for - definition - spiral of the - 5 Elements Mandala - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - need to move - from linear pyramid, neoliberal logic - to trends logic - multi-dimensional - reflexive - feedbacks - intertwingled - need to know what you stand for and - what you stand against ( the dominant neoliberal culture)

for - definition - ahistorical amnesia - plagues philanthropy - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - application - Deep Humanity BEing Journey - onto shift - ontological shift - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - key insight - challenging ourselves for authentic, transformative change - inner and outer work to dismantle oppressive, entrenched systems - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - ontological shift - from totalizing neoliberalism - to spiral logic - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - adjacency - ontological shift - Deep Humanity - asking these fundamental questions - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - definition - ontological shift - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - adjacency - Deep Humanity - can provide new vocabulary and ideas to support - the horizon 3 - ontological shift - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

adjacency - between - ontological shift to reach horizon 3 - Deep Humanity - adjacency relationship - Deep Humanity may offer a new language and vocabulary for this Horizon 3 shift ontology

for - quote - Flow of wealth to the lowest place - Colonial project stops flow to the lowest place - Todd James - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - quote / key insight - must interrogate the deeper thought patterns else - we risk repeating simplistic linear transition social movements that have failed over the past centuries - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - definition - Three Horizon Framework - developed by Bill Sharp - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - example - Three Horizon Framework

example - Three Horizon Framework - horizon 1 - carbon credits - carbon capture - green new deal - green growth - reforming democracy - more humane capitalism - horizon 2 - equity and justice - decolonization - transition pathways to disrupt ideologies - formative stage - ontological - still operating in frame of modernity - still operating in material realm - horizon 3 - new ways of being, living seeing, worldviews - dearth of imagination

for - definition - just transition movement - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - Mexican artist Patrick Cruz - redefining - anthropocene - to age of consequence - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy

for - key insight - Philanthropies have decided on the outside, which communities and which problems need to be solved - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

comment - So true! Who hasn't experienced the NGO coming into the community with a know-it-all attitude and already decided who will receive what funds for what project. It's all decided ahead of time then offered! - We don't want to fall into the same trap!

for - key insight - as individuals, we promote neoliberalism - via entrenched and unconscious colonialism - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - deep entrenchment and entrainment of neolieralism in our bodies - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

comment - The depth of entrainment of neoliberalism in our bodies is very pronounced - This is why it is so difficult to make adhoc change because it faces so much opposition emerging from the unconscious

for - key insight - severe limits of philanthropy - abiding by neoliberal logic severely constrains them - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - progress traps - science - technology - neoliberalism - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

progress traps - science - technology - neoliberalism - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - It is with progress that the modernity shaped by centuries of scaled-out industrial,scientific and technological innovation has created all our crisis. - It is absurd to say that science, technology and industrialization did not play a major role in the creation of all the crisis of modernity - If science, technology and industry inherently embed separation, how do we use it in a meaningful way that doesn't lead to another progress trap? - What are the motives of those who fund technology?

for - key insight - neoliberalism and industrial capitalism were based on Descarte and our separation from the natural world - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - adjacency - materialism, science and neoliberalism - will technology save us? - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - to - The Three Great Separations

key insight / summary - neoliberalism and industrial capitalism were based on Descarte and our separation from the natural world - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - FIrst, Descarte separated the mind from the body. We have the paradox of: - godlike mind housed in - animalistic bodies - (incidentally, this sets us up for the exageration of the existential crisis of the denial of death in modernity - Ernest Becker) - Then we impose separation of external vs internal world - Then, we have separate categories of mind and nature, and we begin othering of: - women - other (indigenous) cultures - What Alnoor and Lynn forgot to mention was that there is another separation that preceded the industrial revolution, the separation of people into distinct classes of: - producer - consumer - Then with the advance of Newtonian physics and the wild success of materialist theory applied to create a plethora of industrial technologies, a wedding occurred between: - dualism and - materialism - Materialism decomposes everything into subatomic particles that a rational mind can understand - To those who think science and technology can save us from the crisis it helped create - the deeper understanding reveals that science and technology are themselves agents of separation.

to - See the three great separations - https://hyp.is/go?url=https%3A%2F%2Finthesetimes.com%2Farticle%2Findustrial-agricultural-revolution-planet-earth-david-korten&group=world

for - definition - neoliberalism - as the name of the dominant, totalizing, cultural operating system of modernity - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - summary - neoliberalism - as the name of the dominant, totalizing, cultural operating system of modernity - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 definition - neoliberalism - as the name of the dominant, totalizing, cultural operating system of modernity - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - Neoliberalism is a totalizing, cultural operating system for modernity - It is all of these things: - a political philosophy - an economic practice - a cosmology - a wordview - an ontology - a theocracy - a religious worldview based on faith - Most of the dogmas of neoliberalism have been proven to be false, and yet it is still taught in most institutions of higher education summary - Some of the premises of neoliberalism are: - 1. humans are homo economicus - our chief concern is our selves and NOT others - Enlightenment theories - Scientism - Evolutionary theory - All our systems are designed on this false premise - 2. Hierarchy is inevitable and necessary for order. Without it, we would revert to beasts - The system embeds - Patriarchism - White Supremacy - Gender inequality - 3. The individual is the primary unit of power - together with 1) and 2), it creates inherent competition - 4. Material wealth and power is the measure of wellbeing - If you have money, you are considered a success, otherwise, you are considered a moral failure

for - objective - of webinar - collective sensemaking - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - adjacency - philanthropy is the upstream driver of - social change - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - stats - philanthropy - possibly the world's 8th largest industry - with little transparency - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - paradox - of philanthropy - People who amass huge fortunes through a lifetime of extracting from nature, people and destroying the fabric of life - present philanthropy as a way to atone for their own sins - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - key objective - of Post Capitalist Philanthropy - call for philanthropy to be in the liberation of capital in a way that supports transition pathways - to explore other ways of being and knowing that are in co-creative relationship with life itself - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - quote - from book - If you do not have a critique of capitalist modernity, you are contextually irrelevant - but if all you have is a critique, you are spiritually incredibly impoverished - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

for - key points - excavate and replace engrained capitalist worldviews and behaviors and replace with healthier alternatives - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

key points - excavate and replace engrained capitalist worldviews and behaviors and replace with healthier alternatives - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023 - For those of western tradition, - find out what deeply engrained capitalist habits must we excavate in our - minds, - bodies, - worldviews, - behaviors, - hearts (feelings) and - ways of being - and replace them with healthier alternatives

for - summary - explaining the paradox of Post Capitalist Philanthropy - a conceptual container - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Lynn Murphy - 2023

summary - explaining the paradox of Post Capitalist Philanthropy - a conceptual container - Using this idea of Post Capitalist Philanthropy not as a simple linear vehicle for transition from old to new system - It is a conceptual container that holds multiple values and ways of being, including: - reciprocity - solidarity - compassion - reverence for life - Recognition of transitioning out of a system that is about: - extractionism - commodification of - humans - nature - our relationships - domination - exploitation - What does an alternative way of being look like?

for - second and ultimate paradox - Post Capitalist Philanthropy itself - paradoxes - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladna - Lynn Murphy - 2023

for - paradoxes - first one - pronouncement - the written word - evocative - but also hegemonic - especially the English language - there are other oral traditions - try to open nondual embodied cognition using English - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladna - Lynn Murphy - 2023

for - quote - power of language - Alnoor Ladha - Lynn Murphy - Post Capitalist Philanthropy Webinar 1 - 2023

quote - power of language - Alnoor Ladha - Lynn Murphy - Post Capitalist Philanthropy Webinar 1 - 2023 - (see below) - We are still performers of the dominant culture

for - youtube - Post Capitalist Philanthropy Webinar 1 - Alnoor Ladha - Culture Hack Labs - Lynn Murphy - 2023

summary - to visit the annotated transcription of this video, please goto: - https://via.hypothes.is/https://www.youtube.com/watch?v=dk6F4IlEbAk - funding bottom-up, transition work in the polycrisis - Alnoor Ladha - Lynn Murphy

Reviewer #1 (Public review):

Summary:

This paper describes molecular dynamics simulations (MDS) of the dynamics of two T-cell receptors (TCRs) bound to the same major histocompatibility complex molecule loaded with the same peptide (pMHC). The two TCRs (A6 and B7) bind to the pMHC with similar affinity and kinetics, but employ different residue contacts. The main purpose of the study is to quantify via MDS the differences in the inter- and intra-molecular motions of these complexes, with a specific focus on what the authors describe as catch-bond behavior between the TCRs and pMHC, which could explain how T-cells can discriminate between different peptides in the presence of weak separating force.

Strengths:

The authors present extensive simulation data that indicates that, in both complexes, the number of high-occupancy inter-domain contacts initially increases with applied load, which is generally consistent with the authors' conclusion that both complexes exhibit catch-bond behavior, although to different extents. In this way, the paper somewhat expands our understanding of peptide discrimination by T-cells.

Weaknesses:

While generally well supported by data, the conclusions would nevertheless benefit from a more concise presentation of information in the figures, as well as from suggesting experimentally testable predictions.

Reviewer #1 (Public review):

Summary:

In the manuscript entitled 'The Role of ATP Synthase Subunit e (ATP5I) in 1 Mediating the Metabolic and Antiproliferative 2 Effects of Biguanides', Lefrancois G et al. identifies ATP5I, a subunit of F1Fo-ATP synthase, as a key target of medicinal biguanides. ATP5I stabilizes F1Fo-ATP synthase dimers, essential for cristae morphology, but its role in cancer metabolism is understudied. The research shows ATP5I interacts with a biguanide analogue, and its knockout in pancreatic cancer cells mimics biguanide treatment effects, including altered mitochondria, reduced OXPHOS, and increased glycolysis. ATP5I knockout cells resist biguanide-induced antiproliferative effects, but reintroducing ATP5I restores the effects of metformin and phenformin. These findings highlight ATP5I as a promising mitochondrial target for cancer therapies. The manuscript is well written.

Strengths:

Demonstrated the experiments in systematic and well-accepted methods.

Weaknesses:

The significance of the target molecule and mechanisms may help in understanding the molecular mechanisms of metformin.

Reviewer #1 (Public review):

Summary:

The authors' goal was to advance the understanding of metabolic flux in the bradyzoite cyst form of the parasite T. gondii, since this is a major form of transmission of this ubiquitous parasite, but very little is understood about cyst metabolism and growth.

