This case ruled that the Sentencing Reform Act of 1984 and the U.S. Sentencing Commission were constitutional. The court's decision was based on delegation of powers. Congress can delegate authority to other branches of government under broad guidelines.

Personification of the ship - genuinely if I heard this out of context and ship-specific stuff wasn't mentioned, I would've just thought of a woman. It's either really pervading personification or I'm just too sleepy lol

this line feels really questionable considering how similar it is to things that have been said to justify slavery

YIKES...

Ghost ship?

Underscores? Also thanks to the person who commented what this is!

the spanish once again being brought up in relation to the slave trade

Why am I reminded of the Creature's appearance on the ship in Frankenstein?

What did I just say about eerie lol?

I feel like there's an interesting, eerie tone in this.

oh...

Religious simile!

character is an unbelievably good person apparently

Very descriptive language.

Super mysterious writing, lots of imagery.

oh, um, that escalated quickly.

Is Magic about to happen? I hope so!

I'm confused with the punctuation.

What exactly is this trying to say? Did they steal it, was it out of kindness? I'm confused.

Who's the "her" referring to?

Self view

Love the word choice.

the grayness mentioned again

i think this is the first piece of action Ive read in this piece omggggg

im wondering the same

interesting statement

im still wondering if the underscores have significance. does it represent them maybe saying it in a different language and it's translated?

I like this phrase idk why

wow

I hate the terms owner and master yuck

if they want to be like the emigrant ship then why aren't they trying harder than they are to be like it?

weaponizing humans

I would be the same ngl. why does kindness matter when you're being physically tortured?

is this worded weird or can I just not read?

wow hello generalization and racism

reminding of before: the calm before the storm. are we now getting to the storm?

ooo gossip

never seen this term before. is it the plural feminine form?

for - group dynamics of expanding and converging groups

group dynamics of expanding and converging groups - It is natural for groups to expand and grow and when they do, it changes the dynamics of the social interactions - Effort is required to know each other. It requires time to share and absorb what is shared - That legacy knowledge becomes the unspoken and implicit ground for future discourse - When new people are introduced to a group, or new groups are introduced to each other, - a minimum amount of sharing is required to establish common ground, common understanding - When members of a group have unique ideas to share, - a standardized, shareable documentation may become necessary for greater efficacy of sharing - the constitutions that are often at the heart of institutions became necessary for the same reasons

for - similarity - not just talk, make an impact

similarity - not just talk, make an impact - I think many of us are of like-mind. Surveying the precarity of the current polycrisis, there is immense complexity and very little time - Given these challenging circumstances, it behooves us to perform very careful sense-making to identify both the individual and the collective leverage points that will have the greatest impact in the shortest time - This also means we have to be careful of which groups we choose to work with as an optimal set of synergies is required if the group is to have possibility of reaching the greatest impact collectively

for - example - people- centered, interpersonal network

example - people-centered, interpersonal network - This is the scenario that innovators find themselves in always - you are at the center of multiple networks, each exploring an idea of interest to you - By its very nature, we often form silos in these groups, as they are sometimes mutually exclusive - for instance, our family group does not often overlap with this group - Sometimes we feel there is enough synergy to pursue de-siloing and introduce members of one group to other groups - If we have a people-centered software system that locates ourselves precisely at the center of all our groups, - then at least we have a uniform information system that can allow us to associate ideas across group silos without friction - As Gyuri says: - https://hyp.is/RVVayCOKEe2OJnff8kssaA/iopcommunity.com/what-is-the-internet-of-people-iop/ - - All financially stable organizations begin as an idea between people, with uncertainty of whether it will succeed

for - reply to - @Michael - annotation for annotation sake

reply to- @Michael - annotation for annotation sake - I think of annotation in the broadest possible sense - as social learning - Annotating is "making a note" and that is effectively noticing how I respond to the idea of another person. - If I am digesting ideas and suddenly a particular idea resonates with an idea in my salience landscape, my attention will be drawn to it. - That is, there is a salient reaction of my own consciousness with the ideas of another consciousness - If I react strongly to an idea, with my own ideas and feelings, then that moment of social learning is worth noting and recording, and hence annotating. - There's absolutely no point in annotating unless it is relevant to you - For me, it is the most powerful way to keep track of the evolution of my own intertwingled individual / collective learning journey - If that becomes a modus operandi for your annotation, then by definition they are all relevant, and not done simply for some external, dogmatic reason of conventionality

All of these together provide a comprehensive picture of parasitism in a population.

This would make sense since they most likely had increased exposure.

I never thought about how something so subtle could have such a significant effect on bacterial infections.

Hastanın problemli dişi dışında periodontal sorunların olmaması.

Klinik belirtiler periodontal hastalığa çok benzediğinden, doğru teşhis için dikkatli bir muayene gerekmektedir.

So where the defendant is legally responsible for having caused injury to the plaintiff, corrective justice insists that the defendant is answerable to the plaintiff for this result

Author response:

Public Reviews:

Reviewer #1 (Public review):

Summary:

This study evaluates whether species can shift geographically, temporally, or both ways in response to climate change. It also teases out the relative importance of geographic context, temperature variability, and functional traits in predicting the shifts. The study system is large occurrence datasets for dragonflies and damselflies split between two time periods and two continents. Results indicate that more species exhibited both shifts than one or the other or neither, and that geographic context and temp variability were more influential than traits. The results have implications for future analyses (e.g. incorporating habitat availability) and for choosing winner and loser species under climate change. The methodology would be useful for other taxa and study regions with strong community/citizen science and extensive occurrence data.

We thank Reviewer 1 for their time and expertise in reviewing our study. The suggestions are very helpful and will improve the quality of our manuscript.

Strengths:

This is an organized and well-written paper that builds on a popular topic and moves it forward. It has the right idea and approach, and the results are useful answers to the predictions and for conservation planning (i.e. identifying climate winners and losers). There is technical proficiency and analytical rigor driven by an understanding of the data and its limitations.

We thank Reviewer 1 for this assessment.

Weaknesses:

(1) The habitat classifications (Table S3) are often wrong. "Both" is overused. In North America, for example, Anax junius, Cordulia shurtleffii, Epitheca cynosura, Erythemis simplicicollis, Libellula pulchella, Pachydiplax longipennis, Pantala flavescens, Perithemis tenera, Ischnura posita, the Lestes species, and several Enallagma species are not lotic breeding. These species rarely occur let alone successfully reproduce at lotic sites. Other species are arguably "both", like Rhionaeschna multicolor which is mostly lentic. Not saying this would have altered the conclusions, but it may have exacerbated the weak trait effects.

We thank the reviewer for their expertise on this topic. We obtained these habitat classifications from field guides and trait databases, and we will review our primary sources to clarify the trait classifications. We will also reclassify the species according to the expertise of this reviewer and perform our analysis again. 

(2) The conservative spatial resolution (100 x 100 km) limits the analysis to wide- ranging and generalist species. There's no rationale given, so not sure if this was by design or necessity, but it limits the number of analyzable species and potentially changes the inference.

It is really helpful to have the opportunity to contextualize study design decisions like this one, and we thank the reviewer for the query. Sampling intensity is always a meaningful issue in research conducted at this scale, and we addressed it head-on in this work.

Very small quadrats covering massive geographical areas will be critically and increasingly afflicted by sampling weaknesses, as well as creating a potentially large problem with pseudoreplication. There is no simple solution to this problem. It would be possible to create interpolated predictions of species’ distributions using Species Distribution Models, Joint Species Distribution Models, or various kinds of Occupancy Models. None of these approaches then leads to analyses that rely on directly observed patterns. Instead, they are extrapolations, and those extrapolations typically fail when tested, (for example, papers by Lee-Yaw demonstrate that it is rare for SDMs to predict things well; occupancy models often perform less well than SDMs and do not capture how things change over time - Briscoe et al. 2021, Global Change Biology). The result of employing such techniques would certainly be to make all conclusions speculative, rather than directly observable. 

Rather than employing extrapolative models, we relied on transparent techniques that are used successfully in the core macroecology literature that address spatial variation in sampling explicitly and simply. Moreover, we constructed extensive null models that show that range and phenology changes, respectively, are contrary to expectations that arise from sampling difference. 100km quadrats make for a reasonable “middle-ground” in terms of the effects of sampling, and we will add a reference to the methods section to clarify this.

(3) The objective includes a prediction about generalists vs specialists (L99-103) yet there is no further mention of this dichotomy in the abstract, methods, results, or discussion.

Thank you for pointing this out - it is an editing error that should have been resolved prior to submission. We will replace the terms specialist and generalist with specific predictions based on traits.

(4) Key references were overlooked or dismissed, like in the new edition of Dragonflies & Damselflies model organisms book, especially chapters 24 and 27.

We thank Reviewer 1 for making us aware of this excellent reference. We will review this text and include it as a reference, in addition to other references recommended by Reviewer 1 and other reviewers.

Reviewer #2 (Public review):

Summary:

This paper explores a highly interesting question regarding how species migration success relates to phenology shifts, and it finds a positive relationship. The findings are significant, and the strength of the evidence is solid. However, there are substantial issues with the writing, presentation, and analyses that need to be addressed. First, I disagree with the conclusion that species that don't migrate are "losers" - some species might not migrate simply because they have broad climatic niches and are less sensitive to climate change. Second, the results concerning species' southern range limits could provide valuable insights. These could be used to assess whether sampling bias has influenced the results. If species are truly migrating, we should observe northward shifts in their southern range limits. However, if this is an artifact of increased sampling over time, we would expect broader distributions both north and south. Finally, Figure 1 is missed panel B, which needs to be addressed.

We thank Reviewer 2 for their time and expertise in reviewing our study.

It is possible that some species with broad niches may not need to migrate, although in general failing to move with climate change is considered an indicator of “climate debt”, signaling that a species may be of concern for conservation (ex. Duchenne et al. 2021, Ecology Letters). We will revise the discussion to acknowledge potential differences in outcomes.

We used null models to test whether our results regarding range shifts were robust, and if they varied due to increased sampling over time. We found that observed northern range limit shifts are not consistent with expectations derived from changes in sampling intensity (Figure S1, S2). 

We thank Reviewer 2 for pointing out this error in Figure 1. This conceptual figure was a challenge to construct, as it must illustrate how phenology and range shifts can occur simultaneously or uniquely to enable a hypothetic odonate to track its thermal niche over time. In a previous version of the figure, we had a second panel and we failed to remove the reference to that panel when we simplified the figure. 

Reviewer #3 (Public review):

Summary:

In their article "Range geographies, not functional traits, explain convergent range and phenology shifts under climate change," the authors rigorously investigate the temporal shifts in odonate species and their potential predictors. Specifically, they examine whether species shift their geographic ranges poleward or alter their phenology to avoid extreme conditions. Leveraging opportunistic observations of European and North American odonates, they find that species showing significant range shifts also exhibited earlier phenological shifts. Considering a broad range of potential predictors, their results reveal that geographical factors, but not functional traits, are associated with these shifts.

We thank Reviewer 3 for their expertise and the time they spent reviewing our study. Their suggestions are very helpful and will improve the quality of our manuscript.

Strengths:

The article addresses an important topic in ecology and conservation that is particularly timely in the face of reports of substantial insect declines in North America and Europe over the past decades. Through data integration the authors leverage the rich natural history record for odonates, broadening the taxonomic scope of analyses of temporal trends in phenology and distribution to this taxon. The combination of phenological and range shifts in one framework presents an elegant way to reconcile previous findings improving our understanding of the drivers of biodiversity loss.

We thank Reviewer 3 for this assessment.

Weaknesses:

The introduction and discussion of the article would benefit from a stronger contextualization of recent studies on biological responses to climate change and the underpinning mechanism.

The presentation of the results (particularly in figures) should be improved to address the integrative character of the work and help readers extract the main results. While the writing of the article is generally good, particularly the captions and results contain many inconsistencies and lack important detail. With the multitude of the relationships that were tested (the influence of traits) the article needs more coherence.

We thank Reviewer 3 for these suggestions. We will revise the introduction and discussion to better contextualize species’ responses to climate change and the mechanisms behind them. We will carefully review all figures and captions, and we will make changes to improve the clarity of the text and the presentation of results.

eLife Assessment

This fundamental work by Mäkelä et al. presents compelling experimental evidence supported by a theoretical model that the amount of chromosomal DNA can become limiting for the total rate of mRNA transcription and consequently protein production in the model bacterium Escherichia coli. The work is based on a mutant that allows inhibition of DNA replication while following growth at the single-cell level due to cell filamentation. The work significantly advances our understanding of growth and of the central dogma, and will be of considerable interest within both systems biology and microbial physiology.

Reviewer #1 (Public review):

Summary:

The manuscript by Mäkelä et al. presents compelling experimental evidence that the amount of chromosomal DNA can become limiting for the total rate of mRNA transcription and consequently protein production in the model bacterium Escherichia coli. Specifically, the authors demonstrate that upon inhibition of DNA replication the rate of RNA transcription and the single-cell growth rate continuously decrease, the latter in direct proportion to the concentration of active ribosomes, as measured indirectly by single-particle tracking. The decrease of ribosomal activity with filamentation is likely caused by a decrease of the concentration of mRNAs, as suggested by an observed plateau of the total number of active RNA polymerases. These observations are compatible with the hypothesis that DNA limits the total rate of transcription and thus, indirectly, translation.

The authors also demonstrate that the decrease of RNAp activity is independent of two candidate stress response pathways, the SOS stress response and the stringent response, as well as an anti-sigma factor previously implicated in variations of RNAp activity upon variations of nutrient sources.

Remarkably, the reduction of growth rate is observed soon after the inhibition of DNA replication, suggesting that the amount of DNA in wild-type cells is tuned to provide just as much substrate for RNA polymerase as needed to saturate most ribosomes with mRNAs. While previous studies of bacterial growth have most often focused on ribosomes and metabolic proteins, this study provides important evidence that chromosomal DNA has a previously underestimated important and potentially rate-limiting role for growth.

Strengths:

This article links the growth of single cells to the amount of DNA, the number of active ribosomes and to the number of RNA polymerases, combining quantitative experiments with theory. The correlations observed during depletion of DNA, notably in M9gluCAA medium, are compelling and point towards a limiting role of DNA for transcription and subsequently for protein production soon after reduction of the amount of DNA in the cell. The article also contains a theoretical model of transcription-translation that contains a Michaelis-Menten type dependency of transcription on DNA availability and is fit to the data.

At a technical level, single-cell growth experiments and single-particle tracking experiments are well described, suggesting that different diffusive states of molecules represent different states of RNAp/ribosome activities, which reflect the reduction of growth.

Apart from correlations in DNA-deplete cells, the article also investigates the role of candidate stress response pathways for reduced transcription, demonstrating that neither the SOS nor the stringent response are responsible for the reduced rate of growth. Equally, the anti-sigma factor Rsd recently described for its role in controlling RNA polymerase activity in nutrient-poor growth media, seems also not involved according to mass-spec data. While other (unknown) pathways might still be involved in reducing the number of active RNA polymerases, the proposed hypothesis of the DNA substrate itself being limiting for the total rate of transcription is appealing.

Finally, the authors confirm the reduction of growth in the distant Caulobacter crescentus, which lacks overlapping rounds of replication and could thus have shown a different dependency on DNA concentration.

Weaknesses:

The study has no apparent weaknesses after review.

Reviewer #2 (Public review):

In this work, the authors uncovered the effects of DNA dilution on E. coli, including a decrease in growth rate and a significant change in proteome composition. The authors demonstrated that the decline in growth rate is due to the reduction of active ribosomes and active RNA polymerases because of the limited DNA copy numbers. They further showed that the change in the DNA-to-volume ratio leads to concentration changes in almost 60% of proteins, and these changes mainly stem from the change in the mRNA levels.

Comments on revised version:

The authors have satisfyingly answered all of our questions.

Reviewer #3 (Public review):

Mäkelä et al. here investigate genome concentration as a limiting factor on growth. Previous work has identified key roles for transcription (RNA polymerase) and translation (ribosomes) as limiting factors on growth, which enable an exponential increase in cell mass. While a potential limiting role of genome concentration under certain conditions has been explored theoretically, Mäkelä et al. here present direct evidence that when replication is inhibited, genome concentration emerges as a limiting factor.

A major strength of this paper is the diligent and compelling combination of experiment and modeling used to address this core question. The use of origin- and ftsZ-targeted CRISPRi is a very nice approach that enables dissection of the specific effects of limiting genome dosage in the context of a growing cytoplasm. While it might be expected that genome concentration eventually becomes a limiting factor, what is surprising and novel here is that this happens very rapidly, with growth transitioning even for cells within the normal length distribution for E. coli. Fundamentally, it demonstrates the fine balance of bacterial physiology, where the concentration of the genome itself (at least under rapid growth conditions) is no higher than it needs to be. A further surprising finding of this study is that susceptibility to this genome-limiting effect is felt differently by different genes, with unstable transcripts more affected and rRNA and many essential genes being more robust to it.

It should be noted that the authors do not identify a "smoking gun" - a gene or small number of genes that mediate the effects of genome concentration-dependent growth limitation. However, what they do achieve is to develop plausible criteria for identifying such a gene - through investigating essential genes that decrease in their abundance more rapidly than others.

Overall, this study provides a fundamental contribution to bacterial physiology by illuminating the relationship between DNA, mRNA, and protein in determining growth rate. While coarse-grained, the work invites exciting questions about how the composition of major cellular components is fine-tuned to a cell's needs and which specific gene products mediate this connection. The work also suggests the presence of buffering mechanisms that allow essential proteins such as RNA polymerase to be robust to fluctuations in genome concentration, which is an exciting area for future exploration. This work has implications not only for biotechnology, as the authors discuss, but potentially also for our understanding of how DNA-targeted antibiotics limit bacterial growth.

Comments on revised version:

Nothing left to add - the authors did a fantastic job addressing my points. In some ways doing so opened up even more interesting questions, but I happily accept that those are best left to future investigations.

Author response:

The following is the authors’ response to the original reviews.

