significant markers on the plot outside of the stated range in the text.

      Thank you for your careful observations, these issues reflect the same inconsistency as raise above, where the text describes two-way ANOVAs and the figures refers to results obtained with multiple t tests. We shall adjust the markers in the figures to be only shown when the ANOVA is significant and show the results of posthoc tests after ANOVAs instead of the results of multiple t tests.

      (7) Some important details are only available in figure captions, making it difficult to understand the main text. For example, when describing Figure 3c in the main text on page 7, it is not clear what type of transitions are being discussed without reading the figure caption. Likewise, a "decrease," "shift," and "change" are mentioned, but relative to what? Similar comment for the EEG theta activity description on pages 7 - 8. Please add relevant details to the main text.

      We will adjust the wording in the main text to reflect more precisely which comparisons are shown in the figures.

      (8) Statistical comparisons for data in Figure 3e, post hoc analyses for data in Figure S7a-b REM data, and post hoc analyses for Figure S7c (not b) occipital EEG should be included to support differences claims. Please denote these differences on the respective plots.

      We have added the statistical comparisons for Figure 3e to the results section.

      We have added the statistical comparisons for Figure S7A to the results section.

      We have added the statistical comparison for Figure S7b to the results section.

      In Figure S7c, there was an overall genotype difference, but there was not a time x genotype interaction, so we have not performed posthoc tests and did not plot posthoc significance markers for this figure. We have adjusted the wording in the results section to make this clearer.

      We have adjusted the reference to the figure S7c which was incorrect, thank you for your careful attention.

      (9) In the subsection titled "Layer 6b mediates effects of orexin on vigilance states (pg. 8)," there does not seem to be any stated differences between control and L6b silenced mice. A more accurate subtitle is needed.

      We shall change the subtitle to: “The effects of orexin on vigilance states in L6b silenced mice”. The main finding described in this section is that the increase in EEG theta frequency after ORXB infusion is attenuated in L6b silenced mice, so a statement summarizing this finding could be an alternative title. However, then it would not accurately reflect other, less conspicuous, yet potentially important findings described in this section (during NREM sleep, only in L6b silenced animals there is an increase in power in the lower frequency bins in the frontal derivation; in the occipital derivation, levels of relative SWA during NREM sleep after ORXA infusion were lower in L6b silenced than in control animals).

      Reviewer #2 (Public review):

      Weaknesses:

      (1) Although the authors used a highly selective approach to silence layer 6b neurons, the observed changes in EEG oscillations cannot be solely attributed to layer 6b neurons because of the ICV route for orexin administration.

      We completely agree, and did not want to imply that orexin administered through the ICV route reaches cortical Drd1a Cre expressing neurons only. We will re-word the corresponding sentences accordingly throughout the manuscript.

      (2) The rationale for using only male rats is not provided.

      We agree that this is an important limitation and will acknowledge and discuss it further in the revised manuscript. Unfortunately, our experimental protocol precluded the possibility of monitoring accurately the oestrous cycle, which as well-known has an influence on sleep-wake architecture, brain oscillations as well as orexin signalling and receptor abundance. We therefore decided to use male mice only for the current study, but planning to use both sexes in our follow up work.

    1. eLife Assessment

      In this valuable study, the authors use a cutting-edge method to perform voltage imaging of CA1 pyramidal cells in head-fixed mice running on a track while local field potentials (LFPs) were recorded in the contralateral hemisphere. The authors provide solid evidence of synchronous ensembles of CA1 pyramidal neurons that are associated with contralaterally recorded theta rhythms but not with contralaterally recorded sharp wave-ripples during exploration of a novel environment. The paper will be of interest to scientists who are interested in hippocampal neuronal coding of novel environments, particularly those with experimental questions that can benefit from this cutting-edge imaging technique.

    2. Joint Public Review:

      Summary:

      There has been extensive electrophysiological research investigating the relationship between local field potential patterns and individual cell spike patterns in the hippocampus. In this study, the authors used innovative imaging techniques to examine spike synchrony of hippocampal cells during locomotion and immobility states. The authors report that hippocampal place cells exhibit prominent synchronous spikes that co-occur with theta oscillations during exploration of novel environments.

      Strengths:

      The single cell voltage imaging used in this study is a highly novel method that may allow recordings that were not previously possible using traditional methods.

      Weaknesses:

      Local field potential recordings were obtained from the contralateral hemisphere for technical reasons, which limits some of the study's claims.

    3. Author response:

      The following is the authors’ response to the previous reviews

      Joint Public Review:

      Summary:

      For many years, there has been extensive electrophysiological research investigating the relationship between local field potential patterns and individual cell spike patterns in the hippocampus. In this study, using innovative imaging techniques, they examined spike synchrony of hippocampal cells during locomotion and immobility states. The authors demonstrated that hippocampal place cells exhibit prominent synchronous spikes locked to theta oscillations.

      Strengths:

      The single cell voltage imaging used in this study is a highly novel method that may allow recordings that were not previously possible using existing methods.

      We thank the reviewer for recognizing the strengths of our study.

      Weaknesses:

      The strength of evidence remains incomplete because of the main claim that synchronous events are not associated with ripples. As was mentioned in previous rounds of review, ripples emerge locally and independently in the two hemispheres. Thus, obtaining ripple recordings from the contralateral hemisphere does not provide solid evidence for this claim. The papers the authors are citing to make the claim that "Additionally, we implanted electrodes in the contralateral CA1 region to monitor theta and ripple oscillations, which are known to co-occur across hemispheres (29-31)" do not support this claim. For example, reference 29 contains the following statement: "These findings suggest that ripples emerge locally and independently in the two hemispheres".

      In our previous revisions, we took care to limit our claim to what our data directly supported: that synchronous ensembles of CA1 neurons were not associated with ripple oscillations recorded in the contralateral hippocampus. To address reviewer concerns, we changed the Title, modified the Abstract, adjusted relevant text in the Results, and explicitly acknowledged the methodological limitations in the Discussion. 

      In this round, we further revised the manuscript to directly address the editor’s and reviewer’s remaining concerns: 

      (1) We replaced the word “surprisingly” with a more neutral “Moreover” to avoid implying that the observed dissociation was unexpected given the use of contralateral recordings.

      Introduction (line 67-69):

      “Moreover, these synchronous ensembles occurred outside of contralateral ripples (c-ripples) …”

      (2) We removed the clause stating that ripples “co-occur across hemispheres”, along with the associated citation to Buzsaki et al. (2003), to avoid potential misinterpretation. The sentence now simply states that we recorded ripple and theta oscillations in the contralateral CA1.

      Introduction (line 63-64):

      “Additionally, we implanted electrodes in the contralateral CA1 region to monitor theta and ripple oscillations.” (co-occurrence claim removed)

      (3) We carefully replaced all mentions of “ripples” in the manuscript with “c-ripples” (i.e., contralateral ripples) to ensure that the scope of our findings is clearly defined and cannot be misinterpreted.

      (4) We strengthened the acknowledgment of the methodological limitations in the Discussion. 

      Discussion (line 528-533): 

      “While contralateral LFP recordings can capture large-scale hippocampal theta and ripple oscillations, they do not fully reflect ipsilateral-specific dynamics, such as variation in theta phase alignment or locally generated ripple events (Buzsaki et al., 2003; Szabo et al., 2022; Huang et al., 2024). Given that ripple oscillations can emerge locally and independently in each hemisphere, interpretations based on contralateral recordings must be made with caution. Further studies incorporating simultaneous ipsilateral field potential recordings will be essential to more precisely understand local-global network interactions.”

      These revisions ensure that our manuscript now presents a consistent and appropriately limited interpretation across all sections. We hope these clarifications address all remaining concerns and accurately reflect the scope of our findings.

    1. 海洋植物地理一直研究的很少,所以现在的植物地理学主要指陆地植物地理学。

      海洋植物地理研究滞后的原因是什么?

    2. 每一个种(或属、科)都不是在地球表面普遍分布,而只是出现于某种生境,占据地表某一有限范围,它的分布的地理范围也不断地发生变化。

      分布有限

    3. 生态植物地理学与植物生理学的成就结合,已经发展成为植物生态学

      两个科目最初的侧重点是分别什么,形成后有什么改变,并且形成的原因是什么

    4. 传统的植物地理学分为三个部分:区系植物地理学、生态植物地理学和历史植物地理学

      传统植物地理学的种类

  4. drive.google.com drive.google.com
    1. constant background noise.

      This description captures how anxiety often isn’t about isolated panic episodes but a persistent, underlying tension. The phrase “background noise” reflects the way anxiety can subtly interfere with daily functioning — always present, even when not overwhelming. It aligns with how chronic stress can become normalized yet still impact focus, mood, and wellbeing.

    1. eLife Assessment

      This paper reports a valuable discovery that specific-mode electroacupuncture (EA) transiently opens the blood-brain barrier (BBB) in rats. The evidence is solid but lacks functional validation of BBB permeability changes. The work will be of interest to medical scientists working in the field of electroacupuncture and drug delivery.

    2. Reviewer #1 (Public review):

      Summary:

      The work from this paper successfully mapped transcriptional landscape and identified EA-responsive cell types (endothelial, microglia). Data suggest EA modulates BBB via immune pathways and cell communication. However, claims of "BBB opening" are not directly proven (no permeability data).

      Strengths:

      First scRNA-seq atlas of EA effects on BBB, revealing 23 cell clusters and 8 cell types. High cell throughput (98,338 cells), doublet removal, and robust clustering (Seurat, SingleR). Comprehensive bioinformatics (GO/KEGG, CellPhoneDB for ligand-receptor interactions). Raw data were deposited in GEO (GSE272895) and can be accessed.

      Weaknesses:

      (1) No in vivo/in vitro assays confirm BBB permeability changes (e.g., Evans blue leakage, TEER).

      (2) Only male rats were used, ignoring sex-specific BBB differences.

      (3) Pericytes and neurons, critical for the BBB, were not captured, likely due to dissociation artifacts.

      (4) Protein-level validation (Western blot, IHC) absent for key genes (e.g., LY6E, HSP90).

      (5) Fixed stimulation protocol (2/100 Hz, 40 min); no dose-response or temporal analysis.

    3. Reviewer #2 (Public review):

      Summary:

      This study uses single-cell RNA sequencing to explore how electroacupuncture (EA) stimulation alters the brain's cellular and molecular landscape after blood-brain barrier (BBB) opening. The authors aim to identify changes in gene expression and signaling pathways across brain cell types in response to EA stimulation using single-cell RNA sequencing. This direction holds promise for understanding the consequences of noninvasive methods of BBB opening for therapeutic drug delivery across the BBB.

      Strengths:

      (1) The study addresses an emerging and potentially important application of noninvasive stimulation methods to manipulate BBB permeability.

      (2) The dataset provides broad transcriptional profiling across multiple brain cell types using single-cell resolution, which could serve as a valuable community resource.

      (3) Analyses of receptor-ligand signaling and cell-cell communication are included and have the potential to offer mechanistic insight into BBB regulation.

      Weaknesses:

      (1) The work falls short in its current form. The experimental design lacks a clear justification, and readers are not provided with sufficient background information on the extent, timing, or regional specificity of BBB opening in this EA model. These details, established in prior work, are critical to understanding the rationale behind the current transcriptomic analyses.

      (2) Further, the results are often presented with minimal context or interpretation. There is no model of intercellular or molecular coordination to explain the BBB-opening process, despite the stated goal of identifying such mechanisms. The statement that EA induces a "unique frontal cortex-specific transcriptome signature" is not supported, as no data from other brain regions are presented. Biological interpretation is at times unclear or inaccurate - for instance, attributing astrocyte migration effects to endothelial cell clusters or suggesting microglial tight junction changes without connecting them meaningfully to endothelial function.

      (3) The study does include analyses of receptor-ligand signaling and cell-cell communication, which could be among its most biologically rich outputs. However, these are relegated to supplementary material and not shown in the leading figures. This choice limits the utility of the manuscript as a hypothesis-generating resource.

      (4) Overall, while the dataset may be of interest to BBB researchers and those developing technologies for drug delivery across the BBB, the manuscript in its current form does not yet fulfill its interpretive goals. A more integrated and biologically grounded analysis would be beneficial.

    4. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      The work from this paper successfully mapped transcriptional landscape and identified EA-responsive cell types (endothelial, microglia). Data suggest EA modulates BBB via immune pathways and cell communication. However, claims of "BBB opening" are not directly proven (no permeability data).

      (1) No in vivo/in vitro assays confirm BBB permeability changes (e.g., Evans blue leakage, TEER).  

      (2) Only male rats were used, ignoring sex-specific BBB differences.

      (3) Pericytes and neurons, critical for the BBB, were not captured, likely due to dissociation artifacts.

      (4) Protein-level validation (Western blot, IHC) absent for key genes (e.g., LY6E, HSP90).

      (5) Fixed stimulation protocol (2/100 Hz, 40 min); no dose-response or temporal analysis.

      (1) We sincerely apologize for the oversight regarding the description of changes in blood-brain barrier permeability. In fact, our team conducted a series of preliminary studies that verified this aspect, but we did not provide a more detailed introduction in the introduction section. We will address and improve this in the revised manuscript. (2) We are very grateful to the reviewers for pointing out the important and meaningful issue of "gender-specific BBB differences." We will make this a focal point in our future research.

      (2) As for pericytes and neurons, we acknowledge their importance in the function of the blood-brain barrier. We acknowledge the importance of pericytes and neurons in the blood-brain barrier. However, neurons are absent because our sample processing method involves dissociation. During the dissociation procedure, neuronal axons, which are relatively long, are filtered out during the frequent cell suspension steps and cannot enter the downstream microfluidic system for analysis, so they are not present in our data. Since this experiment is primarily focused on non-neuronal cells, we did not choose to use nucleus extraction for sample processing. As for pericytes, we believe they are not captured because their proportion in our samples is extremely low, which is why they are not present in the data. Further research may require single-nucleus transcriptomics or the separate isolation of these two cell types for study. Of course, in our current mechanistic studies, we are also fully considering the important roles these two cell types play in BBB function.

      (3) In addition, for verification at the protein level, we have recently conducted some experiments and will include these results in the revised version.

      (5) Lastly, regarding our electroacupuncture intervention model, we actually conducted a series of parameter optimization experiments during the preliminary exploration phase. This part is indeed lacking in our current introduction, and we will add it to the research background and introduction.

      Reviewer #2 (Public review):

      Summary:

      This study uses single-cell RNA sequencing to explore how electroacupuncture (EA) stimulation alters the brain's cellular and molecular landscape after blood-brain barrier (BBB) opening. The authors aim to identify changes in gene expression and signaling pathways across brain cell types in response to EA stimulation using single-cell RNA sequencing. This direction holds promise for understanding the consequences of noninvasive methods of BBB opening for therapeutic drug delivery across the BBB.

      (1) The work falls short in its current form. The experimental design lacks a clear justification, and readers are not provided with sufficient background information on the extent, timing, or regional specificity of BBB opening in this EA model. These details, established in prior work, are critical to understanding the rationale behind the current transcriptomic analyses.

      (2) Further, the results are often presented with minimal context or interpretation. There is no model of intercellular or molecular coordination to explain the BBB-opening process, despite the stated goal of identifying such mechanisms. The statement that EA induces a "unique frontal cortex-specific transcriptome signature" is not supported, as no data from other brain regions are presented. Biological interpretation is at times unclear or inaccurate - for instance, attributing astrocyte migration effects to endothelial cell clusters or suggesting microglial tight junction changes without connecting them meaningfully to endothelial function.<br /> (3) The study does include analyses of receptor-ligand signaling and cell-cell communication, which could be among its most biologically rich outputs. However, these are relegated to supplementary material and not shown in the leading figures. This choice limits the utility of the manuscript as a hypothesis-generating resource.

      (4) Overall, while the dataset may be of interest to BBB researchers and those developing technologies for drug delivery across the BBB, the manuscript in its current form does not yet fulfill its interpretive goals. A more integrated and biologically grounded analysis would be beneficial.

      (1) It was indeed our mistake that we did not pay attention to the importance of research background factors such as the degree, timing, or regional specificity of BBB opening for the rationale and purpose of this experimental design. In our revision, we will thoroughly elaborate on the relevant previous studies.

      (2) Our current study is actually based on previous findings that electroacupuncture can open the BBB, with a more pronounced effect observed in the frontal lobe (this aspect should be further described in the research background). Building on this foundation, our aim is to delineate the potential biological mechanisms involved. Therefore, we selected frontal lobe tissue as our primary choice for sequencing and have not yet investigated differences across other brain regions, although this may become a focus of future research. Additionally, we recognize that the mechanism underlying BBB opening is complex, and at present, we cannot determine whether it is driven by a single direct factor or by coordinated actions between cells or molecules. As such, our results are presented only briefly for now, and we will carefully consider whether to supplement our findings by incorporating insights from other studies.

      (3) Thank you very much for bringing this to our attention. We will include the key results of the receptor-ligand signaling and cell-cell communication analysis in the main manuscript.

      (4) Indeed, our current dataset and analysis tend to present objective data results. We are also conducting a series of validations that may be related to the biology of the blood-brain barrier, and we look forward to sharing and discussing any future research findings with you and everyone.

    1. eLife Assessment

      This study presents valuable computational findings on the neural basis of learning new motor memories without interfering with previously learned behaviours using recurrent neural networks. The evidence supporting the claims of the authors is solid, but it would benefit from stronger and clearer links with experimental findings. This work will be of interest to computational and experimental neuroscientists working in motor learning.

    2. Reviewer #1 (Public review):

      Summary:

      This work investigates the neural basis of continual motor learning, specifically how brains might accommodate new motor memories without interfering with previously learned behaviours. Mainly drawing inspiration from recent experimental studies in monkeys (Losey et al. and Sun, O'Shea et al.), the authors use recurrent neural networks (RNNs) to model sequential learning and examine the emergence and properties of two proposed neural signatures of motor memory: the "uniform shift" observed in preparatory activity and the "memory trace" observed in execution activity.

      Strengths:

      The work's main contribution is demonstrating that both uniform shifts and memory traces emerge in RNN models trained on a sequential BCI task, without requiring explicit additional mechanisms. The work explores the relationship between these signatures and behavioural savings, finding that the memory trace correlates with immediate retention savings in networks without context, while the uniform shift does not. The study also investigates how properties of the new task perturbation (within- vs. outside-manifold) and the presence of explicit context cues affect these signatures and their relationship to savings, generally finding that context signals and outside-manifold perturbations reduce savings by decreasing the inherent overlap in the neural strategies used to solve the task.