Nonetheless, this is an important advance in understanding and targeting bradyzoite growth.

Strengths:

The study used a newly developed technique for growing T. gondii cystic parasites in a human muscle-cell myotube format, which enables culturing and analysis of cysts. This enabled the screening of a set of anti-parasitic compounds to identify those that inhibit growth in both vegetative (tachyzoite) forms and bradyzoites (cysts). Three of these compounds were used for comparative Metabolomic profiling to demonstrate differences in metabolism between the two cellular forms.

One of the compounds yielded a pattern consistent with targeting the mitochondrial bc1 complex and suggests a role for this complex in metabolism in the bradyzoite form, an important advance in understanding this life stage.

Weaknesses:

Studies such as these provide important insights into the overall metabolic differences between different life stages, and they also underscore the challenge of interpreting individual patterns caused by metabolic inhibitors due to the systemic level of some of the targets, so that some observed effects are indirect consequences of the inhibitor action. While the authors make a compelling argument for focusing on the role of the bc1 complex, there are some inconsistencies in the patterns that underscore the complexity of metabolic systems.

Reviewer #1 (Public review):

Neuronal activity spatiotemporal fine-tuning of cerebral blood flow balances metabolic demands of changing neuronal activity with blood supply. Several 'feed-forward' mechanisms have been described that contribute to activity-dependent vasodilation as well as vasoconstriction leading to a reduction in perfusion. Involved messengers are ionic (K+), gaseous (NO), peptides (e.g., NPY, VIP), and other messengers (PGE2, GABA, glutamate, norepinephrine) that target endothelial cells, smooth muscle cells, or pericytes. Contributions of the respective signaling pathways likely vary across brain regions or even within specific brain regions (e.g., across the cortex) and are likely influenced by the brain's physiological state (resting, active, sleeping) or pathological departures from normal physiology.

The manuscript "Elevated pyramidal cell firing orchestrates arteriolar vasoconstriction through COX-2-derived prostaglandin E2 signaling" by B. Le Gac, et al. investigates mechanisms leading to activity-dependent arteriole constriction. Here, mainly working in brain slices from mice expressing channelrhodopsin 2 (ChR2) in all excitatory neurons (Emx1-Cre; Ai32 mice), the authors show that strong optogenetic stimulation of cortical pyramidal neurons leads to constriction that is mediated through the cyclooxygenase-2 / prostaglandin E2 / EP1 and EP3 receptor pathway with contribution of NPY-releasing interneurons and astrocytes releasing 20-HETE. Specifically, using a patch clamp, the authors show that 10-s optogenetic stimulation at 10 and 20 Hz leads to vasoconstriction (Figure 1), in line with a stimulation frequency-dependent increase in somatic calcium (Figure 2). The vascular effects were abolished in the presence of TTX and significantly reduced in the presence of glutamate receptor antagonists (Figure 3). The authors further show with RT-PCR on RNA isolated from patched cells that ~50% of analyzed cells express COX-1 or -2 and other enzymes required to produce PGE2 or PGF2a (Figure 4). Further, blockade of COX-1 and -2 (indomethacin), or COX-2 (NS-398) abolishes constriction. In animals with chronic cranial windows that were anesthetized with ketamine and medetomidine, 10-s long optogenetic stimulation at 10 Hz leads to considerable constriction, which is reduced in the presence of indomethacin. Blockade of EP1 and EP3 receptors leads to a significant reduction of the constriction in slices (Figure 5). Finally, the authors show that blockade of 20-HETE synthesis caused moderate and NPY Y1 receptor blockade a complete reduction of constriction.

The mechanistic analysis of neurovascular coupling mechanisms as exemplified here will guide further in-vivo studies and has important implications for human neuroimaging in health and disease. Most of the data in this manuscript uses brain slices as an experimental model which contrasts with neurovascular imaging studies performed in awake (headfixed) animals. However, the slice preparation allows for patch clamp as well as easy drug application and removal. Further, the authors discuss their results in view of differences between brain slices and in vivo observations experiments, including the absence of vascular tone as well as blood perfusion required for metabolite (e.g., PGE2) removal, and the presence of network effects in the intact brain. The manuscript and figures present the data clearly; regarding the presented mechanism, the data supports the authors' conclusions. Some of the data was generated in vivo in head-fixed animals under anesthesia; in this regard, the authors should revise the introduction and discussion to include the important distinction between studies performed in slices, or in acute or chronic in-vivo preparations under anesthesia (reduced network activity and reduced or blockade of neuromodulation, or in awake animals (virtually undisturbed network and neuromodulatory activity). Further, while discussed to some extent, the authors could improve their manuscript by more clearly stating if they expect the described mechanism to contribute to CBF regulation under 'resting state conditions' (i.e., in the absence of any stimulus), during short or sustained (e.g., visual, tactile) stimulation, or if this mechanism is mainly relevant under pathological conditions; especially in the context of the optogenetic stimulation paradigm being used (10-s long stimulation of many pyramidal neurons at moderate-high frequencies) and the fact that constriction leading to undersupply in response to strongly increased neuronal activity seems counterintuitive?

Reviewer #1 (Public review):

Dwulet et al. combined experimental and modeling approaches to investigate how correlated spontaneous activity in the mouse's primary visual (V1) and primary somatosensory (S1) areas drives the development of multisensory integration in area RL. Notably, they focused on early developmental stages, before sensory experience occurs. Consistent with previous experimental findings, the authors first demonstrated that spontaneous activity becomes more sparse across development in all three areas, as measured by event amplitude, event duration, and participation ratio. Using a linear mixed model analysis to compare the maturation of this spontaneous activity, they found evidence that S1 matured the fastest. The authors then presented experimental evidence suggesting that these spontaneous events were moderately correlated both spatially and temporally.

They hypothesized that activity-dependent mechanisms use these correlations to establish connectivity across these regions. To test this hypothesis, the authors modeled a feedforward network with connections from S1 to RL and from V1 to RL, where the strength of connections depended on a Hebbian term for potentiation and a heterosynaptic term for depression. By investigating different levels of V1-S1 correlations, they found that moderate levels of correlation led to the significant development of topographically organized connectivity while maintaining a mix of bimodal and unimodal cells in RL. Additionally, when simulating a network with a more mature S1, they observed that topographical maps improved not only between S1 and RL but also between V1 and RL. Finally, the authors use linear regression to suggest that the mixture of bimodal and unimodal cells in RL is optimal for encoding the maximum amount of information from both V1 and S1.

However, there are significant gaps between the experimental data and the modeling setup, which weaken the paper's conclusions. Additionally, some key details are omitted, making it difficult to fully assess their analysis and interpret some of their figures.

(1) Some of the statistical measures and techniques in Figure 1 could benefit from clearer definitions. While the thresholds for activation (peak with at least 5% dF/F0) and events (20% of recorded cells activated simultaneously) are provided, event duration and participation rate are not clearly defined. Based on this definition of event alone, it is unclear why the minimum participation rate in Figure 1F is not 20%. Additionally, the conclusion that S1 matures earlier than RL and V1 could be strengthened by including a direct comparison between S1 and RL, as the current analysis only compares these areas to V1.

(2) The wide-field experiments in Figure 2 could be expanded to support the feedforward modeling assumptions. Currently, the spatial and temporal correlations presented leave open the possibility that these spontaneous events are traveling waves propagating from V1 to RL to S1 (or vice versa). This scenario would suggest a different connectivity scheme for the model. Clarifying this point with additional data analysis, specifically including temporal correlations involving RL, could provide stronger support for the model's assumptions.

(3) The functional correlation map in Figure 2D appears contradictory to the authors' modeling assumption that inputs are correlated spatially in V1 and S1. While V1 seed points align topographically with RL, this organization breaks down when extended into S1. In contrast, and in support of the modeling assumption, Figure 2E shows clearer topography across all three regions. A discussion of this discrepancy would be helpful, as it's a key conclusion of the figure. Additionally, it is unclear when this data was collected during development. Clarifying the developmental stage and analyzing how this map changes over time could strengthen the results.

(4) The modeling of spontaneous events with fixed amplitude and duration seems inconsistent with the experimental data in Figure 1, which shows variability in these parameters. This is particularly confusing in Figure 4, where S1 maturation is modeled as a stronger topographical alignment with RL, but the experimental data defines maturation based on amplitude, duration, and event rates. Justifying these modeling choices or adapting the model to reflect experimental variability would create a better connection between the theory and data.

(5) Several important details of the mathematical model are missing or unclear, partly due to typos. The Results section mentions the general framework of the input correlation matrix (e.g., "S1 and V1 neurons were driven by a combination of events, independent and shared in each V1 and S1" and "each independent event activated a randomly chosen, contiguous set of neurons"), but the specifics are not fully explained. Additionally, the caption of Figure 5 refers to a non-linear transfer function (a sigmoid), but these details are not provided in the Methods section, which instead suggests a linear model was used. A careful review of the main text and Methods section would help ensure that all the necessary details are included and that the story is both complete and accurate.

(6) While Figure 5 supports the paper's conclusion that a mixture of unimodal and bimodal neurons in RL optimizes information encoding, the authors missed an opportunity to strengthen the connection between the model and experimental data. Specifically, they could apply this reconstruction method to the experimental data and examine how RL's ability to reconstruct V1/S1 activity changes across development. Their model predicts that this performance would improve over time, and if this trend is observed in the experimental data, it would provide strong validation that these feedforward connections are developing in line with the model's predictions.

Reviewer #1 (Public review):

Summary:

The authors report the structure of the human CTF18-RFC complex bound to PCNA. Similar structures (and more) have been reported by the O'Donnell and Li labs. This study should add to our understanding of CTF18-RFC in DNA replication and clamp loaders in general. However, there are numerous major issues that I recommend the authors fix.

Strengths:

The structures reported are strong and useful for comparison with other clamp loader structures that have been reported lately.

Weaknesses:

The structures don't show how CTF18-RFC opens or loads PCNA. There are recent structures from other groups that do examine these steps in more detail, although this does not really dampen this reviewer's enthusiasm. It does mean that the authors should spend their time investigating aspects of CTF18-RFC function that were overlooked or not explored in detail in the competing papers. The paper poorly describes the interactions of CTF18-RFC with PCNA and the ATPase active sites, which are the main interest points. The nomenclature choices made by the authors make the manuscript very difficult to read.