Public Reviews: 

Reviewer #1 (Public Review): 

Summary: 

The manuscript by Mäkelä et al. presents compelling experimental evidence that the amount of chromosomal DNA can become limiting for the total rate of mRNA transcription and consequently protein production in the model bacterium Escherichia coli. Specifically, the authors demonstrate that upon inhibition of DNA replication the single-cell growth rate continuously decreases, in direct proportion to the concentration of active ribosomes, as measured indirectly by single-particle tracking. The decrease of ribosomal activity with filamentation, in turn, is likely caused by a decrease of the concentration of mRNAs, as suggested by an observed plateau of the total number of active RNA polymerases. These observations are compatible with the hypothesis that DNA limits the total rate of transcription and thus translation. The authors also demonstrate that the decrease of RNAp activity is independent of two candidate stress response pathways, the SOS stress response and the stringent response, as well as an anti-sigma factor previously implicated in variations of RNAp activity upon variations of nutrient sources.

Remarkably, the reduction of growth rate is observed soon after the inhibition of DNA replication, suggesting that the amount of DNA in wild-type cells is tuned to provide just as much substrate for RNA polymerase as needed to saturate most ribosomes with mRNAs. While previous studies of bacterial growth have most often focused on ribosomes and metabolic proteins, this study provides important evidence that chromosomal DNA has a previously underestimated important and potentially rate-limiting role for growth. 

Thank you for the excellent summary of our work.

Strengths: 

This article links the growth of single cells to the amount of DNA, the number of active ribosomes and to the number of RNA polymerases, combining quantitative experiments with theory. The correlations observed during depletion of DNA, notably in M9gluCAA medium, are compelling and point towards a limiting role of DNA for transcription and subsequently for protein production soon after reduction of the amount of DNA in the cell. The article also contains a theoretical model of transcription-translation that contains a Michaelis-Menten type dependency of transcription on DNA availability and is fit to the data. While the model fits well with the continuous reduction of relative growth rate in rich medium (M9gluCAA), the behavior in minimal media without casamino acids is a bit less clear (see comments below). 

At a technical level, single-cell growth experiments and single-particle tracking experiments are well described, suggesting that different diffusive states of molecules represent different states of RNAp/ribosome activities, which reflect the reduction of growth. However, I still have a few points about the interpretation of the data and the measured fractions of active ribosomes (see below). 

Apart from correlations in DNA-deplete cells, the article also investigates the role of candidate stress response pathways for reduced transcription, demonstrating that neither the SOS nor the stringent response are responsible for the reduced rate of growth. Equally, the anti-sigma factor Rsd recently described for its role in controlling RNA polymerase activity in nutrient-poor growth media, seems also not involved according to mass-spec data. While other (unknown) pathways might still be involved in reducing the number of active RNA polymerases, the proposed hypothesis of the DNA substrate itself being limiting for the total rate of transcription is appealing. 

Finally, the authors confirm the reduction of growth in the distant Caulobacter crescentus, which lacks overlapping rounds of replication and could thus have shown a different dependency on DNA concentration. 

Weaknesses: 

There are a range of points that should be clarified or addressed, either by additional experiments/analyses or by explanations or clear disclaimers. 

First, the continuous reduction of growth rate upon arrest of DNA replication initiation observed in rich growth medium (M9gluCAA) is not equally observed in poor media. Instead, the relative growth rate is immediately/quickly reduced by about 10-20% and then maintained for long times, as if the arrest of replication initiation had an immediate effect but would then not lead to saturation of the DNA substrate. In particular, the long plateau of a constant relative growth rate in M9ala is difficult to reconcile with the model fit in Fig 4S2. Is it possible that DNA is not limiting in poor media (at least not for the cell sizes studied here) while replication arrest still elicits a reduction of growth rate in a different way? Might this have something to do with the naturally much higher oscillations of DNA concentration in minimal medium?

The reviewer is correct that there are interesting differences between nutrient-rich and -poor conditions. They were originally noted in the discussion, but we understand how our original presentation made it confusing. We reorganized the text and figures to better explain our results and interpretations. In the revised manuscript, the data related to the poor media are now presented separately (new Figure 6) from the data related to the rich medium (Figures 1-3).  The total RNAP activity (abundance x active fraction) is significantly reduced in poor media (Figure 6A-B) similarly to rich medium (Figure 3H). Thus, DNA is limiting for transcription across conditions. However, the total ribosome activity in poor media (Figure 6C-D) and thus the growth rate (Figure 6EF) was less affected in comparison to rich media (Figure 2H and 1C). Our interpretation of these results is that while DNA is limiting for transcription in all tested nutrient conditions (as shown by the total active RNAP data), post-transcriptional buffering activities compensate for the reduction in transcription in poor media, thereby maintaining a better scaling of growth rates under DNA limitation. 

The authors argue that DNA becomes limiting in the range of physiological cell sizes, in particular for M9glCAA (Fig. 1BC). It would be helpful to know by how much (fold-change) the DNA concentration is reduced below wild-type (or multi-N) levels at t=0 in Fig 1B and how DNA concentration decays with time or cell area, to get a sense by how many-fold DNA is essentially 'overexpressed/overprovided' in wild-type cells. 

We now provide crude estimates in the Discussion section. The revised text reads: “Crude estimations suggest that ≤ 40% DNA dilution is sufficient to negatively affect transcription (total RNAP activity) in M9glyCAAT, whereas the same effect was observed after less than 10% dilution in nutrient-poor media (M9gly or M9ala) (see Materials and Methods).” We obtained these numbers based on calculations and estimates described in the Materials and Methods section and Appendix 1 (Appendix 1 – Table 1).

Fig. 2: The distribution of diffusion coefficients of RpsB is fit to Gaussians on the log scale. Is this based on a model or on previous work or simply an empirical fit to the data? An exact analytical model for the distribution of diffusion constants can be found in the tool anaDDA by Vink, ..., Hohlbein Biophys J 2020. Alternatively, distributions of displacements are expressed analytically in other tools (e.g., in SpotOn). 

We use an empirical fit of Gaussian mixture model (GMM) of three states to the data and extract the fractions of molecules in each state. This avoids making too many assumptions on the underlying processes, e.g. a Markovian system with Brownian diffusion. The model in anaDDA (Vink et al.) is currently limited to two-transitioning states with a maximal step number of 8 steps per track for a computationally efficient solution (longer tracks are truncated). Using a short subset of the trajectories is less accurate than using the entire trajectory and because of this, we consider full tracks with at least 9 displacements. Meanwhile, Spot-On supports a three-state model but it is still based on a semi-analytical model with a pre-calculated library of parameters created by fitting of simulated data. Neither of these models considers the effect of cell confinement, which plays a major role in single-molecule diffusion in small-sized cells such as bacteria. For these reasons, we opted to use an empirical fit to the data. We note that the fractions of active ribosomes in WT cells, which we extracted from these diffusion measurements, are consistent with the range of estimates obtained by others using similar or different approaches (Forchhammer and Lindhal 1971; Mohapatra and Weisshaar, 2018; Sanamrad et al., 2014). 

The estimated fraction of active ribosomes in wild-type cells shows a very strong reduction with decreasing growth rate (down from 75% to 30%), twice as strong as measured in bulk experiments (Dai et al Nat Microbiology 2016; decrease from 90% to 60% for the same growth rate range) and probably incompatible with measurements of growth rate, ribosome concentrations, and almost constant translation elongation rate in this regime of growth rates. Might the different diffusive fractions of RpsB not represent active/inactive ribosomes? See also the problem of quantification above. The authors should explain and compare their results to previous work. 

We agree that our measured range is somewhat larger than the estimated range from Dai et al, 2016. However, they use different media, strains, and growth conditions. We also note that Dai et al did not make actual measurements of the active ribosome fraction. Instead, they calculate the “active ribosome equivalent” based on a model that includes growth rate, protein synthesis rate, RNA/protein abundance, and the total number of amino acids in all proteins in the cell. Importantly, our measurements show the same overall trend (a ~30% decrease) as Dai et al, 2016. Furthermore, our results are within the range of previous experimental estimates from ribosome profiling (Forchhammer and Lindhal 1971) or single-ribosome tracking (Mohapatra and Weisshaar, 2018; Sanamrad et al., 2014). We clarified this point in the revised manuscript. 

To measure the reduction of mRNA transcripts in the cell, the authors rely on the fluorescent dye SYTO RNAselect. They argue that 70% of the dye signal represents mRNA. The argument is based on the previously observed reduction of the total signal by 70% upon treatment with rifampicin, an RNA polymerase inhibitor (Bakshi et al 2014). The idea here is presumably that mRNA should undergo rapid degradation upon rif treatment while rRNA or tRNA are stable. However, work from Hamouche et al. RNA (2021) 27:946 demonstrates that rifampicin treatment also leads to a rapid degradation of rRNA. Furthermore, the timescale of fluorescent-signal decay in the paper by Bakshi et al. (half life about 10min) is not compatible with the previously reported rapid decay of mRNA (24min) but rather compatible with the slower, still somewhat rapid, decay of rRNA reported by Hamouche et al.. A bulk method to measure total mRNA as in the cited Balakrishnan et al. (Science 2022) would thus be a preferred method to quantify mRNA. Alternatively, the authors could also test whether the mass contribution of total RNA remains constant, which would suggest that rRNA decay does not contribute to signal loss. However, since rRNA dominates total RNA, this measurement requires high accuracy. The authors might thus tone down their conclusions on mRNA concentration changes while still highlighting the compelling data on RNAp diffusion. 

Thank you for bringing the Hamouche et al 2021 paper to our attention. To address this potential issue, we have performed fluorescence in situ hybridization (FISH) microscopy using a 16S rRNA probe (EUB338) to quantify rRNA concentration in 1N cells. We found that the rRNA signal only slightly decreases with cell size (i.e., genome dilution) compared to the RNASelect signal (e.g., a ~5% decrease for rRNA signal vs. 50% for RNASelect for a cell size range of 4 to 10 µm2). We have revised the text and added a figure to include the new rRNA FISH data (Figure 4). In addition, as a control, we validated our rRNA FISH method by comparing the intracellular concentration of 16S rRNA in poor vs. rich media (new Figure 4 – Figure supplement 3).

The proteomics experiments are a great addition to the single-cell studies, and the correlations between distance from ori and protein abundance is compelling. However, I was missing a different test, the authors might have already done but not put in the manuscript: If DNA is indeed limiting the initiation of transcription, genes that are already highly transcribed in non-perturbed conditions might saturate fastest upon replication inhibition, while genes rarely transcribed should have no problem to accommodate additional RNA polymerases. One might thus want to test, whether the (unperturbed) transcription initiation rate is a predictor of changes in protein composition. This is just a suggestion the authors may also ignore, but since it is an easy analysis, I chose to mention it here. 

We did not find any correlation when we examined the potential relation between RNA slopes and mRNA abundance (from our first CRISPRi oriC time point) or the transcription initiation rate (from Balakrishnan et al., 2022, PMID: 36480614) across genes. These new plots are presented in Figure 7 – Figure supplement 2B. In contrast, we found a small but significant correlation between RNA slopes and mRNA decay rates (from Balakrishnan et al., 2022, PMID: 36480614), specifically for genes with short mRNA lifetimes (new Figure 7F). This effect is consistent with our model prediction (Figure 5 – Figure supplement 2). 

Related to the proteomics, in l. 380 the authors write that the reduced expression close to the ori might reflect a gene-dosage compensatory mechanism. I don't understand this argument. Can the authors add a sentence to explain their hypothesis? 

We apologize for the confusion. While performing additional analyses for the revisions, we realized that while the proteins encoded by genes close to oriC tend to display subscaling behavior, this is not true at the mRNA level (new Figure 7 – Figure supplement 3B). In light of this result, we no longer have a hypothesis for the observed negative correlation at the protein level (originally Figure 5D, now Figure 7 – Figure supplement 3A). The text was revised accordingly.  

In Fig. 1E the authors show evidence that growth rate increases with cell length/area. While this is not a main point of the paper it might be cited by others in the future. There are two possible artifacts that could influence this experiment: a) segmentation: an overestimation of the physical length of the cell based on phase-contrast images (e.g., 200 nm would cause a 10% error in the relative rate of 2 um cells, but not of longer cells). b) timedependent changes of growth rate, e.g., due to change from liquid to solid or other perturbations. To test for the latter, one could measure growth rate as a function of time, restricting the analysis to short or long cells, or measuring growth rate for short/long cells at selected time points. For the former, I recommend comparison of phase-contrast segmentation with FM4-64-stained cell boundaries.

As the reviewer notes, the small increase in relative growth was just a minor observation that does not affect our story whether it is biologically meaningful or the result of a technical artefact. But we agree with the reviewer that others might cite it in future works and thus should be interpreted with caution.

An artefact associated with time-dependent changes (e.g. changing from liquid cultures to more solid agarose pads) is unlikely for two reasons. 1. We show that varying the time that cells spend on agarose pads relative to liquid cultures does not affect the cell size-dependent growth rate results (Figure 1 – supplement 5A). 2. We show that the growth rate is stable from the beginning of the time-lapse with no transient effects upon cell placement on agarose pads for imaging (Figure 1 – supplement 1). These results were described in the Methods section where they could easily be missed. We revised the text to discuss these controls more prominently in the Results section.

As for cell segmentation, we have run simulations and agree with the reviewer that a small overestimation of cell area (which is possible with any cell segmentation methods including ours) could lead to a small increase in relative growth with increasing cell areas (new Figure 1 – Figure supplement 3). Since the finding is not important to our story, we simply revised the text and added the simulation results to alert the readers to the possibility that the observation may be due to a small cell segmentation bias.

Reviewer #2 (Public Review): 

In this work, the authors uncovered the effects of DNA dilution on E. coli, including a decrease in growth rate and a significant change in proteome composition. The authors demonstrated that the decline in growth rate is due to the reduction of active ribosomes and active RNA polymerases because of the limited DNA copy numbers. They further showed that the change in the DNA-to-volume ratio leads to concentration changes in almost 60% of proteins, and these changes mainly stem from the change in the mRNA levels. 

Thank you for the support and accurate summary!

Reviewer #3 (Public Review): 

Summary: 

Mäkelä et al. here investigate genome concentration as a limiting factor on growth.

Previous work has identified key roles for transcription (RNA polymerase) and translation (ribosomes) as limiting factors on growth, which enable an exponential increase in cell mass. While a potential limiting role of genome concentration under certain conditions has been explored theoretically, Mäkelä et al. here present direct evidence that when replication is inhibited, genome concentration emerges as a limiting factor. 

Strengths: 

A major strength of this paper is the diligent and compelling combination of experiment and modeling used to address this core question. The use of origin- and ftsZ-targeted CRISPRi is a very nice approach that enables dissection of the specific effects of limiting genome dosage in the context of a growing cytoplasm. While it might be expected that genome concentration eventually becomes a limiting factor, what is surprising and novel here is that this happens very rapidly, with growth transitioning even for cells within the normal length distribution for E. coli. Fundamentally, it demonstrates the fine balance of bacterial physiology, where the concentration of the genome itself (at least under rapid growth conditions) is no higher than it needs to be. 

Thank you!

Weaknesses: 

One limitation of the study is that genome concentration is largely treated as a single commodity. While this facilitates their modeling approach, one would expect that the growth phenotypes observed arise due to copy number limitation in a relatively small number of rate-limiting genes. The authors do report shifts in the composition of both the proteome and the transcriptome in response to replication inhibition, but while they report a positional effect of distance from the replication origin (reflecting loss of high-copy, origin-proximal genes), other factors shaping compositional shifts and their functional effects on growth are not extensively explored. This is particularly true for ribosomal RNA itself, which the authors assume to grow proportionately with protein. More generally, understanding which genes exert the greatest copy number-dependent influence on growth may aid both efforts to enhance (biotechnology) and inhibit (infection) bacterial growth. 

We agree but feel that identifying the specific limiting genes is beyond the scope of the study. This said, we carried out additional experiments and analyses to address the reviewer’s comment and identify potential contributing factors and limiting gene candidates. First, we examined the intracellular concentration of 16S ribosomal RNA (rRNA) by rRNA FISH microscopy and found that it decays much slower than the bulk of mRNAs as measured using RNASelect staining (new Figure 4 and Figure 4 – Figure supplements 1 and 3). We found that the rRNA signal is far more stable in 1N cells than the RNASelect signal, the former decreasing by only ~5% versus ~50% for the later in response to the same range of genome dilution (Figure 4C).  Second,  we carried out new correlation analyses between our proteomic/transcriptomic datasets and published genome-wide datasets that report various variables under unperturbed conditions (e.g., mRNA abundance, mRNA degradation rates, fitness cost, transcription initiation rates, essentiality for viability); see new Figure 7E-G and Figure 7 – Figure supplement 2. In the process, we found that genes essential for viability tend, on average, to display superscaling behavior (Figure 7G). This suggests that cells have evolved mechanisms that prioritize expression of essential genes over nonessential ones during DNA-limited growth. Furthermore, this analysis identified a small number of essential genes that display strong negative RNA slopes (Figure 7C, Datasets 1 and 2), indicating that the concentration of their mRNA decreases rapidly relative to the rest of the transcriptome upon genome dilution. These essential genes with strong subscaling behavior are candidates for being growth-limiting. 

The text and figures were revised to include these new results.

Overall, this study provides a fundamental contribution to bacterial physiology by illuminating the relationship between DNA, mRNA, and protein in determining growth rate. While coarse-grained, the work invites exciting questions about how the composition of major cellular components is fine-tuned to a cell's needs and which specific gene products mediate this connection. This work has implications not only for biotechnology, as the authors discuss, but potentially also for our understanding of how DNA-targeted antibiotics limit bacterial growth. 

Thank you!

Recommendations for the authors:

Reviewer #2 (Recommendations For The Authors): 

Below are my comments. 

(1) I noticed that a paper by Li et al. on biorxiv has found similar results as this work ("Scaling between DNA and cell size governs bacterial growth homeostasis and resource allocation," https://doi.org/10.1101/2021.11.12.468234), including the linear growth of E. coli when the DNA concentration is low. This relevant reference was not cited or discussed in the current manuscript. 