      Weaknesses:

      A primary weakness is the lack of clear definitions of the uniform shift and the memory trace, which are quite different metrics. Another primary weakness is that the task modelled is well-matched to the Losey et al. BCI paradigm, but not well-matched to the Sun, O'Shea et al.'s curl field paradigm, which is likely impacting some of the results, primarily the lack of a relationship between the uniform shift and motor memories. While there are improvements that could be made in this work, we think it is a demonstration that modeling learning in neural activity using neural network models continues to be a valuable tool, moving the field forward.

    3. Reviewer #2 (Public review):

      Summary:

      Chang et al. develop an RNN model of a BCI sequential learning task to examine the emergence of motor memory in the network. They use this system to quantify signatures of memory in continual learning, comparing their model with experimental observations from monkeys in prior publications. They show that the RNN model has signatures of shifts associated with sequential learning without any non-standard learning rules. This convincing study contributes to the knowledge of how motor memories are formed and shaped so that they are flexible in acquiring multiple behaviors.

      Strengths:

      This paper describes a well-designed numerical experiment that comes to a clear interpretation of a set of neural BCI experiments. The learning signatures the authors describe are interesting and well laid out, and the paper is well written. I find it insightful that the neural signature of motor learning emerges in a trained network without special learning rules.

      Weaknesses:

      The paper could be stronger if it made a stronger interpretation of how memory traces and uniform shifts are related. These two observations are taken from the BCI sequential learning literature and introduced by two different prior experimental papers on two different tasks, so it seems like there is an opportunity here to use the RNN model to unite these concepts, or define another metric for signatures of learning from a more normative approach.

    4. Reviewer #3 (Public review):

      Summary:

      The authors build and analyze recurrent neural network (RNN) models of brain-computer interface (BCI) multi-task learning, developing a valuable theoretical understanding of learning-related neural population phenomena ("memory traces" and "uniform shifts") that have been reported in recent experimental studies of BCI and motor learning. The authors find that both phenomena emerge in their RNN models, and both correlate in some manner to learning-related behavioral phenomena ("savings" and "forgetting"). The authors also reveal that RNN training details, in particular, incorporating a task-indicating contextual input, can impact these population-level signatures of learning in RNN activity and their relation to those behavioral phenomena.

      Strengths:

      The text is well written, and the figures are clearly composed to convey the core concepts and findings. The RNN studies are elegant in their ability to recapitulate the memory trace and uniform shift phenomena, and further allow evaluations of novel scenarios that were not tested in the original corpus of the modeled animal experiments. The authors assess the sensitivity of their results to multiple approaches to RNN training, including training connectivity within a model of motor cortex, training only an upstream model that provides inputs to the motor cortex model, and providing task-indicating contextual inputs.

      Weaknesses:

      (1) It is unclear to what extent these RNN models operate in regimes relevant to biological neural networks (e.g., motor cortex), even at the neural-population level of abstraction studied here. Can the authors speak to how sensitive their results are to details that might speak to these operating regimes (e.g., signal-to-noise ratios or dimensionality of the RNN activities)?

      (2) The work could be further strengthened by analyses demonstrating a more direct link between the neural population phenomena (memory trace and uniform shift) and the behavioral phenomena (savings, forgetting, etc). While in animal experiments, it can be exceedingly difficult to demonstrate links beyond correlative effects, the promise of a model is the relative tractability of implementing manipulations that might establish something closer to a causal link between phenomena. Is it the case that the memory trace is a task-dependent, mean-preserving rotation of the across-target task-relevant activity space? And that the uniform shift is a translation (non-mean-preserving) of that space? If so, could the authors design regularization schemes that specifically target each of these effects, enabling a more direct test of the functional role the effects play in driving behavioral phenomena?

      Minor Comments:

      The current study is based on BCI learning of center-out tasks, analogous to the Losey et al. task that initially reported the memory trace phenomena. However, a rather different behavioral task - involving arm movements through curl force fields - was employed by the Sun, O'Shea, et al. study that originally reported the uniform shift phenomena. How should readers interpret the current study's findings related to the uniform shift? To what extent might the behavioral implications of the uniform shift depend on the demands of the task, e.g., the biomechanics, day-to-day experiencing of different curl-field perturbations, etc.?

    5. Author response:

      We thank the reviewers for their thoughtful comments, and we plan to implement many of their suggestions to improve the paper. We agree that the paper can benefit from clearer links between the two neural signatures (memory traces and uniform shifts) themselves, and between the neural signatures and behavioral phenomena. We will address these limitations in multiple ways. First, as the reviewers noted, RNN models have the potential to probe these relationships, so we plan to perform further analyses and modeling experiments to uncover any causal relationships. Second, we will also establish clearer definitions of the neural signatures and explore how these signatures can be unified using our models. Finally, we will compare the experimental paradigms between Losey et al and Sun, O’Shea et al, and discuss how differences between the paradigms may have impacted our observations, particularly in the context of other experimental and modeling papers.

    1. eLife Assessment

      This important study introduces the Life Identification Number (LIN) coding system as a powerful and versatile approach for classifying Neisseria gonorrhoeae lineages. The authors show that LIN codes capture both previously defined lineages and their relationships in a way that aligns with the species' phylogenetic structure. The compelling evidence presented, together with its integration into the PubMLST platform, underscores its strong potential to enhance epidemiological surveillance and advance our understanding of gonococcal population biology.

    2. Reviewer #1 (Public review):

      Summary:

      Bacterial species that frequently undergo horizontal gene transfer events tend to have genomes that approach linkage equilibrium, making it challenging to analyze population structure and establish the relationships between isolates. To overcome this problem, researchers have established several effective schemes for analyzing N. gonorrhoeae isolates, including MLST and NG-STAR. This report shows that Life Identification Number (LIN) Codes provide for a robust and improved discrimination between different N. gonorrhoeae isolates.

      Strengths:

      The description of the system is clear, the analysis is convincing, and the comparisons to other methods show the improvements offered by LIN Codes.

      Weaknesses:

      No major weaknesses were identified by this reviewer.

    3. Reviewer #2 (Public review):

      Summary:

      This paper describes a new approach for analyzing genome sequences.

      Strengths:

      The work was performed with great rigor and provides much greater insights than earlier classification systems.

      Weaknesses:

      A minor weakness is that the clinical application of LIN coding could be articulated in a more in-depth way. The LIN coding system is very impressive and is certainly superior to other protocols. My recommendation, although not necessary for this paper, is that the authors expand their analysis to noncoding sequences, especially those upstream of open reading frames. In this respect, important cis-acting regulatory mutations that might help to further distinguish strains could be identified.

    4. Reviewer #3 (Public review):

      Summary:

      In this well-written manuscript, Unitt and colleagues propose a new, hierarchical nomenclature system for the pathogen Neisseria gonorrhoeae. The proposed nomenclature addresses a longstanding problem in N. gonorrhoeae genomics, namely that the highly recombinant population complicates typing schemes based on only a few loci and that previous typing systems, even those based on the core genome, group strains at only one level of genomic divergence without a system for clustering sequence types together. In this work, the authors have revised the core genome MLST scheme for N. gonorrhoeae and devised life identification numbers (LIN) codes to describe the N. gonorrhoeae population structure.

      Strengths:

      The LIN codes proposed in this manuscript are congruent with previous typing methods for Neisseria gonorrhoeae, like cgMLST groups, Ng-STAR, and NG-MAST. Importantly, they improve upon many of these methods as the LIN codes are also congruent with the phylogeny and represent monophyletic lineages/sublineages.

      The LIN code assignment has been implemented in PubMLST, allowing other researchers to assign LIN codes to new assemblies and put genomes of interest in context with global datasets.

      Weaknesses:

      The authors correctly highlight that cgMLST-based clusters can be fused due to "intermediate isolates" generated through processes like horizontal gene transfer. However, the LIN codes proposed here are also based on single linkage clustering of cgMLST at multiple levels. It is unclear if future recombination or sequencing of previously unsampled diversity within N. gonorrhoeae merges together higher-level clusters, and if so, how this will impact the stability of the nomenclature.

      The authors have defined higher resolution thresholds for the LIN code scheme. However, they do not investigate how these levels correspond to previously identified transmission clusters from genomic epidemiology studies. It would be useful for future users of the scheme to know the relevant LIN code thresholds for these investigations.

    5. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      Summary:

      Bacterial species that frequently undergo horizontal gene transfer events tend to have genomes that approach linkage equilibrium, making it challenging to analyze population structure and establish the relationships between isolates. To overcome this problem, researchers have established several effective schemes for analyzing N. gonorrhoeae isolates, including MLST and NG-STAR. This report shows that Life Identification Number (LIN) Codes provide for a robust and improved discrimination between different N. gonorrhoeae isolates.

      Strengths:

      The description of the system is clear, the analysis is convincing, and the comparisons to other methods show the improvements offered by LIN Codes.

      Weaknesses:

      No major weaknesses were identified by this reviewer.

      We thank the reviewer for their assessment of our paper.

      Reviewer #2 (Public review):

      Summary:

      This paper describes a new approach for analyzing genome sequences.

      Strengths:

      The work was performed with great rigor and provides much greater insights than earlier classification systems.

      Weaknesses:

      A minor weakness is that the clinical application of LIN coding could be articulated in a more in-depth way. The LIN coding system is very impressive and is certainly superior to other protocols. My recommendation, although not necessary for this paper, is that the authors expand their analysis to noncoding sequences, especially those upstream of open reading frames. In this respect, important cis-acting regulatory mutations that might help to further distinguish strains could be identified.

      We thank the reviewer for their comments. LIN code could be applied clinically, for example in the analysis of antibiotic resistant isolates, or to investigate outbreaks associated with a particular lineage. We will update the text to describe this more thoroughly.

      In regards to non-coding sequences: unfortunately, intergenic regions are generally unsuitable for use in typing systems as (i) they are subject to phase variation, which can occlude relationships based on descent; (ii) they are inherently difficult to assemble and therefore can introduce variation due to the sequencing procedure rather than biology. For the type of variant typing that LIN code represents, which aims to replicate phylogenetic clustering, protein encoding sequences are the best choice for convenience, stability, and accuracy. This is not to say that it is not a valid object to base a nomenclature on intergenic regions, which might be especially suitable for predicting some phenotypic characters, but this will still be subject to problem (ii), depending on the sequencing technology used.  Such a nomenclature system should stand beside, rather than be combined with or used in place of, phylogenetic typing. However, we could certainly investigate the relationship between an isolates LIN code and regulatory mutations in the future.

      Reviewer #3 (Public review):

      Summary:

      In this well-written manuscript, Unitt and colleagues propose a new, hierarchical nomenclature system for the pathogen Neisseria gonorrhoeae. The proposed nomenclature addresses a longstanding problem in N. gonorrhoeae genomics, namely that the highly recombinant population complicates typing schemes based on only a few loci and that previous typing systems, even those based on the core genome, group strains at only one level of genomic divergence without a system for clustering sequence types together. In this work, the authors have revised the core genome MLST scheme for N. gonorrhoeae and devised life identification numbers (LIN) codes to describe the N. gonorrhoeae population structure.

      Strengths:

      The LIN codes proposed in this manuscript are congruent with previous typing methods for Neisseria gonorrhea, like cgMLST groups, Ng-STAR, and NG-MAST. Importantly, they improve upon many of these methods as the LIN codes are also congruent with the phylogeny and represent monophyletic lineages/sublineages.

      The LIN code assignment has been implemented in PubMLST, allowing other researchers to assign LIN codes to new assemblies and put genomes of interest in context with global datasets.

      Weaknesses:

      The authors correctly highlight that cgMLST-based clusters can be fused due n to "intermediate isolates" generated through processes like horizontal gene transfer. However, the LIN codes proposed here are also based on single linkage clustering of cgMLST at multiple levels. It is unclear if future recombination or sequencing of previously unsampled diversity within N. gonorrhoeae merges together higher-level clusters, and if so, how this will impact the stability of the nomenclature.

      The authors have defined higher resolution thresholds for the LIN code scheme. However, they do not investigate how these levels correspond to previously identified transmission clusters from genomic epidemiology studies. It would be useful for future users of the scheme to know the relevant LIN code thresholds for these investigations.

      We thank the reviewer for their insightful comments. LIN codes do use multi-level single linkage clustering to define the cluster number of isolates. However, unlike previous applications of simple single linkage clustering such as N. gonorrhoeae core genome groups (Harrison et al., 2020), once assigned in LIN code, these cluster numbers are fixed within an unchanging barcode assigned to each isolate. Therefore, the nomenclature is stable, as the addition of new isolates cannot change previously established LIN codes.

      Cluster stability was considered during the selection of allelic mismatch thresholds. By choosing thresholds based on natural breaks in population structure (Figure 3), applying clustering statistics such as the silhouette score, and by assessing where cluster stability has been maintained within the previous core genome groups nomenclature, we can have confidence that the thresholds which we have selected will form stable clusters. For example, with core genome groups there has been significant group fusion with clusters formed at a threshold of 400 allelic differences, while clustering at a threshold of 300 allelic differences has remained cohesive over time (supported by a high silhouette score) and so was selected as an important threshold in the gonococcal LIN code. LIN codes have now been applied to >27000 isolates in PubMLST, and the nomenclature has remained effective despite the continual addition of new isolates to this collection. The manuscript will be revised to emphasise these points.

      Work is in progress to explore what LIN code thresholds are generally associated with transmission chains. These will likely be the last 7 thresholds (25, 10, 7, 5, 3, 1, 0) as previous work has suggested that isolates linked by transmission within one year are associated with <14 single nucleotide polymorphism differences (De Silva et al., 2016). The results of this analysis will be described in a future article, currently in preparation.

      Harrison, O.B., et al. Neisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance. The Journal of Infectious Diseases 2020.

      De Silva, D., et al. Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study. The Lancet Infectious Diseases 2016;16(11):1295-1303.

    1. Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

      Learn more at Review Commons


      Reply to the reviewers

      Proposed revision plan

      Based on the below reviews, we propose the following revision plan. Briefly:

      • We will remove the functional data on TGFβ signaling and mechanical loading/mechanosensing. We agree with the reviewers that we would need to generate additional histological and molecular data from conditional knockout mice, antibody and (ant)agonist treatments and the optogenetic model to determine their exact involvement in lining macrophage maturation. These experiments require significant time and other resources.
      • We would therefore like to uncouple this question for a follow-on manuscript.We will re-focus the manuscript on the developmental data providing a molecular and cellular blueprint of lining macrophage development. This will include our data on CSF1 as a key signal. The novelty and relevance of our developmental data have been highlighted by all three reviewers, and they have also praised the rigor of these experiments and their interpretation. We thus believe that this re-focus will improve the manuscript message.
      • To further enhance this, we are proposing to include additional data delineating the developmental dynamics of synovial fibroblasts. We have generated an in-depth single cell RNAsequencing dataset but did not include fibroblast-specific analyses in the original manuscript. This is not a change proposed by the reviewers, but we are proposing this because we believe this would be an impactful addition to a revised version of our study, providing data also on the maturation of the synovial (lining) macrophage niche.
      • We will otherwise respond to all individual reviewer comments and implement the requested changes, unless technically not possible. Please find below detailed point-by-point answers.

      Reviewer #1

      Evidence, reproducibility and clarity

      In their manuscript entitled "The synovial lining macrophage layer develops in the first weeks of life in a CSF1- and TGFβ-dependent but monocyte-independent process," the authors explore the developmental trajectory of synovial lining macrophages. They demonstrate that the formation of this specialized macrophage layer is age-dependent and governed by a distinct developmental program that proceeds independently of circulating monocytes. Through scRNA-Seq, the authors show that synovial lining macrophages originate locally from Aqp1⁺ macrophages and are marked by the expression of Csf1r, Tgfbr, and Piezo1. Notably, genetic ablation of each of these factors impaired the development of lining macrophages to varying degrees, suggesting differential contributions of CSF1, TGFβ, and PIEZO1 signaling pathways to their maturation and maintenance.

      The manuscript is well written, and the data quality and representation is of a high standard. The authors have employed a sophisticated array of state-of-the-art mouse models and cutting-edge technologies to elucidate the developmental origin of synovial lining macrophages. Notably, the supporting scRNA-Seq datasets are of excellence and provide valuable insights that will likely be of significant interest to researchers in the field of immunology and joint biology. Accordingly, the experimental approach and interpretations regarding macrophage origin are well-founded and compelling. However, in the eye of the reviewer, the section addressing the underlying molecular mechanisms is a bit less convincing. This part of the study appears slightly underdeveloped, and some of the mechanistic claims lack sufficient experimental clarity. A more rigorous experimental investigation would be essential to reinforce the manuscript's conclusions, particularly concerning the data related to Tgfbr and Piezo1, where the current evidence appears insufficiently substantiated.

      We thank the reviewer for their positive and constructive evaluation of our manuscript. We agree with them (and the other reviewers) that our functional data on the involvement of TGFβ signaling and mechanical loading/mechanosensing are comparably less convincing and substantiated than our developmental data. We are very grateful for their (and the other reviewers’) suggestions to provide more support for the involvement of these factors in lining macrophage development. However, we think that carrying this out to the same high standard will require substantial time and other resources. We have therefore decided to uncouple this from the developmental data and pursue this in follow-up work. We will re-focus the current manuscript on the developmental data. We have proposed to the editors to instead include additional data on synovial fibroblast development, to complement our macrophage data and also delineate the maturation of their niche, thereby providing a conclusive developmental atlas.

      Major point:

      1. The numbers of VSIG4⁺ macrophages appear either unaffected or only minimally altered in both Csf1rMerCreMer Tgfbr2floxed and Fcgr1Cre Piezo1floxed mouse models, respectively. This raises an important question: was the gene deletion efficiency sufficient in each model? Accordingly, the authors are encouraged to include quantitative data on gene deletion efficiency for both mouse models, as this information is critical for interpreting the observed phenotypic outcomes and validating the conclusions regarding gene function. Furthermore, to better assess the impact of Tgfbr2 and Piezo1 disruption, the authors should provide more comprehensive flow cytometry analyses and histological data for these mouse models. Given the apparent homogeneity of VSIG4⁺ macrophages (as shown by the authors themselves), bulk RNA-Seq of sorted Tgfbr2- and Piezo1-deficient VSIG4⁺ macrophages (or from TGFβ-treated animals) would offer valuable insights into both the effectiveness of gene deletion and the molecular pathways governed by TGFβ and PIEZO1 in lining macrophages.