Reviewer #1 (Public review):

This study presents Jyvaskylavirus, a new member of the Marseilleviridae family, infecting Acanthamoeba castellanii. The study provides a detailed and comprehensive genomic and structural analysis of Jyvaskylavirus. The authors identified ORF142 as the capsid penton protein and additional structural proteins that comprise the virion. Using a combination of imaging techniques the authors provide new insights into the giant virus architecture and lifecycle. The study could be improved by providing atomic coordinates and refinement statistics, comparisons with available giant virus structures could be expanded, and the novelty in terms of the first isolated example of a giant virus from Finland could be expounded upon.

The study contributes new structural and genomic diversity to the Marseilleviridae family, hinting at a broader distribution and ecological significance of giant viruses than previously thought.

Reviewer #1 (Public review):

Summary:

The authors report the role of a novel gene Aff3ir-ORF2 in flow-induced atherosclerosis. They show that the gene is anti-inflammatory in nature. It inhibits the IRF5-mediated athero-progression by inhibiting the causal factor (IRF5). Furthermore, the authors show a significant connection between shear stress and Aff3ir-ORF2 and its connection to IRF5 mediated athero-progression in different established mice models which further validates the ex vivo findings.

Strengths:

(1) An adequate number of replicates were used for this study.<br /> (2) Both in vitro and in vivo validation was done.<br /> (3) The figures are well presented.<br /> (4) In vivo causality is checked with cleverly designed experiments.

Weaknesses:

(1) Inflammatory proteins must be measured with standard methods e.g ELISA as mRNA level and protein level does not always correlate.

(2) RNA seq analysis has to be done very carefully. How does the euclidean distance correlate with the differential expression of genes. Do they represent the neighborhood? If they do how does this correlation affect the conclusion of the paper?

(3) The volcano plot does not indicate the q value of the shown genes. It is advisable to calculate the q value for each of the genes which represents the FDR probability of the identified genes.

(4) GO enrichment was done against the Global gene set or a local geneset? The authors should provide more detailed information about the analysis.

(5) If the analysis was performed against a global gene set. How does that connect with this specific atherosclerotic microenvironment?

(6) What was the basal expression of genes and how did the DGE (differential gene expression) values differ?

(7) How was IRF5 picked from GO analysis? was it within the 20 most significant genes?

(8) Microscopic studies should be done more carefully? There seems to be a global expression present on the vascular wall for Aff3ir-ORF2 and the expression seems to be similar to AFF3 in Figure 1.

Reviewer #1 (Public review):

Summary:

Multiple compounds that inhibit ATP-sensitive potassium (KATP) channels also chaperone channels to the surface membrane. The authors used an artificial intelligence (AI)-based virtual screening (AtomNet) to identify novel compounds that exhibit chaperoning effects on trafficking-deficient disease-causing mutant channels. One compound, which they named Aekatperone, acts as a low affinity, reversible inhibitor and effective chaperone. A cryoEM structure of KATP bound to Aekatperone showed that the molecule binds at the canonical inhibitory site.

Strengths and weaknesses:

The details of the AI screening itself are inevitably opaque but appear to differ from classical virtual screening in not involving any physical docking of test compounds into the target site. The authors mention criteria that were used to limit the number of compounds so that those with high similarity to known binders and 'sequence identity' (does this mean structural identity) were excluded. The identified molecules contain sulfonylurea-like moieties. How different are they from other sulfonylure4as?

The experimental work confirming that Aekatperone acts to traffic mutant KATP channels to the surface and acts as a low affinity, reversible, inhibitor is comprehensive and clear, with very convincing cell biological and patch-clamp data, as is the cryoEM structural analysis, for which the group are leading experts. In addition to the three positive chaperone-effective molecules, the authors identified a large number of compounds that are predicted binders but apparently have no chaperoning effect. Did any of them have an inhibitory action on channels? If so, does this give clues to separating chaperoning from inhibitory effects?

The authors suggest that the novel compound may be a promising therapeutic for the treatment of congenital hyperinsulinism due to trafficking defective KATP mutations. Because they are low-affinity, reversible, inhibitors. This is a very interesting concept, and perhaps a pulsed dosing regimen would allow trafficking without constant channel inhibition (which otherwise defeats the therapeutic purpose), although it is unclear whether the new compound will offer advantages over earlier low-affinity sulfonylurea inhibitor chaperones. These include tolbutamide which has very similar affinity and effect to Aekatperone. As the authors point out this (as well as other sulfonylureas) is currently out of favor because of potential adverse cardiovascular effects, but again, it is unclear why Aekatperone should not have the same concerns.

Reviewer #1 (Public review):

Summary:

This manuscript is a focused investigation of the phosphor-regulation of a C. elegans kinesin-2 motor protein, OSM-3. In C-elegans sensory ciliary, kinesin-2 motor proteins Kinesin-II complex and OSM-3 homodimer transport IFT trains anterogradely to the ciliary tip. Kinesin-II carries OSM-3 as an inactive passenger from the ciliary base to the middle segment, where kinesin-II dissociates from IFT trains and OSM-3 gets activated and transports IFT trains to the distal segment. Therefore, activation/inactivation of OSM-3 plays an essential role in its ciliary function.

Strengths:

In this study, using mass spectrometry, the authors have shown that the NEKL-3 kinase phosphorylates a serine/threonine patch at the hinge region between coiled coils 1 and 2 of an OSM-3 dimer, referred to as the elbow region in ubiquitous kinesin-1. Phosphomimic mutants of these sites inhibit OSM-3 motility both in vitro and in vivo, suggesting that this phosphorylation is critical for the autoinhibition of the motor. Conversely, phospho-dead mutants of these sites hyperactivate OSM-3 motility in vitro and affect the localization of OSM3 in C. elegans. The authors also showed that Alanine to Tyrosine mutation of one of the phosphorylation rescues OS-3 function in live worms.

Weaknesses:

Collectively, this study presents evidence for the physiological role of OSM-3 elbow phosphorylation in its autoregulation, which affects ciliary localization and function of this motor. Overall, the work is well performed, and the results mostly support the conclusions of this manuscript. However, the work will benefit from additional experiments to further support conclusions and rule out alternative explanations, filling some logical gaps with new experimental evidence and in-text clarifications, and improving writing.

Reviewer #1 (Public review):

In this manuscript, Dillard and colleagues integrate cross-species genomic data with a systems approach to identify potential driver genes underlying human GWAS loci and establish the cell type(s) within which these genes act and potentially drive disease. Specifically, they utilize a large single-cell RNA-seq (scRNA-seq) dataset from an osteogenic cell culture model - bone marrow-derived stromal cells cultured under osteogenic conditions (BMSC-OBs) - from a genetically diverse outbred mouse population called the Diversity Outbred (DO) stock to discover network driver genes that likely underlie human bone mineral density (BMD) GWAS loci. The DO mice segregate over 40M single nucleotide variants, many of which affect gene expression levels, therefore making this an ideal population for systems genetic and co-expression analyses. The current study builds on previously published work from the same group that used co-expression analysis to identify co-expressed "modules" of genes that were enriched for BMD GWAS associations. In this study, the authors utilize a much larger scRNA-seq dataset from 80 DO BMSC-OBs, infer co-expression-based and Bayesian networks for each identified mesenchymal cell type, focused on networks with dynamic expression trajectories that are most likely driving differentiation of BMSC-OBs, and then prioritized genes ("differentiation driver genes" or DDGs) in these osteogenic differentiation networks that had known expression or splicing QTLs (eQTL/sQTLs) in any GTEx tissue that colocalized with human BMD GWAS loci. The systems analysis is impressive, the experimental methods are described in detail, and the experiments appear to be carefully done. The computational analysis of the single-cell data is comprehensive and thorough, and the evidence presented in support of the identified DDGs, including Tpx2 and Fgfrl1, is for the most part convincing. Some limitations in the data resources and methods hamper enthusiasm somewhat and are discussed below. Overall, while this study will no doubt be valuable to the BMD community, the cross-species data integration and analytical framework may be more valuable and generally applicable to the study of other diseases, especially for diseases with robust human GWAS data but for which robust human genomic data in relevant cell types is lacking.

Specific strengths of the study include the large scRNA-seq dataset on BMSC-OBs from 80 DO mice, the clustering analysis to identify specific cell types and sub-types, the comparison of cell type frequencies across the DO mice, and the CELLECT analysis to prioritize cell clusters that are enriched for BMD heritability (Figure 1). The network analysis pipeline outlined in Figure 2 is also a strength, as is the pseudotime trajectory analysis (results in Figure 3). One weakness involves the focus on genes that were previously identified as having an eQTL or sQTL in any GTEx tissue. The authors rightly point out that the GTEx database does not contain data for bone tissue, but the reason that eQTLs can be shared across many tissues - this assumption is valid for many cis-eQTLs, but it could also exclude many genes as potential DDGs with effects that are specific to bone/osteoblasts. Indeed, the authors show that important BMD driver genes have cell-type-specific eQTLs. Furthermore, the mesenchymal cell type-specific co-expression analysis by iterative WGCNA identified an average of 76 co-expression modules per cell cluster (range 26-153). Based on the limited number of genes that are detected as expressed in a given cell due to sparse per-cell read depth (400-6200 reads/cell) and dropouts, it's hard to believe that as many as 153 co-expression modules could be distinguished within any cell cluster. I would suspect some degree of model overfitting here and would expect that many/most of these identified modules have very few gene members, but the methods list a minimum module size of 20 genes. How do the numbers of modules identified in this study compare to other published scRNA-seq studies that use iterative WGCNA?

In the section "Identification of differentiation driver genes (DDGs)", the authors identified 408 significant DDGs and found that 49 (12%) were reported by the International Mouse Knockout [sic] Consortium (IMPC) as having a significant effect on whole-body BMD when knocked out in mice. Is this enrichment significant? E.g., what is the background percentage of IMPC gene knockouts that show an effect on whole-body BMD? Similarly, they found that 21 of the 408 DDGs were genes that have BMD GWAS associations that colocalize with GTEx eQTLs/sQTLs. Given that there are > 1,000 BMD GWAS associations, is this enrichment (21/408) significant? Recommend performing a hypergeometric test to provide statistical context to the reported overlaps here.