We agree that authors should cite and discuss relevant peer-reviewed literature. But broadly speaking, we feel that extending this responsibility to all preprints (and by extension any online material) that have not been reviewed is a bit dangerous. It would effectively legitimize unreviewed claims and risk their propagation in future publications. We think that while imperfect, the peer-reviewing process still plays an important role. 

Regarding the specific 2021 preprint that the reviewer pointed out, we think that the presented growth rate data are quite noisy and that the experiments lack a critical control (multi-N cells), making interpretation difficult. Their report that plasmid-borne expression is enhanced when DNA is severely diluted is certainly interesting and makes sense in light of our measurements that the activities, but not the concentrations, of RNA polymerases and ribosomes are reduced in 1N cells. However, we do not know why this preprint has not yet been published since 2021. There could be many possible reasons for this. Therefore, we feel that it is safer to limit our discussion to peer-reviewed literature.

(2) I think the kinetic Model B in the Appendix has been studied in previous works, such as Klump & Hwa, PNAS 2008, https://doi.org/10.1073/pnas.0804953105

Indeed, Klumpp & Hwa 2008 modeled the kinetics of RNA polymerase and promoter association prior to our study. But there is a difference between their model and ours. Their model is based on Michaelis Menten-type (MM) functions in which the RNAP is analogous to the “substrate” and the promoter to the “enzyme” in the MM equation. In contrast, our model uses functions based on the law of mass action (instead of MMtype of function). We have revised the text, included the Klumpp & Hwa 2008 reference, and revised the Materials & Methods section to clarify these points. 

(3) On lines 284-285, if I understand correctly, the fractions of active RNAPs and active ribosomes are relative to the total protein number. It would be helpful if the authors could mention this explicitly to avoid confusion. 

The fractions of active RNAPs and active ribosomes are expressed as the percentage of the total RNAPs and ribosomes. We have revised the text to be more explicit. Thank you.

(4) On line 835, I am not sure what the bulk transcription/translation rate means. I guess it is the maximum transcription/translation rate if all RNAPs/ribosomes are working according to Eq. (1,2). It would be helpful if the authors could explain the meaning of r_1 and r_2 more explicitly. 

Our apology for the lack of clarity. We have added the following equations:

(5) Regarding the changes in protein concentrations due to genome dilution, a recent theoretical paper showed that it may come from the heterogeneity in promoter strengths (Wang & Lin, Nature Communications 2021). 

In the Wang and Lin model, the heterogeneity in promoter strength predicts that the “mRNA production rate equivalent”, which is the mRNA abundance multiplied by the mRNA decay rate, will correlate the RNA slopes. However, we found these two variables to be uncorrelated (see below, The Spearman correlation coefficient ρ was 0.02 with a p-value of 0.24, indicating non-significance (NS).

Author response image 1.

The mRNA production rate equivalent (mRNA abundance at the first time point after CRISPRi oriC induction multiplied by the mRNA degradation rate measured by Balakrishnan et al., 2022, PMID: 36480614, expressed in transcript counts per minute) does not correlate (Spearman correlation’s p-value = 0.24) with the RNA slope in 1N-rich cells.  Data from 2570 genes are shown (grey markers, Gaussian kernel density estimation - KDE), and their binned statistics (mean +/- SEM, ~280 genes per bin, orange markers). 

In addition, we found no significant correlation between RNA slopes and mRNA abundance or transcription initiation rate. These plots are now included in Figure 7E and Figure 7 –Figure supplement 2B. Thus, the promoter strength does not appear to be a predictor of the RNA (and protein) scaling behavior under DNA limitation. 

Reviewer #3 (Recommendations For The Authors): 

One general area that could be developed further is analysis of changes in the proteome/transcriptome composition, given that there may be specific clues here as to the phenotypic effects of genome concentration limitation. Specifically: 

• In Figure 5D, the authors demonstrate an effect of origin distance on sensitivity to replication inhibition, presumably as a copy number effect. However, the authors note that the effect was only slight and postulated a compensatory mechanism. Due to the stability of proteins, one should expect relatively small effects - even if synthesis of a protein stopped completely, its concentration would only decrease twofold with a doubling of cell area (slope = -1, if I'm interpreting things correctly). It would be helpful to display the same information shown in Figure 5D at the mRNA level, since I would anticipate that higher mRNA turnover rates mean that effects on transcription rate should be felt more rapidly. 

We thank the reviewer for this suggestion. To our surprise, we found that there is no correlation between gene location relative to the origin and RNA slope across genes. This suggests that the observed correlation between gene location and protein slopes does not occur at the mRNA level. Given that we do not have an explanation for the underlying mechanism, we decided to present these data (the original data in Figure 5D and the new data for the RNA slope) in a supplementary figure (Figure 7 – Figure supplement 3).

• Related to this, did the authors see any other general trends? For example, do highly expressed genes hit saturation faster, making them more sensitive to limited genome concentration? 

We found that the RNA slopes do not correlate with mRNA abundance or transcription initiation rates. However, they do correlate with mRNA decay. That is, short-lived mRNAs tend to have negative RNA slopes. The new analyses have been added as Figure 7E-F and Figure 7 – Figure supplement 2B. The text has been revised to incorporate this information. 

• Presumably loss of growth is primarily driven by a subset of genes whose copy number becomes limiting. Previously, it has been reported that there is a wide variety among "essential" genes in their expression-fitness relationship - i.e. how much of a reduction in expression you need before growth is reduced (e.g. PMID 33080209). It would be interesting to explore the shifts in proteome/transcriptome composition to see whether any genes particularly affected by restricted genome concentration are also especially sensitive to reduced expression - overlap in these datasets may reveal which genes drive the loss of growth. 

This is a very interesting idea – thank you! We did not find a correlation between the protein/RNA slope and the relative gene fitness as previously calculated (PMID 33080209), as shown below.

Author response image 2.

The relative fitness of each gene (data by Hawkins et al., 2020, PMID: 33080209, median fitness from the highest sgRNA activity bin) plotted versus the gene-specific RNA and protein slopes that we measured in 1Nrich cells after CRISPRi oriC induction. More than 260 essential genes are shown (262 RNA slopes and 270 protein slopes, grey markers), and their binned statistics (mean +/- SEM, 43-45 essential genes per bin, orange markers). The spearman correlations (ρ) with p-values above 10-3 are considered not significant (NS). In our analyses, we only considered correlations significant if they have a Spearman correlation p-value below 10-10.

However, while doing this suggested analysis, we noticed that the essential genes that were included in the forementioned study have RNA slopes above zero on average. This led us to compare the RNA slope distributions of essential genes relative to all genes (now included in Figure 7G). We found that they tend to display superscaling behavior (positive RNA slopes), suggesting the existence of regulatory mechanisms that prioritize the expression of essential genes over less important ones when genome concentration becomes limiting for growth.  The text has been revised to include this new information.

Other suggestions: 

• In Figure 3 the authors report that total RNAP concentration increases with increasing cytoplasmic volume. This is in itself an interesting finding as it may imply a compensatory mechanism - can the authors offer an explanation for this? 

We do not have a straightforward explanation. But we agree that it is very interesting and should be investigated in future studies given that this superscaling behavior is common among essential genes. 

• The explanation of the modeling within the main text could be improved. Specifically, equations 1 and 2, as well as a discussion of models A and B (lines 290-301), do not explicitly relate DNA concentration to downstream effects. The authors provide the key information in Appendix 1, but for a general reader, it would be helpful to provide some intuition within the main text about how genome concentration influences transcription rate (i.e. via 𝛼RNAP).  

We apologize for the lack of clarity. We have added information that hopefully improves clarity.

eLife Assessment

This valuable study uses dynamic metabolic models to compare perturbation responses in a bacterial system, analyzing whether they return to their steady state or amplify beyond the initial perturbation. The evidence supporting the emergent properties of perturbed metabolic systems to network topology and sensitivity to specific metabolites is solid, although the authors do not explain the origin of some significant inconsistencies between models.

Reviewer #1 (Public review):

(1a) Summary:

The author studied metabolic networks for central metabolism, focusing on how system trajectories returned to their steady state. To quantify the response, systematic perturbation was performed in simulation and the maximal destabilization away from steady state (compared with initial perturbation distance) was characterized. The author analyzed the perturbation response and found that sparse network and networks with more cofactors are more "stable", in the sense that the perturbed trajectories have smaller deviation along the path back to the steady state.

(1b) Strengths and major contributions:

The author compared three metabolic models and performed systematic perturbation analysis in simulation. This is the first work characterized how perturbed trajectories deviate from equilibrium in large biochemical systems and illustrated interesting findings about the difference between sparse biological systems and randomly simulated reaction networks.

(1c) Weaknesses:

There are two main weaknesses in this study:

First, the metabolic network in this study is incomplete. For example, amino acid synthesis and lipid synthesis are important for biomass and growth, but they are not included in the three models used in this study. NADH and NADPH are as important as ATP/ADP/AMP, but they are not included in the models. In the future, a more comprehensive metabolic and biosynthesis model is required.

Second, this work does not provide mathematics explanation on the perturbation response χ. Since the perturbation analysis are performed closed to steady state (or at least belongs to the attractor of single steady state), local linear analysis would provide useful information. By complement with other analysis in dynamical systems (described in below) we can gain more logical insights about perturbation response.

(1d) Discussion and impact for the field:

Metabolic perturbation is an important topic in cell biology and has important clinical implication in pharmacodynamics. The computational analysis in this study provides an initiative for future quantitative analysis on metabolism and homeostasis.

Comments on revised version:

The revised version of this manuscript made some clarifications, while I think the analysis of response coefficients is still numerical and model-specific, being unclear under dynamical systems of views.

Reviewer #2 (Public review):

The authors have conducted a valuable comparative analysis of perturbation responses in three nonlinear kinetic models of E. coli central carbon metabolism found in the literature. They aimed to uncover commonalities and emergent properties in the perturbation responses of bacterial metabolism. They discovered that perturbations in the initial concentrations of specific metabolites, such as adenylate cofactors and pyruvate, significantly affect the maximal deviation of the responses from steady-state values. Furthermore, they explored whether the network connectivity (sparse versus dense connections) influences these perturbation responses. The manuscript is reasonably well written.

Comments on revised version:

The authors have addressed my concerns to a large extent. However, a few minor issues remain, as listed below:

(1) The authors identified key metabolites affecting responses to perturbations in two ways: (i) by fixing a metabolite's value and (ii) by performing a sensitivity analysis. It would be helpful for the modeling community to understand better the differences and similarities in the obtained results. Do both methods identify substrate-level regulators? Is freezing a metabolite's dynamics dramatically changing the metabolic response (and if yes, which ones are so different in the two cases)? Does the scope of the network affect these differences and similarities?

(2) Regarding the issues the authors encountered when performing the sensitivity analysis, they can be approached in two ways. First, the authors can check the methods for computing conserved moieties nicely explained by Sauro's group (doi:10.1093/bioinformatics/bti800) and compute them for large-scale networks (but beware of metabolites that belong to several conserved pools). Otherwise, the conserved pools of metabolites can be considered as variables in the sensitivity analysis-grouping multiple parameters is a common approach in sensitivity analysis.

Author response:

The following is the authors’ response to the original reviews.

Reviewer #1 (Public Reviews):  

First, the metabolic network in this study is incomplete. For example, amino acid synthesis and lipid synthesis are important for biomass and growth, but they4 are not included in the three models used in this study. NADH and NADPH are as important as ATP/ADP/AMP, but they are not included in the models. In the future, a more comprehensive metabolic and biosynthesis model is required.  

Thank you for the critical comment on the weakness of the present study. We actually tried to study a larger model like Turnborg et al (2021), which is a model of JCVI-syn3A, but we give up to include it in our model list to study in depth. This is because we noticed that the concentration of ATP in the model can be negative (we confirmed this with one of the authors of the paper). Another "big" kinetic model of metabolism that we could list would be Khodayari et al (2017). However, we could not find the models to compare the dynamics of this big model with. Therefore, we decided to use the model only for the central carbon metabolism for now. We would like to leave a more extended study for the near future.  

We would like to mention that NADH and NADPH are included in Khodayari model and Boecker model, while NADH and NADPH are ramped up to NADH in the latter model.  

Second, this work does not provide a mathematical explanation of the perturbation response χ. Since the perturbation analysis is performed close to the steady state (or at least belongs to the attractor of single-steady-state), local linear analysis would provide useful information. By complementing with other analysis in dynamical systems (described below) we can gain more logical insights about perturbation response.  

We tried a linear stability analysis. However, with the perturbation strength we used here, the linearization of the model is no longer valid, in the sense that the linearized model

leads to negative concentrations of the metabolites (xst+Δx < 0 for some metabolites). We have added a scatter plot of the response coefficient of trajectories sharing the initial condition, while the dynamics are computed by the original model and the linearized model, respectively. (Fig. S1). 

Since the response coefficient is based on the logarithm of the concentrations, as the metabolite concentrations approach zero, the response coefficient becomes larger. The high response coefficient in the Boecker and Chassagnole model would be explained by this artifact.  The linearized Khodayari model shows either χ~1 or χ = 0 (one or more metabolite concentrations become negative). This could be due to the number of variables in the model. For the response coefficient to have a larger value, the perturbation should be along the eigenvector that leads to oscillatory dynamics with long relaxation time (i.e., the corresponding eigenvalue has a small real part in terms of absolute value and a non-zero imaginary part). However, since the Khodayari model has about 800 variables, if perturbations are along such directions, there is a high probability that one or more metabolite concentrations will become negative.

We fully agree that if the perturbations on the metabolite concentrations are in the linear regime, the response to the perturbations can be estimated by checking the eigenvalues and eigenvectors. However, we would say that the relationship between the linearized model (and thus the spectrum of eigenvalues) and the original model is unclear in this regime.  We remarked this in Lines 158160.

Recommendations for the authors:

My major suggestion is about understanding the key quantity in this study: the response coefficient χ. When the perturbed state is close to the fixed point, one could adopt local stability analysis and consider the linearized system. For a linear system with one stable fixed point P, we consider the Jacobian matrix M on P. If all eigenvalues of M are real and negative, the perturbed trajectory will return to P with each component monotonically varies. If some eigenvalues have negative real part and nonzero imaginary part, then the perturbed trajectory will spiral inward to the fixed point. Depending on the spiral trajectory and the initially perturbed state, some components would deviate furthermore (transiently) from the fixed point on the spiral trajectory. This explains why the response coefficient χ can be greater than 1. 

Mathematically, a locally linearized system has similar behavior to the linear system, and the examples in this study can be analyzed in the similar way. Specifically, if a system has many complex eigenvalues, then the perturbed trajectory is more likely to have further deviation. The metabolic network models investigated in this work are not extremely large, and hence the author could analyze its spectrum of the Jacobian matrix at the steady state. Since the steady state is stable, I expect the spectrum located in the left half of the complex plane. If the spectrum spread out away from the real axis, we expect to see more spiral trajectories under perturbation. I think the spectrum analysis will provide a complementary view with respect to analysis on χ.  The authors' major findings, about the network sparsity and cofactors, can also be investigated under the framework of the spectrum analysis.  

Of course, when the nonlinear system is perturbed far away from the fixed point, there are other geometrical properties of the vector field that can cause the response coefficient χ to be greater than 1. This could also be investigated in the future by testing the behavior of small and large perturbations and observing if the systems have signatures of nonlinearity.  

Since all perturbed states return to the steady state, the eigenvalues of the Jacobi matrix accompanying the linearized system around the steady state are in the left half complex plane (negative real value). Also, some eigenvalues have non-zero imaginary parts.    

The reason we emphasize the "nonlinear regime" is that the linearization is no longer valid in this regime, i.e. the metabolite concentrations can be negative when we calculate the linearized system. Certainly, there are complex eigenvalues in the Jacobi matrix of any model. However, we would say that there is no clear relationship between the eigenvalues and the response coefficient.      

Minor suggestions:  

Line 127: Regarding the source of perturbation, cell division also generates unequal concentration of proteins and metabolites for two daughter cells, and it is an interesting mechanism to create metabolic perturbation. 

Thank you for the insightful suggestion. We mentioned the cell division as another source of perturbation (Lines 130-131).

Line 175: I do not quite understand the statement "fixing each metabolite concentration...", since the metabolite concentration in the ODE simulation would change immediately after this fixing.  

We meant in the sentence that we fixed the concentration of the selected metabolite as the steady state concentration and set the dx/dt of that metabolite to zero. We have rewritten the sentences to avoid confusion (Lines 180-181).

Figure 2: There are a lot of inconsistencies between the three models. Could we learn which model is more reasonable, or the conclusion here is that the cellular response under perturbation is model-specific? The latter explanation may not be quite satisfactory since we expect the overall cellular property should not be sensitive to the model details. 

Ideally, the overall cellular property should be insensitive to model details. However, the reality is that the behavior of the models (e.g., steady-state properties, relaxation dynamics, etc.) depends on the specific parameter choices, including what regulation is implemented. I think this situation is part of the motivation for the ensemble modeling (by J. Liao and colleague) that has been developed.  

Detailed responsiveness would be model specific. For example, FBP has a fairly strong effect in the Boecker model, but less so in the Khodayari model, and the opposite effect in the Chassagnole model (Fig. 2). Our question was whether there are common tendencies among kinetic models that tend to show model-specific behavior.  

Reviewer 2 (Public Review):

(1) In the study on determining key metabolites affecting responses to perturbations (starting from line 171), the authors fix the values of individual concentrations to their steady-state values and observe the responses. Such a procedure adds artificial constraints to the network because, in the natural responses of cells (and models) to perturbations, it is highly unlikely that metabolites will not evolve in time. By fixing the values of specific metabolites, the authors prohibit the metabolic network from evolving in the most optimal way to compensate for the perturbation. Instead of this procedure, have the authors considered for this task applying techniques from variance-based sensitivity analysis (Sobol, global sensitivity analysis), where they can calculate the first-order sensitivity index and total effect index? Using this technique, the authors would be able to determine the key metabolites while allowing for metabolic responses to perturbations without unnatural constraints. 