      As outlined above, we have decided to uncouple our functional data on TGFβ, Piezo1 and mechanical loading. The points raised here are all very valid, and we will implement your suggestions in our follow-up functional work focusing on signaling events regulating lining macrophage development. On the suggestion to perform bulk RNA sequencing for VSIG4+ macrophages: This is a good one in principle – although we will not be able to use this strategy where we want to assess the consequences of experimental treatments or genetic models on lining macrophage maturation, because acquisition of VSIG4 is a key maturation event that might be impaired in these conditions.

      Minor points:

      Consistent usage of Cx3cr1-GFP+ nomenclature (for instance: Fig. S1 legend "adult mouse synovial tissue, showing PDGFRα⁺ fibroblasts (yellow) and CX3CR1-GFP⁺ cells (cyan)." versus Fig. 1 legend "Automated spot detection highlights Cx3cr1-GFP⁺ macrophages)".

      We will implement these changes.

      Unclear Fig. 3 legend: "Representative immunofluorescence images of synovial tissue from Clec9aCre:Rosa26lsl-tdT mice at 3 weeks and in adulthood, showing and tdTomato (yellow) and stained for DAPI (blue), VSIG4 (cyan)" Check 'showing and tdTomato.'

      We will implement these changes.

      For greater clarity, it would have been helpful if the transcript names had been directly included within Figures 3C, S3A, and S3C.

      We will implement these changes.

      Page 24: "(Mki67CreERT2:Rosa26lsl-tdT)" Last bracket not superscript.

      We will implement these changes.

      Page 25: "we again leveraged our scRNAsequencing dataset" Missing punctuation.

      We will implement these changes.

      Page 27: Fig. 5C legend: " of synovial tissue of 1 week-old, 3 weeks-old and adult mice." Please specify and change to 'adult Csf1rΔFIRE/ΔFIRE mice'.

      We will implement these changes.

      Page 30: The outcome observed in the Acta1-rtTA:tetO-Cre:ChR2-V5fl mouse model appears to be inconclusive: "This approach resulted in an increased density of VSIG4+ and total (F4/80+) macrophages in the exposed leg of some 5 days-old pups, but others showed the opposite trend (Figure S5D)." This variability may reflect low efficiency of the model or other technical limitations (e.g. muscle contractions frequency or time point of analysis). Given this ambiguity, it is worth reconsidering whether the data are sufficiently robust to warrant inclusion. Should the authors choose to include these findings, further experimentation of appropriate depth and precision is required to allow a conclusive interpretation (either it increases the density of VSIG4+ macrophages or not). The same applies to the Yoda1-treated mice, for which additional data are needed to determine whether VSIG4⁺ macrophage density is truly affected.

      We have decided to remove the data on the optogenetic mouse model and Yoda1 treatment and follow-on separately, implementing these suggestions, including proof of concept data for optogenetically induced muscle contractions.

      Significance

      General assessment: provide a summary of the strengths and limitations of the study. What are the strongest and most important aspects? What aspects of the study should be improved or could be developed? This is a well-designed study that uses cutting-edge methodologies to investigate the developmental trajectory of synovial lining macrophages under homeostatic conditions. The authors present robust experimental evidence and compelling interpretations concerning synovial macrophage origin, which are both well-substantiated and impactful. Nonetheless, from the reviewer's perspective, the section exploring the molecular mechanisms underlying macrophage differentiation is comparatively less convincing. This section appears somewhat underdeveloped, as some of the mechanistic claims lack sufficient depth and experimental rigor to fully substantiate the conclusions.

      Describe the nature and significance of the advance (e.g. conceptual, technical, clinical) for the field: In contrast to earlier studies (PMID: 31391580, 32601335), the inclusion of fate-mapping experiments adds an important dimension, offering novel insight into the ontogeny of synovial macrophages. This expanded perspective may prove particularly valuable in advancing our understanding of joint immunology, especially regarding the local origins and lineage relationships of macrophage populations.

      Furthermore, the authors present novel insights into the molecular pathways underlying the differentiation and development of synovial lining macrophages. By demonstrating previously unrecognized regulatory mechanisms, this work significantly deepens our understanding of the cellular and transcriptional programs that drive macrophage specialization within the joint microenvironment.

      Place the work in the context of the existing literature (provide references, where appropriate): This study builds upon previous work characterizing the macrophage compartment in the joint (PMID: 31391580, 32601335), yet provides a substantially more comprehensive dataset that spans multiple developmental time points and data on the origin of this specialized macrophage subset.

      State what audience might be interested in and influenced by the reported findings: Immunologist, clinicians

      Define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate. This study falls well within the scope of the reviewer's expertise in innate immunity.

      Reviewer #2

      Evidence, reproducibility and clarity

      In the manuscript „The synovial lining macrophage layer develops in the first weeks of life in a CSF1- and TGFβ- dependent but monocyte-independent process", Magalhaes Pinto and colleagues carefully employ a wide range of technologies including single cell profiling, imaging and an exceptional combination of fate mapping models to characterize the ontogeny and development of lining macrophages in the joint, thus dissecting their maturation during postnatal development. Over the last decade, several landmark studies highlighted the imprinting of tissue-resident macrophages by a combination of ontogenetic and tissue-specific niche factors during development. So far, the ontogeny and the tissue niche factors governing the development and maturation of lining macrophages have not been described. Therefore, the results of this study offers insights on a small highly adapted macrophage population with relevance in many disease settings in the joint. Furthermore, the findings are nicely showcasing how macrophages are specializing to even very small tissue niches across development within one bigger anatomical compartment to serve dedicated functions within this niche.

      This manuscript is beautifully written and highlights many novel, highly relevant findings on lining macrophage biology and the authors employ a wide range of different technologies to carefully dissect the postnatal development of lining macrophages.

      In particular, the combination of scRNA-seq and fate mapping is providing a unique the link of transcriptional programs to ontogeny within the tissue niche. Furthermore, the integrative use of distinct fate mapping strategies, transgenic mouse lines, and treatment paradigms to elucidate key niche factors guiding the development and maturation of lining macrophages provides many interesting findings and data that are highly relevant to the field. I really enjoyed reading this manuscript.

      Thank you for your complimentary and constructive assessment of our manuscript, and the detailed comments below, which are very helpful. Please find point-by-point responses below.

      Major points:

      The authors show dynamic regulation of VSIG4 in lining macrophages during development, therefore VSIG4 is maybe not an ideal choice for gating strategies to define lining macrophages or to show as a single markers in immunofluorescence (IF) stainings to demonstrate their abundance across development (even though it is clear that this is the reason why the F4/80 staining is shown next to it). To demonstrate the increase of lining macrophages during development in IF, it would be more helpful if the authors would show quantifications of all F4/80+ cells and additionally VSIG4+ as a proportion of F4/80+ cells (or VSIG4+ F4/80+ and all F4/80+ in a stacked bar plot). We agree with the assessment of VSIG4 not being ideal since this is a key marker of mature lining macrophages only.

      We will provide these additional analyses.

      In Figure 1C, the authors nicely demonstrate that the lining macrophages get closer in their distance across development to build the epithelial-like macrophage structure along the adult lining. Is the close proximity between lining macrophages already fully "matured" at 3 weeks of age and comparable to adults? Please quantify the distance in adult linings.

      We will provide data for adult joints.

      Can the authors explain how the grouping was performed between the analyzed human fetal joints? It is not clear why the cut was chosen between the groups at 16/17 weeks of age. Maybe it would be also beneficial if the authors would consider not grouping these samples but rather show the specific quantifications for each samples individually and estimate via linear regression the expansion over time across human development. Furthermore, can the authors give additional information about the distancing of lining macrophages in the human fetal samples, it would be great to see if they follow the same dynamics as in mouse. Maybe comparison to human juvenile/adult joints would also add on to substantiate the findings in human samples (if possible).

      We will show samples ungrouped and perform linear regression analysis as suggested.

      The scRNA-seq analysis leaves several questions open and some conclusions and workflows cannot be easily followed.

      We appreciate this comment and the complexity of the data, and will implement the below recommendations, and clarify the issues raised.

      It is not clear how and especially why the signature genes to define macrophages vs. monocytes were chosen. Especially as the signature genes for monocytes would not include patrolling monocytes and the macrophage signature genes seem to be highly regulated during development, see also Apoe expression in NB vs. adult in Figure S2e. Why did the authors not take classical markers such as Itgam, Fcgr1a, Csf1r?

      Can dendritic cell signatures be excluded? Cluster 11 and 12 show indeed some DC markers, are these really macrophages?

      The authors provide several figure panels showing TOP marker genes or key marker genes for the identified clusters, however it is not clear if these are TOP DE genes or if the genes were hand chosen. Somehow, the authors give the impression that the clusters were chosen and labeled not based on DE genes, but more on existing literature that previously reported these macrophage populations. DE gene lists for all annotated cell types and macrophage clusters need to be provided within the manuscript.

      The authors claim that Clusters 1 and 4 are "developing" macrophages. How is this defined? Why are these developing cells compared to other clusters? And why are these clusters later on not considered as progenitors of Aqp1 macrophages and Vsig4 macrophages? Why are Aqp1+ macrophages not labeled as developing when they are later on in the manuscript shown as potential intermediate progenitors of lining macrophages?

      Furthermore, it is again confusing that markers are used throughout Figure 2 which are labeled as "key marker genes" for a population and then later on they are claimed to be regulated during development within this population, see for example Figure 2D and 2H.

      It is appreciated that the authors distinguished cycling clusters such as 8, 9, and 10 based on their cycling gene signature. Here it would be very exciting to see a cell cycle analysis across all clusters and time points to see when exactly the cells are expanding during development; this would also substantiate the data later shown for the Mki67-CreERT2 mouse model.

      Can the authors identify certain gene modules during development of lining macrophages (and/or their progenitors) which are associated with certain functions (e.g. GO terms, GSEA enrichment)?

      To determine the actual presence of the identified macrophage clusters from the scRNA-seq as macrophage populations in the joint, the authors should perform IF or FACS for key markers. Especially, Aqp1+ macrophages should be shown in the developing joint.

      We will provide additional data, but would also like to reference a study by collaborators currently in revision at Immunity, which characterizes the Aqp1+ population in detail. We are hoping to have a doi available during our revision process.

      The authors used a wide range of fate mapping models, which is quite unique and highly appreciated. The obtained results and the conclusions made from the models raise a couple of questions: Whereas contribution of HSC-derived/monocyte-derived macrophages to the lining compartment seems to be minor, there is still labeling across different models. Various aspects would need to be clarified.

      We will clarify these data throughout as per below suggestions.

      For example, the authors employ Ms4a3-Cre as a tracing model for GMP-derived monocytes, however all quantifications of the labeling efficiency are not normalized to the labeling in monocytes or another highly recombined cell population. This should be shown, similar to the other fate mapping models (Figure 3 F-I).

      Labelling efficacy for Ms4a3-Cre is near complete for GMP-derived monocytes (and neutrophils) with the Rosa-lsl-tdT (aka Ai14) reporter we have used (see also PMID: 31491389 and doi: 10.1101/2024.12.03.626330); but we will include normalized data as requested.

      Please show Ms4a3 expression across clusters across time points, to exclude expression in fetal-derived clusters.

      We will include this in the revised supplementary information, but there is indeed very little at birth (in line with the original report for other tissues PMID: 31491389).

      In line with the question raised above, if the authors can exclude a development of the Egfr1+ and Clec4n+ developing macrophages into Aqp1+ macrophages and subsequently into Vsig4 lining macrophages, the obtained data from the Ms4a3-Cre model highly suggests a correlative labeling across these clusters what could implicate a relation. However, the authors do not discuss throughout the manuscript the role of these developing macrophages. It is highly encouraged to include this into the manuscript and it would be of high relevance to understand lining macrophage development.

      This is an interesting point and we agree it deserves consideration in the revised manuscript. Indeed, our trajectory analyses do not predict differentiation of the Egfr1+ and Clec4n+ developing macrophages into Aqp1+ macrophages, and hence, ultimately lining macrophages. Conversely, Aqp1+ cells might also convert into Egfr1+ and Clec4n+ developing macrophages. We will elaborate on this more in the revised manuscript.

      The authors conclude from the pseudo bulk transcriptomic profiling of the different macrophage clusters that TdT+ and TdT- macrophages do not differ in their gene expression profile and that this is due to niche imprinting rather than origin imprinting. Even though the data supports that conclusion, the authors should verify if inkling cells early during development also show this similar gene expression profile and gene expression should be compared at the different developmental time points. Tissue niche imprinting is happening within the niche during development, most likely in a stepwise progress, and therefore there should be differences in the beginning.

      This is another important point that we will address in the revised manuscript by performing additional differential gene expression analyses at the different developmental time points, including the earliest stages, as suggested.

      The trajectorial analysis using different pseudotime pipelines is very interesting and nicely points out the potential role of Aqp1 macrophages as intermediates of Vsig4 lining macrophages. From my point of view, all trajectories seem to suggest that Egfr1 developing macrophages and Clec4n developing macrophages might differentiate into Aqp1 macrophages, however the authors are not exploring this further and the role of both developing macrophage clusters is not further discussed (see also comments above).

      We will address and discuss this in the revised manuscript.

      How was the starting point of the trajectorial analyses defined and is it the same for each pipeline used?

      We will clarify this in the revised manuscript.

      Are there potentially two trajectories? It looks like there is one in the beginning of postnatal life and a second one appearing from the monocyte-compartment later in life. If this is true, that would rather speak for a dual ontogeny of Vsig4+ macrophages, wouldn't it?

      We will discuss this in the revised manuscript.

      A heatmap (transcriptional shift) of trajectories between more clusters should be shown at least for Cluster 0,1,2, and 3. It is not sufficient to demonstrate this only between two clusters.

      We will add these analyses during revision.

      To show the similarity between Aqp1 macrophages and proliferating macrophage clusters, the authors should remove the cycling signature and compare these clusters to show that the cycling cells might be Aqp1 macrophages or earlier developing macrophage progenitors aka Clec4n or Egfr1 macrophages.

      We will address this in the revised manuscript.

      The conclusions made from the Mki67-CreERT2 data are a bit difficult to understand, whereas all progenitors (monocyte progenitors and macrophage progenitors will proliferate at the neonatal time point and no conclusions can be made if the cells expand in the niche. The authors should employ Confetti mice or other models (Ubow mice) to analyze clonal expansion in the niche.

      We agree that interpretation of the Mki67-CreERT2 data is complicated by labeling of other cells, and notably, labeling observed in BM-derived cells. We will highlight this better in the revised manuscript. We have tried using Ubow mice to address this issue, but the recombination efficacy we yielded was too low to draw conclusions. We will address this during revision.

      All predicted cell-cell interactions between macrophages and fibroblasts should be provided in a supplementary table. Are the interactions shown in Figure 5 chosen interactions or the TOP predicted ones? Whereas the authors show different numbers of interactions, it is most likely hand-picked and therefore biased.

      We will provide a full list of all predicted interactions in the revised supplementary material in addition to a list of the full differential gene expression analysis.

      The authors further aim to dissect the factors involved in the developmental niche imprinting of lining macrophages. Even though it is highly appreciated that the authors used so many experimental setups to show the reliance of lining macrophages on Csf1 and TGF-beta as well as mechanosensation, the wide range of models the different methods used and selected developmental time points make it very difficult to really interpret the data. The authors should carefully choose time points and methods (either FACS analysis across all models or IF across all, or both). Often deletion efficiencies for transgenic models and proof of concept that the inhibitors and agonists are working in the treatment paradigm are not provided. For example, Csf1rMer-iCre-Mer Tgfbr2fl/fl mice are used but no deletion efficiency is shown or different time points of analysis, maybe the macrophages are not properly targeted in the set up.

      We have decided to uncouple our experimental data on Tgfb, Piezo1 and mechanosensing/mechanical loading, but are taking this into consideration for revision. In many cases, we have in fact performed flow cytometry and imaging analyses, and agree, we should be showing this consistently.

      The authors have shown the role of Csf1 and Tgfbr2 only for lining macrophages, is this specific in the joint to this population of are subliming macrophages affected in a similar manner.

      We will include data on sublining macrophages in the revised figure (for CSF1; Tgfb data will be uncoupled from this current manuscript).

      Can the authors confirm their results in CSF1R-FIRE mice with anti-Csf1 injections or in Csf1op/op mice?

      We will expand our discussion of the Csf1 findings, and will consider including anti-CSF1 data during revision. Phenotypes on other Csf1(r) deficient mice are published, if not with the same developmental resolution as our time course in Csf1rFIRE knockout mice and with simpler readouts. Csf1op/op mice are indeed deficient in synovial lining macrophages, from 2 days of age onwards (PMID: 8050349), and lining macrophages are also absent from 2-weeks-old and adult Csf1r-/- mice (PMID: 11756160).

      The setup in Figure S5G is very interesting to test the role of movement and mechanical load on the joint, however, there is basically no data on the model provided showing the efficiency of the induced optogenetic muscle contractions, and only one time point is shown.

      Data on mechanical loading will be uncoupled from the current manuscript and substantiated in a separate follow-up.

      The results regarding the role of Piezo1 and mechanosensation vary a lot. Could it be that analyses were done too early or that actually proper weight load on the joint must be applied for the maturation of the macrophages? The authors should test this to.

      We will uncouple these data from the current manuscript during revision. However, this is a possibility that we have discussed. In fact, the most appropriate experimental approach to address the involvement of mechanical loading, onset of walking and specifically, weight bearing would be a loss-of-function approach (i.e. paralysis at the newborn stage), for which we unfortunately could not obtain ethics approval from the UK Home Office.

      The Rolipram experiment is shown in Figure S5G, but is not described in the result section. It only appears at some point in the discussion part. The authors should move it to results or remove it from the manuscript.

      We will incorporate these data with the revised section on developing synovial macrophage populations.

      Minor points:

      Please reference the Figure panels in numeric order throughout the text.

      We will change this where not the case.

      Figure 2a and 2b are a bit out of the storyline, it is not obvious why this is shown here and maybe it would be good to move it to the supplements. Gating strategy is also not used for scRNA-seq. Therefore, it would better fit to the later analysis of joint macrophages across different transgenic mouse models and treatment paradigms. The gating strategies are changing across different experiments throughout the figures, it would be nice to have a similar gating strategy for all experiments, see also Figure 3 where the defining markers for joint macrophages are changing between models.

      We will revise Figures 2, 3 and the related supplementary figures.

      A lot of figure panels have very small labeling that is basically unreadable. Axes at FACS plots for example. Sometimes, it is even impossible to distinguish cluster labels especially when they have similar colors.

      We will revise this, thanks for pointing it out.

      In the text on page 14, many markers are named which are specifically regulated during development in lining macrophages, but these factors are not labeled anywhere in the volcano plot. It would be good to showcase at least some of these named genes in the figure panel, e.g. Trem2.