Reviewer #1 (Public review):

Summary:

The manuscript by Bindu et al. created an AAV-based tool (GEARAOCS) to perform in vivo genome editing of mouse astrocytes. The authors engineered a versatile AAV vector that allows for gene deletion through NHNJ, site-specific knock-in by HDR, and gene trap. By utilizing this tool, the authors deleted Sparcl1 virally in subsets of astrocytes and showed that thalamocortical synapses in cortical layer IV are indeed reduced during a critical period of ocular dominance plasticity and in adulthood, whereas there is no change in excitatory synapse number in cortical layer II/III. Furthermore, the authors made a VAMP2 gene-trap AAV vector and showed that astrocyte-derived VAMP2 is required for the maintenance of both excitatory and inhibitory synapses.

Strengths:

This AAV-based tool is versatile for astrocytic gene manipulation in vivo. The work is innovative and exciting, given the paucity of tools available to probe astrocytes in vivo.

Weaknesses:

Several important considerations need to be made for the validation and usage of this tool, including:

Major points:

(1) Efficiency and specificity of spCas9-sgRNA mediated gene knockout in astrocytes. In Figure 3, the authors utilized Sparcl1 gene deletion as the proof-of-principle experiment. The readout for Sparcl1 KO efficiency is solely the immunoreactivity using an antibody raised against Sparcl1. As the method is based on NHEJ, the indels can be diverse and can occur in one allele or two. For the tool and proof-of-principle experiment, it will be important to know the percentage of editing near the PAM site, as well as the actual sequences of indels. This can be done by single-cell PCR of edited astrocytes, similar to the published work (Ye... Chen, Nature Biotechnology 2019).

(2) Along the same line, the authors showed that GEARBOCS TagIn of Sparcl1 resulted in 12.49% efficiency based on the immunohistochemistry of mCherry tag. It is understandable that the knock-in efficiency is much reduced as compared to gene knockout. However, it remains unclear if those 12.49% knock-in cells represent sequence-correct ones, as spCas9-mediated HDR is also an error-prone process, and it may accidentally alter nucleotides near the PAM site without causing the frameshift. The author will need to consider the related evidence or make comments in the discussion.

(3) What are the efficiencies of Sparcl1 GEARBOCS GeneTrap (Figure 3V) and Vamp2 GeneTrap and HA TagIn (Figure 5)?

Minor points:

(1) Figure 3H-J. The authors only showed the representative images of Sparcl1 KO. Please consider including the control (without gRNA), given that there are still many Sparcl1+ signals in Figure 3I (likely because of its expression in other cell types?).

(2) In figure 3Q-T, it appears that some Cas9-EGFP+ astrocytes (Q) do not express Sparcl1 (R). Is Sparcl1 expressed in subsets of astrocytes? Does Cas9-EGFP or Sparcl1-TagIn alter Sparcl1 endogenous expression?

(3) On Page 8, for the explanation of the design of the GEARBOCS construct, the authors have made a self-citation (#43). That was a BioRxiv paper that is being reviewed currently.

(4) For Figures 4 and 6, the graphs seem to be made in R with the x-axis labeled as "Condition". The y-axis labels are too small to read properly, especially in print. It would be better to make the graphs clearer like Figure 2 and Figure 3.

(5) On Page 13, "Figures 3V-Y" were referred to. However, there are no Figures 3W, X, and Y.

(6) There are a few typos in the manuscript, including line 900 "immunofluorescence microscopy images of a Cas9-EGFP-positive astrocytes (green)".

Reviewer #1 (Public review):

Summary:

Wang et al. created a series of specific FLIM-FRET sensors to measure the activity of different Rab proteins in small cellular compartments. They apply the new sensors to monitor Rab activity in dendritic spines during induction of LTP. They find sustained (30 min) inactivation of Rab10 and transient (5 min) activation of Rab4 after glutamate uncaging in zero Mg. NMDAR function and CaMKII activation are required for these effects. Knockdown of Rab4 reduced spine volume change while knockdown of Rab10 boosted it and enhanced functional LTP (in KO mice). To test Rab effects on AMPA receptor exocytosis, the authors performed FRAP of fluorescently labeled GluA1 subunits in the plasma membrane. Within 2-3 min, new AMPARs appear on the surface via exocytosis. This process is accelerated by Rab10 knock-down and slowed by Rab4 knock-down. The authors conclude that CaMKII promotes AMPAR exocytosis by i) activating Rab4, the exocytosis driver and ii) inhibiting Rab10, possibly involved in AMPAR degradation.

Strengths:

The work is a technical tour de force, adding fundamental insights to our understanding of the crucial functions of different Rab proteins in promoting/preventing synaptic plasticity. The complexity of compartmentalized Ras signaling is poorly understood and this study makes substantial inroads. The new sensors are thoroughly characterized, seem to work very well, and will be quite useful for the neuroscience community and beyond (e.g. cancer research). The use of FLIM for read-out is compelling for precise activity measurements in rapidly expanding compartments (i.e., spines during LTP).

Weaknesses:

The interpretation of the FRAP experiments (Figure 5, Ext. Data Figure 13) is not straightforward as spine volume and surface area greatly expand during uncaging. I appreciate the correction for the added spine membrane shown in Extended Data Figure 14i, but shouldn't this be a correction factor (multiplication) derived from the volume increase instead of a subtraction?

Also, experiments were not conducted or analyzed blind, risking bias in the selection/exclusion of experiments for analysis. This reduces my confidence in the results.

Reviewer #1 (Public review):

Summary:

This paper investigates how recurrent neural networks (RNNs) can perform context-dependent decision-making (CDM). The authors use low-rank RNN modeling and focus on a CDM task where subjects are presented with sequences of auditory pulses that vary in location and frequency, and they must determine either the prevalent location or frequency based on an external context signal. In particular, the authors focus on the problem of differentiating between two distinct selection mechanisms: input modulation, which involves altering the stimulus input representation, and selection vector modulation, which involves altering the "selection vector" of the dynamical system.

First, the authors show that rank-one networks can only implement input modulation and that higher-rank networks are required for selection vector modulation. Then, the authors use pathway-based information flow analysis to understand how information is routed to the accumulator based on context. This analysis allows the authors to introduce a novel definition of selection vector modulation that explicitly links it to changes in the effective coupling along specific pathways within the network.

The study further generates testable predictions for differentiating selection vector modulation from input modulation based on neural dynamics. In particular, the authors find that:<br /> (1) A larger proportion of selection vector modulation is expected in networks with high-dimensional connectivity.<br /> (2) Single-neuron response kernels exhibiting specific profiles (peaking between stimulus onset and choice onset) are indicative of neural dynamics in extra dimensions, supporting the presence of selection vector modulation.<br /> (3) The percentage of explained variance (PEV) of extra dynamical modes extracted from response kernels at the population level can serve as an index to quantify the amount of selection vector modulation.

Strengths:

The paper is clear and well-written, and it draws bridges between two recent important approaches in the study of CDM: circuit-level descriptions of low-rank RNNs, and differentiation across alternative mechanisms in terms of neural dynamics. The most interesting aspect of the study involves establishing a link between selection vector modulation, network dimensionality, and dimensionality of neural dynamics. The high correlation between the networks' mechanisms and their dimensionality (Figure 7d) is surprising since differentiating between selection mechanisms is generally a difficult task, and the strength of this result is further corroborated by its consistency across multiple RNN hyperparameters (Figure 7-Figure Supplement 1 and Figure 7-figure supplement 2). Interestingly, the correlation between the selection mechanism and the dimensionality of neural dynamics is also high (Figure 7g), potentially providing a promising future avenue for the study of neural recordings in this task.

Weaknesses:

The first part of the manuscript is not particularly novel, and it would be beneficial to clearly state which aspects of the analyses and derivations are different from previous literature. For example, the derivation that rank-1 RNNs cannot implement selection vector modulation is already present in the Extended Discussion of Pagan et al., 2022 (Equations 42-43). Similarly, it would be helpful to more clearly explain how the proposed pathway-based information flow analysis differs from the circuit diagram of latent dynamics in Dubreuil et al., 2022.

With regard to the results linking selection vector modulation and dimensionality, more work is required to understand the generality of these results, and how practical it would be to apply this type of analysis to neural recordings. For example, it is possible to build a network that uses input modulation and to greatly increase the dimensionality of the network simply by adding additional dimensions that do not directly contribute to the computation. Similarly, neural responses might have additional high-dimensional activity unrelated to the task. My understanding is that the currently proposed method would classify such networks incorrectly, and it is reasonable to imagine that the dimensionality of activity in high-order brain regions will be strongly dependent on activity that does not relate to this task.

Finally, a number of aspects of the analysis are not clear. The most important element to clarify is how the authors quantify the "proportion of selection vector modulation" in vanilla RNNs (Figures 7d and 7g). I could not find information about this in the Methods, yet this is a critical element of the study results. In Mante et al., 2013 and in Pagan et al., 2022 this was done by analyzing the RNN linearized dynamics around fixed points: is this the approach used also in this study? Also, how are the authors producing the trial-averaged analyses shown in Figures 2f and 3f? The methods used to produce this type of plot differ in Mante et al., 2013 and Pagan et al., 2022, and it is necessary for the authors to explain how this was computed in this case.

I am also confused by a number of analyses done to verify mathematical derivations, which seem to suggest that the results are close to identical, but not exactly identical. For example, in the histogram in Figure 6b, or the histogram in Figure 7-figure supplement 3d: what is the source of the small variability leading to some of the indices being less than 1?

Reviewer #1 (Public review):

Summary:

This paper advances a new understanding of plasticity in artificial neural networks. It shows that weight changes can be decomposed into two components: the first governs the magnitude (or gain) of responses in a particular layer; the second governs the relationship of those responses to the input to that layer. Then, it shows that separate control of these two factors via a surprise-based metaplasticity can avoid catastrophic forgetting as well as induce successful generalization in different conditions, through a series of simulation experiments in linear networks. The authors argue that separate control of the two factors may be at work in the brain and may underlie the ability of humans and other animals to perform successful sequential learning. The paper is hampered by confusing terminology and the precise setup of some of the simulations is unclear. The paper also focuses exclusively on the linear case, which limits confidence in the generality of the results. The paper would also benefit from the inclusion of specific predictions for neural data that would confirm the idea that the separate control of these two factors underlies successful continual learning in the brain.

Strengths:

(1) The theoretical framework developed by the paper is interesting, and could have wide applicability for both training networks and for understanding plasticity.

(2) The simulations convincingly show benefits to the coordinated eligibility model of plasticity advanced by the authors.