Thank you for the useful suggestion for studying the roles of each metabolite for responsiveness. We have computed the total sensitivity index (Homma and Salteli, 1996) for each metabolite of each model (Fig.S5). The total sensitivity indices of ATP are high-ranked in Khodayari- and Chassagnole model, while it is middle-ranked in the Boecker model. We believe that the importance of the adenyl cofactors is highlighted also in terms of the Sobol’ sensitivity analysis (the figure is referred in Lines 193-195). 

We have encountered a minor difficulty for computing the sensitivity index. For the computation of the sensitivity index, we need to carry out the following Monte Carlo integral, 

where the superscript (m) is the sample number index. The subscript i represents the ith element of the vector x, and ~i represents the vector x except for the ith element. The tilde stands for resampling.  

There are several conserved quantities in each model. For independent resampling, we need to deal with the conserved quantities. For the Boecker and Chassagnole models, we picked a single metabolite from each conservation law and solved its concentration algebraically to make the metabolite concentration the dependent variable. Then, we can resample the metabolite concentration of one metabolite without changing the concentrations of other metabolites, which are independent variables.  

However, in the Khodayari model, it was difficult to solve the dependent variables because the model has about 800 variables. Therefore, we gave up the computations of the sensitivity indices of the metabolites whose concentration is part of any conserved quantities, namely NAD, NADH, NADP, NADPH, Q8, and Q8H2.

(2) To follow up on the previous remark, the authors state that the metabolites that augment the response coefficient when their concentration is fixed tend to be allosteric regulators. The authors should report which allosteric regulations are implemented in each of the models so that one can compare against Figure 2. Again, the effect of allosteric regulation by a specific metabolite that is quantified the way the authors did is biased by fixing the concentration value - it is true that negative feedback is broken when the metabolite concentration is fixed, however, in the rate law, there is still the fixed inhibition term with its value corresponding to the inhibition at the steady state. To see the effect of allosteric regulation by a metabolite, one can change the inhibition constants instead of constraining the responses with fixed concentrations.  

We have listed the substrate-level regulations (Table S1-3). Also, we re-ran the simulation with reduced the effect of the substrate-level regulations for the reactions that are suspected to influence the change of the response coefficient. Instead of fixing the concentrations (Fig. S6). 

The impact of substrate-level regulations is discussed in Lines 203-212.   

We replaced "allosteric regulation" with "substrate-level regulation" because we noticed that some regulations are not necessarily allosteric.

(3) Given the role of ATP in metabolic processes, the authors' finding of the sensitivity of the three networks' responses to perturbations in the AXP concentrations seems reasonable. However, drawing such firm conclusions from only three models, with each of them built around one steady state and having one kinetic parameter set despite that they were built for different physiologies, raises some questions. It is well-known in studies related to basins of attraction of the steady states that the nonlinear responses also depend on the actual steady states, the values of kinetic parameters, and implemented kinetic rate law, i.e., not only on the topology of the underlying systems. In the population of only three models, we cannot exclude the possibility of overlaps and strong similarities in the values of kinetic parameters, steady states, and enzyme saturations that all affect and might bias the observed responses. Ideally, to eliminate the possibility of such biases, one should simulate responses of a large population of models for multiple physiologies (and the corresponding steady states) and multiple parameter sets per physiology. This can be a difficult task, but having more kinetic models in this work would go a long way toward more convincing results. Recently, E. coli nonlinear kinetic models from several groups appeared that might help in this task, e.g., Haiman et al., PLoS Comput Biol, 17(1): e1008208, (2021), Choudhury et al., Nat Mach Intell, 4, 710-719, (2022); Hu et al., Metab Eng, 82, 123-133 (2024), Narayanan et al., Nat Commun, 15:723, (2024). 

We have computed the responsiveness of 215 models generated by the MASSpy package (Haiman et al, 2021). Several model realizations showed a strong responsiveness, i.e. a broader distribution of the response coefficient (Fig.S8), and mentioned in Lines 339-341.

We would like to mention that the three models studied in the present manuscript have limited overlap in terms of kinetic rate law and, accordingly, parameter values. In the Khodayari model, all reactions are bi-uni or uni-uni reactions implemented by mass-action kinetics, while the Boecker and Chassagnole models use the generalized Michaelis-Menten type rate laws. Also, the relationship between the response coefficients of the original model and the linearized model highlights the differences between the models (Fig. S1). If the models were somewhat effectively similar, the scatter plots of the response coefficient of the original- and linearized model should look similar among the three models. However, the three panels show completely different trends. Thus, the three models have less similarity even when they are linearized around the steady states. 

(4) Can the authors share their insights on what could be the underlying reasons for the bimodal distribution in Figure 1E? Even after adding random reactions, the distribution still has two modes - why is that?  

We have not yet resolved why only the Khodayari model shows the bimodal distribution of the response coefficient. However, by examining the time courses, the dynamics of the Khodayari model look like those of the excitable systems. This feature may contribute to the bimodal distribution of the response coefficient. In the future, we would like to show whether the system is indeed the excitable system and whcih reactions contribute to such dynamics.

(5) Considering the effects of the sparsity of the networks on the perturbation responses (from line 223 onwards), when we compare the three analyzed models, it is clear that the Khodayari et al. model is a superset of the other two models. Therefore, this model can be considered as, e.g., Chassagnole model with Nadd reactions (though not randomly added). Based on Figures 1b and S2, one can observe that the responses of the Khodayari models have stronger responses, which is exactly opposite to the authors' conclusion that adding the reactions weakens the responses.

The authors should comment on this.  

The sparsity of the network is defined by the ratio of the number of metabolites to the number of reactions. Note that the Khodayari model is a superset of the Boecker and Chassagnole models in terms of the number of reactions, but also in terms of the number of metabolites (Boecker does not have the pentose phosphate pathway, Chassagnole does not have the TCA cycle, and neither has oxyative phosphorylation). Thus, even if we manually add reactions to the Boecker model, for example, we cannot obtain a network that is equivalent to the Khodayari model.  We added one sentence to clarify the point (Lines 254-255).

Recommendations for the authors: 

(1) Some typos: Line 57, remove ?; Line 134, correct "relaxation". 

Thank you for pointing out. We fixed the typos.

(2) Lines 510-515, please rewrite/clarify, it is confusing what are you doing. 

We rewrote the sentences (Lines 529-532). We are sorry for the confusion.

(3) Line 522, where are the expressions above Leq and K*? 

Leq appears in the original paper of the Boecker model, but we decided not to use Leq. We apologize for not removing Leq from the present manuscript. The * in K* is the wildcard for representing the subscripts. We added a description for the role of “*”. 

(4) Lines 525-530, based on the wording, it seems like you test first for 128 initial concentrations if the models converge back to the steady state and then you generate another set of 128 initial concentrations - is this what you are doing, or you simply use the 128 initial concentrations that have passed the test? 

We apologize for the confusion. We did the first thing. We have rewritten the sentence to make it clearer. 

(5) Figure 3, caption, by "broken line," did the authors mean "dashed line"? 

We meant dashed line. We changed “broken line” to “dashed line”.

Why was marijuana so popular and mainstream in the past???

Diaspora: the jews living outside Israel (https://www.merriam-webster.com/dictionary/diaspora)

Interesting musical roots for Reggae... Wonder if this is still present?

Mystical roots.

(Note, I give this the fiction tag because I might want to look into this mystical religion for fiction writing as inspiration)

Logical that marijuana (a drug) is correlated with the mystical concept of communicating with diseased spirits for marijuana makes you hallucinate (or perhaps it's demonic in nature?)

Main early pioneers: - Toots and the Maytals (band) - Wailers (band)

Notable members of these bands: Toots and Maytals - Paul Douglas - Radcliffe "Dougie" Bryan - Jackie Jackson - Carl Harvey - Marie "Twiggi" Gitten - Stephen Stewart - Charles Farquarson - Frederick "Toots" Hibbert - Henry "Raleigh" Gordon - Nathaniel "Jerry" Matthias - Hux Brown - Harold Butler - Michelle Eugene - Winston Wright - Winston Grennan - Andy Bassford - Leba Hibbert - Thomas Copied from: https://en.wikipedia.org/wiki/Toots_and_the_Maytals

Wailers: * Aston Barrett Jr. * Owen "Dreadie" Reid * Josh David Barrett * Glen DaCosta * Andres Lopez * Junior Jazz * Aston "Familyman" Barrett * Donald Kinsey * Junior Marvin * Carlton Barrett * Alvin "Seeco" Patterson * Tyrone Downie * Earl "Wire" Lindo * Al Anderson * Gary "Nesta" Pine * Joe Yamanaka * Elan Atias * Anthony Watson * Chico Chin * Everald Gayle * Irvin "Carrot" Jarrett * Brady Walters * Basil Creary * Keith Sterling * Kevin "Yvad" Davy * Ras Mel Glover * "Drummie Zeb" Williams * Audley Chisholm * Koolant Brown * Dwayne Anglin * Ceegee Victory * Javaughn Bond * Shema McGregor Copied from: https://en.wikipedia.org/wiki/The_Wailers_Band

Other notable pioneers: - Bob Marley

Reggae is known to have depth and meaning to its tracks due to tackling of social and economic issue as well as injustice in general.

Reggae came to be during a time of subjugation to Britain?

Emerged in Jamaica

Mainstream perception of Reggae Music

eLife Assessment

This fundamental study generated a single cell atlas of mouse periosteal cells under both steady-state and fracture healing conditions to address the knowledge gap regarding cellular composition of the periosteum and their responses to injury. Based on convincing transcriptome analyses and experimental validation, the authors identified the injury induced fibrogenic cell (IIFC) as a characteristic cell type appearing in the bone regeneration process and proposed that the IIFC is a progenitor undergoing osteochondrogenic differentiation. This study will provide a significant publicly accessible dataset to reexamine the expression of the reported periosteal stem and progenitor cell markers.

Reviewer #1 (Public review):

This study delineates an important set of uninjured and injured periosteal snRNAseq data that provides an overview of periosteal cell responses to fracture healing. The authors also took additional steps to validate some of the findings using immunohistochemistry and transplantation assays. This study will provide a valuable publicly accessible dataset to reexamine the expression of the reported periosteal stem and progenitor cell markers.

Strengths:

(1) This is the first single-nuclei atlas of periosteal cells that are obtained without enzymatic cell dissociation or targeted cell purification by FACS. This integrated snRNAseq dataset will provide additional opportunities for the community to revisit the expression of many periosteal cell markers that have been reported to date.<br /> (2) The authors delved further into the dataset using cutting-edge algorithms, including CytoTrace, SCENIC, Monocle, STRING and CellChat, to define potential roles of identified cell populations in the context of fracture healing. These additional computation analyses generate many new hypotheses regarding periosteal cell reactions.<br /> (3) The authors also sought to validate some of the computational findings using immunohistochemistry and transplantation assays to support the conclusion.

Weaknesses:

(1) The current snRNAseq datasets contain only a small number of nuclei (1,189 nuclei at day 0, 6,213 nuclei day 0-7 combined). It is possible that these datasets are underpowered to discern subtle biological changes in skeletal stem/progenitor cell populations during fracture healing.<br /> (2) POSTN is expressed in the cambium layer of the periosteum without fracture. The current data do not exclude the possibility that these pre-existing POSTN+ cells are the main responder of fracture healing.

Reviewer #2 (Public review):

Summary:

The authors described cell type mapping was conducted for both WT and fracture types. Through this, unique cell populations specific to fracture conditions were identified. To determine these, the most undifferentiated cells were initially targeted using stemness-related markers and CytoTrace scoring. This led to the identification of SSPC differentiating into fibroblasts. It was observed that the fibroblast cell type significantly increased under fracture conditions, followed by subsequent increases in chondrocytes and osteoblasts.

Strengths:

This study presented the injury-induced fibrogenic cell (IIFC) as a characteristic cell type appearing in the bone regeneration process and proposed that the IIFC is a progenitor undergoing osteochondrogenic differentiation.

Comments on revised version:

The authors have thoroughly addressed the reviewer's comments and have conducted additional experiments.

she would not be able to see this

do they though?

somewhere outside the shop, a person screamed.

why is she with him?

'the shop was eerily quiet except for its ambient music'

syntax is off here - 'the great cruise ships, that had once polluted the city's harbours, docked elsewhere'

this is very interesting but too expositional here i think

you use this tense a lot and you don't need to. just say 'the tram arrived'

'with her index finger, she slowly traced the outline of her features'

this seems inconsistent with her character

inconsistent voice here

this is funny but it takes away from the tension in the scene

how would she know this?

you could make this sentence sharper to mirror the feeling of the paper cut

this is a great way of showing us her internal monologue without taking us out of the usual style

this is funny but keep in mind who is narrating

where has this come from?

'she tried, unsuccessfully, to cut the image of her mother's new face out of her mind. taking a deep breath and adopting an expression of composure, she opened the door.'

too long

i see what you're trying to do but this doesn't give us a deeper image as much as just hammering home the same thing over and over

one or the other, you don't need both

too long

Jamaica became independent in 1962

eLife Assessment

This manuscript describes an important study of a new lipid-mediated regulation mechanism of adenylyl cyclases. The biochemical evidence provided is convincing and will trigger more research in this mechanism. This manuscript will be of interest to all scientists working on lipid regulation and adenylyl cyclases.

Reviewer #1 (Public review):

Summary:

The authors show that the Gαs-stimulated activity of human membrane adenylyl cyclases (mAC) can be enhanced or inhibited by certain unsaturated fatty acids (FA) in an isoform-specific fashion. Thus, with IC50s in the 10-20 micromolar range, oleic acid affects 3-fold stimulation of membrane-preparations of mAC isoform 3 (mAC3) but it does not act on mAC5. Enhanced Gαs-stimulated activities of isoforms 2, 7, and 9, while mAC1 was slightly attenuated, but isoforms 4, 5, 6, and 8 were unaffected. Certain other unsaturated octadecanoic FAs act similarly. FA effects were not observed in AC catalytic domain constructs in which TM domains are not present. Oleic acid also enhances the AC activity of isoproterenol-stimulated HEK293 cells stably transfected with mAC3, although with lower efficacy but much higher potency. Gαs-stimulated mAC1 and 4 cyclase activity were significantly attenuated in the 20-40 micromolar by arachidonic acid, with similar effects in transfected HEK cells, again with higher potency but lower efficacy. While activity mAC5 was not affected by unsaturated FAs, neutral anandamide attenuated Gαs-stimulation of mAC5 and 6 by about 50%. In HEK cells, inhibition by anandamide is low in potency and efficacy. To demonstrate isoform specificity, the authors were able to show that membrane preparations of a domain-swapped AC bearing the catalytic domains of mAC3 and the TM regions of mAC5 are unaffected by oleic acid but inhibited by anandamide. To verify in vivo activity, in mouse brain cortical membranes 20 μM oleic acid enhanced Gαs-stimulated cAMP formation 1.5-fold with an EC50 in the low micromolar range.

Strengths:

(1) A convincing demonstration that certain unsaturated FAs are capable of regulating membrane adenylyl cyclases in an isoform-specific manner, and the demonstration that these act at the AC transmembrane domains.

(2) Confirmation of activity in HEK293 cell models and towards endogenous AC activity in mouse cortical membranes.

(3) Opens up a new direction of research to investigate the physiological significance of FA regulation of mACs and investigate their mechanisms as tonic or regulated enhancers or inhibitors of catalytic activity.

(4) Suggests a novel scheme for the classification of mAC isoforms.

Comments on revised version:

The issues I raised have largely been addressed. A minor concern relates to the legend for Figure 2C, where, according to the author's rebuttal, the vertical axis is "The ratio would be (Gsα + oleic acid stimulation) / (Gsα stimulation)" Otherwise, my general evaluation of the importance of the manuscript stands as stated in my initial review, namely, that the manuscript presents data and results that add a new dimension to existing paradigms for AC regulation, and will prompt future research into the role of physiological lipids in isoform-specific activation or inhibition of AC in tissues.

Reviewer #3 (Public review):

Summary:

Landau et al. have submitted a manuscript describing for the first time that mammalian adenylyl cyclases can serve as membrane receptors. They have also identified the respective endogenouse ligands which act via AC membrane linkers to modify and control Gs-stimulated AC activity either towards enhancement or inhibition of ACs which is family and ligand-specific. Overall, they have used classical assays such as adenylyl cyclase and cAMP accumulation assays combined with molecular cloning and mutagenesis to provide exceptionally strong biochemical evidence for the mechanism of the involved pathway regulation.

Strengths:

The authors have gone the whole long classical way from having a hypothesis that ACs could be receptors to a series of MS studies aimed at ligand indentification, to functional studies of how these candidate substances affect the activity of various AC families in intact cells. They have used a large array of techniques with a paper having clear conceptual story and several strong lines of evidence.

Comments on revised version:

In general, the authors have addressed my comments satisfactorily apart from the suggestion to use a lower ISO concentration in their assay or at least to discuss this issue, cite relevant literature etc. Pending this small amendment I would to fine to proceed.

Author response:

The following is the authors’ response to the original reviews.

Public Reviews:

Reviewer #1 (Public review):

Summary:

The authors show that the Gαs-stimulated activity of human membrane adenylyl cyclases (mAC) can be enhanced or inhibited by certain unsaturated fatty acids (FA) in an isoform-specific fashion. Thus, with IC50s in the 10-20 micromolar range, oleic acid affects 3-fold stimulation of membrane-preparations of mAC isoform 3 (mAC3) but it does not act on mAC5. Enhanced Gαs-stimulated activities of isoforms 2, 7, and 9, while mAC1 was slightly attenuated, but isoforms 4, 5, 6, and 8 were unaffected. Certain other unsaturated octadecanoic FAs act similarly. FA effects were not observed in AC catalytic domain constructs in which TM domains are not present. Oleic acid also enhances the AC activity of isoproterenol-stimulated HEK293 cells stably transfected with mAC3, although with lower efficacy but much higher potency. Gαs-stimulated mAC1 and 4 cyclase activity were significantly attenuated in the 20-40 micromolar by arachidonic acid, with similar effects in transfected HEK cells, again with higher potency but lower efficacy. While activity mAC5 was not affected by unsaturated FAs, neutral anandamide attenuated Gαs-stimulation of mAC5 and 6 by about 50%. In HEK cells, inhibition by anandamide is low in potency and efficacy. To demonstrate isoform specificity, the authors were able to show that membrane preparations of a domain-swapped AC bearing the catalytic domains of mAC3 and the TM regions of mAC5 are unaffected by oleic acid but inhibited by anandamide. To verify in vivo activity, in mouse brain cortical membranes 20 μM oleic acid enhanced Gαs-stimulated cAMP formation 1.5-fold with an EC50 in the low micromolar range.