      We will do this for revision.

      Figure 2F and Figure S2F are really nicely showing the percentage of cells per cluster in each analyzed biological sample. Maybe the authors could additionally consider to show a stacked bar plot with the mean percentage of cells per cluster and how the clusters are distributed across time points?

      We will include this in the revised manuscript.

      Figure 3A: IF for adult lining macrophages and the quantification are missing.

      This will be included in the revised version.

      Significance

      This manuscript highlights novel, highly relevant findings on lining macrophage biology and the authors employ a wide range of different technologies to carefully dissect the postnatal development of lining macrophages. Furthermore, this study showcases in a very elegant and detailed way the adaptation of macrophage progenitors to a highly specific anatomical tissue niche.

      The manuscript is of high interest to basic scientists focussing on macrophage biology and immune cell development and clinicians and clinician scientists focussing on joint diseases such as RA.

      Therefore the manuscript is of interest to a wide community working in immunology.

      Reviewer #3

      Summary:

      Magalhaes Pinto, Malengier-Devlies, and co-authors investigated the developmental origins and maturation of synovial (lining and sublining) macrophages across embryonic, newborn, and postnatal stages in mouse. The authors used multiple transgenic reporter lines, lineage tracing, scRNA-seq, 2D confocal and 3D lightsheet imaging, and perturbations to delineate the macrophage states and ontogeny. They propose a model in which the majority of the joint lining macrophages has a fetal (EMP-derived) origin and a small proportion has a definitive HSC-derived monocyte origin, which both seed and mature within the synovial space in the postnatal period in the first 3 weeks of life. Using cell-cell communication analysis on their scRNA-seq data, they identified Fgf2, Csf1, and Tgfb as candidate signaling pathways that support (lining) macrophage development and maturation. Functional experiments indicate that the process is CSF1 and TGFb-dependent and also partly dependent on mechanosensing through Piezo1.

      The key conclusions on the composition of the synovial macrophages are convincing based on the presented results, and are carefully phrased. The study is very comprehensive, yet the description and organization of the results of the different mouse models could be altered to improve the storyline. Several refinements in data presentation, formulation, and minor validation experiments would further improve the clarity of the story, as well as summary recaps of the major findings throughout the text.

      We thank this reviewer for their detailed review. We will be implementing the requested changes wherever technically feasible.

      Major comments:

      Generally, the story could be more streamlined by introducing earlier reporter lines and lineage-origin logic. Clearly state which reporter/CreERT2 lines and acrosses are used. It was unclear in Figure 2 that cells of the cross of the Cx3cr1-GFP and Ms4a3Cre:Rosa26lsl-tdT reporter lines were used for the scRNA-seq. The principle that there are fetal-derived and bone marrow (GMP)-derived monocytes and macrophages doesn't need to be "hidden" until Figure 3. For example, also the imaging of Ms4a3Cre could be introduced before the scRNA-seq.

      We will revise the structure and order of the manuscript during revision.

      Figure 1 could benefit from a cartoon visualizing the anatomy of the knee joint. The terms "sublining" and "synovium" are now a bit unclear, as it appears that sometimes the synovium is indicated as sublining and vice versa. Additionally, a schematic developmental timeline could be added to indicate the parallels between mouse and human development (fetal and postnatal development in mouse versus gestational age in human). Also, the various waves of hematopoiesis could be indicated in this timeline, which would be particularly helpful for Figure 3 for the lineage-tracing readouts. Lastly, the authors could end the manuscript (a new Figure 6) with a general cartoon summarizing all the results presented.

      We will include illustrations as suggested.

      Figure 1 could be rearranged: first introduce the markers CX3CR1 and VSIG4 (Figure 1D) and then present the quantifications (Figure 1B/E). Where possible, co-visualization CX3CR1-GFP and VSIG4 on tissue sections to strengthen the claims on the relationship between these 2 markers. Tying the scRNA-seq insights (Figure 2) to the imaging would be elegant. Moreover, it would be informative to represent the CX3CR1+ and VSIG4+ macrophages as a percentage of F4/80+ macrophages (Figure 1B/E). Similarly, for the flow cytometry data in Figure 2, the relationship between the markers CX3CR1 and VSIG4 on macrophages could be more clearly displayed and discussed.

      Thanks for this remark. We will endeavor to show co-localization and analysis of both markers wherever possible. However, where we did not use Cx3cr1gfp mice, co-staining was limited by antibody choice.

      The 3D imaging of the joint is a nice addition to the manuscript, as it provides more context to the anatomical structure; however, while the text suggests several newborn joints were imaged, Figure 1F visualizes (again) the knee joint. Could other joints also be represented by 3D imaging? If the knee joint is the only joint available for imaging, and previous confocal imaging focused specifically on the meniscus in the knee joint, could the meniscus also be highlighted in the lightsheet imaging?

      Apologies if this was not clear from the original manuscript text, but we have only imaged the knee joint in 3D. We will clarify this during revision and consider inclusion of additional imaging data.

      Clarification is requested regarding the imaging quantification representation. The M&M section under "Statistical analysis and reproducibility" states that individual data points are displayed, and bars represent the mean. However, some of the Figure legends (e.g., Figures 1B and S1C) specify that each dot corresponds to an individual mouse, with quantification based on 2-3 sections per mouse. While this appears to be a very reasonable representation of the data, does this mean that for each dot, the mean value from the 2-3 sections per mouse was calculated and plotted?

      We will clarify this.

      It is not clear how the differential expression analysis was performed on the Vsig4+ cells. Please specify if Cluster 0 was used for analysis, or all Vsig4-expressing cells? Not all cells in Cluster 0 have Vsig4+ expression. The authors described the expression dynamics of Aqp1 as intriguing, but lack a reasoning on why this is interesting.

      We will revise this section.

      Figure S3E: In line with the previous comment, can the authors justify that the tdTomato+/- comparisons are not biased by scRNA-seq dropout (scRNA-seq is zero-inflated, so some tdTomato- cells could be false negatives), and provide methodological details (thresholds, ambient RNA correction, etc.) to support this?

      We will clarify this and include additional representations of the tdTomato transcript data.

      Although the sex-related differences in macrophage composition and the absence of differential expression are interesting, they distract from the manuscript's main messages. Moreover, the Discussion does not elaborate on how these observations relate to joint (disease) biology. Consider removing this section or integrating it clearly into the relevant biological context.

      We will remove this section as suggested.

      CreERT2 transgenic lines are often not 100% efficient in recombination, also depending on whether tamoxifen or 4-OHT is used. Could the authors report the percentage of tdTomato+ cells in the joints and compare them to the recombination efficiencies in the monocytes/microglia under the same tamoxifen or 4-OHT conditions? This would help clarify how the interpret the macrophage labeling %'s.

      We will report labelling efficacies and/or show normalized data in the revised manuscript.

      Could the authors draw parallels between the observations in the mouse knee joint macrophage populations and literature on other joints in mouse and the knee joint in human (for example, as described in Alivernini et al., 2020 and in the very recent Raut et al., 2025)?

      We will include a section on this in the revised manuscript.

      Minor comments:

      In general, the authors should clarify in the Results what each marker used for imaging, flow cytometry, or in the mouse reporter lines delineates. For example, mention that F4/80 is a marker for tissue-resident macrophages (correct?) in immunofluorescence, that IBA1 is a marker for macrophages on human tissue sections (Figure S1), and PDPN is GP38 (Figure S2 - align usage of marker reference across main text and figures).

      We will implement this request.

      For clarity in the microscopy representation, the single channels should be represented in a grey scale.

      We will revise image presentation.

      Figure S1B: Is CX3CR1 also restricted to the lining macrophages in human? Could a co-staining with IBA1 be performed to strengthen the species similarities?

      To our knowledge, there is no antibody available that works for imaging of human CX3CR1. Moreover, CX3CR1 is only limited to the lining population in adult joints, in fetal and newborn (mouse) joints, all macrophages express this receptor, as do fetal progenitors to macrophages. However, Alivernini and colleagues have reported that TREM2high macrophages are the human counterpart of the mouse CX3CR1+ lining population (PMID: 32601335).

      Adipocyte diameter quantification: Avoid plotting individual adipocytes from 2 mice without per-mouse visualization. Instead, report the mean adipocyte diameter per mouse and plot those means.

      We will implement this change.

      A little typo was spotted in the "Statistical analysis and reproducibility" section: it is Dunn's, not Bunn's multiple-comparison correction.

      Thanks for spotting this.

      Figure 2A: The gating strategy for the CX3CR1-GFP cells is missing.

      We will provide this in the revised manuscript or supplementary material.

      Improve the visualization of some plots. For example, Figure 2F is hard to read because of the big dot size. The dots seem to add no information to the graph and could be removed. Additionally, for comparing the clusters across the different time points, one could project the cells from the other time points in grey in the background.

      We will revise the presentation of these data.

      Figure S2: The dotplot is more informative than the heatmap, consider removing the heatmap.

      We will do that.

      Figure 3A: If technically feasible, image and visualize both the GFP and tdTomato expression. It would be informative to see the Cx3cr1+ and Ms4a3-derived cells in the same specimen.

      We will thrive to show this in the revised manuscript.

      Figure 3C: Highlight that tdTomato expression is visualized here.

      We will do that.

      Figure 3G,F: The authors should place the schematics and graphs next to each other, so the data points can be more easily compared.

      We aim to do this in the revised manuscript.

      Figure 4B: Which co-staining was performed for the immunofluorescence to quantify the % of tdTomato+ cells?

      We co-stained for F4/80 and assessed localization in the lining or sublining. This will be clarified in the revised Figure legend.

      Figure 4C: The trajectory analysis appears to have an arrow pointing from the Ccr2+ macrophages to the Ly6c+ monocytes. Please verify this directionality, as its seems against the known biology.

      This will be addressed during revision.

      Figure 5 mentions that the Csfr1 levels were reduced in a tissue-specific manner, but it is unclear how this tissue specificity was achieved.

      We apologize for this misunderstanding. Csfr1FIRE mice are not tissue-specific knockouts, but they are more specific than global knockout mice, since only a (myeloid-specific) enhancer is affected. We will clarify this in the relevant section.

      For the TGFb perturbations (Tgfbr2 KO and systemic TGFb depletion): did the authors validate reduced TGFb pathway activity in the macrophages, for example, reduced pSMAD2/3 levels? This would validate the effectiveness of the perturbations. This is an important point, and assessing signaling events downstream of TGFb is a very good suggestion.

      As per above comment, we have decided to uncouple the functional data with exception of CSF1 from the revised version of the current manuscript, but we will be taking this into account for substantiating our functional data in follow-up work.

      Figure 5F could benefit from a timeline of the treatment.

      As for the previous point raised, we will be taking this into account for follow-up work on the uncoupled functional data.

      The Methods mention that Gene Ontology analysis was performed on the single-cell data, but the results are not plotted in a figure. It would be informative to include this GO/pathway analysis in the appropriate figure(s).

      We will include this in the revised (supplementary) information.

      Significance:

      This work provides a high temporal-resolution and "spatial" resolution reference map of the ontogeny and maturation of the synovial lining macrophages in the knee joint. It complements existing literature that demonstrated the presence of tissue-resident macrophages in the synovial space and lining (Culemann, et al., 2019 and others) by charting the embryonic-to-postnatal emergence of lining and sublining subsets. In particular, this mouse work identified some key signaling pathways in shaping this tissue compartment. This dataset serves as a robust, steady-state reference for joint pathology and can be implemented with human studies on disease biology of the knee joint (e.g., Alivernini et al., 2020; Raut et al., 2025). Insights into the exact developmental origins, mechanisms contributing to diverse or seemingly similar cell types, and distinct maturation processes are crucial to understanding disease biology, in which developmental processes can be hijacked/reactivated.

      These findings will interest researchers in joint disease biology (osteoarthritis and immune-mediated arthritides such as RA and psoriasis), macrophage development (tissue-resident vs monocyte-derived lineages), the bone/joint microenvironment, and joint mechanobiology.

      The reviewer's expertise is in developmental biology, mesoderm, bone biology, hematopoiesis, and monocyte/macrophage biology in disease

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      Referee #3

      Evidence, reproducibility and clarity

      Summary:

      Magalhaes Pinto, Malengier-Devlies, and co-authors investigated the developmental origins and maturation of synovial (lining and sublining) macrophages across embryonic, newborn, and postnatal stages in mouse. The authors used multiple transgenic reporter lines, lineage tracing, scRNA-seq, 2D confocal and 3D lightsheet imaging, and perturbations to delineate the macrophage states and ontogeny. They propose a model in which the majority of the joint lining macrophages has a fetal (EMP-derived) origin and a small proportion has a definitive HSC-derived monocyte origin, which both seed and mature within the synovial space in the postnatal period in the first 3 weeks of life. Using cell-cell communication analysis on their scRNA-seq data, they identified Fgf2, Csf1, and Tgfb as candidate signaling pathways that support (lining) macrophage development and maturation. Functional experiments indicate that the process is CSF1 and TGFb-dependent and also partly dependent on mechanosensing through Piezo1. The key conclusions on the composition of the synovial macrophages are convincing based on the presented results, and are carefully phrased. The study is very comprehensive, yet the description and organization of the results of the different mouse models could be altered to improve the storyline. Several refinements in data presentation, formulation, and minor validation experiments would further improve the clarity of the story, as well as summary recaps of the major findings throughout the text.

      Major comments:

      1. Generally, the story could be more streamlined by introducing earlier reporter lines and lineage-origin logic. Clearly state which reporter/CreERT2 lines and acrosses are used. It was unclear in Figure 2 that cells of the cross of the Cx3cr1-GFP and Ms4a3Cre:Rosa26lsl-tdT reporter lines were used for the scRNA-seq. The principle that there are fetal-derived and bone marrow (GMP)-derived monocytes and macrophages doesn't need to be "hidden" until Figure 3. For example, also the imaging of Ms4a3Cre could be introduced before the scRNA-seq.
      2. Figure 1 could benefit from a cartoon visualizing the anatomy of the knee joint. The terms "sublining" and "synovium" are now a bit unclear, as it appears that sometimes the synovium is indicated as sublining and vice versa. Additionally, a schematic developmental timeline could be added to indicate the parallels between mouse and human development (fetal and postnatal development in mouse versus gestational age in human). Also, the various waves of hematopoiesis could be indicated in this timeline, which would be particularly helpful for Figure 3 for the lineage-tracing readouts. Lastly, the authors could end the manuscript (a new Figure 6) with a general cartoon summarizing all the results presented.
      3. Figure 1 could be rearranged: first introduce the markers CX3CR1 and VSIG4 (Figure 1D) and then present the quantifications (Figure 1B/E). Where possible, co-visualization CX3CR1-GFP and VSIG4 on tissue sections to strengthen the claims on the relationship between these 2 markers. Tying the scRNA-seq insights (Figure 2) to the imaging would be elegant. Moreover, it would be informative to represent the CX3CR1+ and VSIG4+ macrophages as a percentage of F4/80+ macrophages (Figure 1B/E). Similarly, for the flow cytometry data in Figure 2, the relationship between the markers CX3CR1 and VSIG4 on macrophages could be more clearly displayed and discussed.
      4. The 3D imaging of the joint is a nice addition to the manuscript, as it provides more context to the anatomical structure; however, while the text suggests several newborn joints were imaged, Figure 1F visualizes (again) the knee joint. Could other joints also be represented by 3D imaging? If the knee joint is the only joint available for imaging, and previous confocal imaging focused specifically on the meniscus in the knee joint, could the meniscus also be highlighted in the lightsheet imaging?
      5. Clarification is requested regarding the imaging quantification representation. The M&M section under "Statistical analysis and reproducibility" states that individual data points are displayed, and bars represent the mean. However, some of the Figure legends (e.g., Figures 1B and S1C) specify that each dot corresponds to an individual mouse, with quantification based on 2-3 sections per mouse. While this appears to be a very reasonable representation of the data, does this mean that for each dot, the mean value from the 2-3 sections per mouse was calculated and plotted?
      6. It is not clear how the differential expression analysis was performed on the Vsig4+ cells. Please specify if Cluster 0 was used for analysis, or all Vsig4-expressing cells? Not all cells in Cluster 0 have Vsig4+ expression. The authors described the expression dynamics of Aqp1 as intriguing, but lack a reasoning on why this is interesting.
      7. Figure S3E: In line with the previous comment, can the authors justify that the tdTomato+/- comparisons are not biased by scRNA-seq dropout (scRNA-seq is zero-inflated, so some tdTomato- cells could be false negatives), and provide methodological details (thresholds, ambient RNA correction, etc.) to support this?
      8. Although the sex-related differences in macrophage composition and the absence of differential expression are interesting, they distract from the manuscript's main messages. Moreover, the Discussion does not elaborate on how these observations relate to joint (disease) biology. Consider removing this section or integrating it clearly into the relevant biological context.
      9. CreERT2 transgenic lines are often not 100% efficient in recombination, also depending on whether tamoxifen or 4-OHT is used. Could the authors report the percentage of tdTomato+ cells in the joints and compare them to the recombination efficiencies in the monocytes/microglia under the same tamoxifen or 4-OHT conditions? This would help clarify how the interpret the macrophage labeling %'s.
      10. Could the authors draw parallels between the observations in the mouse knee joint macrophage populations and literature on other joints in mouse and the knee joint in human (for example, as described in Alivernini et al., 2020 and in the very recent Raut et al., 2025)?