Weaknesses:

(1) The simulation results are limited to simple tasks in linear networks, it would be interesting to see how the intuitions developed in the linear case extend to nonlinear networks.

(2) The terminology is somewhat confusing and this can make the paper difficult to follow in some places.

(3) The details of some of the simulations are lacking.

Reviewer #1 (Public review):

This paper presents a comprehensive study of how neural tracking of speech is affected by background noise. Using five EEG experiments and Temporal response function (TRF), it investigates how minimal background noise can enhance speech tracking even when speech intelligibility remains very high. The results suggest that this enhancement is not attention-driven but could be explained by stochastic resonance. These findings generalize across different background noise types and listening conditions, offering insights into speech processing in real-world environments.

I find this paper well-written, the experiments and results are clearly described. However, I have a few comments that may be useful to address.

(1) The behavioral accuracy and EEG results for clear speech in Experiment 4 differ from those of Experiments 1-3. Could the author provide insights into the potential reasons for this discrepancy? Might it be due to linguistic/ acoustic differences between the passages used in experiments? If so, what was the rationale behind using different passages across different experiments?

(2) Regarding peak amplitude extraction, why were the exact peak amplitudes and latencies of the TRFs for each subject not extracted, and instead, an amplitude average within a 20 ms time window based on the group-averaged TRFs used? Did the latencies significantly differ across different SNR conditions?

(3) How is neural tracking quantified in the current study? Does improved neural tracking correlate with EEG prediction accuracy or individual peak amplitudes? Given the differing trends between N1 and P2 peaks in babble and speech-matched noise in experiment 3, how is it that babble results in greater envelope tracking compared to speech-matched noise?

(4) The paper discusses how speech envelope-onset tracking varies with different background noises. Does the author expect similar trends for speech envelope tracking as well? Additionally, could you explain why envelope onsets were prioritized over envelope tracking in this analysis?

Reviewer #1 (Public review):

Summary:

Sun et al. are interested in how experience can shape the brain and specifically investigate the plasticity of the Toll-6 receptor-expressing dopaminergic neurons (DANs). To learn more about the role of Toll-6 in the DANs, the authors examine the expression of the Toll-6 receptor ligand, DNT-2. They show that DNT-2 expressing cells connect with DANs and that loss of function of DNT-2 in these cells reduces the number of PAM DANs, while overexpression causes alterations in dendrite complexity. Finally, the authors show that alterations in the levels of DNT-2 and Toll-6 can impact DAN-driven behaviors such as climbing, arena locomotion, and learning and long-term memory.

Strengths:

The authors methodically test which neurotransmitters are expressed by the 4 prominent DNT-2 expressing neurons and show that they are glutamatergic. They also use Trans-Tango and Bac-TRACE to examine the connectivity of the DNT-2 neurons to the dopaminergic circuit and show that DNT-2 neurons receive dopaminergic inputs and output to a variety of neurons including MB Kenyon cells, DAL neurons, and possibly DANS.

Weaknesses:

(1) To identify the DNT-2 neurons, the authors use CRISPR to generate a new DN2-GAL4. They note that they identified at least 12 DNT-2 plus neurons. In Supplementary Figure 1A, the DNT-2-GAL4 driver was used to express a UAS-histoneYFP nuclear marker. From these figures, it looks like DNT-2-GAL4 is labeling more than 12 neurons. Is there glial expression? This question is relevant as it is not clear how many other cell types are being manipulated with the DNT-2-GAL4 driver is used in subsequent experiments. For example, is DNT-2-GAL4--> DNT-2-RNAi is reducing DNT2 in many neurons or glia effects could be indirect.

(2) In Figure 2C the authors show that DNT-2 upregulation leads to an increase in TH levels using q-RT-PCR from whole heads. However, in Figure 3G they also show that DNT-2 overexpression also causes an increase in the number of TH neurons. It is unclear whether TH RNA increases due to expression/cell or number of TH neurons in the head.

(3)DNT-2 is also known as Spz5 and has been shown to activate Toll-6 receptors in glia (McLaughlin et al., 2019), resulting in the phagocytosis of apoptotic neurons. In addition, the knockdown of DNT-2/Spz5 throughout development causes an increase in apoptotic debris in the brain, which can lead to neurodegeneration. Indeed Figure 3H shows that an adult-specific knockdown of DNT-2 using DNT2-GAL4 causes an increase in Dcp1 signal in many neurons and not just TH neurons.

Comments on revisions:

The authors have made some changes in the text to tone down their claims. They have also provided additional images to support their work. However, requested controls are not provided, and new experiments are not added to address reviewer concerns.

Reviewer #2 (Public review):

Summary:

The authors investigated the roles of IncRNA Malat1 in bone homeostasis which was initially believed to be non-functional for physiology. They found that both Malat1 KO and conditional KO in osteoblast lineage exhibit significant osteoporosis due to decreased osteoblast bone formation and increased osteoclast resorption. More interestingly, they found that deletion of Matat1 in osteoclast lineage cell does not affect osteoclast differentiation and function. Mechanistically, they found that Malat1 acts as an co-activator of b-Catenin directly regulating osteoblast activity and indirectly regulating osteoclast activity via mediating OPG, but not RANKL expression in osteoblast and chondrocyte. Their discoveries establish a previous unrecognized paradigm model of Malat1 function in the skeletal system, providing novel mechanistic insights into how a lncRNA integrates cellular crosstalk and molecular networks to fine tune tissue homeostasis, remodeling.

Strengths:

The authors generated global and conditional KO mice in osteoblast and osteoclast lineage cells and carefully analyzed the role of Matat1 with both in vivo and in vitro system. The conclusion of this paper is mostly well supported by data.

Comments on revised version:

The authors have addressed all my concerns.

Reviewer #1 (Public review):

Summary:

SUFU modulates Sonic hedgehog (SHH) signaling and is frequently mutated in the B-subtype of SHH driven medulloblastoma. The B-subtype occurs mostly in infants, is often metastatic, and lacks specific treatment. Yabut et al. found Fgf5 was highly expressed in the B-subtype of SHH driven medulloblastoma by examining a published microarray expression dataset. They then investigated how Fgf5 functions in the cerebellum of mice that have embryonic Sufu loss of function. This loss was induced using the hGFAP-cre transgene, which is expressed multiple cell types in the developing cerebellum, including granule neuron precursors (GNPs) derived from the rhombic lip. By measuring the area of Pax6+ cells in the external granule cell layer (EGL) of Sufu-cKO mice at postnatal day 0, they find Pax6+ cells occupy a larger area in the posterior lobe adjacent to the secondary fissure, which is poorly defined. They show that Fgf5 RNA and phosphoErk1/2 immunostaining are also higher in the same disrupted region. Some of the phosphoErk1/2+ cells are proliferative in the Sufu-cKO. Western blot analysis of Gli proteins that modulate SHH signaling found reduced expression and absence of Gli1 activity in the region of cerebellar dysgenesis in Sufu-cKO mice. This suggests the GNP expansion in this region is independent of SHH signaling. Amazingly, intraventricular injection of the FGFR1-2 antagonist AZD4547 from P0-4 and examined histologoically at P7 found the treatment restored cytoarchitecture in the cerebella of Sufu-cKO mice. This is further supported by NeuN immunostaining in the internal granule cell layer, which labels mature, non-diving neurons, and KI67 immunostaining, indicating dividing cells, and primarily found in the EGL. The mice were treated beginning at a timepoint when cerebellar cytoarchitecture was shown to be disrupted and it is indistinguishable from control following treatment. Fig.3 presents the most convincing and exciting data in this manuscript.

Sufu-cKO do not readily develop cerebellar tumors. The authors detected phosphorylated H2AX immunostaining, which labels double strand breaks, was in some cells in the EGL in regions of cerebellar dysgenesis in the Sufu-cKO, as was cleaved Caspase 3, a marker of apoptosis. P53, downstream of the double strand break pathway, protein was reduced in Sufu-cKO cerebellum. Genetically removing p53 from the Sufu-cKO cerebellum resulted in cerebellar tumors in 2 mo mice. The Sufu;p53-dKO cerebella at P0 lacked clear foliation, and the secondary fissure, even more so than the Sufu-cKO. Fgf5 RNA and signaling (pERK1/2) were also expressed ectopically.

In the revised manuscript, additional details have been added to clarify statistical analyses and to state limitations of the reported results in the absence of further experimental analyses.

Joint Public Review:

Summary:

If synaptic input is functionally clustered on dendrites, nonlinear integration could increase the computational power of neural networks. But this requires the right synapses to be located in the right places. This paper aims to address the question of whether such synaptic arrangements could arise by chance (i.e. without special rules for axon guidance or structural plasticity), and could therefore be exploited even in randomly connected networks. This is important, particularly for the dendrites and biological computation communities, where there is a pressing need to integrate decades of work at the single-neuron level with contemporary ideas about network function.

Using an abstract model where ensembles of neurons project randomly to a postsynaptic population, back-of-envelope calculations are presented that predict the probability of finding clustered synapses and spatiotemporal sequences. Using data-constrained parameters, the authors conclude that clustering and sequences are indeed likely to occur by chance (for large enough ensembles), but require strong dendritic nonlinearities and low background noise to be useful.

Strengths:

- The back-of-envelope reasoning presented can provide fast and valuable intuition. The authors have also made the effort to connect the model parameters with measured values. Even an approximate understanding of cluster probability can direct theory and experiments towards promising directions, or away from lost causes.

- I found the general approach to be refreshingly transparent and objective. Assumptions are stated clearly about the model and statistics of different circuits. Along with some positive results, many of the computed cluster probabilities are vanishingly small, and noise is found to be quite detrimental in several cases. This is important to know, and I was happy to see the authors take a balanced look at conditions that help/hinder clustering, rather than just focus on a particular regime that works.

- This paper is also a timely reminder that synaptic clusters and sequences can exist on multiple spatial and temporal scales. The authors present results pertaining to the standard `electrical' regime (~50-100 µm, <50 ms), as well as two modes of chemical signaling (~10 µm, 100-1000 ms). The senior author is indeed an authority on the latter, and the simulations in Figure 5, extending those from Bhalla (2017), are unique in this area. In my view, the role of chemical signaling in neural computation is understudied theoretically, but research will be increasingly important as experimental technologies continue to develop.