Strengths:

(1) A convincing demonstration that certain unsaturated FAs are capable of regulating membrane adenylyl cyclases in an isoform-specific manner, and the demonstration that these act at the AC transmembrane domains.

(2) Confirmation of activity in HEK293 cell models and towards endogenous AC activity in mouse cortical membranes.

(3) Opens up a new direction of research to investigate the physiological significance of FA regulation of mACs and investigate their mechanisms as tonic or regulated enhancers or inhibitors of catalytic activity.

(4) Suggests a novel scheme for the classification of mAC isoforms.

Weaknesses:

(1) Important methodological details regarding the treatment of mAC membrane preps with fatty acids are missing.

We will address this issue in more detail.

(2) It is not evident that fatty acid regulators can be considered as "signaling molecules" since it is not clear (at least to this reviewer) how concentrations of free fatty acids in plasma or endocytic membranes are hormonally or otherwise regulated.

Although this question is not the subject of this ms., we will address this question in more detail in the discussion of the revision.

Reviewer #2 (Public review):

Summary:

The authors extend their earlier findings with bacterial adenylyl cyclases to mammalian enzymes. They show that certain aliphatic lipids activate adenylyl cyclases in the absence of stimulatory G proteins and that lipids can modulate activation by G proteins. Adding lipids to cells expressing specific isoforms of adenylyl cyclases could regulate cAMP production, suggesting that adenylyl cyclases could serve as 'receptors'.

Strengths:

This is the first report of lipids regulating mammalian adenylyl cyclases directly. The evidence is based on biochemical assays with purified proteins, or in cells expressing specific isoforms of adenylyl cyclases.

Weaknesses:

It is not clear if the concentrations of lipids used in assays are physiologically relevant. Nor is there evidence to show that the specific lipids that activate or inhibit adenylyl cyclases are present at the concentrations required in cell membranes. Nor is there any evidence to indicate that this method of regulation is seen in cells under relevant stimuli.

Although this question is not the subject of this ms., we will address this question in more detail in the discussion of the revision.

Reviewer #3 (Public review):

Summary:

Landau et al. have submitted a manuscript describing for the first time that mammalian adenylyl cyclases can serve as membrane receptors. They have also identified the respective endogenouse ligands which act via AC membrane linkers to modify and control Gs-stimulated AC activity either towards enhancement or inhibition of ACs which is family and ligand-specific. Overall, they have used classical assays such as adenylyl cyclase and cAMP accumulation assays combined with molecular cloning and mutagenesis to provide exceptionally strong biochemical evidence for the mechanism of the involved pathway regulation.

Strengths:

The authors have gone the whole long classical way from having a hypothesis that ACs could be receptors to a series of MS studies aimed at ligand indentification, to functional studies of how these candidate substances affect the activity of various AC families in intact cells. They have used a large array of techniques with a paper having clear conceptual story and several strong lines of evidence.

Weaknesses:

(1) At the beginning of the results section, the authors say "We have expected lipids as ligands". It is not quite clear why these could not have been other substances. It is because they were expected to bind in the lipophilic membrane anchors? Various lipophilic and hydrophilic ligands are known for GPCR which also have transmembrane domains. Maybe 1-2 additional sentences could be helpful here.

Will be done as suggested.

(2) In stably transfected HEK cells expressing mAC3 or mAC5, they have used only one dose of isoproterenol (2.5 uM) for submaximal AC activation. The reference 28 provided here (PMID: 33208818) did not specifically look at Iso and endogenous beta2 adrenergic receptors expressed in HEK cells. As far as I remember from the old pharmacological literature, this concentration is indeed submaximal in receptor binding assays but regarding AC activity and cAMP generation (which happen after signal amplification with a so-called receptor reserve), lower Iso amounts would be submaximal. When we measure cAMP, these are rather 10 to 100 nM but no more than 1 uM at which concentration response dependencies usually saturate. Have the authors tried lower Iso concentrations to prestimulate intracellular cAMP formation? I am asking this because, with lower Iso prestimulation, the subsequent stimulatory effects of AC ligands could be even greater.

The best way to address this issue is to establish a concentration-response curve for Iso-stimulated cAMP formation using the permanently transfected cells. We note that in the past isoproterenol concentrations used in biochemical or electrophysiological experiments differed substantially.

(3) The authors refer to HEK cell models as "in vivo". I agree that these are intact cells and an important model to start with. It would be very nice to see the effects of the new ligands in other physiologically relevant types of cells, and how they modulate cAMP production under even more physiological conditions. Probably, this is a topic for follow-up studies.

The last sentence is correct.

Appraisal of whether the authors achieved their aims, and whether the results support their conclusions:

The authors have achieved their aims to a very high degree, their results do nicely support their conclusions. There is only one point (various classical GPCR concentrations, please see above) that would be beneficial to address.

Without any doubt, this is a groundbreaking study that will have profound implications in the field for the next years/decades. Since it is now clear that mammalian adenylyl cyclases are receptors for aliphatic fatty acids and anandamide, this will change our view on the whole signaling pathway and initiate many new studies looking at the biological function and pathophysiological implications of this mechanism. The manuscript is outstanding.

Recommendations for the authors:

Reviewer #1 (Recommendations for the authors):

It is not clear from the methods section how free FAs were applied to membrane preparations or HEK293 cells. Were FAs solubilized in organic solvents, or introduced as micelles?

The requested info is inserted into the M&M section

Could the authors comment on what is known about the concentration of oleic acid and other non-saturated fatty acids in plasma membranes relative to those required to produce allosteric effects on cyclase activity?

This info is now included in the last paragraph of the discussion.

It would be worthwhile to test the effect of FAs on basal (not Gαs-stimulated) activity of mACs.

This has been carried with mAC isoforms 2, 3, 7, and 9 in which oleic acid enhances Gsα-stimulated activity. Due to the low levels of basal activities interpretable data were not obtained.

Do triglycerides esterified with oleic acid stimulate mAC3 and other sensitive isoforms?

Experiments were done with triolein and 2-oleoyl-glycerol (the answer is no). The data are presented in Fig. 3 and in the appendix Fig.’s 8, 9, 14; structural formulas in appendix 2 Fig. 4 were updated.

Does the quantity plotted on the vertical axis of Figure 1, right panel represent "Fractional Stimulation by Oleic acid" rather than simply "Fold Stimulation"? Clearly, as shown in the two left-most panels, Gαs stimulates both mAC and mAC5. Rather it seems that the ratio (oleic acid stimulation) / (Gαs stimulation) remains constant. This observation supports the statement in the discussion that "We suppose that in mAC3 the equilibrium of two differing ground states favors a Gαs-unresponsive state and the effector oleic acid concentration-dependently shifts this equilibrium to a Gαs-responsive state". It could also be said that the effect of oleic acid is additive, and in constant proportion to that of Gαs.

This comment certainly is related to Fig. 2:

The ratio would be (Gsα + oleic acid stimulation) / (Gsα-stimulation), i.e., fractional stimulation by addition of oleic acid is identical to fold stimulation.

We have amended the legend to fig. 2C for clarification.

The last sentence is wrong because oleic acid alone does not stimulate.

It is stated on page 3, 2nd to last line that "The action of oleic acid on mAC3 was instantaneous...". Since the earliest time point is taken at 5 minutes, the claim that the action of the lipid is instantaneous cannot be made. Information about kinetics would be useful to have, since it is possible that the lipid must be released from a micelle and be incorporated into the AC membrane fraction before it is active.

The first point is 3 min.

We deleted the word “instantaneous” and added the correlation coefficients for both conditions in the legend to appendix 2; fig. 1 for clarification.

The data spread in Figure 4 and other figures showing similar data is significant, to the extent that the computed value for EC50 may not be of high precision. Authors should cite the correlation coefficient for the overall fit and uncertainty for the EC50 value (in addition to significances by t-test of individual data points).

This will not add valuable information. Pearsons correlation coefficients are only for linear relationships.

(cf. N.N. Kachouie, W. Deebani (2020) Association Factor for Identifying Linear and Nonlinear Correlations in Noisy Conditions. Entropy 22:440)

The "switch" between relatively low potency and high efficacy in membrane preps to high potency and low efficacy in cells is remarkable. Could this have a methodological basis or is it reflective of the mechanism by which FAs access mACs in membrane preps vs. cell membranes, or perhaps some biochemical transformation of the lipid in cells?

Honestly, we do not know.

The authors should note that there is some precedence for this work:

J Nakamura , N Okamura, S Usuki, S Bannai, Inhibition of adenylyl cyclase activity in brain membrane fractions by arachidonic acid and related unsaturated fatty acids. Arch Biochem Biophys. 2001 May 1;389(1):68-76. doi: 10.1006/abbi.2001.2315.

The effects of FA deficiencies on AC and related activities have been noted:

Alam SQ, Mannino SJ, Alam BS, McDonough K Effect of essential fatty acid deficiency on forskolin binding sites, adenylate cyclase, and cyclic AMP-dependent protein kinase activity, the levels of G proteins and ventricular function in rat heart. J Mol Cell Cardiol. 1995 Aug;27(8):1593-604. doi: 10.1016/s0022-2828(95)90491-3. PMID: 8523422

The latter publications are supportive of, and provide context to, the author's findings.

Both references are mentioned and cited.

Minor points:

The significance of the coloring scheme in Figure 5C bar graph should be stated in the legend.

Done.

In the introduction, it is stated that "The protein displayed two similar catalytic domains (C1 and C2) and two dissimilar hexahelical membrane anchors (TM1 and TM2)". In both cases, the respective domains can be said to be similar in overall fold, but - certainly in the case of the catalytic domains - different in amino acid sequence in functionally important regions of the domain.

Done: Changed wording.

The statement in the introduction that "The domain architecture, TM1-C1-TM2-C2, clearly indicated a pseudoheterodimeric protein composed of two concatenated bacterial precursor proteins" The authors refer to the fact that mammalian enzymes are pseudo heterodimers whereas bacterial type III cyclases are dimers of identical subunits.

Done.

Reviewer #2 (Recommendations for the authors):

The title need not state that a 'new class of receptors' has been identified. There is no direct evidence that the lipids bind to the enzymes, and the affinities can only be surmised from the EC50 graphs. To call a protein a receptor requires evidence to show that the binding is specific by showing that binding can be inhibited by a large excess of 'unlabelled' ligand. This could have been done by procuring labelled lipids for experimental verification.

As is well known, lipids easily bind to proteins. In this study no purified proteins were used. Therefore, binding assays most likely would result in unreliable data.

The paper would have benefitted from showing sequence alignments in the TM domains of the ACs discussed in the paper. Further, a phylogenetic tree of mammalian ACs would also reveal which enzymes from other species may be regulated similarly to those described in the paper. This would be important for researchers who use other model organisms to study cAMP signalling.

Such data are in multiple papers accessible in the literature. Where deemed appropriate we inserted references.

Figures 1A and 1B show data from only two experiments. A third experiment would have been useful in order to show the statistical significance of the data.

At this stage more experiments would not have affected further experimental plans.

Statements made in the text (for example, the last paragraph on page 6) state only the mean value and not the SDs. This would have been important to include even if the data is shown in the appendix. The same is true in the Legend of Figure 2. Why have the authors decided to use SEM and not SDs?

The reason is specified in M&M.

Concentrations of lipids used in biochemical assays are in the micromolar range. This suggests that we have moderate affinity binding, more in the range of an enzyme for a substrate rather than a receptor-ligand interaction.

We happen to disagree. Clearly, the differential activities, enhancing or attenuating Gsα-stimulated mAC activities is most plausibly explained by mAC receptor properties. mACs have enzyme activities using fatty acids as substrates.

The authors add lipids to cells and show changes in cAMP levels in their presence and absence. They also discuss how these extracellular lipids could be produced. Do you think this is necessary in vivo, though? Could the lipids present in membranes naturally act as regulators? Do specific lipid concentrations differ in different cell types, suggesting tissue-specific regulation of these mammalian Acs?

These are things that could be discussed in the manuscript.

The last paragraph of the discussion deals with these questions.

This guy learns music creation efficiently, by learning the theory first and really analyzing worked examples (the masters). Positively surprises me. I rarely come across a non-learning expert who intuitively uses proper processes for skill acquisition.

Levels of understanding genres: - 0) No understanding Like the song, never heard anything like it before, but no idea about anything. - 1) Basic Understanding Knowing a bit about the name of the genre and subgenres, but you can be wrong. - 2) Immersion Really dive into subgenres and flavors of the main genre... Also a bit of history about the genre. Research. - 3) Structure Breaking down the structure of the tracks in the genre. For example through DAW. Basically first-principles thinking.

To level 1: Song Analyzer tools (for example musicstax or AI). The author recommends everynoise.com too to gain a basic understanding of genres.

To level 2: Find similar songs and artists for your playlists with that genre. Perhaps playlists. Important to understand the origin of the genre.

Author response:

The following is the authors’ response to the current reviews.

We thank you for sending our manuscript for the second round of review.  We are encouraged by the comments from reviewer #2 that our supplementary work on naïve T cells and antibody blockade work satisfied their previous concerns and is important for our work.

The Editors raised concerns that we have shared preliminary data on Nrn1 and AMPAR double knockout mice.  We apologize for our enthusiasm for these studies.  Because of the publication model by eLife, we shared that data not because we needed to persuade the reviewer for publication purposes but rather to agree with the reviewer that the molecular target of Nrn1 is important, and we are progressing in understanding this subject.

The following is the authors’ response to the original reviews.

To Reviewer #1:

Thank you for your thorough review and comments on our work, which you described as “the role of neuritin in T cell biology studied here is new and interesting.”.  We have summarized your comments into two categories: biology and investigation approach, experimental rigor, and data presentation.

Biology and Investigation approach comments:

(1) Questions regarding the T cell anergy model:

Major point “(4) Figure 1E-H. The authors assume that this immunization protocol induces anergic cells, but they provide no experimental evidence for this. It would be useful to show that T cells are indeed anergic in this model, especially those that are OVA-specific. The lack of IL-2 production by Cltr cells could be explained by the presence of fewer OVA-specific cells, rather than by an anergic status.”

T cell anergy is a well-established concept first described by Schwartz’s group. It refers to the hyporesponsive T cell functional state in antigen-experienced CD4 T cells (Chappert and Schwartz, 2010; Fathman and Lineberry, 2007; Jenkins and Schwartz, 1987; Quill and Schwartz, 1987).  Anergic T cells are characterized by their inability to expand and to produce IL2 upon subsequent antigen re-challenge. In this paper, we have borrowed the existing in vivo T cell anergy induction model used by Mueller’s group for T cell anergy induction (Vanasek et al., 2006).  Specifically, Thy1.1+ Ctrl or Nrn1-/- TCR transgenic OTII cells were co-transferred with the congenically marked Thy1.2+ WT polyclonal Treg cells into TCR-/- mice.  After anergy induction, the congenically marked TCR transgenic T cells were recovered by sorting based on Thy1.1+ congenic marker, and subsequently re-stimulation ex vivo with OVA323-339 peptide. We evaluated the T cell anergic state based on OTII cell expansion in vivo and IL2 production upon OVA323-339 restimulation ex vivo.  

“The authors assume that this immunization protocol induces anergic cells, but they provide no experimental evidence for this.”

Because the anergy model by Mueller's group is well established (Vanasek et al., 2006), we did not feel that additional effort was required to validate this model as the reviewer suggested. Moreover, the limited IL2 production among the control cells upon restimulation confirms the validity of this model.

“The lack of IL-2 production by Cltr cells could be explained by the presence of fewer OVAspecific cells, rather than by an anergic status”.

Cells from Ctrl and Nrn1-/- mice on a homogeneous TCR transgenic (OTII) background were used in these experiments. The possibility that substantial variability of TCR expression or different expression levels of the transgenic TCR could have impacted IL2 production rather than anergy induction is unlikely.

Overall, we used this in vivo anergy model to evaluate the Nrn1-/- T cell functional state in comparison to Ctrl cells under the anergy induction condition following the evaluation of Nrn1 expression, particularly in anergic T cells.  Through studies using this anergy model, we observed a significant change in Treg induction among OTII cells. We decided to pursue the role of Nrn1 in Treg cell development and function rather than the biology of T cell anergy as evidenced by subsequent experiments.

Minor points “(6) On which markers are anergic cells sorted for RNAseq analysis?”

Cells were sorted out based on their congenic marker marking Ctrl or Nrn1-/- OTII cells transferred into the host mice.  We did not specifically isolate anergic cells for sequencing.

(2) Question regarding the validity of iTreg differentiation model.

Major point: “(5) Figure 2A-C and Figure 3. The use of iTregs to try to understand what is happening in vivo is problematic. iTregs are cells that have probably no equivalent in vivo, and so may have no physiological relevance. In any case, they are different from pTreg cells generated in vivo. Working with pTreg may be challenging, that is why I would suggest generating data with purified nTreg. Moreover, it was shown in the article of Gonzalez-Figueroa 2021 that Nrn1-/- nTreg retained a normal suppressive function, which would not be what is concluded by the authors of this manuscript. Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”.

We thank Reviewer #1 for their feedback. While it is true that iTregs made in vitro and in vivo generated pTregs display several distinctions (e. g., differences in Foxp3 expression stability, for example), we strongly disagree with this statement by Revieweer#1 “The use of iTregs to try to understand what is happening in vivo is problematic. iTregs are cells that have probably no equivalent in vivo, and so may have no physiological relevance.”  The induced Treg cell (iTreg) model was established over 20 years ago (Chen et al., 2003; Zheng et al., 2002), and the model is widely adopted with over 2000 citations. Further, it has been instrumental in understanding different aspects of regulatory T cell biology (Hurrell et al., 2022; John et al., 2022; Schmitt and Williams, 2013; Sugiura et al., 2022).   