      Minor comments:

      1. In general, the authors should clarify in the Results what each marker used for imaging, flow cytometry, or in the mouse reporter lines delineates. For example, mention that F4/80 is a marker for tissue-resident macrophages (correct?) in immunofluorescence, that IBA1 is a marker for macrophages on human tissue sections (Figure S1), and PDPN is GP38 (Figure S2 - align usage of marker reference across main text and figures).
      2. For clarity in the microscopy representation, the single channels should be represented in a grey scale.
      3. Figure S1B: Is CX3CR1 also restricted to the lining macrophages in human? Could a co-staining with IBA1 be performed to strengthen the species similarities?
      4. Adipocyte diameter quantification: Avoid plotting individual adipocytes from 2 mice without per-mouse visualization. Instead, report the mean adipocyte diameter per mouse and plot those means.
      5. A little typo was spotted in the "Statistical analysis and reproducibility" section: it is Dunn's, not Bunn's multiple-comparison correction.
      6. Figure 2A: The gating strategy for the CX3CR1-GFP cells is missing.
      7. Improve the visualization of some plots. For example, Figure 2F is hard to read because of the big dot size. The dots seem to add no information to the graph and could be removed. Additionally, for comparing the clusters across the different time points, one could project the cells from the other time points in grey in the background.
      8. Figure S2: The dotplot is more informative than the heatmap, consider removing the heatmap.
      9. Figure 3A: If technically feasible, image and visualize both the GFP and tdTomato expression. It would be informative to see the Cx3cr1+ and Ms4a3-derived cells in the same specimen.
      10. Figure 3C: Highlight that tdTomato expression is visualized here.
      11. Figure 3G,F: The authors should place the schematics and graphs next to each other, so the data points can be more easily compared.
      12. Figure 4B: Which co-staining was performed for the immunofluorescence to quantify the % of tdTomato+ cells?
      13. Figure 4C: The trajectory analysis appears to have an arrow pointing from the Ccr2+ macrophages to the Ly6c+ monocytes. Please verify this directionality, as its seems against the known biology.
      14. Figure 5 mentions that the Csfr1 levels were reduced in a tissue-specific manner, but it is unclear how this tissue specificity was achieved.
      15. For the TGFb perturbations (Tgfbr2 KO and systemic TGFb depletion): did the authors validate reduced TGFb pathway activity in the macrophages, for example, reduced pSMAD2/3 levels? This would validate the effectiveness of the perturbations.
      16. Figure 5F could benefit from a timeline of the treatment.
      17. The Methods mention that Gene Ontology analysis was performed on the single-cell data, but the results are not plotted in a figure. It would be informative to include this GO/pathway analysis in the appropriate figure(s).

      Significance

      This work provides a high temporal-resolution and "spatial" resolution reference map of the ontogeny and maturation of the synovial lining macrophages in the knee joint. It complements existing literature that demonstrated the presence of tissue-resident macrophages in the synovial space and lining (Culemann, et al., 2019 and others) by charting the embryonic-to-postnatal emergence of lining and sublining subsets. In particular, this mouse work identified some key signaling pathways in shaping this tissue compartment. This dataset serves as a robust, steady-state reference for joint pathology and can be implemented with human studies on disease biology of the knee joint (e.g., Alivernini et al., 2020; Raut et al., 2025). Insights into the exact developmental origins, mechanisms contributing to diverse or seemingly similar cell types, and distinct maturation processes are crucial to understanding disease biology, in which developmental processes can be hijacked/reactivated.

      These findings will interest researchers in joint disease biology (osteoarthritis and immune-mediated arthritides such as RA and psoriasis), macrophage development (tissue-resident vs monocyte-derived lineages), the bone/joint microenvironment, and joint mechanobiology.

      The reviewer's expertise is in developmental biology, mesoderm, bone biology, hematopoiesis, and monocyte/macrophage biology in disease

    3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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      Referee #2

      Evidence, reproducibility and clarity

      In the manuscript „The synovial lining macrophage layer develops in the first weeks of life in a CSF1- and TGFβ- dependent but monocyte-independent process", Magalhaes Pinto and colleagues carefully employ a wide range of technologies including single cell profiling, imaging and an exceptional combination of fate mapping models to characterize the ontogeny and development of lining macrophages in the joint, thus dissecting their maturation during postnatal development. Over the last decade, several landmark studies highlighted the imprinting of tissue-resident macrophages by a combination of ontogenetic and tissue-specific niche factors during development. So far, the ontogeny and the tissue niche factors governing the development and maturation of lining macrophages have not been described. Therefore, the results of this study offers insights on a small highly adapted macrophage population with relevance in many disease settings in the joint. Furthermore, the findings are nicely showcasing how macrophages are specializing to even very small tissue niches across development within one bigger anatomical compartment to serve dedicated functions within this niche.

      This manuscript is beautifully written and highlights many novel, highly relevant findings on lining macrophage biology and the authors employ a wide range of different technologies to carefully dissect the postnatal development of lining macrophages.

      In particular, the combination of scRNA-seq and fate mapping is providing a unique the link of transcriptional programs to ontogeny within the tissue niche. Furthermore, the integrative use of distinct fate mapping strategies, transgenic mouse lines, and treatment paradigms to elucidate key niche factors guiding the development and maturation of lining macrophages provides many interesting findings and data that are highly relevant to the field. I really enjoyed reading this manuscript.

      Major points:

      1) The authors show dynamic regulation of VSIG4 in lining macrophages during development, therefore VSIG4 is maybe not an ideal choice for gating strategies to define lining macrophages or to show as a single markers in immunofluorescence (IF) stainings to demonstrate their abundance across development (even though it is clear that this is the reason why the F4/80 staining is shown next to it). To demonstrate the increase of lining macrophages during development in IF, it would be more helpful if the authors would show quantifications of all F4/80+ cells and additionally VSIG4+ as a proportion of F4/80+ cells (or VSIG4+ F4/80+ and all F4/80+ in a stacked bar plot).

      2) In Figure 1C, the authors nicely demonstrate that the lining macrophages get closer in their distance across development to build the epithelial-like macrophage structure along the adult lining. Is the close proximity between lining macrophages already fully "matured" at 3 weeks of age and comparable to adults? Please quantify the distance in adult linings.

      3) Can the authors explain how the grouping was performed between the analyzed human fetal joints? It is not clear why the cut was chosen between the groups at 16/17 weeks of age. Maybe it would be also beneficial if the authors would consider not grouping these samples but rather show the specific quantifications for each samples individually and estimate via linear regression the expansion over time across human development. Furthermore, can the authors give additional information about the distancing of lining macrophages in the human fetal samples, it would be great to see if they follow the same dynamics as in mouse. Maybe comparison to human juvenile/adult joints would also add on to substantiate the findings in human samples (if possible).

      4) The scRNA-seq analysis leaves several questions open and some conclusions and workflows cannot be easily followed.

      a. It is not clear how and especially why the signature genes to define macrophages vs. monocytes were chosen. Especially as the signature genes for monocytes would not include patrolling monocytes and the macrophage signature genes seem to be highly regulated during development, see also Apoe expression in NB vs. adult in Figure S2e. Why did the authors not take classical markers such as Itgam, Fcgr1a, Csf1r?

      b. Can dendritic cell signatures be excluded? Cluster 11 and 12 show indeed some DC markers, are these really macrophages?

      c. The authors provide several figure panels showing TOP marker genes or key marker genes for the identified clusters, however it is not clear if these are TOP DE genes or if the genes were hand chosen. Somehow, the authors give the impression that the clusters were chosen and labeled not based on DE genes, but more on existing literature that previously reported these macrophage populations. DE gene lists for all annotated cell types and macrophage clusters need to be provided within the manuscript.

      d. The authors claim that Clusters 1 and 4 are "developing" macrophages. How is this defined? Why are these developing cells compared to other clusters? And why are these clusters later on not considered as progenitors of Aqp1 macrophages and Vsig4 macrophages? Why are Aqp1+ macrophages not labeled as developing when they are later on in the manuscript shown as potential intermediate progenitors of lining macrophages?

      e. Furthermore, it is again confusing that markers are used throughout Figure 2 which are labeled as "key marker genes" for a population and then later on they are claimed to be regulated during development within this population, see for example Figure 2D and 2H.

      f. It is appreciated that the authors distinguished cycling clusters such as 8, 9, and 10 based on their cycling gene signature. Here it would be very exciting to see a cell cycle analysis across all clusters and time points to see when exactly the cells are expanding during development; this would also substantiate the data later shown for the Mki67-CreERT2 mouse model.

      g. Can the authors identify certain gene modules during development of lining macrophages (and/or their progenitors) which are associated with certain functions (e.g. GO terms, GSEA enrichment)?

      5) To determine the actual presence of the identified macrophage clusters from the scRNA-seq as macrophage populations in the joint, the authors should perform IF or FACS for key markers. Especially, Aqp1+ macrophages should be shown in the developing joint.

      6) The authors used a wide range of fate mapping models, which is quite unique and highly appreciated. The obtained results and the conclusions made from the models raise a couple of questions: Whereas contribution of HSC-derived/monocyte-derived macrophages to the lining compartment seems to be minor, there is still labeling across different models. Various aspects would need to be clarified.

      a. For example, the authors employ Ms4a3-Cre as a tracing model for GMP-derived monocytes, however all quantifications of the labeling efficiency are not normalized to the labeling in monocytes or another highly recombined cell population. This should be shown, similar to the other fate mapping models (Figure 3 F-I).

      b. Please show Ms4a3 expression across clusters across time points, to exclude expression in fetal-derived clusters.

      c. In line with the question raised above, if the authors can exclude a development of the Egfr1+ and Clec4n+ developing macrophages into Aqp1+ macrophages and subsequently into Vsig4 lining macrophages, the obtained data from the Ms4a3-Cre model highly suggests a correlative labeling across these clusters what could implicate a relation. However, the authors do not discuss throughout the manuscript the role of these developing macrophages. It is highly encouraged to include this into the manuscript and it would be of high relevance to understand lining macrophage development.

      d. The authors conclude from the pseudo bulk transcriptomic profiling of the different macrophage clusters that TdT+ and TdT- macrophages do not differ in their gene expression profile and that this is due to niche imprinting rather than origin imprinting. Even though the data supports that conclusion, the authors should verify if inkling cells early during development also show this similar gene expression profile and gene expression should be compared at the different developmental time points. Tissue niche imprinting is happening within the niche during development, most likely in a stepwise progress, and therefore there should be differences in the beginning.

      7) The trajectorial analysis using different pseudotime pipelines is very interesting and nicely points out the potential role of Aqp1 macrophages as intermediates of Vsig4 lining macrophages. From my point of view, all trajectories seem to suggest that Egfr1 developing macrophages and Clec4n developing macrophages might differentiate into Aqp1 macrophages, however the authors are not exploring this further and the role of both developing macrophage clusters is not further discussed (see also comments above).

      8) How was the starting point of the trajectorial analyses defined and is it the same for each pipeline used?

      9) Are there potentially two trajectories? It looks like there is one in the beginning of postnatal life and a second one appearing from the monocyte-compartment later in life. If this is true, that would rather speak for a dual ontogeny of Vsig4+ macrophages, wouldn't it?

      10) A heatmap (transcriptional shift) of trajectories between more clusters should be shown at least for Cluster 0,1,2, and 3. It is not sufficient to demonstrate this only between two clusters.

      11) To show the similarity between Aqp1 macrophages and proliferating macrophage clusters, the authors should remove the cycling signature and compare these clusters to show that the cycling cells might be Aqp1 macrophages or earlier developing macrophage progenitors aka Clec4n or Egfr1 macrophages.

      12) The conclusions made from the Mki67-CreERT2 data are a bit difficult to understand, whereas all progenitors (monocyte progenitors and macrophage progenitors will proliferate at the neonatal time point and no conclusions can be made if the cells expand in the niche. The authors should employ Confetti mice or other models (Ubow mice) to analyze clonal expansion in the niche.

      13) All predicted cell-cell interactions between macrophages and fibroblasts should be provided in a supplementary table. Are the interactions shown in Figure 5 chosen interactions or the TOP predicted ones? Whereas the authors show different numbers of interactions, it is most likely hand-picked and therefore biased.

      14) The authors further aim to dissect the factors involved in the developmental niche imprinting of lining macrophages. Even though it is highly appreciated that the authors used so many experimental setups to show the reliance of lining macrophages on Csf1 and TGF-beta as well as mechanosensation, the wide range of models the different methods used and selected developmental time points make it very difficult to really interpret the data. The authors should carefully choose time points and methods (either FACS analysis across all models or IF across all, or both). Often deletion efficiencies for transgenic models and proof of concept that the inhibitors and agonists are working in the treatment paradigm are not provided. For example, Csf1rMer-iCre-Mer Tgfbr2fl/fl mice are used but no deletion efficiency is shown or different time points of analysis, maybe the macrophages are not properly targeted in the set up.

      15) The authors have shown the role of Csf1 and Tgfbr2 only for lining macrophages, is this specific in the joint to this population of are subliming macrophages affected in a similar manner.

      16) Can the authors confirm their results in CSF1R-FIRE mice with anti-Csf1 injections or in Csf1op/op mice?

      17) The setup in Figure S5G is very interesting to test the role of movement and mechanical load on the joint, however, there is basically no data on the model provided showing the efficiency of the induced optogenetic muscle contractions, and only one time point is shown.

      18) The results regarding the role of Piezo1 and mechanosensation vary a lot. Could it be that analyses were done too early or that actually proper weight load on the joint must be applied for the maturation of the macrophages? The authors should test this to

      19) The Rolipram experiment is shown in Figure S5G, but is not described in the result section. It only appears at some point in the discussion part. The authors should move it to results or remove it from the manuscript.

      Minor points:

      1) Please reference the Figure panels in numeric order throughout the text.

      2) Figure 2a and 2b are a bit out of the storyline, it is not obvious why this is shown here and maybe it would be good to move it to the supplements. Gating strategy is also not used for scRNA-seq. Therefore, it would better fit to the later analysis of joint macrophages across different transgenic mouse models and treatment paradigms. The gating strategies are changing across different experiments throughout the figures, it would be nice to have a similar gating strategy for all experiments, see also Figure 3 where the defining markers for joint macrophages are changing between models.

      3) A lot of figure panels have very small labeling that is basically unreadable. Axes at FACS plots for example. Sometimes, it is even impossible to distinguish cluster labels especially when they have similar colors.

      4) In the text on page 14, many markers are named which are specifically regulated during development in lining macrophages, but these factors are not labeled anywhere in the volcano plot. It would be good to showcase at least some of these named genes in the figure panel, e.g. Trem2.

      5) Figure 2F and Figure S2F are really nicely showing the percentage of cells per cluster in each analyzed biological sample. Maybe the authors could additionally consider to show a stacked bar plot with the mean percentage of cells per cluster and how the clusters are distributed across time points?

      6) Figure 3A: IF for adult lining macrophages and the quantification are missing

      Significance

      This manuscript highlights novel, highly relevant findings on lining macrophage biology and the authors employ a wide range of different technologies to carefully dissect the postnatal development of lining macrophages. Furthermore, this study showcases in a very elegant and detailed way the adaptation of macrophage progenitors to a highly specific anatomical tissue niche.

      The manuscript is of high interest to basic scientists focussing on macrophage biology and immune cell development and clinicians and clinician scientists focussing on joint diseases such as RA

      Therefore the manuscript is of interest to a wide community working in immunology.

    4. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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      Referee #1

      Evidence, reproducibility and clarity

      In their manuscript entitled "The synovial lining macrophage layer develops in the first weeks of life in a CSF1- and TGFβ-dependent but monocyte-independent process," the authors explore the developmental trajectory of synovial lining macrophages. They demonstrate that the formation of this specialized macrophage layer is age-dependent and governed by a distinct developmental program that proceeds independently of circulating monocytes. Through scRNA-Seq, the authors show that synovial lining macrophages originate locally from Aqp1⁺ macrophages and are marked by the expression of Csf1r, Tgfbr, and Piezo1. Notably, genetic ablation of each of these factors impaired the development of lining macrophages to varying degrees, suggesting differential contributions of CSF1, TGFβ, and PIEZO1 signaling pathways to their maturation and maintenance.

      The manuscript is well written, and the data quality and representation is of a high standard. The authors have employed a sophisticated array of state-of-the-art mouse models and cutting-edge technologies to elucidate the developmental origin of synovial lining macrophages. Notably, the supporting scRNA-Seq datasets are of excellence and provide valuable insights that will likely be of significant interest to researchers in the field of immunology and joint biology. Accordingly, the experimental approach and interpretations regarding macrophage origin are well-founded and compelling. However, in the eye of the reviewer, the section addressing the underlying molecular mechanisms is a bit less convincing. This part of the study appears slightly underdeveloped, and some of the mechanistic claims lack sufficient experimental clarity. A more rigorous experimental investigation would be essential to reinforce the manuscript's conclusions, particularly concerning the data related to Tgfbr and Piezo1, where the current evidence appears insufficiently substantiated.

      Major point:

      • The numbers of VSIG4⁺ macrophages appear either unaffected or only minimally altered in both Csf1rMerCreMer Tgfbr2floxed and Fcgr1Cre Piezo1floxed mouse models, respectively. This raises an important question: was the gene deletion efficiency sufficient in each model? Accordingly, the authors are encouraged to include quantitative data on gene deletion efficiency for both mouse models, as this information is critical for interpreting the observed phenotypic outcomes and validating the conclusions regarding gene function. Furthermore, to better assess the impact of Tgfbr2 and Piezo1 disruption, the authors should provide more comprehensive flow cytometry analyses and histological data for these mouse models. Given the apparent homogeneity of VSIG4⁺ macrophages (as shown by the authors themselves), bulk RNA-Seq of sorted Tgfbr2- and Piezo1-deficient VSIG4⁺ macrophages (or from TGFβ-treated animals) would offer valuable insights into both the effectiveness of gene deletion and the molecular pathways governed by TGFβ and PIEZO1 in lining macrophages.

      Minor points:

      • Consistent usage of Cx3cr1-GFP+ nomenclature (for instance: Fig. S1 legend "adult mouse synovial tissue, showing PDGFRα⁺ fibroblasts (yellow) and CX3CR1-GFP⁺ cells (cyan)." versus Fig. 1 legend "Automated spot detection highlights Cx3cr1-GFP⁺ macrophages)"
      • Unclear Fig. 3 legend: "Representative immunofluorescence images of synovial tissue from Clec9aCre:Rosa26lsl-tdT mice at 3 weeks and in adulthood, showing and tdTomato (yellow) and stained for DAPI (blue), VSIG4 (cyan)" Check 'showing and tdTomato.'
      • For greater clarity, it would have been helpful if the transcript names had been directly included within Figures 3C, S3A, and S3C.
      • Page 24: "(Mki67CreERT2:Rosa26lsl-tdT)" Last bracket not superscript.
      • Page 25: "we again leveraged our scRNAsequencing dataset" Missing punctuation.
      • Page 27: Fig. 5C legend: " of synovial tissue of 1 week-old, 3 weeks-old and adult mice." Please specify and change to 'adult Csf1rΔFIRE/ΔFIRE mice'.
      • Page 30: The outcome observed in the Acta1-rtTA:tetO-Cre:ChR2-V5fl mouse model appears to be inconclusive: "This approach resulted in an increased density of VSIG4+ and total (F4/80+) macrophages in the exposed leg of some 5 days-old pups, but others showed the opposite trend (Figure S5D)." This variability may reflect low efficiency of the model or other technical limitations (e.g. muscle contractions frequency or time point of analysis). Given this ambiguity, it is worth reconsidering whether the data are sufficiently robust to warrant inclusion. Should the authors choose to include these findings, further experimentation of appropriate depth and precision is required to allow a conclusive interpretation (either it increases the density of VSIG4+ macrophages or not). The same applies to the Yoda1-treated mice, for which additional data are needed to determine whether VSIG4⁺ macrophage density is truly affected.