(Editors' note: the paper has been through two rounds of revisions and the authors are encouraged to finalise this as the Version of Record. The earlier reviews are here: https://elifesciences.org/reviewed-preprints/100664v2/reviews)

Joint Public Review:

Summary:

If synaptic input is functionally clustered on dendrites, nonlinear integration could increase the computational power of neural networks. But this requires the right synapses to be located in the right places. This paper aims to address the question of whether such synaptic arrangements could arise by chance (i.e. without special rules for axon guidance or structural plasticity), and could therefore be exploited even in randomly connected networks. This is important, particularly for the dendrites and biological computation communities, where there is a pressing need to integrate decades of work at the single-neuron level with contemporary ideas about network function.

Using an abstract model where ensembles of neurons project randomly to a postsynaptic population, back-of-envelope calculations are presented that predict the probability of finding clustered synapses and spatiotemporal sequences. Using data-constrained parameters, the authors conclude that clustering and sequences are indeed likely to occur by chance (for large enough ensembles), but require strong dendritic nonlinearities and low background noise to be useful.

Strengths:

- The back-of-envelope reasoning presented can provide fast and valuable intuition. The authors have also made the effort to connect the model parameters with measured values. Even an approximate understanding of cluster probability can direct theory and experiments towards promising directions, or away from lost causes.

- I found the general approach to be refreshingly transparent and objective. Assumptions are stated clearly about the model and statistics of different circuits. Along with some positive results, many of the computed cluster probabilities are vanishingly small, and noise is found to be quite detrimental in several cases. This is important to know, and I was happy to see the authors take a balanced look at conditions that help/hinder clustering, rather than just focus on a particular regime that works.

- This paper is also a timely reminder that synaptic clusters and sequences can exist on multiple spatial and temporal scales. The authors present results pertaining to the standard `electrical' regime (~50-100 µm, <50 ms), as well as two modes of chemical signaling (~10 µm, 100-1000 ms). The senior author is indeed an authority on the latter, and the simulations in Figure 5, extending those from Bhalla (2017), are unique in this area. In my view, the role of chemical signaling in neural computation is understudied theoretically, but research will be increasingly important as experimental technologies continue to develop.

(Editors' note: the paper has been through two rounds of revisions and the authors are encouraged to finalise this as the Version of Record. The earlier reviews are here: https://elifesciences.org/reviewed-preprints/100664v2/reviews#tab-content)

Reviewer #1 (Public review):

In the current manuscript, the authors use theoretical and analytical tools to examine the possibility of neural projections to engage ensembles of synaptic clusters in active dendrites. The analysis is divided into multiple models that differ in the connectivity parameters, speed of interactions and identity of the signal (electric vs. second messenger). They first show that random connectivity almost ensures the representation of presynaptic ensembles. As expected, this convergence is much more likely for small group sizes and slow processes, such as calcium dynamics. Conversely, fast signals (spikes and postsynaptic potentials) and large groups are much less likely to recruit spatially clustered inputs. Dendritic nonlinearity in the postsynaptic cells was found to play a highly important role in distinguishing these clustered activation patterns, both when activated simultaneously and in sequence. The authors tackled the difficult issue of noise, showing a beneficiary effect when noise 'happen' to fill in gaps in a sequential pattern but degraded performance at higher background activity levels. Last, the authors simulated selectivity to chemical and electrical signals. While they find that longer sequences are less perturbed by noise, in more realistic activation conditions, the signals are not well resolved in the soma.

While I think the premise of the manuscript is worth exploring, I have a number of reservations regarding the results.

(1) In the analysis, the authors made a simplifying assumption that the chemical and electrical processes are independent. However, this is not the case; excitatory inputs to spines often trigger depolarization combined with pronounced calcium influx; this mixed signaling could have dramatic implications on the analysis, particularly if the dendrites are nonlinear (see below)<br /> (2) Sequence detection in active dendrites is often simplified to investigating activation in a part of or the entirety of individual branches. However, the authors did not do that for most of their analysis. Instead, they treat the entire dendritic tree as one long branch and count how many inputs form clusters. I fail to see why the simplification is required and suspect it can lead to wrong results. For example, two inputs that are mapped to different dendrites in the 'original' morphology but then happen to fall next to each other when the branches are staggered to form the long dendrites would be counted as neighbors.<br /> (3) The simulations were poorly executed. Figures 5 and 6 show examples but no summary statistics. The authors emphasize the importance of nonlinear dendritic interactions, but they do not include them in their analysis of the ectopic signals! I find it to be wholly expected that the effects of dendritic ensembles are not pronounced when the dendrites are linear.

To provide a comprehensive analysis of dendritic integration, the authors could simulate more realistic synaptic conductances and voltage-gated channels. They would find much more complicated interactions between inputs on a single site, a sliding temporal and spatial window of nonlinear integration that depends on dendritic morphology, active and passive parameters and synaptic properties. At different activation levels, the rules of synaptic integration shift to cooperativity between different dendrites and cellular compartments, further complicated by nonlinear interactions between somatic spikes and dendritic events.

While it is tempting to extend back-of-the-napkin calculations of how many inputs can recruit nonlinear integration in active dendrites, the biological implementation is very different from this hypothetical. It is important to consider these questions, but I am not convinced that this manuscript adequately addressed the questions it set out to probe, nor does it provide information that was unknown beforehand.

Update after the first revision:

In this revision, the authors significantly improved the manuscript. They now address some of my concerns. Specifically, they show the contribution of end-effects on spreading the inputs between dendrites. This analysis reveals greater applicability of their findings to cortical cells, with long, unbranching dendrites than other neuronal types, such as Purkinje cells in the cerebellum.

They now explain better the interactions between calcium and voltage signals, which I believe improve the take-away message of their manuscript. They modified and added new figures that helped to provide more information about their simulations.<br /> However, some of my points remain valid. Figure 6 shows depolarization of ~5mV from -75. This weak depolarization would not effectively recruit nonlinear activation of NMDARs. In their paper, Branco and Hausser (2010) showed depolarizations of ~10-15mV. More importantly, the signature of NMDAR activation is the prolonged plateau potential and activation at more depolarized resting membrane potentials (their Figure 4). Thus, despite including NMDARs in the simulation, the authors do not model functional recruitment of these channels. Their simulation is thus equivalent to AMPA only drive, which can indeed summate somewhat nonlinearly.

Reviewer #1 (Public review):

De Seze et al. investigated the role of guanine exchange factors (GEFs) in controlling cell protrusion and retraction. In order to causally link protein activities to the switch between the opposing cell phenotypes, they employed optogenetic versions of GEFs which can be recruited to the plasma membrane upon light exposure and activate their downstream effectors. Particularly the RhoGEF PRG could elicit both protruding and retracting phenotypes. Interestingly, the phenotype depended on the basal expression level of the optoPRG. By assessing the activity of RhoA and Cdc42, the downstream effectors of PRG, the mechanism of this switch was elucidated: at low PRG levels, RhoA is predominantly activated and leads to cell retraction, whereas at high PRG levels, both RhoA and Cdc42 are activated but PRG also sequesters the active RhoA, therefore Cdc42 dominates and triggers cell protrusion. Finally, they create a minimal model that captures the key dynamics of this protein interaction network and the switch in cell behavior.

The conclusions of this study are strongly supported by data, harnessing the power of modelling and optogenetic activation. The minimal model captures well the dynamics of RhoA and Cdc42 activation and predicts that by changing the frequency of optogenetic activation one can switch between protruding and retracting behaviour in the same cell of intermediate optoPRG level. The authors are indeed able to demonstrate this experimentally albeit with a very low number of cells. A major caveat of this study is that global changes due to PRG overexpression cannot be ruled out. Also, a quantification of absolute protein concentration, which is notoriously difficult, would be useful to put the level of overexpression here in perspective with endogenous levels. Furthermore, it remains unclear whether in cases of protein overexpression in vivo such as cancer, PRG or other GEFs can activate alternative migratory behaviours.

Previous work has implicated RhoA in both protrusion and retraction depending on the context. The mechanism uncovered here provides a convincing explanation for this conundrum. In addition to PRG, optogenetic versions of two other GEFs, LARG and GEF-H1, were used which produced either only one phenotype or less response than optoPRG, underscoring the functional diversity of RhoGEFs. The authors chose transient transfection to achieve a large range of concentration levels and, to find transfected cells at low cell density, developed a small software solution (Cell finder), which could be of interest for other researchers.

Reviewer #2 (Public review):

Summary:

This study investigated the effects of transcutaneous auricular vagus nerve stimulation (taVNS) on cardiovascular dynamics in subarachnoid hemorrhage (SAH) patients. The researchers conducted a randomized clinical trial with 24 SAH patients, comparing taVNS treatment to a Sham treatment group (20 minutes per day twice a day during the ICU stay). They monitored electrocardiogram (ECG) readings and vital signs to assess acute as well as middle -term changes in heart rate, heart rate variability, QT interval, and blood pressure between the two groups. The results showed that repetitive taVNS did not significantly alter heart rate, corrected QT interval, blood pressure, or intracranial pressure. However, it increased overall heart rate variability and parasympathetic activity after 5-10 days of treatment compared to the sham treatment. Acute taVNS led to an increase in heart rate, blood pressure, and peripheral perfusion index without affecting corrected QT interval, intracranial pressure, or heart rate variability. The acute post-treatment elevation in heart rate was more pronounced in patients who showed clinical improvement. In conclusion, the study found that taVNS treatment did not cause adverse cardiovascular effects, suggesting it as a safe immunomodulatory treatment for SAH patients. The mild acute increase in heart rate post-treatment could potentially serve as a biomarker for identifying SAH patients who may benefit more from taVNS therapy.

Strengths:

The paper is overall well written, and the topic is of great interest. The methods are solid and the presented data are convincing.

Comments on revisions:

The main previous weaknesses of the paper have now been fixed.

Reviewer #1 (Public review):

Summary:

The authors introduced neutron crystallography coupled with room temperature X-ray crystallography to exam the redox properties of the BtFt [4Fe-4S] cluster expressed in E. coli. Neutron structure allowed the authors to exam the influence of Asp64 on the redox properties of the [4Fe-4S] cluster. The neutron structure also allowed for the identification of the hydrogen network around the [4Fe-4S] structure. This work was followed by density functional theory calculation to examine different redox states which also pointed to the role of Asp64 in affecting or dictating redox function of the [4Fe-4S] cluster. Based on the DFT work the authors examine the redox properties under oxic and anoxic conditions in wild type enzymes and in a D64N mutant again showing the role of Asp64 on the redox kinetics and redox potential of the [4Fe-4S] cluster. Lastly, the authors examined similar [4Fe-4S] ferredoxins from several organisms and with a Asp64 or Glu64 observed a similar role of Asp64 on the low potential state of the [4Fe-4S] cluster. The major conclusion of the study was to identify the role of specific amino acids, in this case Asp64, in controlling the redox state and kinetics of [4Fe-4S] clusters. The authors also demonstrate the strength of neutron crystallography when combined with classical X-ray crystallography and classical spectral/redox studies.