Because we have observed reduced pTreg generation in vivo, we choose to use the in vitro iTreg model system to understand the mechanistic changes involved in Treg cell differentiation and function, specifically, neuritin’s role in this process. We have made no claim that iTreg cell biology is identical to pTreg generated in vivo or nTreg cells. However, the iTreg culture system has proved to be a good in vitro system for deciphering molecular events involved in complex processes. As such, it remains a commonly used approach by many research groups in the Treg cell field (Hurrell et al., 2022; John et al., 2022; Sugiura et al., 2022). Moreover, applying the iTreg in vitro culture system has been instrumental in helping us identify the cell electrical state change in Nrn1-/- CD4 cells and revealed the biological link between Nrn1 and the ionotropic AMPA receptor (AMPAR), which we will discuss in the subsequent discussion. It is technically challenging to use nTreg cells for T cell electrical state studies due to their heterogeneous nature from development in an in vivo environment and the effect of manipulation during the nTreg cell isolation process, which can both affect the T cell electrical state.   

“Moreover, it was shown in the article of Gonzalez-Figueroa 2021 that Nrn1-/- nTreg retained a normal suppressive function, which would not be what is concluded by the authors of this manuscript.” 

We have also carried out nTreg studies in vitro in addition to iTreg cells. Similar to Gonzalez-Figueroa et al.'s findings, we did not observe differences in suppression function between Nrn1-/- and WT nTreg using the in vitro suppression assay. However, Nrn1-/- nTreg cells revealed reduced suppression function in vivo (Fig. 2D-L). In fact, Gonzalez-Figueroa et al. observed reduced plasma cell formation after OVA immunization in Treg-specific Nrn1-/- mice, implicating reduced suppression from Nrn1-/- follicular regulatory T (Tfr) cells. Thus, our observation of the reduced suppression function of Nrn1-/- nTreg toward effector T cell expansion, as presented in Fig. 2D-L, does not contradict the results from Gonzalez-Figueroa et al. Rather, the conclusions of these two studies agree that Nrn1 can play important roles in immune suppression observable in vivo that are not captured readily by the in vitro suppression assay.

“Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”

We have stated in the manuscript on page 7 line 208 that “Similar proportions of Foxp3+ cells were observed in Nrn1-/- and Ctrl cells under the iTreg culture condition, suggesting that Nrn1 deficiency does not significantly impact Foxp3+ cell differentiation”. In the revised manuscript, we will include the data on the proportion of Foxp3+ cells before iTreg restimulation.

(3) Confirmation of transcriptomic data regarding amino acids or electrolytes transport change

Minor point“(3) Would not it be possible to perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane? This would be a more interesting demonstration than transcriptomic data.”

We appreciate Review# 1’s suggestion regarding “perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane”.  We have indeed already performed such experiments corroborating the transcriptomics data on differential amino acid and nutrient transporter expression. Specifically, we loaded either iTreg or Th0 cells with membrane potential (MP) dye and measured MP level change after adding the complete set of amino acids (complete AA).  Upon entry, the charge carried by AAs may transiently affect cell membrane potential. Different AA transporter expression patterns may show different MP change patterns upon AA entry, as we showed in Author response image 1. We observed reduced MP change in Nrn1-/- iTreg compared to the Ctrl, whereas in the context of Th0 cells, Nrn1-/- showed enhanced MP change than the Ctrl. We can certainly include these data in the revised manuscript.

Author response image 1.

Membrane potential change induced by amino acids entry. a. Nrn1-/- or WT iTreg cells loaded with MP dye and MP change was measured upon the addition of a complete set of AAs. b. Nrn1-/- or WT Th0 cells loaded with MP dye and MP change was measured upon the addition of a complete set of AAs.

(4) EAE experiment data assessment

Minor point ”(5) Figure 5F. How are cells re-stimulated? If polyclonal stimulation is used, the experiment is not interesting because the analysis is done with lymph node cells. This analysis should either be performed with cells from the CNS or with MOG restimulation with lymph node cells.”

In the EAE study, the Nrn1-/- mice exhibit similar disease onset but a protracted non-resolving disease phenotype compared to the WT control mice.  Several reasons may contribute to this phenotype: 1. Enhanced T effector cell infiltration/persistence in the central nervous system (CNS); 2. Reduced Treg cell-mediated suppression to the T effector cells in the CNS; 3. Protracted non-resolving inflammation at the immunization site has the potential to continue sending T effector cells into CNS, contributing to persistent inflammation. Based on this reasoning, we examined the infiltrating T effector cell number and Treg cell proportion in the CNS.  We also restimulated cells from draining lymph nodes close to the inflammation site, looking for evidence of persistent inflammation.  When mice were harvested around day 16 after immunization, the inflammation at the local draining lymph node should be at the contraction stage.  We stimulated cells with PMA and ionomycin intended to observe all potential T effector cells involved in the draining lymph node rather than only MOG antigen-specific cells.  We disagree with Reviewer #1’s assumption that “This analysis should either be performed with cells from the CNS or with MOG restimulation with lymph node cells.”. We think the experimental approach we have taken has been appropriately tailored to the biological questions we intended to answer.

Experimental rigor and data presentation.

(1) data labeling and additional supporting data

Major points

(2) The authors use Nrn1+/+ and Nrn1+/- cells indiscriminately as control cells on the basis of similar biology between Nrn1+/+ and Nrn1+/- cells at homeostasis. However, it is quite possible that the Nrn1+/- cells have a phenotype in situations of in vitro activation or in vivo inflammation (cancer, EAE). It would be important to discriminate Nrn1+/- and Nrn1+/+ cells in the data or to show that both cell types have the same phenotype in these conditions too.

(3) Figure 1A-D. Since the authors are using the Nrp1 KO mice, it would be important to confirm the specificity of the anti-Nrn1 mAb by FACS. Once verified, it would be important to add FACS results with this mAb in Figures 1A-C to have single-cell and quantitative data as well.

Minor points  

(1) Line 119, 120 of the text. It is said that one of the most up-regulated genes in anergic cells is Nrn1 but the data is not shown.

(2) For all figures showing %, the titles of the Y axes are written in an odd way. For example, it is written "Foxp3% CD4". It would be more conventional and clearer to write "% Foxp3+ / CD4+" or "% Foxp3+ among CD4+".

(4) For certain staining (Figure 3E, H) it would be important to show the raw data, in addition to MFI or % values.

We can adapt the labeling and provide additional data, including Nrn1 staining on Treg cells and flow graphs for pmTOR and pS6 staining (Fig. 3H), as requested by Reviewer #1.

(2) Experimental rigor:

General comments:

“However, it is disappointing that reading this manuscript leaves an impression of incomplete work done too quickly.”

We were discouraged to receive the comment, “this manuscript leaves an impression of incomplete work done too quickly.” Our study of this novel molecule began without any existing biological tools such as antibodies, knockout mice, etc.  Over the past several years, we have established our own antibodies for Nrn1 detection, obtained and characterized Nrn1 knockout mice, and utilized multiple approaches to identify the molecular mechanism of Nrn1 function. Through the use of the in vitro iTreg system described in this manuscript, we identified the association of Nrn1 deficiency with cell electrical state change, potentially connected to AMPAR function. We have further corroborated our findings by generating Nrn1 and AMPAR T cell specific double knockout mice and confirmed that T cell specific AMPAR deletion could abrogate the phenotype caused by the Nrn1 deficiency (see Support Figure 2).  We did not include the double knockout data in the current manuscript because AMPAR function has not yet been studied thoroughly in T cell biology, and we feel this topic warrants examination in its own right.  However, the unpublished data support the finding that Nrn1 modulates the T cell electrical state and, consequently, metabolism, ultimately influencing tolerance and immunity.  In its current form, the manuscript represents the first characterization of the novel molecule Nrn1 in anergic cells, Tregs, and effector T cells. While this work has led to several exciting additional questions, we disagree that the novel characterization we have presented Is incomplete. We feel that our present data set, which squarely highlights Nrn1’s role as an important immune regulator while shedding unprecedented light on the molecular events involved, will be of considerable interest to a broad field of researchers.

“Multiple models have been used, but none has been studied thoroughly enough to provide really conclusive and unambiguous data. For example, 5 different models were used to study T cells in vivo. It would have been preferable to use fewer, but to go further in the study of mechanisms.”

We have indeed used multiple in vivo models to reveal Nrn1's function in Treg differentiation, Treg suppression function, T effector cell differentiation and function, and the overall impact on autoimmune disease. Because the impact of ion channel function is often context-dependent, we examined the biological outcome of Nrn1 deficiency in several in vivo contexts.  We would appreciate it if Reviewer#1 would provide a specific example, given the Nrn1 phenotype, of how to proceed deeper to investigate the electrical change in the in vivo models.

“Major points

(1) A real weakness of this work is the fact that in most of the results shown, there are few biological replicates with differences that are often small between Ctrl and Nrn1 -/-. The systematic use of student's t-test may lead to thinking that the differences are significant, which is often misleading given the small number of samples, which makes it impossible to know whether the distributions are Gaussian and whether a parametric test can be used. RNAseq bulk data are based on biological duplicates, which is open to criticism.”

We respectfully disagree with Reviewer #1 on the question of statistical power and significance to our work. We have used 5-8 mice/group for each in vivo model and 3-4 technical replicates for the in vitro studies, with a minimum of 2-3 replicate experiments. These group sizes and replication numbers are in line with those seen in high-impact publications. While some differences between Ctrl and Nrn1-/- appear small, they have significant biological consequences, as evidenced by the various Nrn1-/- in vivo phenotypes. Furthermore, we believe we have subjected our data to the appropriate statistical tests to ensure rigorous analysis and representation of our findings.

To Reviewer #2.

We thank Reviewer #2 for the careful review of the manuscript. We especially appreciate the comments that “The characterizations of T cell Nrn1 expression both in vitro and in vivo are comprehensive and convincing. The in vivo functional studies of anergy development, Treg suppression, and EAE development are also well done to strengthen the notion that Nrn1 is an important regulator of CD4 responsiveness.”

“The major weakness of this study stems from a lack of a clear molecular mechanism involving Nrn1. “  

We fully understand this comment from Reviewer #2. The main mechanism we identified contributing to the functional defect of Nrn1-/- T cells involves novel effects on the electric and metabolic state of the cells. Although we referenced neuronal studies that indicate Nrn1 is the auxiliary protein for the ionotropic AMPA-type glutamate receptor (AMPAR) and may affect AMPAR function, we did not provide any evidence in this manuscript as the topic requires further in-depth study.   

For the benefit of this discussion, we include our preliminary Nrn1 and AMPAR double knockout data (Author response image 2), which indicates that abrogating AMPAR expression can compensate for the defect caused by Nrn1 deficiency in vitro and in vivo. This preliminary data supports the notion that Nrn1 modulates AMPAR function, which causes changes in T cell electric and metabolic state, influencing T cell differentiation and function.  

Author response image 2.

Deletion of AMPAR expression in T cells compensates for the defect caused by

Nrn1 deficiency. Nrn1-/- mice were crossed with T cell-specific AMPAR knockout mice (AMPARfl/flCD4Cre+) mice. The following mice were generated and used in the experiment: T cell specific AMPAR-knockout and Nrn1 knockout mice (AKONKO), Nrn1 knockout mice (AWTNKO), Ctrl mice (AWTNWT). a. Deletion of AMPAR compensates for the iTreg cell defect observed in Nrn1-/- CD4 cells. iTreg live cell proportion, cell number, and Ki67 expression among Foxp3+ cells 3 days after aCD3 restimulation. b. Deletion of AMPAR in T cells abrogates the enhanced autoimmune response in Nrn1-/- Mouse in the EAE disease model. Mouse relative weight change and disease score progression after EAE disease induction.  

Ion channels can influence cell metabolism through multiple means (Vaeth and Feske, 2018; Wang et al., 2020). First, ion channels are involved in maintaining cell resting membrane potential. This electrical potential difference across the cell membrane is essential for various cellular processes, including metabolism (Abdul Kadir et al., 2018; Blackiston et al., 2009; Nagy et al., 2018; Yu et al., 2022). Second, ion channels facilitate the movement of ions across cell membranes. These ions are essential for various metabolic processes. For example, ions like calcium (Ca2+), potassium (K+), and sodium (Na+) play crucial roles in signaling pathways that regulate metabolism (Kahlfuss et al., 2020). Third, ion channel activity can influence cellular energy balance due to ATP consumption associated with ion transport to maintain ion balances (Erecińska and Dagani, 1990; Gerkau et al., 2019). This, in turn, can impact processes like ATP production, which is central to cellular metabolism. Thus, ion channel expression and function determine the cell’s bioelectric state and contribute to cell metabolism (Levin, 2021).

Because the AMPAR function has not been thoroughly studied using a genetic approach in T cells, we do not intend to include the double knockout data in this manuscript before fully characterizing the T cell-specific AMPAR knockout mice.  

“Although the biochemical and informatics studies are well-performed, it is my opinion that these results are inconclusive in part due to the absence of key "naive" control groups. This limits my ability to understand the significance of these data.

Specifically, studies of the electrical and metabolic state of Nrn1-/- inducible Treg cells (iTregs) would benefit from similar data collected from wild-type and Nrn1-/- naive CD4 T cells.”

We appreciate the reviewer’s comments. This comment reflects two concerns in data interpretation:

(1) Are Nrn1-/- naïve T cells fundamentally different from WT cells? Does this fundamental difference contribute to the observed electrical and metabolic phenotype in iTreg or Th0 cells? This is a very good question we will perform the experiments as the reviewer suggested. While Nrn1 is expressed at a basal (low) level in naïve T cells, deletion of Nrn1 may cause changes in naïve T cell phenotype.   

(2) Is the Nrn1-/- phenotype caused by Nrn1 functional deficiency or due to the secondary effect of Nrn1 deletion, such as non-physiological cell membrane structure changes?

We have done the following experiment to address this concern.  We have cultured WT T cells in the presence of Nrn1 antibody and compared the outcome with Nrn1-/- iTreg cells (Figure 3-figure supplement 2D,E,F). WT iTreg cells under antibody blockade exhibited similar changes as Nrn1-/- iTreg cells, confirming the physiological relevance of the Nrn1-/- phenotype.

Manuscript Revision based on the Reviewer’s suggestions:

Reviewer #1:

Major points (3) Figure 1A-D. Since the authors are using the Nrp1 KO mice, it would be important to confirm the specificity of the anti-Nrn1 mAb by FACS. 

Following the suggestion by Reviewer#1, We have included the Nrn1 Ab staining on activated Nrn1-/- CD4 cells in Figure 1D. We have also added the staining of cell surface Nrn1 on Treg cells in Figure 1-figure supplement 1D.

Major point: (5) “Moreover, we do not even know what the % of Foxp3 cells is in the iTreg used (after differentiation and 20h of re-stimulation) and whether this % is the same between Ctlr and Nrn1 KO cells.”

In the revised manuscript, we have included the proportion of Foxp3+ cells among Nrn1-/- and ctrl iTreg cells developed under the iTreg culture condition in Figure 2A.

Minor points  

(2) For all figures showing %, the titles of the Y axes are written in an odd way. For example, it is written "Foxp3% CD4". It would be more conventional and clearer to write "% Foxp3+ / CD4+" or "% Foxp3+ among CD4+".

Following reviewer#1’s suggestion, we have changed the Y-axis label in all the relevant figures.

(3) Would not it be possible to perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane? This would be a more interesting demonstration than transcriptomic data.”

We appreciate Review# 1’s suggestion regarding “perform experiments showing the ability of cells to transport amino acids or electrolytes across the plasma membrane”.  We have used AAinduced cellular MP changes to confirm differential AA transporter expression patterns and their impact on cellular MP levels.  The data are included in the revised manuscript in Figure 3H and Figure 4K.

(4) For certain staining (Figure 3E, H) it would be important to show the raw data, in addition to MFI or % values.

We appreciated Reviewer #1’s suggestion and have included the histogram staining data for Figure 3E. We have moved the original Figure 3H to the supplemental figure and included the histogram staining data in Figure 3-figure supplement 1C.  Similarly, we have included the histogram staining data in Figure 4-figure supplement 1C.

Reviewer#2:

“Although the biochemical and informatics studies are well-performed, it is my opinion that these results are inconclusive in part due to the absence of key "naive" control groups. This limits my ability to understand the significance of these data.

Specifically, studies of the electrical and metabolic state of Nrn1-/- inducible Treg cells (iTregs) would benefit from similar data collected from wild-type and Nrn1-/- naive CD4 T cells.”

We greatly appreciate Reviewer#2’s suggestion and have carried out experiments on naïve CD4 cells derived from Nrn1-/- and WT mice. We have compared membrane potential, AA-induced MP change between Nrn1-/- and WT naïve T cells, and the metabolic state of Nrn1-/- and WT naïve T cells by carrying out glucose stress tests and mitochondria stress tests using a seahorse assay.  Moreover, to investigate whether the phenotype revealed in Nrn1-/- CD4 cells was caused by a secondary effect of cell membrane structure change due to Nrn1 deletion, we carried out Nrn1 antibody blockade in WT CD4 cells and investigated the phenotypic change. These new results are included in Figure 3-figure supplement 2.

Reference:

Abdul Kadir, L., M. Stacey, and R. Barrett-Jolley. 2018. Emerging Roles of the Membrane Potential: Action Beyond the Action Potential. Front Physiol 9:1661.

Blackiston, D.J., K.A. McLaughlin, and M. Levin. 2009. Bioelectric controls of cell proliferation: ion channels, membrane voltage and the cell cycle. Cell Cycle 8:3527-3536.

Chappert, P., and R.H. Schwartz. 2010. Induction of T cell anergy: integration of environmental cues and infectious tolerance. Current opinion in immunology 22:552-559.

Chen, W., W. Jin, N. Hardegen, K.J. Lei, L. Li, N. Marinos, G. McGrady, and S.M. Wahl. 2003. Conversion of peripheral CD4+CD25- naive T cells to CD4+CD25+ regulatory T cells by TGF-beta induction of transcription factor Foxp3. The Journal of experimental medicine 198:1875-1886.