      Significance

      • General assessment: provide a summary of the strengths and limitations of the study. What are the strongest and most important aspects? What aspects of the study should be improved or could be developed?

      This is a well-designed study that uses cutting-edge methodologies to investigate the developmental trajectory of synovial lining macrophages under homeostatic conditions. The authors present robust experimental evidence and compelling interpretations concerning synovial macrophage origin, which are both well-substantiated and impactful. Nonetheless, from the reviewer's perspective, the section exploring the molecular mechanisms underlying macrophage differentiation is comparatively less convincing. This section appears somewhat underdeveloped, as some of the mechanistic claims lack sufficient depth and experimental rigor to fully substantiate the conclusions. - Describe the nature and significance of the advance (e.g. conceptual, technical, clinical) for the field:

      In contrast to earlier studies (PMID: 31391580, 32601335), the inclusion of fate-mapping experiments adds an important dimension, offering novel insight into the ontogeny of synovial macrophages. This expanded perspective may prove particularly valuable in advancing our understanding of joint immunology, especially regarding the local origins and lineage relationships of macrophage populations. Furthermore, the authors present novel insights into the molecular pathways underlying the differentiation and development of synovial lining macrophages. By demonstrating previously unrecognized regulatory mechanisms, this work significantly deepens our understanding of the cellular and transcriptional programs that drive macrophage specialization within the joint microenvironment. -Place the work in the context of the existing literature (provide references, where appropriate):

      This study builds upon previous work characterizing the macrophage compartment in the joint (PMID: 31391580, 32601335), yet provides a substantially more comprehensive dataset that spans multiple developmental time points and data on the origin of this specialized macrophage subset. - State what audience might be interested in and influenced by the reported findings:

      Immunologist, clinicians - Define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate.

      This study falls well within the scope of the reviewer's expertise in innate immunity.

    1. Description

      Essential guidance for new users on the Hive Blockchain. Understanding community etiquette. Avoiding plagiarism. Engaging meaningfully with content. To foster growth and success within the platform. Learn best practices for content creation and community involvement. To enhance reputation and rewards.

    1. Трепещущую, дрожащую мысль, легко уязвимую и с трудом сдерживаемую, мудрец направляет, как лучник стрелу. 34 Как рыба, вырванная из своей стихии и брошенная на сушу, дрожит эта мысль: лишь бы вырваться из-под власти Мары. 35 Обуздание мысли, едва сдерживаемой, легковесной, спотыкающейся где попало, – благо. Обузданная мысль приводит к счастью. 36 Пусть мудрец стережёт свою мысль, трудно постижимую, крайне изощрённую, спотыкающуюся где попало. Стережённая мысль приводит к счастью. 37 Те, которые смирят свою мысль, блуждающую вдалеке, бредущую в одиночку, бестелесную, скрытую в сердце, освободятся от Мары. 38 У того, чья мысль нестойка, кто не знает истинной дхаммы, чья вера колеблется, – мудрость не становится совершенной. 39 В непорочной мысли, в невсполошенной мысли, отказавшейся от добра и зла, в бодрствующей нет страха. 40 Зная, что это тело подобно скудели, превратив эту мысль в подобие крепости, пусть он с оружием мудрости нападет на Мару, и да сохранит он победу и да будет он свободен от привязанностей. 41 Увы! Недолго это тело проживёт на земле, отверженное, бесчувственное, бесполезное, как чурбан. 42 Что бы ни сделал враг врагу или же ненавистник ненавистнику, ложно направленная мысль может сделать еще худшее. 43 Что бы ни сделали мать, отец или какой другой родственник, истинно направленная мысль может сделать еще лучшее.
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    1. eLife Assessment

      This study provides valuable insights into microtubule remodeling during liver-stage Plasmodium berghei development, demonstrating that deletion of the alpha-tubulin C-terminal tail impairs parasite growth in mosquitoes and abolishes infection in HeLa cells. The work is technically ambitious, employing advanced microscopy, genetic mutants, and pharmacological approaches. However, key claims are only partially supported due to incomplete evidence linking tubulin modifications to microtubule dynamics and uncertain antibody-based PTM detection.

    2. Reviewer #1 (Public review):

      The authors try to investigate how the population of microtubules (LSPMB) that originate from sporozoite subpellicular microtubules (SSPM) and are remodelled during liver-stage development of malaria parasites. These bundles shrink over time and help form structures needed for cell division. The authors have used expansion microscopy, live-cell imaging, genetically engineered mutants, and pharmacological perturbation to study parasite development with liver cells.

      A major strength of the manuscript is the live cell imaging and expansion microscopy to study this challenging liver stage of parasite development. It gives important knowledge that PTMs of α-tubulin, such as polyglutamylation and tyrosination/detyrosination, are crucial for microtubule stability. Mutations in α-tubulin reduce the parasite's ability to move and proliferate in the liver cells. The drug oryzalin, which targets microtubules, also blocks parasite development, showing how important dynamic microtubules are at this stage.

      The major problem in the manuscript was the way it flows, as the authors keep shifting from the liver stage to the sporogony stages and then back to the liver stages. It was very confusing at times to know what the real focus of the study is, whether sporozoite development or liver stage development. The flow of the manuscript could be improved. Some of the findings reported here substantiate the previous electron microscopy.

      Overall, the study represents an important contribution towards understanding cytoskeletal remodelling during liver stage infection. The study suggests that tubulin modifications are key for the parasite's survival in the liver and could be targets for new malaria treatments. This is also the stage that has been used for vaccine development, so any knowledge of how parasites proliferate in the liver cells will be beneficial towards intervention approaches.

    3. Reviewer #2 (Public review):

      Summary:

      The authors investigated microtubule distribution and their possible post-translational modifications (PTM) in Plasmodium berghei during development of the liver stage, using either hepatocytes or HeLa cells as models. They used conventional immunofluorescence assays and expansion microscopy with various antibodies recognising tubulin and, in the second part of the work, its candidate PTMs, as well as markers of Plasmodium, in addition to live imaging with a fluorescent marker for tubulin. In the third part of the study, they generated 3 mutants deprived of either the last four residues or the last 11 residues, or where a candidate polyglutamylation site was substituted by an alanine residue.

      Strengths:

      In the first part, microtubules are monitored by a combination of two approaches (IFA and live), revealing nicely the evolution of the sporozoite subpellicular microtubules (SSPM, the sporozoite is the developmental stage present in salivary glands of the mosquitoes and that infects hepatocytes) into a different structure termed liver-stage parasite microtubule bundle (LSPMB). The LSPMB shrinks during the course of parasite development and finally disappears while hemi-spindles emerge over time. Contact points between these two structures are observed frequently in live cells and occasionally in fixed cells, suggesting the intriguing possibility that tubulin might be recycled from the LSPMB to contribute to hemi-spindle formation.

      In the second part, antibodies recognising (1) the final tyrosine found at the C-terminal tail and (2) a stretch of 3 glutamate residues in a side chain are used to monitor these candidate PTMs. Signals are positive at the SSPM, and while it remains positive for polyglutamylation, it becomes negative for the final tyrosine at the LSPM, while a positive signal emerges at hemi-spindles at later stages of development.

      In the last part, the three mutants are fed to mosquitoes, where they show reduced development, the one lacking the alpha-tubulin tail even failing to reach the salivary glands. However, the two other mutants infect HeLa cells normally, whereas sporozoites with the C-terminal tail deletion recovered from the haemolymph did not develop in these cells.

      The first part provides convincing evidence that microtubules are extensively remodelled during the infection of hepatocytes and HeLa cells, in agreement with the spectacular Plasmodium morphogenetic changes accompanying massive and rapid proliferation. The third part brings further confirmation that the C-terminal tail of alpha-tubulin is essential for multiple stages of parasite development, in agreement with previous work (50). Since it is the region where several post-translational modifications take place in other organisms (detyrosination, polyglutamylation, glycylation), it makes sense to propose that the essential function is related to these PTMs also in Plasmodium.

      Weaknesses:

      The significance of tubulin PTM relies on two antibodies whose reactivity to Plasmodium tubulins is unclear (see below). The interpretation of the literature on detyrosination and polyglutamylation is confusing in several places, meaning that the statements about the possible role of these PTMs need to be carefully revisited.

      The authors use the term "tyrosination" but the alpha1-tubulin studied here possesses the final tyrosine when it is synthesised, so it is "tyrosinated" by default. It could potentially be removed by a tyrosine carboxypeptidase of the vasoinhibin family (VASH) as reported in other species. After removal, this tyrosine can be added again by a tubulin-tyrosine ligase (TTL) enzyme. It is therefore more appropriate to talk about detyrosination-retyrosination rather than tyrosination (this confusion is unfortunately common in the literature, see Janke & Magiera, 2020).

      The difficulty here is that there is so far no evidence that detyrosination takes place in Plasmodium. Neither VASH nor TTL could be identified in the Plasmodium genome (ref 31, something we can confirm with our unsuccessful BLAST analyses), and mass spectrometry studies of purified tubulin, albeit from blood stages, did not find evidence for detyrosination (reference 43). Western blots using an antibody against detyrosinated tubulin did not produce a positive signal, neither on purified tubulin, nor on whole parasites (43). Of course, the situation could be different in liver stages, but the question of the detyrosinating enzyme is still there. The existence of a unique Plasmodium system for detyrosination cannot be formally ruled out, but given the high degree of conservation of these PTMs and their associated enzymes, it sounds difficult to imagine.

      The fact that the anti-tyrosinated antibody still produced a signal in the cell line where the final tyrosine is deleted raises issues about its specificity. A cross-reactivity with beta-tubulin is proposed, but the Plasmodium beta-tubulin does not carry a final tyrosine, further raising concerns about antibody specificity.

      The interpretation of these results should therefore be considered carefully. There also seems to be some confusion in the function of detyrosination cited from the literature. It is said in line 229 that "tyrosination has been associated with stable microtubules" (33, 34, 50, 55). References 33 and 34 actually show that tyrosinated microtubules turn over faster in neurons or in epithelial cells, respectively, while references 50 and 55 do not study de/retyrosination. The general consensus is that tyrosinated microtubules are more dynamic (see reference 24).

      The situation is a bit different for polyglutamylation since several candidate poly- or mono-glutamylases have been identified in the Plasmodium genome, and at least mono-glutamylation of beta-tubulin has been formally proven, still in bloodstream stages (ref 43). The authors propose that the residue E445 is the polyglutamylation site. To our knowledge, this has not been demonstrated for Plasmodium. This residue is indeed the favourite one in several organisms such as humans and trypanosomes (Eddé et al., Science 1990; Schneider et al., JCS, 1997), and it is tempting to propose it would be the same here. However, TTLLs bind the tubulin tails from their C-terminal end like a glove on a finger (Garnham et al., Cell, 2015), and the presence of two extra residues in Plasmodium tubulins would mean that the reactive glutamate might be in position E447 rather than E445. This is worth discussing.<br /> On the positive side, it is encouraging to see that signals for both anti-tyrosinated tail and poly-glutamylated side chain are going down in the various mutants, but this would need validation with a comparison for alpha-tubulin signal.

      Line 316: polyglutamylation "is commonly associated with dynamic microtubule behavior (78-80)". Actually, references 78 and 79 show the impact of this PTM on interaction with spastin, and reference 80 discusses polyglutamylation as a marker of stable microtubules in the context of cilia and flagella. The consensus is that polyglutamylated microtubules tend to be more stable (ref24).

      Conclusion:

      The first and the third parts of this manuscript - evolution of microtubules and importance of the C-terminal tails for Plasmodium development - are convincing and well supported by data. However, the presence and role of tubulin PTM should be carefully reconsidered.

      Plasmodium tubulins are more closely related to plant tubulins and are sensitive to inhibitors that do not affect mammalian microtubules. They therefore represent promising drug targets as several well-characterised compounds used as herbicides are available. The work produced here further defines the evolution of the microtubule network in sporozoites and liver stages, which are the initial and essential first steps of the infection. Moreover, Plasmodium has multiple specificities that make it a fascinating organism to study both for cell biology and evolution. The data reported here are elegant and will attract the attention of the community working on parasites but also on the cytoskeleton at large. It will be interesting to have the feedback of other people working on tubulin PTMs to figure out the significance of this part of the work.

    4. Reviewer #3 (Public review):

      Summary:

      The manuscript by Atchou et al. investigates the role of the microtubule cytoskeleton in sporozoites of Plasmodium berghei, including possible functions of microtubule post-translational modifications (tyrosination and polyglutamylation) in the development of sporozoites in the liver. They also assessed the development of sporozoites in the mosquito. Using cell culture models and in vivo infections with parasites that contain tubulin mutants deficient in certain PTMs, they show that may aspects of the life cycle progression are impaired. The main conclusion is that microtubule PTMs play a major role in the differentiation processes of the parasites.

      However, there are a number of major and minor points of criticism that relate to the interpretation of some of the data.

      Comments:

      (1) The first paragraph of "Results" almost suggests that the presence of a subpellicular MT-array in sporozoites is a new discovery. This is not the case, see e.g. the recent publication by Ferreira et al. (Nature Communications, 2023).

      (2) Why were HeLa cells and not hepatocytes (as in Figure 3) used for measuring infection rates of the mutants in Figure 5H and 5L? As I understand, HeLa cells are not natural host cells for invading sporozoites. HeLa cells are epithelial cells derived from a cervical tumour. I am not an expert in Plasmodium biology, but is a HeLa infection an accepted surrogate model for liver stage development?

      (3) The tubulin staining in Figures 1A and 1B is confusing and doesn't seem to make sense. Whereas in 1A the antibody nicely stains host and parasite tubulin, in 1B, only parasite tubulin is visible. If the same antibody and the same host cells have been used, HeLa cytoplasmic microtubules should be visible in 1B. In fact, they should be the predominant antigen. The same applies to Figure 2, where host microtubules are also not visible.

      (4) In Figures 2A and B, the host nuclei appear to have very different sizes in the DMSO controls and in the drug-treated cells. For example, in the 20 µM (-) image (bottom right), the nuclei are much larger than in the DMSO (-) control (top left). If this is the case, expansion microscopy hasn't worked reproducibly, and therefore, quantification of fluorescence is problematic. The scalebar is the same for all panels.

      (5) I don't quite follow the argument that spindles and the LSPMB are dynamic structures (e.g., lines 145, 174). That is a trivial statement for the spindle, as it is always dynamic, but beyond that, it has only been shown that the structure is sensitive to oryzalin. That says little about any "natural" dynamic behaviour. Any microtubule structure can be destroyed by a particular physical or chemical treatment, but that doesn't mean all structures are dynamic. It also depends on the definition of "dynamic" in a particular context, for example, the time scale of dynamic behaviour (changes within seconds, minutes, or hours).

      (6) I am not sure what part in the story EB1 plays. The data are only shown in the Supplements and don't seem to be of particular relevance. EB1 is a ubiquitous protein associated with microtubule plus ends. The statement (line 192) that it "may play a broader role..." is unsubstantiated and cannot be based merely on the observation that it is expressed in a particular life cycle stage.

      (7) Line 196 onwards: The antibody IN105 is better known in the field as polyE. Maybe that should be added in Materials and Methods. Also, the antibody T9028 against tyrosinated tubulin is poorly validated in the literature and rarely used. Usually, researchers in this field use the monoclonal antibody YL1/2. I am not sure why this unusual antibody was chosen in this study. In fact, has its specificity against tyrosinated α-tubulin from Plasmodium berghei ever been shown? The original antigen was human and had the sequence EGEEY. The Plasmodium sequence is YEADY and hence very different. It is stated that the LSPMB is both polyglutamylated and tyrosinated. This is unusual because polyglutamylated microtubules are usually indicative of stable microtubules, whereas tyrosinated microtubules are found on freshly polymerised and dynamic microtubules. However, a co-localisation within the same cell has not been attempted. This is, however, possible since polyE is a rabbit antibody and T9028 is a mouse antibody. I suspect that differences or gradients along the LSPMB would have been noticed. Also, in lines 207/208, it is said that tyrosination disappears after hepatocyte invasion, which is shown in Figure 3. However, in Figure 3A, quite a lot of positive signals for tyrosination are visible in the 54 and 56 hpi panels.

      (8) In line 229, it is stated that tyrosination "has previously been associated with stable microtubule in motility". This statement is not correct. In fact, none of the cited references that apparently support this statement show that this is the case. On the contrary, stable microtubules, such as flagellar axonemes, are almost completely detyrosinated. Therefore, tyrosination is a marker for dynamic microtubules, whereas detyrosinated microtubules are indicative of stable microtubules. This is an established fact, and it is odd that the authors claim the opposite.

      (9) Line 236 onwards: Concerning the generation of tubulin mutants, I think it is necessary to demonstrate successful replacement of the wild-type allele by the mutant allele. I am sure the authors have done this by amplification and subsequent sequencing of the genomic locus using PCR primers outside the plasmid sequences. I suggest including this information, e.g., by displaying the chromatograph trace in a supplementary figure. Or are the sequences displayed in Figure S3B already derived from sequenced genomic DNA? This is not described in the Legend or in Materials and Methods. The left PCR products obtained for Figure S3 B would be a suitable template for sequencing.

      (10) It is also important to be aware of the fact that glutamylation also occurs on β-tubulin. This signal will also be detected by polyE (IN105). Therefore, it is surprising that IN105 immunofluorescence is negative on the C-term Δ cells (Figure S3 D). Is there anything known about confirmed polyglutamylation sites on both α- and β-tubulins in Plasmodium, e.g., by MS? In Toxoplasma, both α- and β-tubulin have been shown to be polyglutamylated.

      (11) Figure S3 is very confusing. In the legend, certain intron deletions are mentioned. How does this relate to posttranslational tubulin modifications? The corresponding section in Results (lines 288-292) is also not very helpful in understanding this.

      (12) Figure 4E doesn't look like brightfield microscopy but like some sort of fluorescent imaging. In Figure 4C, were the control (NoΔ) cells with an integrated cassette, but no mutations, or non-transgenic cells?

      (13) It is difficult to understand why the TyΔ and the CtΔ mutants still show quite a strong signal using the anti-tyrosination antibody. If the mutants have replaced all wild-type alleles, the signal should be completely absent, unless the antibody (see my comment above concerning T9028) cross-reacts with detyrosinated microtubules. Therefore, the quantitation in Figures 5F and 5G is actually indicative of something that shouldn't be like that. The quantitation of 5F is at odds with the microscopy image in 5D. If this image is representative, the anti-Ty staining in TyΔ is as strong as in the control NoΔ.