Strengths:

In general, the experimental design is logical and the results are convincing demonstrating the role of Asp64 on the redox properties of [4Fe-4S] clusters in ferredoxins.

Weaknesses:

The role(s) of coordinating amino acids on the redox properties of a functional group is not surprising, this reviewer believes this is a novel result in ferredoxins and does make a nice contribution to the field.

Reviewer #1 (Public review):

This manuscript by Bai et al concerns the expression of Scleraxis (Scx) by muscle satellite cells (SCs) and the role of that gene in regenerative myogenesis. The authors report the expression of this gene associated with tendon development in satellite cells. Genetic deletion of Scx in SCs impairs muscle regeneration, and the authors provide evidence that SCs deficient in Scx are impaired in terms of population growth and cellular differentiation. Overall, this report provides evidence of the role of this gene, unexpectedly, in SC function and adult regenerative myogenesis.

There are a few points of concern.

(1) From the data in Figure 1, it appears that all of the SCs, assessed both in vitro and in vivo, express Scx. The authors refer to a scRNA-seq dataset from their lab and one report from mdx mouse muscle that also reveal this unexpected gene expression pattern. Has this been observed in many other scRNA-seq datasets? If not, it would be important to discuss potential explanations as to why this has not been reported previously.

(2) A major point of the paper, as illustrated in Fig. 3, is that Scx-neg SCs fail to produce normal myofibers and renewed SCs following injury/regeneration. They mention in the text that there was no increased PCD by Caspase staining at 5 DPI. A failure of cell survival during the process of SC activation, proliferation, and cell fate determination (differentiation versus self-renewal) would explain most of the in vivo data. As such, this conclusion that would seem to warrant a more detailed analysis in terms of at least one or two other time points and an independent method for detecting dead/dying cells (the in vitro data in Fig. 4F is also based on assessment of activated Caspase to assess cell death). The in vitro data presented later in Fig. S4G,H do suggest an increase in cell loss during proliferative expansion of Scx-neg SCs. To what extent does cell loss (by whatever mechanism of cell death) explain both the in vivo findings of impaired regeneration and even the in vitro studies showing slower population expansion in the absence of Scx?

(3) I'm not sure I understand the description of the data or the conclusions in the section titled "Basement membrane-myofiber interaction in control and Scx cKO mice". Is there something specific to the regeneration from Scx-neg myogenic progenitors, or would these findings be expected in any experimental condition in which myogenesis was significantly delayed, with much smaller fibers in the experimental group at 5 DPI?

(4) The data presented in Fig. 4B showing differences in the purity of SC populations isolated by FACS depending on the reporter used are interesting and important for the field. The authors offer the explanation of exosomal transfer of Tdt from SCs to non-SCs. The data are consistent with this explanation, but no data are presented to support this. Are there any other explanations that the authors have considered and that could be readily tested?

(5) The Cut&Run data of Fig. 6 certainly provide evidence of direct Scx targets, especially since the authors used a novel knock-in strain for analyses. The enrichment of E-box motifs provides support for the 207 intersecting genes (scRNA-seq and Cut&Run) being direct targets. However, the rationale elaborated in the final paragraph of the Results section proposing how 4 of these genes account for the phenotypes on the Scx-neg cells and tissues is just speculation, however reasonable. These are not data, and these considerations would be more appropriate in the Discussion in the absence of any validation studies.

Comments on revisions:

The authors have adequately addressed all of the concerns I raised regarding the original submission. I have no further issues to be addressed.

Reviewer #1 (Public review):

Summary:

The authors present experimental and numerical results on the motility Magnetospirillum gryphiswaldense MSR-1, a magnetotactic bacterium living in sedimentary environments. The authors manufactured microfluidic chips containing three-dimensional obstacles of irregular shape, that match the statistical features of the grains observed in the sediment via micro-computer tomography. The bacteria are furthermore subject to an external magnetic field, whose intensity can be varied. The key quantity measured in the experiments is the throughput ratio, defined as the ratio between the number of bacteria that reach the end of the microfluidic channel and the number of bacteria entering it. The main result is that the throughput ratio is non-monotonic and exhibits a maximum at magnetic field strength comparable with Earth's magnetic field. The authors rationalize the throughput suppression at large magnetic fields by quantifying the number of bacteria trapped in corners between grains.

Strengths:

While magnetotactic bacteria general motility in bulk has been characterized, we know much less about their dynamics in a realistic setting, such as a disordered porous material. The micro-computer tomography of sediments and their artificial reconstruction in a microfluidic channel is a powerful method that establishes the rigorous methodology of this work. This technique can give access to further characterization of the microbial motility. The coupling of experiments and computer simulations lends considerable strength to the claims of the authors, because the model parameters (with one exception) are directly measured in the experiments.

Weaknesses:

The main weakness of the manuscript pertains to the comparison between simulations and experiments due to limitations in the tracking of bacteria in the experiments.

Impact:

Building on the present work, and refining the experimental setup may shed light on the microbial interactions in an environment such as soil which deserves further studies.

Reviewer #1 (Public review):

Summary:

In this excellent manuscript by Egan et al., the authors very carefully dissect the roles of inflammasome components in restricting Salmonella Typhimurium (STm) replication in human macrophages. They show that caspase-1 is essential to mediating inflammasome responses and that caspase-4 contributes to bacterial restriction at later time points. The authors show very clear roles for the host proteins that mediate terminal lysis, gasdermin D and ninjurin-1. The unique finding in this study is that in the absence of inflammasome responses, Salmonella hypereplicates within the cytosol of macrophages. These findings suggest that caspase-1 and possibly caspase-4 play roles in restricting the replication of Salmonella in the cytosol as well as in the Salmonella containing vacuole.

Strengths:

(1) The genetic and biochemical approaches have shown for the first time in human macrophages that the caspase-1-GSDMD-NINJ1 axis is very important for restricting intracellular STm replication. In addition, they demonstrate a later role for Casp4 in control of intracellular bacterial replication.

(2) In addition, they show that in macrophages deficient in the caspase-1-GSDMD-NINJ1 axis that STm are found replicating in the cytosol, which is a novel finding. The electron microscopy is convincing that STm are in the cytosol.

(3) The authors go on to use a chloroquine resistance assay to show that inflammasome signaling also restricts STm within SCVs in human macrophages.

(4) Finally, they show that the Type 3 Secretion System encoded on Salmonella Pathogenicity Island 1 contributes to STm's cytosolic access in human macrophages.

Weaknesses:

(1) Their results with human macrophages suggest that there are differences between murine and human macrophages in inflammasome-mediated restriction of STm growth. For example, Thurston et al. showed that in murine macrophages that inflammasome activation controls the replication of mutant STm that aberrantly invades the cytosol, but only slightly limits replication of WT STm. In contrast, here the authors found that primed human macrophages rely on caspase-1, gasdermin D and ninjurin-1 to restrict WT STm. I wonder if the priming of the human macrophages in this study could account for the differences in these studies. Along those lines, do the authors see the same results presented in this study in the absence of priming the macrophages with Pam3CSK4. I think that determining whether the control of intracellular STm replication is dependent on priming is very important. Another difference with the Thurston et al. paper is the way that the STm inoculum was prepared - stationary phase bacteria that were opsonized. Could this also account for differences between the two studies rather than differences between murine and human macrophages in inflammasome-dependent control of STm?

(2) The authors show that the pore-forming proteins GSDMD and Ninj1 contribute to control of STm replication in human macrophages. Is it possible that leakage of gentamicin from the media contributes to this control?

(3) One major question that remains to be answered is whether casp-1 plays a direct role in the intracellular localization of STm. If the authors quantify the percentage of vacuolar vs. cytosolic bacteria at early time points in WT and casp-1 KO macrophages, would that be the same in the presence and absence of casp-1? If so, then this would suggest that there is a basal level of bacterial-dependent lysis of the SCV and in WT macrophages the presence of cytosolic PAMPS trigger cell death and bacteria can't replicate in the cytosol. However, in the inflammasome KO macrophages, the host cell remains alive and bacteria can replicate in the cytosol.

Comments on revisions:

The authors have addressed my previous concerns. The addition of the statements indicating the limitations of the study are an important addition.

Reviewer #1 (Public review):

The authors point out that the fitness estimates obtained from different experimental assays (monoculture, pairwise competition, or bulk competition) are not generally equivalent, not even with regard to the fitness ranking of different genotypes. Using a computational model based on experimentally measured growth phenotypes for knockout strains in yeast, as well as data from Lenski's Long Term Evolution Experiment (LTEE), they derive a set of best practice rules aimed at extracting the optimal amount of information from such experiments.

The study is very complete on a technical level and I have no suggestions for further analyses. However, I feel the readability and the conceptual focus of the manuscript could be significantly improved by rearranging the material with regard to the contents of the main text vs. the Methods and the Supplement. Detailed recommendations:

(1) Regarding readability, the large number of references to material in the Methods and Supplement fragment the main text and make it difficult to follow.

(2) Conceptually, it seems to me that the current presentation obscures the reasons why we should care about fitness in the first place. In the first paragraph of Results, the authors define fitness "as any number that is sufficient to predict the genotype's relative abundance x(t) over a short-time horizon". To me, this seems like an extremely narrow and not very interesting definition. Instead, I view fitness as an intrinsic property of a genotype that allows us to predict its performance<br /> under a range of conditions, including in particular conditions that are different from the experimental setup that was used to obtain the fitness estimates. The latter viewpoint is well expressed in Supplementary Section S1, where the authors discuss the notion of fitness potential. I would recommend to move at least part of this discussion to the main text. By comparison, the arguments in favor of the logit encoding that currently opens the Results session are rather straightforward and could be shortened significantly.