Erecińska, M., and F. Dagani. 1990. Relationships between the neuronal sodium/potassium pump and energy metabolism. Effects of K+, Na+, and adenosine triphosphate in isolated brain synaptosomes. J Gen Physiol 95:591-616.

Fathman, C.G., and N.B. Lineberry. 2007. Molecular mechanisms of CD4+ T-cell anergy. Nat Rev Immunol 7:599-609.

Gerkau, N.J., R. Lerchundi, J.S.E. Nelson, M. Lantermann, J. Meyer, J. Hirrlinger, and C.R. Rose. 2019. Relation between activity-induced intracellular sodium transients and ATP dynamics in mouse hippocampal neurons. The Journal of physiology 597:5687-5705.

Hurrell, B.P., D.G. Helou, E. Howard, J.D. Painter, P. Shafiei-Jahani, A.H. Sharpe, and O. Akbari. 2022. PD-L2 controls peripherally induced regulatory T cells by maintaining metabolic activity and Foxp3 stability. Nature communications 13:5118.

Jenkins, M.K., and R.H. Schwartz. 1987. Antigen presentation by chemically modified splenocytes induces antigen-specific T cell unresponsiveness in vitro and in vivo. The Journal of experimental medicine 165:302-319.

John, P., M.C. Pulanco, P.M. Galbo, Jr., Y. Wei, K.C. Ohaegbulam, D. Zheng, and X. Zang. 2022. The immune checkpoint B7x expands tumor-infiltrating Tregs and promotes resistance to anti-CTLA-4 therapy. Nature communications 13:2506.

Kahlfuss, S., U. Kaufmann, A.R. Concepcion, L. Noyer, D. Raphael, M. Vaeth, J. Yang, P. Pancholi, M. Maus, J. Muller, L. Kozhaya, A. Khodadadi-Jamayran, Z. Sun, P. Shaw, D. Unutmaz, P.B. Stathopulos, C. Feist, S.B. Cameron, S.E. Turvey, and S. Feske. 2020. STIM1-mediated calcium influx controls antifungal immunity and the metabolic function of nonpathogenic Th17 cells. EMBO molecular medicine 12:e11592.

Levin, M. 2021. Bioelectric signaling: Reprogrammable circuits underlying embryogenesis, regeneration, and cancer. Cell 184:1971-1989.

Nagy, E., G. Mocsar, V. Sebestyen, J. Volko, F. Papp, K. Toth, S. Damjanovich, G. Panyi, T.A. Waldmann, A. Bodnar, and G. Vamosi. 2018. Membrane Potential Distinctly Modulates Mobility and Signaling of IL-2 and IL-15 Receptors in T Cells. Biophys J 114:2473-2482.

Quill, H., and R.H. Schwartz. 1987. Stimulation of normal inducer T cell clones with antigen presented by purified Ia molecules in planar lipid membranes: specific induction of a long-lived state of proliferative nonresponsiveness. Journal of immunology (Baltimore, Md. : 1950) 138:3704-3712.

Schmitt, E.G., and C.B. Williams. 2013. Generation and function of induced regulatory T cells. Frontiers in immunology 4:152.

Sugiura, A., G. Andrejeva, K. Voss, D.R. Heintzman, X. Xu, M.Z. Madden, X. Ye, K.L. Beier, N.U. Chowdhury, M.M. Wolf, A.C. Young, D.L. Greenwood, A.E. Sewell, S.K. Shahi, S.N. Freedman, A.M. Cameron, P. Foerch, T. Bourne, J.C. Garcia-Canaveras, J. Karijolich, D.C. Newcomb, A.K. Mangalam, J.D. Rabinowitz, and J.C. Rathmell. 2022. MTHFD2 is a metabolic checkpoint controlling effector and regulatory T cell fate and function. Immunity 55:65-81.e69.

Vaeth, M., and S. Feske. 2018. Ion channelopathies of the immune system. Current opinion in immunology 52:39-50.

Vanasek, T.L., S.L. Nandiwada, M.K. Jenkins, and D.L. Mueller. 2006. CD25+Foxp3+ regulatory T cells facilitate CD4+ T cell clonal anergy induction during the recovery from lymphopenia. Journal of immunology (Baltimore, Md. : 1950) 176:5880-5889.

Wang, Y., A. Tao, M. Vaeth, and S. Feske. 2020. Calcium regulation of T cell metabolism. Current opinion in physiology 17:207-223.

Yu, W., Z. Wang, X. Yu, Y. Zhao, Z. Xie, K. Zhang, Z. Chi, S. Chen, T. Xu, D. Jiang, X. Guo, M. Li, J. Zhang, H. Fang, D. Yang, Y. Guo, X. Yang, X. Zhang, Y. Wu, W. Yang, and D. Wang. 2022. Kir2.1-mediated membrane potential promotes nutrient acquisition and inflammation through regulation of nutrient transporters. Nature communications 13:3544.

Zheng, S.G., J.D. Gray, K. Ohtsuka, S. Yamagiwa, and D.A. Horwitz. 2002. Generation ex vivo of TGF-beta-producing regulatory T cells from CD4+CD25- precursors. Journal of immunology (Baltimore, Md. : 1950) 169:4183-4189.

eLife Assessment

The neurotrophic factor Neuritin can moderate T-cell tolerance and immunity through both regulatory T (Treg) and effector T cells, promoting Treg cell expansion and suppression while dampening effector T cells to mediate the inflammatory response. Neuritin expression influences the membrane potential, ion channels, and nutrient transporter expression patterns of CD4+ T cells, contributing to differential metabolic states in Treg and effector T cells. These findings are solid and important for understanding immune regulation involving Treg cells and effector T cells.

Reviewer #1 (Public review):

The manuscript by Yu et al seeks to investigate the role of neuritin (Nrn1), identified as a marker of anergic cells, in the biology of regulatory (Tregs) and conventional (Tconv) T cells. Although the role of Nrn1 expressed by Tregs has already been explored (Gonzalez-Figueroa 2021 cited in the manuscript), this manuscript shows original new data suggesting that this molecule would be important in promoting Treg function and inhibiting Tconv effector function by acting at the level of membrane potential and molecule transport across the plasma membrane. However, multiple models have been used, but none has been studied thoroughly enough to provide really conclusive and unambiguous data. For example, 5 different models were used to study T cells in vivo. It would have been preferable to use fewer, but to go further in the study of mechanisms. In the absence of more in-depth study, the conclusions drawn by the authors are often open to questions. Major points concern the fact that there are not enough biological replicates for most experiments and some critical controls and data are lacking. Also, the authors have used iTregs rather than nTregs for many experiments (see below). This is unfortunate because the role of neuritin in T cell biology studied here is new and interesting.

Major points (in the order in which they appear in the text).

(1) A real weakness of this work is the fact that in most of the results shown, there are few biological replicates with differences that are often small between Ctrl and Nrn1 -/-. The systematic use of student's t test may lead to think that the differences are significant, which is often misleading given the small number of samples, which makes it impossible to know whether the distributions are Gaussian and whether a parametric test can be used. RNAseq bulk data are based on biological duplicates, which is open to criticism.<br /> (2) The authors use Nrn1+/+ and Nrn1+/- cells indiscriminately as control cells on the basis of similar biology between Nrn1+/+ and Nrn1+/- cells at homeostasis. However, it is quite possible that the Nrn1+/- cells have a phenotype in situations of in vitro activation or in vivo inflammation (cancer, EAE). It would be important to discriminate Nrn1+/- and Nrn1+/+ cells in the data or to show that both cell types have the same phenotype in these conditions too.<br /> (3) Fig 1A-D. Since the authors are using the Nrp1 KO mice, it would be important to confirm the specificity of the anti-Nrn1 mAb by FACS. Once verified, it would be important to add FACS results with this mAb in Figs 1A-C to have single-cell and quantitative data as well.<br /> (4) Fig 1E-H. The authors assume that this immunization protocol induces anergic cells, but they provide no experimental evidence for this. It would be useful to show that T cells are indeed anergic in this model, especially those that are OVA-specific. The lack of IL-2 production by Cltr cells could be explained by the presence of fewer OVA-specific cells, rather than by an anergic status.<br /> (5) Fig 2A-C and Fig 3. The use of iTregs to try to understand what is happening in vivo is problematic. iTregs are cells that have probably no equivalent in vivo, and so may have no physiological relevance. In any case, they are different from pTreg cells generated in vivo. Working with pTreg may be challenging, that is why I would suggest to generate data with purified nTreg.<br /> (6) Fig 2D-L. The model is designed to study the role of Nrn1 in nTreg. However, the % of Foxp3+ among CD45.2 nTreg cells fell to 5-15% of CD4+ cells (Fig 2F). Since we do not know what is the % of Foxp3 among the injected cells, we do not know whether this very low % is due to very high Treg instability or to preferential expansion of contaminating Tconvs. It is possible that the % of Tconv contaminant is high since Treg were sorted using beads and not FACS on some experiments. As it is very likely that there are Tconv contaminants that would be Nrn1-/- in the group transferred with Nrn1-/- "nTreg", the higher tumor rejection could be due to an overactivation of Nrn1-/- Tconvs (rather than a defect in Nrn1-/- Treg function).

Reviewer #2 (Public review):

Summary:

This manuscript explores the role of Nrn1 in T cell tolerance. A previous study has demonstrated that Nrn1 is up-regulated in the Tfr fraction of Foxp3+ T regulatory cells. These authors now confirm expression of Nrn1 in iTregs as well as report here that Nrn1 is also greatly over-expressed in anergic CD4 T cells, and this is the stepping off point for this investigation.

Most remarkably, experiments show that anergy induction is defective when T cells cannot express Nrn1. Furthermore, differentiation to a Foxp3+ iTreg phenotype is inhibited in the absence of Nrn1, and the iTregs that do develop appear functionally defective. On the other hand, the differentiation and expansion of Teff cells appears to be enhanced following deletion of Nrn1. With such defects in anergy induction as well as dysregulated Treg and Teff cell survival and function, auto reactive effector T cell activation becomes unrestrained and Nrn1-/- mice are more susceptible to severe EAE development.

Strengths:

The characterizations of T cell Nrn1 expression both in vitro and in vivo are comprehensive and convincing. The author's use of both Nrn1-/- T cells as well as anti-Nrn1 neutralizing Ab to achieve similar results is a strength. The in vivo functional studies of anergy development, Treg suppression, and EAE development are also well performed and strengthen the notion that Nrn1 is an important regulator of CD4 responsiveness.

Weaknesses:

The major weakness of this study stems from a lack of a clear molecular mechanism involving Nrn1. Previous studies of Nrn1 have suggested its role as a soluble molecule involved in intracellular communication, perhaps influencing cellular ion channel function and/or triggering downstream NFAT and mTOR activation. However, a unique receptor for Nrn1 has not been discovered and it remains unclear whether it acts in a cell-intrinsic or cell-extrinsic fashion for any particular cell type.

Data shown here provide evidence for alterations in the electrical and metabolic state of iTreg and Teff cells when the Nrn1 gene is deleted. Nrn1-/- Tregs and Teff cells each express a unique pattern of genes associated with Neurotransmitter receptor, Metal ion transmembrane transport, Amino acid transport, and mTORC1 signaling activities, different than that seen in wild-type mice. It remains unclear how Nrn1 reinforces the membrane potential and facilitates aerobic glycolysis during and after iTreg differentiation, and yet suppresses the membrane potential and restrains aerobic glycolysis during Teff cell differentiation. Importantly, naive cells lacking Nrn1 expression show normal electrical and metabolic behaviors.

eLife Assessment

In this valuable study, Li and others identified cell membrane receptors for juvenile hormone (JH), a terpenoid hormone in insects that regulates their development and reproduction. While intracellular receptors for JH have been well characterized, membrane receptors for JH remained elusive for many years. Although the authors provide solid evidence to indicate that the receptor tyrosine kinases they identified bind to JH in vitro and induce non-genomic responses in cultured cells, their loss-of-function phenotypes are not consistent with known JH functions, so additional work is required to define physiological roles of these receptors.

eLife Assessment

This important work presents data showing that all non-proneural phenotypes of the Inhibitor of DNA binding (Id) protein Emc are mediated through inappropriate nonapoptotic caspase activity. Using the developing Drosophila retina as a model the authors show that Emc acts by transcriptionally regulating the Death-Associated Inhibitor of Apoptosis 1 (diap1) gene, which impacts on Notch signaling by caspase-dependent increase of Delta protein. These are compelling findings, interesting for the caspase/apoptosis field as they add more non-apoptotic functions of caspases to the list, as well as for the Id field, which examines how Id proteins inhibit cell differentiation.

这边需要说明，我们在升级过程中，是通过拿到PPM_HOME/content/conf/menus/custom/update_menu.xml和PPM_HOME/content/conf/menus/custom/delete_menu.xml这两个文件的内容，来决定升级后custom menu的结构的。同时我们会忽略PPM_HOME/content/conf/menus这个目录底下添加过的menu相关的文件。这里的更改不会显示在sidenav menu里面。

Smith Corona Manual Vintage Typewriter Main Spring Removal Flush and Re-Lube Draw Band Attached by [[Phoenix Typewriter]]

Duane puts a few drops of red oil on the mainspring of typewriters as a lubricant before blowing it out to thin it down.

Here he demonstrates how to re-tension the mainspring of a Smith-Corona typewriter.

Smith Corona Typewriters 1935 - 1980 Type Alignment / Shift Motion Upper Lower Case Adjustment by [[Phoenix Typewriter]]

Duane starts out by showing the two adjustment screws for the upper and lower case motion adjustment on a 5 Series Smith-Corona portable. (This should be the same across several decades of machines and include the 4 and 6 series as well.)

This sets the stage by explaining that under typical conditions, nitrogen and oxygen are stable and do not form compounds. This explains that high temperatures are needed for the reaction to occur and are key to forming nitrogen oxides.

Reviewer #2 (Public review):

Summary:

In this study, the authors combine the study of clinical samples of antibiotic resistant bacteria with experimental evolution and evolutionary genomics to address important questions about the propensity for reversion in two different schema: de novo resistance arising within a patient, and transmitted resistance. The authors' use of a combination of methods help to answer the question outlined in their hypothesis, that de novo resistance mechanisms appear to revert to sensitive phenotypes more readily in a drug-free environment.

Strengths:

This study is exceptionally well-written and organized. The authors state their hypothesis clearly, and follow it up with an impressive effort that is truly translational-they make direct use of clinical samples of bacteria, and combine that with approaches in experimental evolution and evolutionary genomics. The conclusions follow naturally from the results, and there are no irresponsible leaps made.

Weaknesses:

I will divide my criticism into two areas, conceptual (most of my critique), with a very small methodological question.

(1) In the end, the authors offer findings that appear to be correct, and (again) are reported very clearly. However, this study is very surface-level in its theoretical underpinnings and construction, which is puzzling, because the field of antibiotic resistance and adaptation more broadly, is full of relevant studies and explanatory tools. Below I'll identify several areas where this manifests.

For one, the authors do not engage with a large recent literature on reversion, reversal, and compensation. It provides much more conceptual grounding for what the authors observe, much of it compatible with the findings from this study:

To offer two quick examples:<br /> - Avrani S, Katz S, Hershberg R. Adaptations accumulated under prolonged resource exhaustion are highly transient. MSphere. 2020 Aug 26;5(4):10-128.<br /> - Pennings, P.S., Ogbunugafor, C.B. and Hershberg, R., 2022. Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs. G3, 12(9), p.jkac190.

Examinations of the studies on adaptation and reversion offer a richer mechanistic take on what was observed. But this literature alone is less of a problem than the general offering of different takes for the results. One can turn to a different literature - from ecology - to find a different explanation that is compatible with the findings.

De novo evolution involves the strong selection and rapid fixation of populations that are evolving largely to a relatively simple ecological milieu: their only primary function is to promote replication and survival of populations experiencing the negative fitness effects of drug pressure. Alternatively, transmitted resistant populations must deal with a multitude of selective pressures, working dynamically across time and space. In such a scenario, one would expect populations to locate places on the fitness landscape that are commensurate with survival in both drug-poor and drug-rich environments, as this is the ecological reality of the transmitted resistant bacteria. I could envision selection for "generalism" in this setting, corresponding to populations that have fixed mutations that promote resistance, but also those that ensure replication in drug-free environments. This regime might even reflect selection for "generalism" or "increased niche breadth." That is, transmitted resistance may have adopted a "jack of all trades, master of none" phenotype. The de novo resistance strains, alternatively, are selected for "generalism."

See the following for examples (there are many):

- Kassen R. The experimental evolution of specialists, generalists, and the maintenance of diversity. Journal of evolutionary biology. 2002 Mar 1;15(2):173-90.<br /> - Bell TH, Bell T. Many roads to bacterial generalism. FEMS microbiology ecology. 2021 Jan;97(1):fiaa240.

Note that this classically ecological explanation is only one of several other literatures that offer models for the findings in this study.

To the authors' credit, their study was about the very real-world problem of antibiotic resistance, using a system that is far less tractable than the model systems research that has generated a lot of data and theory. And sure: the study is valuable because it communicates an interesting finding using a combination of methods (impressively). But in some ways, the study almost reads as a descriptive exercise: it offers a good question (does de novo or transmitted resistance revert more readily), and tells you what they found (de novo does). However the explanatory mechanisms do not advance our understanding much. Reporting the presence of unstable and disruptive mutations in the de novo populations is hardly an explanation. That is, alternatively, data in support of a proper explanation. There is nothing magical about de novo evolution that should be selected for disruptive mutations.

The reasons for the different sorts of mutation could have to do with the population genetic particulars of the de novo regime: large populations, strong selective pressure, relatively static fitness landscape. In such a setting, selection marches a population greedily up a peak. Alternatively, a transmitted population arises from a lineage that has observed a multitude of ecologies, across different fitness landscapes and has fixed mutations that confer survival across all of them.

There's a literature that speaks to this:<br /> - Miller CM, Draghi JA. Range expansion can promote the evolution of plastic generalism in coarse-grained landscapes. Evolution Letters. 2024 Apr 1;8(2):322-30.<br /> - Bono LM, Draghi JA, Turner PE. Evolvability costs of niche expansion. Trends in genetics. 2020 Jan 1;36(1):14-23.