      (14) The statement that the failure of CtΔ mutants to generate viable sporozoites is due to the lack of microtubule PTMs (lines 295-296) is speculative. The lack of the entire C-terminal tail could have a number of consequences, such as impaired microtubule assembly or failure to recruit and bind associated proteins. This is not necessarily linked to PTMs. Also, it has been shown in yeast that for microtubules to form properly and exquisite regulation (proteostasis) of the ratio between α- and β-tubulin is essential (Wethekam and Moore, 2023). I am not sure, but according to Materials and Methods (line 423), the gene cassettes for replacing the wild-type tubulin gene with the mutant versions contain a selectable marker gene for pyrimethamine selection. Are there qPCR data that show that expression levels of mutant α-tubulin are more or less the same as the wild-type levels?

      (15) In the Discussion, my impression is that two recent studies, the superb Expansion Microscopy study by Bertiaux et al. (2021) and the cryo-EM study by Ferreira et al. (2023), are not sufficiently recognised (although they are cited elsewhere in the manuscript). The latter study includes a detailed description of the microtubule cytoskeleton in sporozoites. However, the present study clearly expands the knowledge about the structure of the cytoskeleton in liver stage parasites and is one of the few studies addressing the distribution and function of microtubule post-translational modifications in Plasmodium.

      (16) I somewhat disagree with the statement of a co-occurrence of polyglutamylated and tyrosinated microtubules. I think the resolution is too low to reach that conclusion. As this is a bold claim, and would be contrary to what is known from other organisms, it would require a more rigorous validation. Given the apparent problems with the anti-Ty antibody (signal in the TyΔ mutant), one should be very cautious with this claim.

      (17) In the Discussion (lines 311 and 377), it is again claimed that tyrosinated microtubules are "a well-known marker of stable microtubules". This statement is completely incorrect, and I am surprised by this serious mistake. A few lines later, the authors say that polyglutamylated is "commonly associated with dynamic microtubule behaviour". Again, this is completely incorrect and is the opposite of what is firmly established in the literature. Polyglutamylation and detyrosination are markers of stable microtubules.

      (18) In line 339, the authors interpret the residual antibody staining after the introduction of the mutant tubulin as a compensatory mechanism. There is no evidence for this. More likely explanations are firstly the quality of the anti-Ty-antibody used (see comment above), and the fact that also β-tubulin carries C-terminal polyglutamylation sites, which haven't been investigated in this study. PTMs on β-tubulin are not compensatory, but normal PTMs, at least in all other organisms where microtubule PTMs have been investigated.

    5. Author response:

      Public Reviews:

      Reviewer #1 (Public review):

      The authors try to investigate how the population of microtubules (LSPMB) that originate from sporozoite subpellicular microtubules (SSPM) and are remodelled during liver-stage development of malaria parasites. These bundles shrink over time and help form structures needed for cell division. The authors have used expansion microscopy, live-cell imaging, genetically engineered mutants, and pharmacological perturbation to study parasite development with liver cells.

      A major strength of the manuscript is the live cell imaging and expansion microscopy to study this challenging liver stage of parasite development. It gives important knowledge that PTMs of α-tubulin, such as polyglutamylation and tyrosination/detyrosination, are crucial for microtubule stability. Mutations in α-tubulin reduce the parasite's ability to move and proliferate in the liver cells. The drug oryzalin, which targets microtubules, also blocks parasite development, showing how important dynamic microtubules are at this stage.

      The major problem in the manuscript was the way it flows, as the authors keep shifting from the liver stage to the sporogony stages and then back to the liver stages. It was very confusing at times to know what the real focus of the study is, whether sporozoite development or liver stage development. The flow of the manuscript could be improved. Some of the findings reported here substantiate the previous electron microscopy.

      Overall, the study represents an important contribution towards understanding cytoskeletal remodelling during liver stage infection. The study suggests that tubulin modifications are key for the parasite's survival in the liver and could be targets for new malaria treatments. This is also the stage that has been used for vaccine development, so any knowledge of how parasites proliferate in the liver cells will be beneficial towards intervention approaches.

      We would like to express our sincere gratitude to Reviewer #1 for the positive and encouraging feedback on our manuscript. We are delighted that the reviewer found our experimental design and methodologies appropriate and that our study represents an important contribution to understanding cytoskeletal remodelling during liver stage infection, a critical phase for vaccine development. We are also grateful to the reviewer for highlighting the issue with the manuscript's flow. We acknowledge this limitation and will significantly improve the narrative structure and logical progression in the revised manuscript to ensure clarity and avoid any potential confusion. Thank you again for your thoughtful and constructive comments.

      Reviewer #2 (Public review):

      Summary:

      The authors investigated microtubule distribution and their possible post-translational modifications (PTM) in Plasmodium berghei during development of the liver stage, using either hepatocytes or HeLa cells as models. They used conventional immunofluorescence assays and expansion microscopy with various antibodies recognising tubulin and, in the second part of the work, its candidate PTMs, as well as markers of Plasmodium, in addition to live imaging with a fluorescent marker for tubulin. In the third part of the study, they generated 3 mutants deprived of either the last four residues or the last 11 residues, or where a candidate polyglutamylation site was substituted by an alanine residue.

      Strengths:

      In the first part, microtubules are monitored by a combination of two approaches (IFA and live), revealing nicely the evolution of the sporozoite subpellicular microtubules (SSPM, the sporozoite is the developmental stage present in salivary glands of the mosquitoes and that infects hepatocytes) into a different structure termed liver-stage parasite microtubule bundle (LSPMB). The LSPMB shrinks during the course of parasite development and finally disappears while hemi-spindles emerge over time. Contact points between these two structures are observed frequently in live cells and occasionally in fixed cells, suggesting the intriguing possibility that tubulin might be recycled from the LSPMB to contribute to hemi-spindle formation.

      In the second part, antibodies recognising (1) the final tyrosine found at the C-terminal tail and (2) a stretch of 3 glutamate residues in a side chain are used to monitor these candidate PTMs. Signals are positive at the SSPM, and while it remains positive for polyglutamylation, it becomes negative for the final tyrosine at the LSPM, while a positive signal emerges at hemi-spindles at later stages of development.

      In the last part, the three mutants are fed to mosquitoes, where they show reduced development, the one lacking the alpha-tubulin tail even failing to reach the salivary glands. However, the two other mutants infect HeLa cells normally, whereas sporozoites with the C-terminal tail deletion recovered from the haemolymph did not develop in these cells.

      The first part provides convincing evidence that microtubules are extensively remodelled during the infection of hepatocytes and HeLa cells, in agreement with the spectacular Plasmodium morphogenetic changes accompanying massive and rapid proliferation. The third part brings further confirmation that the C-terminal tail of alpha-tubulin is essential for multiple stages of parasite development, in agreement with previous work (50). Since it is the region where several post-translational modifications take place in other organisms (detyrosination, polyglutamylation, glycylation), it makes sense to propose that the essential function is related to these PTMs also in Plasmodium.

      Weaknesses:

      The significance of tubulin PTM relies on two antibodies whose reactivity to Plasmodium tubulins is unclear (see below). The interpretation of the literature on detyrosination and polyglutamylation is confusing in several places, meaning that the statements about the possible role of these PTMs need to be carefully revisited.

      The authors use the term "tyrosination" but the alpha1-tubulin studied here possesses the final tyrosine when it is synthesised, so it is "tyrosinated" by default. It could potentially be removed by a tyrosine carboxypeptidase of the vasoinhibin family (VASH) as reported in other species. After removal, this tyrosine can be added again by a tubulin-tyrosine ligase (TTL) enzyme. It is therefore more appropriate to talk about detyrosination-retyrosination rather than tyrosination (this confusion is unfortunately common in the literature, see Janke & Magiera, 2020).

      The difficulty here is that there is so far no evidence that detyrosination takes place in Plasmodium. Neither VASH nor TTL could be identified in the Plasmodium genome (ref 31, something we can confirm with our unsuccessful BLAST analyses), and mass spectrometry studies of purified tubulin, albeit from blood stages, did not find evidence for detyrosination (reference 43). Western blots using an antibody against detyrosinated tubulin did not produce a positive signal, neither on purified tubulin, nor on whole parasites (43). Of course, the situation could be different in liver stages, but the question of the detyrosinating enzyme is still there. The existence of a unique Plasmodium system for detyrosination cannot be formally ruled out but given the high degree of conservation of these PTMs and their associated enzymes, it sounds difficult to imagine.

      The fact that the anti-tyrosinated antibody still produced a signal in the cell line where the final tyrosine is deleted raises issues about its specificity. A cross-reactivity with beta-tubulin is proposed, but the Plasmodium beta-tubulin does not carry a final tyrosine, further raising concerns about antibody specificity.

      The interpretation of these results should therefore be considered carefully. There also seems to be some confusion in the function of detyrosination cited from the literature. It is said in line 229 that "tyrosination has been associated with stable microtubules" (33, 34, 50, 55). References 33 and 34 actually show that tyrosinated microtubules turn over faster in neurons or in epithelial cells, respectively, while references 50 and 55 do not study de/retyrosination. The general consensus is that tyrosinated microtubules are more dynamic (see reference 24).

      The situation is a bit different for polyglutamylation since several candidate poly- or mono-glutamylases have been identified in the Plasmodium genome, and at least mono-glutamylation of beta-tubulin has been formally proven, still in bloodstream stages (ref 43). The authors propose that the residue E445 is the polyglutamylation site. To our knowledge, this has not been demonstrated for Plasmodium. This residue is indeed the favourite one in several organisms such as humans and trypanosomes (Eddé et al., Science 1990; Schneider et al., JCS, 1997), and it is tempting to propose it would be the same here. However, TTLLs bind the tubulin tails from their C-terminal end like a glove on a finger (Garnham et al., Cell, 2015), and the presence of two extra residues in Plasmodium tubulins would mean that the reactive glutamate might be in position E447 rather than E445. This is worth discussing.

      On the positive side, it is encouraging to see that signals for both anti-tyrosinated tail and poly-glutamylated side chain are going down in the various mutants, but this would need validation with a comparison for alpha-tubulin signal.

      Line 316: polyglutamylation "is commonly associated with dynamic microtubule behavior (78-80)". Actually, references 78 and 79 show the impact of this PTM on interaction with spastin, and reference 80 discusses polyglutamylation as a marker of stable microtubules in the context of cilia and flagella. The consensus is that polyglutamylated microtubules tend to be more stable (ref24).

      Conclusion:

      The first and the third parts of this manuscript - evolution of microtubules and importance of the C-terminal tails for Plasmodium development - are convincing and well supported by data. However, the presence and role of tubulin PTM should be carefully reconsidered.

      Plasmodium tubulins are more closely related to plant tubulins and are sensitive to inhibitors that do not affect mammalian microtubules. They therefore represent promising drug targets as several well-characterised compounds used as herbicides are available. The work produced here further defines the evolution of the microtubule network in sporozoites and liver stages, which are the initial and essential first steps of the infection. Moreover, Plasmodium has multiple specificities that make it a fascinating organism to study both for cell biology and evolution. The data reported here are elegant and will attract the attention of the community working on parasites but also on the cytoskeleton at large. It will be interesting to have the feedback of other people working on tubulin PTMs to figure out the significance of this part of the work.

      We thank Reviewer #2 for the thoughtful and detailed evaluation of our manuscript. We are pleased that the reviewer found our study elegant and believe it will attract the attention of the broader scientific community, both those working on parasites and those focused on cytoskeleton biology. We also acknowledge the concerns raised regarding the specificity of the antibodies used to detect tubulin post-translational modifications (PTMs), as well as the interpretation of their signals and the current lack of identified detyrosination enzymes in the Plasmodium genome. We agree that these are important limitations, and we will address them thoroughly in the revised manuscript. This includes clarifying our interpretation of tyrosination versus detyrosination, adjusting our claims regarding polyglutamylation sites, and carefully revisiting the literature cited to ensure accurate contextualization of PTM function in microtubule stability.

      We are grateful for the reviewer’s close reading and critical feedback, which will help us substantially improve the clarity, precision, and strength of our manuscript.

      Reviewer #3 (Public review):

      Summary:

      The manuscript by Atchou et al. investigates the role of the microtubule cytoskeleton in sporozoites of Plasmodium berghei, including possible functions of microtubule post-translational modifications (tyrosination and polyglutamylation) in the development of sporozoites in the liver. They also assessed the development of sporozoites in the mosquito. Using cell culture models and in vivo infections with parasites that contain tubulin mutants deficient in certain PTMs, they show that may aspects of the life cycle progression are impaired. The main conclusion is that microtubule PTMs play a major role in the differentiation processes of the parasites.

      However, there are a number of major and minor points of criticism that relate to the interpretation of some of the data.

      We thank Reviewer #3 for the overall positive assessment of our study and for recognizing its contribution to advancing our understanding of Plasmodium biology and malaria pathogenesis. We appreciate the reviewer’s constructive feedback, particularly regarding the interpretation of some of our data. These comments have been very helpful in guiding our revisions, and we have worked to improve both the clarity of our presentation and the precision of our interpretations in the revised manuscript.

      Below, we respond in detail to each of the reviewer’s points.

      Comments:<br /> (1) The first paragraph of "Results" almost suggests that the presence of a subpellicular MT-array in sporozoites is a new discovery. This is not the case, see e.g. the recent publication by Ferreira et al. (Nature Communications, 2023).

      We thank the reviewer for pointing this out and fully agree that the subpellicular microtubule (SPM) array in sporozoites is well established, as documented in earlier work (e.g., Cyrklaff et al., 2007) and more recently by Ferreira et al. (Nat. Commun., 2023). Our intention was not to suggest that the existence of the SSPM is a novel finding. Rather, our study builds on this existing knowledge by demonstrating that these sporozoite-derived microtubules are not disassembled upon hepatocyte entry but are repurposed into a newly described structure, the liver stage parasite microtubule bundle (LSPMB). This reorganization, its persistence into liver stage development, and its dynamic role in microtubule remodeling and nuclear division are, to our knowledge, novel observations. We will revise the manuscript to make this distinction clearer in the introduction and the results section.

      (2) Why were HeLa cells and not hepatocytes (as in Figure 3) used for measuring infection rates of the mutants in Figure 5H and 5L? As I understand, HeLa cells are not natural host cells for invading sporozoites. HeLa cells are epithelial cells derived from a cervical tumour. I am not an expert in Plasmodium biology, but is a HeLa infection an accepted surrogate model for liver stage development?

      We appreciate the opportunity to clarify our experimental model. While HeLa cells are not the natural host cells, they are a well-established and validated in vitro model for studying Plasmodium berghei liver stage development in our lab and others. In this system, the parasite completes its full development and generates infectious merozoites. Numerous studies have successfully used HeLa cells as a liver stage infection model, with key findings subsequently validated in primary hepatocytes or in vivo, confirming its utility as a representative model. We employed this cell line primarily to reduce animal usage in accordance with the 3Rs principles (Replacement, Reduction, Refinement). Importantly, to ensure the biological relevance of our discoveries in HeLa cells, we validated our key findings in primary mouse hepatocytes, as shown in Figure 3. Furthermore, we confirmed the in vivo infectivity of mutant parasite lines that produced typical salivary gland sporozoites through an in vivo infection assay, presented in Figure S4C.

      (3) The tubulin staining in Figures 1A and 1B is confusing and doesn't seem to make sense. Whereas in 1A the antibody nicely stains host and parasite tubulin, in 1B, only parasite tubulin is visible. If the same antibody and the same host cells have been used, HeLa cytoplasmic microtubules should be visible in 1B. In fact, they should be the predominant antigen. The same applies to Figure 2, where host microtubules are also not visible.

      We thank the reviewer for this careful observation regarding the α-tubulin staining in Figures 1A and 1B. The same host cell type (HeLa) and α-tubulin antibody were indeed used in both experiments. Figure 1A shows results from conventional immunofluorescence assays, where both host and parasite microtubules are clearly stained. In contrast, Figure 1B shows the outcome of ultrastructure expansion microscopy (U-ExM), where parasite microtubules appear prominently, while host microtubules are less visible.

      This effect appears to be a technical outcome of the U-ExM protocol, which can differentially preserve or reveal microtubule epitopes. We consistently observed stronger parasite signal across various cell types, including primary hepatocytes (Figure 3A,B). The lack of visible host microtubules in some U-ExM images does not reflect their absence, but rather reduced signal intensity relative to the parasite structures. This is not observed with all antibodies, e.g., host microtubules stain strongly with anti-tyrosinated α-tubulin (Figure 3B), likely reflecting their high tyrosination state.

      To overcome this limitation, we employed PS-ExM and combined PS-ExM/U-ExM approaches (as described in reference 56), which allowed simultaneous high-resolution visualization of both host and parasite microtubule networks. These combined methods are now being used in follow-up studies to investigate host–parasite microtubule interactions in more detail.

      We will clarify this point in the revised manuscript to avoid confusion.

      (4) In Figures 2A and B, the host nuclei appear to have very different sizes in the DMSO controls and in the drug-treated cells. For example, in the 20 µM (-) image (bottom right), the nuclei are much larger than in the DMSO (-) control (top left). If this is the case, expansion microscopy hasn't worked reproducibly, and therefore, quantification of fluorescence is problematic. The scalebar is the same for all panels.

      The expansion microscopy methods used in this study have been rigorously validated for both reproducibility and isotropicity. However, as the reviewer rightly notes, host cell nuclei can vary in size due to several factors, including cell cycle stage, infection status, and the extent of parasite development, all of which can influence host nuclei morphology and size.

      Importantly, the quantifications relevant to our conclusions were focused specifically on parasite structures. We did not rely on host nuclear size or host fluorescence intensity as a quantitative readout in this context. While we acknowledge the observed variability in host nuclear dimensions, it does not compromise the accuracy or reproducibility of the parasite specific measurements central to our study.

      We will clarify this point in the revised figure legend and manuscript.

      (5) I don't quite follow the argument that spindles and the LSPMB are dynamic structures (e.g., lines 145, 174). That is a trivial statement for the spindle, as it is always dynamic, but beyond that, it has only been shown that the structure is sensitive to oryzalin. That says little about any "natural" dynamic behaviour. Any microtubule structure can be destroyed by a particular physical or chemical treatment, but that doesn't mean all structures are dynamic. It also depends on the definition of "dynamic" in a particular context, for example, the time scale of dynamic behaviour (changes within seconds, minutes, or hours).