The findings are simple enough (a testament to the strong study design and execution) that supporting population genetic simulations, or analytical descriptions (maybe not relevant) could offer insight as to what really happened here.

(2) I recognize the challenge of working with clinical samples. It is very difficult to understand everything about them. But even having considered that, I might be missing something.

My main question here involves the origin of the putatively transmitted strains. The authors state that " Isolates were also obtained from six patients with a putatively transmitted resistant bacteria (hereafter PT), where a daptomycin-resistant, E. faecium bacteremia was identified on their first culture."

This seems like an awfully dubious way to identify transmitted resistance. I suppose I understand the logic (de novo evolution requires the observer to have seen the evolution happen in real-time). But this definition leaves the study wide open for an "apples to oranges" comparison that might render the other aspects questionable.

The de novo strains are being compared to transmitted strains that may have been part of lineages that had passed between many, many patients. If this were true, then we should expect the genomic architecture of the transmitted strains to be far different. The transmitted strains might have undergone more selection in different regimes and genetic drift. Drift might have fixed mutations in transmission bottlenecks, altering the genetic architecture. In such a scenario, one might expect these populations to have a more difficult time unwinding their resistance phenotype.

In the end, I applaud the authors on a well-done and well-written study.

eLife Assessment

This important study, which will be of interest to those studying the evolution and maintenance of antibiotic resistance, addresses the hypothesis that antibiotic resistance arising de novo during treatment will carry a higher fitness cost and will revert to susceptibility more readily than resistance that has been transmitted between hosts. There are, however, concerns that the 'putatively transmitted isolates' in this study do not necessarily represent resistant isolates that have been transmitted between hosts. The support for the central claim of different patterns of reversion between isolates with de novo resistance and putatively transmitted resistant isolates is currently incomplete.

Reviewer #1 (Public review):

Summary:

Tracy and colleagues study the loss of daptomycin resistance in Enterococcus faecium isolates from bloodstream infections using in vitro evolution experiments in the absence of antibiotics. They test the hypothesis that antibiotic resistance arising de novo during treatment will carry a higher fitness cost and will revert more readily than resistance isolates which have been transmitted and have therefore already survived in the absence of antibiotic selection pressure.

Strengths:

This is an important question as a fitness cost to resistance is typically found in lab evolution experiments and assumed in modelling studies, but often not identified in clinical isolates. Here the authors find examples of clinical isolates which do and don't revert to sensitivity in in vitro evolution in the absence of antibiotics. Sequencing of the lab evolved isolates revealed that reversal of resistance was often due to mutations in the same gene that evolved in vivo, which is nice evidence that these resistance mutations did confer a fitness cost.

Weaknesses:

Although this is an interesting study on an important topic, currently the results are overinterpreted do not justify the title of the paper 'Reversion to sensitivity explains limited transmission of resistance in a hospital pathogen' for several reasons. Firstly, the patient group, e.g. 'putatively transmitted' isolates vs 'de novo' isolates was not a significant predictor of change in MIC. Instead the change in MIC in the absence of antibiotics was significantly associated with the starting MIC of the isolate in the evolution experiments, but this would be expected since isolates with a higher MIC have more potential to decrease in MIC in the evolution experiments. The abstract and some conclusion do not match the results in some instances, for example the abstract states 'resistance that arose de novo within patients was higher level but exhibited greater declines in resistance in vitro'. In the discussion: they state "these findings support our hypothesis that transmitted resistance strains are less likely to revert". However, on page 14 the initial MICs between DNR and PTR were not significantly different and patient group was not a significant predictor of change in MIC. Sequencing of the lab evolved isolates revealed that reversal of resistance was often due to mutations in the same gene that evolved in vivo. However, there were also some example of mutations in the same genes within the PTR isolates, so it remains unclear if there is a significant difference in behaviour between the DNR and PTR isolates in terms of reversion mutations. Significance testing, controlling for the starting MIC, would help confirm this.

Secondly, the 'putatively transmitted isolates', i.e. isolates that were resistant in the first positive blood culture, do not necessarily represent resistant isolates that have been transmitted between hosts. E. faecium is primarily a commensal of the intestinal tract, but which can cause opportunistic extra-intestinal infections. These bacteremia cases were most likely caused by within-host translocation of a strain already colonizing the intestine to the bloodstream - indeed, it has been shown that antibiotics can lead to Enterococcus overgrowth in the intestine and subsequent bloodstream invasion (DOI: 10.1172/JCI43918). The 'putatively transmitted isolates' may have initially colonised the intestine via between host transmission in an already resistant state, as assumed by the authors, but they may also have evolved resistance de novo within the host's intestine prior to causing bloodstream infections. Since they do not have data on past daptomycin exposure in these individuals it cannot be assumed that these isolates were transmitted with high resistance between hosts. An alternative explanation for any differences between the 'de novo' and 'putatively transmitted' could be the environment where resistance evolved, e.g. the intestine with strong competition from other strains and species, or within the otherwise sterile bloodstream environment. The authors hypothesise that "newly resistant population must continue to transmit between hosts in antibiotic free conditions to ensure its survival" and that "transmission acts as a filter to select for resistance with a lower cost or lower chance of reversion". Rather than transmission per se, it is equally plausible that survival of the newly resistant population within the primary niche, the intestinal microbiota, is the crucial to filter for resistance with a lower cost.

Die von Waldbränden außerhalb der Tropen verursachten Emissionen haben sich seit 2001 fast verdreifacht. Weltweit haben die Emissionen durch Waldbrände in dieser Zeit um 60% zugenommen. Ursache dafür ist die Kombination von heißerem und trockenerem Wetter mit dem schnelleren Wachstum der Wälder durch die höheren Temperaturen. Die Wälder können durch die Brände jahrzehntelang zu Emittenten werden. Damit ist die Funktion der Wälder als Kohlenstoffsenken gefährdet. Das bedeutet auch, dass sie andere anthropogene Emissionen weniger kompensieren und die Fähigkeit verlieren, nach einem Überschreiten der 1,5°-Grenze C0₂ aus der Atmosphäre zu entfernen. Außerdem müssten diese von Menschen verursachten Emissonen den C0₂-Budgets der Nationalstaaten zugeordnet werden.

https://theconversation.com/forest-fires-are-shifting-north-and-intensifying-heres-what-that-means-for-the-planet-241337

So there is a distinction between certain lipid serums but overall there does seem to be a correlation between environmental factors and your epigenome / serum lipid + apolipoproteins

I find it interesting that there is a contradiction in the data they found and this warrants further study.

This is an important thing to clarify as this data is taken from Northern Europe. This also brings up a key point, who were the ethnic groups that were studied? I presume mostly Northern Europeans, I think this study should be replicated for other ethnic groups to see if theres a difference between how much your epigenome is affected by your environment taking into account ethnicity.

I find it interesting that there is chance your epigenome is also affected by your sex and that it actually can affect one sex more than another on average.

I like that they admitted that one model didn't really work for them and that another was better but they left in why they didn't use the first model and why the second was more fitting.

This even further helps prove our case that as time goes on these differences become even more apparent and even more noticeable due to environmental factors.

This section helps further prove that there is an environmental affect on your gene expression, that yes genetics plays a factor but so does your environment. Nurture and Nature are true.

I think the sex correlation was expected, at least from me, usually we have different levels of almost everything in our bodies due to sex.

I believe the prediction model is very important to emphasize the differences as if the prediction is accurate it proves the null, while if it is inaccurate it helps reject the null.

This explanation is very useful and makes it easy to understand how they went about comparing the data of two different groups.

Relying on subject self-reporting is not always the best, if they could've gained access to relevant medical and prescription records I think it would've been better but this is sufficient

Sample size is a large factor in determining the ability to reject the null and while this sample size isn't the biggest, for what they're studying I believe its sufficient.

I'm glad the twins weren't forcefully or purposefully separated, as far as we know at least. The ethics remain intact for now.

I wonder why this is? Is it because the older you get the more environmental factors compound on top of each other and it makes it hard to differentiate what has been caused by what?

While I agree that environmental factors can confound the study, I think that its actually beneficial for them to have similar environments (at least for the purposes of our paper) because it shows that even very minor differences such as outlook (which affects stress/dopamine) can change your epigenome. I also disagree with adoption studies ethically as oftentimes these twins are deliberately separated and siblings should have the chance to grow up together.

Many of these factors being determined by single-genes makes it a lot easier to study and experiment with.

The idea that not all lipids are affected is interesting and I want to learn more

Wise (2022) original comments: “350 years into this society’s existence, laws were finally passed to prohibit the discrimination that had been its hallmark for 15 generations — not because of some grand moral epiphany, mind you, but because the resistance of that society’s victims had finally forced a comeuppance.” “If you’re trying to control for non-racial explanations for racial disparities, you need to make sure your alternative variables are genuinely independent, Chad.”

Conceptionally.org (2024) original comments:<br /> “Public officials cannot enact any policy they please like they’re ordering dessert from a menu. They have to choose from among policies that are politically acceptable at the time. And we believe the Overton window defines that range of ideas.” “Instead of joining a side and pulling on the rope (of the Overton window), pull it sideways in a direction no one will resist.”

can you explain the derivation of this

What is the physical significance of \ddot{v}_y

I can see it looks like \ddot{x} = -\omega^2 x

In electrodynamics div E is a scalar product.

Where E is the electric field which is a vector. And E = nabla • f

But in the context of electrodynamics, what is our scalar field, f?

Erstmals wurde genau erfasst, welcher Teil der von Waldbränden betroffenen Gebiete sich auf die menschlich verursachte Erhitzung zurückführen lässt. Er wächst seit 20 Jahren deutlich an. Insgesamt kompensieren die auf die Erhitzung zurückgehenden Waldbrände den Rückgang an Bränden durch Entwaldung. Der von Menschen verursachte – und für die Berechnung von Schadensansprüchen relevante – Anteil der CO2-Emissione ist damit deutlich höher als bisher angenommen https://www.carbonbrief.org/climate-change-almost-wipes-out-decline-in-global-area-burned-by-wildfires/

why in that case, the second term of the equation is not ignored?

wild that there's shit this fucking weird. you couldn't make it up

we dont need money

Ada berapakah nomina dalam paragraf tersebut? Ada berapa kalimatkah dalam paragraf tersebut?

This is common even outside of the care sector. I think we expect that technology can fix many of our problems in the future.

I wonder if some of the hesitation to use these robots is concern for job replacement by these machines.

Do these care homes really need a robot or just a machine like a automated lifting program.

I think its very shortsighted to not interact with the future users of these robots. The engineers need to see what these users need in addition to the basic care if they want to develop advanced care robots.

This is very forward thinking of the government. I think safety standards for a lot of robots need to be created even before the technology is truly finalized.

So how would they be able to truly come up with an effective solution to the problem that they have not seen themselves?

Which one is the most beneficial for the elderly?

From this perspective, the television workplace operates as what Daphne Spain calls a “spatial institution,” in which “the properties of a social system express themselves through daily activities at the same time

a counteroffer: the freedom to “hire an all-woman staff, producer, director . . . everybody” and to program what she wanted. To her surprise, WBZ management immediately agreed to these terms,

Hamlin recalls coming into a room with eighteen men seated around a big table who assured her that she could retain her position as a cultural reporter for the station while she hosted the morning show because of the formulaic and simplistic nature of programming for women. “It’s easy,” they told Hamlin, since she would have “dodo birds for viewers” and the labor required by the program would involve only “a little make-up, a little hairdo, a chef you can cook with, and from time to time there will be a star coming through.” (intro 3)

With 16 bits, you can represent 2^16 different values, because each bit can have 2 possible states (0 or 1), and there are 16 bits total.

Lets Suppose the roundtrip takes 5ms and retransmission happens every 4ms Then roundtrip exceeds retransmission, means new sync request will be triggered before recieving ack from prev req, which will lead to high number of packet req until the saturation point is reached

They again are referencing their sources. The majority of this article is using information from the prosecutor's office to explain the timeline and event of Payne's passing.

They are using other sources to explain how he died and the author clearly states how they know what they know.

Because Liam Payne is a prominent person, this event is going to attract a lot of attention and the news will effect a lot of fans.

This story focuses on timeliness, magnitude and human interest. It begins with really focusing on timeliness with this mention that there was already information being put out the day after.

Included testimony from the U.S. president of McDonalds. Quoted so that it is not confused with opinion.

BBC includes this statistic to show the reader the effect that this spread is having on the consumers, reiterating why this is a big deal.

BBC is using a credible, factual source for their information about the E. Coli spread.

Of course CD40 signaling inhibits differentiation. The data shows that longer treatment with CD40 antibody decreased differentiation compared to 24h of treatment.

.

UMD's robotics department has student projects in collaboration with gemstone that do very similar things.

I think that's a good idea, especially for elderly who might get confused by a humanoid robot talking to them if they have a cognitive disability.

Why do we think older people will especially resist care from robots?

Japan has a very large elderly population and a smaller population of young people, which is what makes it so difficult to find enough people to take care of the elderly.

This would be very helpful for older people who cannot control their bladder. When people have memory loss, they can forget that they have to use the bathroom, so maybe by having a robot remind them, it can help them slightly with their memory.

In general this document is an educational description of the process of enzymes being used as biological catalysts and the different mechanisms that are utlized in the process as a whole

Does a process like this occur when enzymes are used by bacteria to counter antibiotics?

How substrates bond and what happens once they do

Another key term, includes link with extra information(read later)

Key terminology

The first statement appears to be a general statement of the material to be discuessed further in the document based off the title

General introduction to the purpose of the following subsection of this article

Spending hours on reading the documentation and guide lines of the host Canadian unitiverity

is the only options

This sentence is interesting because it is true that media is a skill to be learned. We must learn how to learn the different types of media in order to gain the knowledge that we need to progress in this world as well as use it in our everyday lives. Without this skill, how can we progress or advance in the world since everything is digitalized?

preload = volume of blood returning to heart to the right atrium

afterload = resistance

contractility = how hard the heart gotta work

Beta 1 adrenergic receptors = gas pedal for the heart, increases HR and contractility

Beta 2, alpha 1 = vasoconstriction

M2 = acetylcholine binds to M2 leads to slowing of heart rate

heart cant pump properly, less blood is reaching the rest of the body

don't take phenylephrine which is worsening the workload of her heart

Dilated cardiomyopathy can lead to atrial fluttering, because heart muscles are stretched and damaged, lead to abnromal condcution

Amlodipine = non-DHP, only works to dilate the blood vessels and has no effects on heart like verapamil (which lowers AV conduction / decreases contractility of the heart)

Phenylephrine = selective alpha 1 agonist, causes vasoconstriction which worsens HTN

more calcium = more contractility

when calcium levels rise it bind to troponin and increase contraction, which increases stroke volume -- more blood pumped out with each beat

Orthopnea is the sensation of shortness of breath (dyspnea) that occurs when a person is lying flat and improves when sitting or standing up. Associated with HF (When lying down, the redistribution of fluid from the lower extremities into the chest increases the pressure on the lungs, exacerbating the difficulty in breathing.)

pulse oximetry = difficulty delivering blood to body

central cyanosis = related too the low oxygen delivery to the body

Jugular Venous Distension = related to right sided HF, dilated and restrictive cardiomyopathy (right atrium pressure builds up because blood keeps regurgitating back to RA, then it backds up into the veins))

Peripheral edema/crackles = from pulmonary congestion since blood be backing up

How will climate change affect this weather? Will it make this area less conducive to farming and growing crops and sustaining life?

Is the conflict being referred to mainly between ethnic groups or tribal conflict? Or is it referring to conflict between the state and the citizens?

• E1 activates ubiquitin and transfers it to E2
• E2 is positioned close to the target by E3
• E3 transfers ubiquitin from E2 to the target

"Eukaryotic cells contain multiple versions of the E3 ubiquitin ligase known as the SCF (Skp1/cullin/F box), each of which is distinguished by a different F box protein that uses a domain at the carboxyl terminus to recognize substrates for ubiquitination. The F box protein Dia2 is an important determinant of genome stability in budding yeast"

Because Mcm7 cannot be ubiquitinated, CMG is constitutively bound to DNA, and will not be removed at any point in the cell cycle. This means that when the cell divides, it will divide it's DNA with CMG still loaded, and the next round of DNA replication will be impaired.

The authors mutated a region of the Mcm complex, specifically Mcm7, seemingly through a mutation at residue 10 from lysine to arginine, making it impossible to be ubiquitinated by SCF-Dia2.

Ubiquitnation leads to CMG unloading, via ubiquitylation, via disassembly by Cdc48/p97, so this mutation makes the CMG constitutively bound to DNA.

Cells with the Mcm7-10R mutation could not be ubiquitated and therefore CMG could not be disassembled.

However, this did not lead to cell death, because a secondary disassembly pathway using Rrm3 and Pif1 helicases was enacted.

Without CMG disassembly, cells were not viable and the ability to ubiquitinate new helicases was lost? It seems.

Cells that have the MCM7-10R mutation will carry the CMG complex on their DNA into the next cell cycle. This helicase must be removed to make way for new helicases and further DNA replication.

The authors found that Rrm3 acts during S-phase to disassemble the CMG complexes from previous cell generations.

This is the recommended reading from our textbook for =Week 9=

Please, try to annotate it as much as possible!

female body is the states means of reproduction!!!!!!!!!!!!

Korean gov institures 3rd plan, effort to improve state of declining marriage and threat of lower birth rate. emphasis on female fertility, extra support for newly married couples blamed womens ferility

blame childless generatoin on neoliberlism

policies and laws did not help

The ship has sailed for Harris when it comes to Middle Eastern voters. Between her administration's involvement in the middle east in the last 4 years and her now attempt to sway voters with Cheney, I think it is best for her to move on from this sector.

I don't like when politicians, on any part of the political spectrum, use people as spearheads for their political campaign. If Michigan voters like Kamala enough, they'll vote for Kamala, I don't believe Liz Cheney(Ex-Rep of Wyoming) is going to sway anyone, especially not Michigan republicans.