      We agree that sensitivity to chemical depolymerization alone does not necessarily indicate dynamic behavior, particularly in the absence of data on turnover kinetics or temporal changes.

      Our interpretation was based on two observations: first, that the LSPMB, which derives from the highly stable sporozoite subpellicular microtubules (known to be drug-resistant), becomes susceptible to depolymerization during the liver stage; and second, that the LSPMB gradually shrinks over time during parasite development. These features suggested a transition toward a more dynamic state compared to its origin. However, we fully agree that “dynamic” is a context-dependent term and that direct evidence such as turnover rates or structural changes on short time scales, is required to rigorously define microtubule dynamics.

      We will revise the manuscript to clarify our use of this term and explicitly acknowledge the need for further studies to characterize the timescale and mechanisms underlying LSPMB remodeling.

      (6) I am not sure what part in the story EB1 plays. The data are only shown in the Supplements and don't seem to be of particular relevance. EB1 is a ubiquitous protein associated with microtubule plus ends. The statement (line 192) that it "may play a broader role..." is unsubstantiated and cannot be based merely on the observation that it is expressed in a particular life cycle stage.

      We agree that EB1 is a ubiquitous microtubule plus-end binding protein and that its presence alone does not imply a novel function. Previous studies (e.g., Maurer et al., 2023; Yang et al., 2023; Zeeshan et al., 2023) have focused on its role during Plasmodium sexual stages, while its expression during liver and mosquito stages has not been previously documented.

      Our data extend this knowledge by showing that EB1 is also expressed during liver stage development, particularly during the highly mitotic schizont phase. While we agree that this observation alone does not prove functional involvement, it raises the possibility of a broader role for EB1 in regulating microtubule dynamics beyond sexual stages. To avoid overinterpretation, we have presented these findings in the supplementary material and will revise the manuscript to tone down speculative statements and clearly frame this as a preliminary observation that warrants further investigation.

      (7) Line 196 onwards: The antibody IN105 is better known in the field as polyE. Maybe that should be added in Materials and Methods. Also, the antibody T9028 against tyrosinated tubulin is poorly validated in the literature and rarely used. Usually, researchers in this field use the monoclonal antibody YL1/2. I am not sure why this unusual antibody was chosen in this study. In fact, has its specificity against tyrosinated α-tubulin from Plasmodium berghei ever been shown? The original antigen was human and had the sequence EGEEY. The Plasmodium sequence is YEADY and hence very different. It is stated that the LSPMB is both polyglutamylated and tyrosinated. This is unusual because polyglutamylated microtubules are usually indicative of stable microtubules, whereas tyrosinated microtubules are found on freshly polymerised and dynamic microtubules. However, a co-localisation within the same cell has not been attempted. This is, however, possible since polyE is a rabbit antibody and T9028 is a mouse antibody. I suspect that differences or gradients along the LSPMB would have been noticed. Also, in lines 207/208, it is said that tyrosination disappears after hepatocyte invasion, which is shown in Figure 3. However, in Figure 3A, quite a lot of positive signals for tyrosination are visible in the 54 and 56 hpi panels.

      First, we acknowledge that the IN105 antibody is more widely known as "polyE" in the field. We will update the Materials and Methods section accordingly to reflect this nomenclature.

      Regarding the use of the T9028 antibody against tyrosinated α-tubulin: we agree that this monoclonal antibody is less commonly used than YL1/2, and we appreciate the reviewer drawing attention to this. The original antigen for T9028 is based on the mammalian C-terminal sequence EGEEY, which differs from the Plasmodium α1-tubulin sequence (YEADY). Like many in the field, we face the challenge that most available antibodies are raised against mammalian epitopes, and specificity in Plasmodium can vary. Nonetheless, the literature (e.g., Hirst et al., 2022; Fennell et al., 2008) has demonstrated that tyrosination occurs in Plasmodium α1-tubulin, using anti-tyrosination antibodies including YL1/2.

      Following the reviewer’s excellent suggestion, we are currently repeating the key experiments using the YL1/2 antibody to compare staining patterns directly with those obtained using T9028. We will include these results in the revised manuscript.

      Concerning the potential co-localization of polyglutamylation and tyrosination on the LSPMB: we agree that this is an interesting and testable hypothesis. In the current manuscript, Figures 3A and 3B were generated from independent experiments, and thus co-localization was not assessed. However, as the reviewer correctly notes, polyE and T9028 antibodies are raised in rabbit and mouse, respectively, making co-staining feasible. We will follow up on this experimentally and, if feasible within our revision timeline, include data in the revised version or highlight this as a future direction.

      Finally, with regard to Figure 3 and the observation that tyrosination appears to persist at 54 and 56 hpi (Figure 3B): the reviewer is correct that tyrosination signal is still detectable at these time points. Our statement that tyrosination “disappears after hepatocyte invasion” was intended to refer to an overall decrease in signal intensity during early liver stage development, with a reappearance at later stages (e.g., cytomere formation). We will rephrase this section for greater clarity and ensure that figure annotations and legends unambiguously reflect the dynamics observed.

      (8) In line 229, it is stated that tyrosination "has previously been associated with stable microtubule in motility". This statement is not correct. In fact, none of the cited references that apparently support this statement show that this is the case. On the contrary, stable microtubules, such as flagellar axonemes, are almost completely detyrosinated. Therefore, tyrosination is a marker for dynamic microtubules, whereas detyrosinated microtubules are indicative of stable microtubules. This is an established fact, and it is odd that the authors claim the opposite.

      We fully agree that in canonical eukaryotic systems, tyrosinated microtubules are generally markers of dynamic microtubule populations, whereas detyrosinated microtubules are typically associated with stability particularly in structures such as flagellar axonemes.

      Our original statement will be corrected. In our study, we observed that tyrosinated microtubules are prevalent in invasive stages (sporozoites and merozoites), while detyrosinated forms become more prominent during intracellular liver stage development. This pattern is consistent with the established link between tyrosination and dynamic microtubules.

      What is particularly intriguing in Plasmodium is the apparent cycling of tyrosination despite the absence of known tubulin tyrosine ligase (TTL) homologs in the genome. This suggests either a highly divergent enzyme or the involvement of host cell factors, a hypothesis supported by the reappearance of tyrosinated microtubules during liver stage schizogony (Figure 3B).

      We will revise the relevant text and the Discussion section to reflect these mechanistic considerations more accurately and to avoid misrepresenting established principles of microtubule biology.

      (9) Line 236 onwards: Concerning the generation of tubulin mutants, I think it is necessary to demonstrate successful replacement of the wild-type allele by the mutant allele. I am sure the authors have done this by amplification and subsequent sequencing of the genomic locus using PCR primers outside the plasmid sequences. I suggest including this information, e.g., by displaying the chromatograph trace in a supplementary figure. Or are the sequences displayed in Figure S3B already derived from sequenced genomic DNA? This is not described in the Legend or in Materials and Methods. The left PCR products obtained for Figure S3 B would be a suitable template for sequencing.

      Indeed, these data are presented in Figure 4B and the corresponding sequence data are shown in Figure S3B. We appreciate the reviewer’s suggestion, which will help improve the transparency and reproducibility of our methodology.

      (10) It is also important to be aware of the fact that glutamylation also occurs on β-tubulin. This signal will also be detected by polyE (IN105). Therefore, it is surprising that IN105 immunofluorescence is negative on the C-term Δ cells (Figure S3 D). Is there anything known about confirmed polyglutamylation sites on both α- and β-tubulins in Plasmodium, e.g., by MS? In Toxoplasma, both α- and β-tubulin have been shown to be polyglutamylated.

      Indeed, polyglutamylation is known to occur not only on α-tubulin but also on β-tubulin in many organisms, including Toxoplasma gondii, and the polyE (IN105) antibody is expected to detect polyglutamylation on both tubulin isoforms.

      The parasites shown in Figure S3D correspond to mutant lines originally generated by Spreng et al. (2019): the IntronΔ mutant (with deletion of introns in the Plasmodium α1-tubulin gene) and the C-termΔ mutant (with deletion of the final three C-terminal residues: ADY). As the reviewer correctly notes, this particular C-terminal deletion does not include the predicted polyglutamylation site (E445 or E447, depending on alignment), and thus should not abolish all polyglutamylation. However, in our experiments, the IN105 signal is substantially reduced in this mutant. This may suggest that structural alterations in the tubulin tail affect accessibility of the polyglutamylation epitope or influence the modification itself though we cannot exclude other possibilities, including changes in antibody recognition.

      To date, polyglutamylation sites in Plasmodium tubulins have not been definitively confirmed by mass spectrometry. However, a recent MS-based study (reference 43) detected monoglutamylation on β-tubulin in blood stage parasites. Direct MS evidence for polyglutamylation of either α- or β-tubulin in Plasmodium liver stages is still lacking. We will clarify these points in the revised manuscript to avoid potential confusion and to highlight the need for future biochemical validation of PTM sites.

      (11) Figure S3 is very confusing. In the legend, certain intron deletions are mentioned. How does this relate to posttranslational tubulin modifications? The corresponding section in Results (lines 288-292) is also not very helpful in understanding this.

      The parasite lines shown in Figure S3D were originally generated by Spreng et al. (2019) and are not directly part of the main set of PTM-targeted mutants described in our study. Specifically, the IntronΔ line carries deletions in introns of the Plasmodium α1-tubulin gene, while the C-termΔ line lacks the final three C-terminal residues (ADY). These lines were included for comparative purposes to explore whether structural changes in α-tubulin could impact polyglutamylation signal, as detected by the polyE (IN105) antibody.

      We acknowledge that the figure legend and corresponding text (lines 288–292) did not adequately explain the rationale for including these control lines. We will revise both the legend and Results section to more clearly describe the origin, purpose, and relevance of these mutants to the overall study.

      (12) Figure 4E doesn't look like brightfield microscopy but like some sort of fluorescent imaging. In Figure 4C, were the control (NoΔ) cells with an integrated cassette, but no mutations, or non-transgenic cells?

      The reviewer is absolutely correct: Figure 4E shows a fluorescent image acquired using widefield microscopy and not a brightfield image. We will revise the figure legend accordingly to avoid confusion. The “BF” (brightfield) label applies only to the left panel in Figure 4C, which depicts oocysts imaged using transmitted light.

      Regarding the controls labeled "NoΔ" in Figure 4C, we confirm that these parasites contain the integrated selection cassette but do not harbor any mutations in the target gene. They serve as proper integration controls, allowing us to distinguish the effects of the point mutations or deletions introduced in the experimental lines.

      (13) It is difficult to understand why the TyΔ and the CtΔ mutants still show quite a strong signal using the anti-tyrosination antibody. If the mutants have replaced all wild-type alleles, the signal should be completely absent, unless the antibody (see my comment above concerning T9028) cross-reacts with detyrosinated microtubules. Therefore, the quantitation in Figures 5F and 5G is actually indicative of something that shouldn't be like that. The quantitation of 5F is at odds with the microscopy image in 5D. If this image is representative, the anti-Ty staining in TyΔ is as strong as in the control NoΔ.

      We agree that the persistence of anti-tyrosination signal in the TyΔ and CtΔ mutant lines is unexpected, given that all wild-type alleles were replaced. This discrepancy has led us to further investigate the specificity of the T9028 antibody, as raised in the reviewer’s earlier comment. To address this concern, we are currently repeating the key experiments using the well-established YL1/2 monoclonal antibody, which is widely accepted for detecting tyrosinated α-tubulin in other systems.

      We also acknowledge that Figure 5F shows residual tyrosination signal, and the reviewer is correct that this should not occur if the modified residues are the exclusive PTM sites. One possible explanation is that adjacent residues or even alternative tubulin isoforms may serve as substrates. While α1-tubulin is the dominant isoform in Plasmodium, low-level expression of α2-tubulin has been detected in liver stages based on transcriptomic data, and it may contribute to the observed signal.

      Regarding the apparent discrepancy between the quantification in Figure 5F and the representative image in Figure 5D, we will revise the figure legend to clarify that image selection aimed to show detectable signal, not necessarily the average phenotype. We will also reassess and, if needed, repeat the quantification with improved image sets to ensure accuracy and consistency.

      We will revise the manuscript to reflect these points and include a more nuanced interpretation of the residual staining in the mutant lines.

      (14) The statement that the failure of CtΔ mutants to generate viable sporozoites is due to the lack of microtubule PTMs (lines 295-296) is speculative. The lack of the entire C-terminal tail could have a number of consequences, such as impaired microtubule assembly or failure to recruit and bind associated proteins. This is not necessarily linked to PTMs. Also, it has been shown in yeast that for microtubules to form properly and exquisite regulation (proteostasis) of the ratio between α- and β-tubulin is essential (Wethekam and Moore, 2023). I am not sure, but according to Materials and Methods (line 423), the gene cassettes for replacing the wild-type tubulin gene with the mutant versions contain a selectable marker gene for pyrimethamine selection. Are there qPCR data that show that expression levels of mutant α-tubulin are more or less the same as the wild-type levels?

      We agree that attributing the developmental failure of the CtΔ mutants solely to the absence of microtubule post-translational modifications (PTMs) is speculative. As the reviewer rightly points out, deletion of the entire C-terminal tail may have multiple effects, including impaired microtubule assembly, altered α/β-tubulin stoichiometry, or disruption of interactions with essential microtubule-associated proteins (MAPs). These consequences may arise independently of PTMs.

      That said, we note that PTMs particularly polyglutamylation, can modulate MAP binding by altering the surface charge of microtubules (Genova et al., 2023; Mitchell et al., 2010). Therefore, while PTM loss may be a contributing factor, we acknowledge that the phenotype likely results from a combination of mechanisms. We will revise the relevant section of the manuscript to present a more cautious and balanced interpretation.

      Regarding the reviewer’s question on expression levels: although the replacement constructs include a pyrimethamine resistance cassette, we have not yet quantified α-tubulin transcript levels by qPCR. In the interim, the study by Spreng et al. (2019) (reference 50) on a related α1-tubulin nutations provides valuable insight. They observed no difference in mRNA levels in day 12 oocysts, yet reported fainter microtubule staining and shorter sporozoites, suggesting a post-transcriptional mechanism affecting protein expression or function in later stages. Furthermore, the phenotypic spectrum across their mutant panel (Suppl. Fig. 3 D and E) implies that robust α-tubulin regulation is highly sensitive to specific sequences.

      We acknowledge this as a current limitation in our study and will address it in the revised manuscript, noting that direct measurement of transcript levels is a key area for future investigation.

      (15) In the Discussion, my impression is that two recent studies, the superb Expansion Microscopy study by Bertiaux et al. (2021) and the cryo-EM study by Ferreira et al. (2023), are not sufficiently recognised (although they are cited elsewhere in the manuscript). The latter study includes a detailed description of the microtubule cytoskeleton in sporozoites. However, the present study clearly expands the knowledge about the structure of the cytoskeleton in liver stage parasites and is one of the few studies addressing the distribution and function of microtubule post-translational modifications in Plasmodium.

      Indeed, our work builds upon the established knowledge from Bertiaux et al. (2021) and the cryo-EM study by Ferreira et al. (2023), as rightly mentioned by the reviewer. We agree that these foundational studies, combined with our findings, will significantly expand the understanding of Plasmodium biology and cytoskeleton dynamics across its life cycle and will open the door for further investigations. We are grateful for this suggestion and will ensure these key studies are appropriately acknowledged in the revised manuscript.

      (16) I somewhat disagree with the statement of a co-occurrence of polyglutamylated and tyrosinated microtubules. I think the resolution is too low to reach that conclusion. As this is a bold claim, and would be contrary to what is known from other organisms, it would require a more rigorous validation. Given the apparent problems with the anti-Ty antibody (signal in the TyΔ mutant), one should be very cautious with this claim.

      This is a very important point to clarify. As mentioned previously, the initial experiments for these modifications were performed independently. It is established that sporozoite subpellicular microtubules exhibit both tyrosination and polyglutamylation. We will revise the manuscript to temper this statement and clearly indicate that the co-occurrence of these PTMs remains a hypothesis that requires more rigorous validation. As suggested, we are now conducting additional co-staining experiments using the better validated YL1/2 antibody to re-express and directly compare the distribution of both PTMs within the same cell. These follow-up experiments will help clarify whether both modifications occur simultaneously on the same microtubule structures in Plasmodium liver stages.

      (17) In the Discussion (lines 311 and 377), it is again claimed that tyrosinated microtubules are "a well-known marker of stable microtubules". This statement is completely incorrect, and I am surprised by this serious mistake. A few lines later, the authors say that polyglutamylated is "commonly associated with dynamic microtubule behaviour". Again, this is completely incorrect and is the opposite of what is firmly established in the literature. Polyglutamylation and detyrosination are markers of stable microtubules.

      Indeed, in canonical eukaryotic systems, tyrosinated microtubules are generally considered markers of dynamic microtubule populations, whereas detyrosinated and polyglutamylated microtubules are more commonly associated with stability.

      We acknowledge this mistake and will revise the Discussion to correct these statements accordingly. In the context of Plasmodium, our observations suggest an unusual regulation of microtubule dynamics, which may reflect parasite-specific adaptations. For example, we observed tyrosinated α-tubulin in the stable subpellicular microtubules of sporozoites structures typically known for their exceptional stability. This atypical association implies either non-canonical roles for tyrosination or parasite-specific mechanisms for modulating microtubule properties. Additionally, the presence of both PTMs at different stages of development and on different microtubule populations suggests tightly regulated spatial and temporal modulation of microtubule function.

      We will carefully revise the relevant sections of the manuscript to remove incorrect generalizations and ensure accurate representation of the current consensus in the field, while emphasizing the possibility of Plasmodium-specific adaptations that merit further study.

      (18) In line 339, the authors interpret the residual antibody staining after the introduction of the mutant tubulin as a compensatory mechanism. There is no evidence for this. More likely explanations are firstly the quality of the anti-Ty-antibody used (see comment above), and the fact that also β-tubulin carries C-terminal polyglutamylation sites, which haven't been investigated in this study. PTMs on β-tubulin are not compensatory, but normal PTMs, at least in all other organisms where microtubule PTMs have been investigated.

      As mentioned above, we are currently repeating the key experiments with the [YL1/2] antibody, as suggested. Furthermore, we fully agree with the reviewer's point regarding polyglutamylation on β-tubulin. The C-terminal tail of β-tubulin does indeed contain polyglutamylation sites. As we noted in the manuscript (Lines 340-352), this aspect has not been investigated in the present study, and we acknowledge it as a valuable direction for future research. We will revise the text accordingly to avoid overinterpretation and to more accurately reflect the limitations of our current data.

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