(3) Similarly, the modeling strategy used in this work is quite subtle and needs to be explained more fully in the main text. The authors use growth traits (lag time, growth rate, and yield) extracted from monoculture experiments on a yeast knockout collection and feed them into a specific mathematical model to simulate pairwise and bulk competition scenarios. Since a key claim of the work is that monoculture experiments are generally poor predictors of competitive fitness, the basis for this conclusion and the assumptions on which it is based need to be described clearly in the main text. In the current version of the manuscript, this information has<br /> been largely relegated to the Methods section.

Reviewer #1 (Public review):

Summary:

This study introduces a novel therapeutic strategy for patients with high-risk HER2-positive breast cancer and demonstrates that the incorporation of pyrotinib into adjuvant trastuzumab therapy can improve invasive disease-free survival.

Strengths:

The study features robust logic and high-quality data. Data from 141 patients across 23 centers were analyzed, thereby effectively mitigating regional biases and endowing the research findings with high applicability.

Weaknesses:

(1) Introduction and Discussion: Update the literature regarding the efficacy of pyrotinib combined with trastuzumab in treating HER2-positive advanced breast cancer.

(2) Did all the data have a normal distribution? Expand the description of statistical analysis.

(3) The novelty and innovative potential of your manuscript compared to the published literature should be described in more detail in the abstract and discussion section.

(4) Figure legend should provide a bit more detail about what readers should focus on.

(5) P-values should be clarified for the analysis.

(6) The order (A, B, and C) in Figure 3 should be labeled in the upper left corner of the Figure.

Reviewer #1 (Public review):

Summary:

This study adapts a previously published model of the cat spinal locomotor network to make predictions of how phase durations of swing and stance at different treadmill speeds in tied-belt and split-belt conditions would be altered following a lateral hemisection. The simulations make several predictions that are replicated in experimental settings.

Strengths:

(1) Despite only altering the connections in the model, the model is able to replicate very well several experimental findings. This provides strong validation for the model and highlights its utility as a tool to investigate the operations of mammalian spinal locomotor networks.

(2) The study provides insights about interactions between the left and right sides of the spinal locomotor networks, and how these interactions depend on the mode of operation, as determined by speed and state of the nervous system.

(3) The writing is logical, clear, and easy to follow.

Weaknesses:

(1) Could the authors provide a statement in the methods or results to clarify whether there were any changes in synaptic weight or other model parameters of the intact model to ensure locomotor activity in the hemisected model?

(2) The authors should remind the reader what the main differences are between state-machine, flexor-driven, and classical half-center regimes (lines 77-79).

(3) There may be changes in the wiring of spinal locomotor networks after the hemisection. Yet, without applying any sort of plasticity, the model is able to replicate many of the experimental data. Based on what was experimentally replicated or not, what does the model tell us about possible sites of plasticity after hemisection?

(4) Why are the durations on the right hemisected (fast) side similar to results in the full spinal transected model (Rybak et al. 2024)? Is it because the left is in slow mode and so there is not much drive from the left side to the right side even though the latter is still receiving supraspinal drive, as opposed to in the full transection model? (lines 202-203).

(5) There is an error with probability (line 280).

Reviewer #1 (Public review):

Summary:

This manuscript uses the eye lens as a model to investigate basic mechanisms in the Fgf signaling pathway. Understanding Fgf signaling is of broad importance to biologists as it is involved in the regulation of various developmental processes in different tissues/organs and is often misregulated in disease states. The Fgf pathway has been studied in embryonic lens development, namely with regards to its involvement in controlling events such as tissue invagination, vesicle formation, epithelium proliferation, and cellular differentiation, thus making the lens a good system to uncover the mechanistic basis of how the modulation of this pathway drives specific outcomes. Previous work has suggested that proteins, other than the ones currently known (e.g., the adaptor protein Frs2), are likely involved in Fgfr signaling. The present study focuses on the role of Shp2 and Shc1 proteins in the recruitment of Grb2 in the events downstream of Fgfr activation.

Strengths:

The findings reveal that the juxtamembrane region of the Fgf receptor is necessary for proper control of downstream events such as facilitating key changes in transcription and cytoskeleton during tissue morphogenesis. The authors conditionally deleted all four Fgfrs in the mouse lens that resulted in molecular and morphological lens defects, most importantly, preventing the upregulation of the lens induction markers Sox2 and Foxe3 and the apical localization of F-actin, thus demonstrating the importance of Fgfrs in early lens development, i.e. during lens induction. They also examined the impact of deleting Fgfr1 and 2, on the following stage, i.e. lens vesicle development, which could be rescued by expressing constitutively active KrasG12D. By using specific mutations (e.g. Fgfr1ΔFrs lacking the Frs2 binding domain and Fgfr2LR harboring mutations that prevent binding of Frs2), it is demonstrated that the Frs2 binding site on Fgfr is necessary for specific events such as morphogenesis of lens vesicle. Further, by studying Shp2 mutations and deletions, the authors present a case for Shp2 protein to function in a context-specific manner in the role of an adaptor protein and a phosphatase enzyme. Finally, the key surprising finding from this study is that downstream of Fgfr signaling, Shc1 is an important alternative pathway - in addition to Shp2 - involved in the recruitment of Grb2 and in the subsequent activation of Ras. The methodologies, namely, mouse genetics and state-of-the-art cell/molecular/biochemical assays are appropriately used to collect the data, which are soundly interpreted to reach these important conclusions. Overall, these findings reveal the flexibility of the Fgf signaling pathway and its downstream mediators in regulating cellular events. This work is expected to be of broad interest to molecular and developmental biologists.

Weaknesses:

A weakness that needs to be discussed is that Le-Cre depends on Pax6 activation, and hence its use in specific gene deletion will not allow evaluation of the requirement of Fgfrs in the expression of Pax6 itself. But since this is the earliest Cre available for deletion in the lens, mentioning this in the discussion would make the readers aware of this issue. Referring to Jag1 among "lens-specific markers" (page 5) is debatable, suggesting changing to the lines of "the expected upregulation of Jag1 in lens vesicle". The Abstract could be modified to clearly convey the existing knowledge gap and the key findings of the present study. As it stands now, it is a bit all over the place. Some typos in the manuscript need to be fixed, e.g. "...yet its molecular mechanism remains largely resolved" - unresolved? "...in the development lens" - in the developing lens? In Figure 4 legend, "(B) Grb2 mutants Grb2 mutants displayed...", etc.

Reviewer #1 (Public review):

Summary:

mRNA decapping and decay factors play critical roles in post-transcriptionally regulating gene expression. Here, Kumar and colleagues investigate how deleting two yeast decapping enhancer proteins (Edc3 and Scd6), either alone or in tandem, influences the transcriptome. Using RNA-Seq and ribosome profiling, they come to the conclusion that these factors generally act in a redundant fashion, with a mutant lacking both proteins showing an increased abundance of select mRNAs. As these upregulated transcripts are also upregulated in mutants lacking the decapping enzyme, Dcp2, and show no increases in transcription of their cognate genes, they come to the conclusion that this is at the level of mRNA decapping and decay. Their ribosome profiling data also led them to conclude that Scd6 and Edc3 display functional redundancy and cooperativity with Dhh1/Pat1 in repressing the translation of specific transcripts. Finally, as their data suggest that Scd6 and Edc3 repress mRNAs coding for proteins involved in cellular respiration, as well as proteins involved in the catabolism of alternative carbon sources, they go on to show that these decapping activators play a role in repressing oxidative phosphorylation.

Strengths:

Overall, this manuscript is well-written and contains a large amount of high-quality data and analyses. At its core, it helps to shed light on the overlapping roles of Edc3 and Scd6 in sculpting the yeast transcriptome.

Weaknesses:

(1) While the data presented makes conclusions about mRNA stability based on corresponding ChIP-Seq analyses and analyzing other mutants (e.g. Dcp2 knockout), at no point is mRNA stability actually ever directly assessed. This direct assessment, even for select transcripts, would further strengthen their conclusions.

(2) Scd6 and Edc3 show a high level of functional redundancy, as demonstrated by the double mutant. As these proteins form complexes with other decapping factors/activators, I'm curious if depleting both proteins in the double mutant destabilizes any of these other factors. Have the authors ever assessed the levels of other key decapping factors in the double mutants (i.e. Dhh1, Pat1, Dcp2...etc)? I wonder if depleting both proteins leads to a general destabilization of key complexes. It would also be interesting to see if depleting Edc3 or Scd6 leads to a concomitant increase in the other protein as a compensatory mechanism.

(3) While not essential, it would be interesting if the authors carried out add-back experiments to determine which domain within Scd6/Edce3 plays a critical role in enforcing the regulation that they see. Their double mutant now puts them in a perfect position to carry out such experiments.

Reviewer #1 (Public review):

The manuscript titled "Evolutionary and Functional Analyses Reveal a Role for the RHIM in Tuning RIPK3 Activity Across Vertebrates" by Fay et al. explores the function of RIPK gene family members across a wide range of vertebrate and invertebrate species through a combination of phylogenomics and functional studies. By overexpressing these genes in human cell lines, the authors examine their capacity to activate NF-κB and induce cell death. The methods employed are appropriate, with a thorough analysis of gene loss, positive selection, and functionality. While the study is well-executed and comprehensive, its broader relevance remains limited, appealing mainly to specialists in this specific field of research. It misses the opportunity to extract broader insights that could extend the understanding of these genes beyond evolutionary conservation, particularly by employing evolutionary approaches to explore more generalizable functions.

Major comments:

The main issue I encounter is distinguishing between what is novel in this study and what has been previously demonstrated. What new insights have been gained here that are of broader relevance? The discussion, which would be a good place to do so, is very speculative and has little to do with the actual results. Throughout the manuscript, there is little explanation of the study's importance beyond the fact that it was possible to conduct it. Is the evolutionary analysis being used to advance our understanding of gene function, or is the focus merely on how these genes behave across different species? The former would be exciting, while the latter feels less impactful.

for - regenerative company - principle 1 of 8 - agency-based instead of ownership-based - implementation - via leveraging full extent of legal personhood

Comment - Graham points out an interesting insight, that organisations are given legal personhood status -namely, we test a group of people as a person itself - This reminds me of Michael Levin's Multi Scale Competency Architecture

Involucrar a los grupos marginados en funciones técnicas y no técnicas en todo el ecosistema de IA

Invertir en el desarrollo de capacidades para la inclusión institucional

Permiso para el tratamiento de categorías especiales de datos

Financiar la investigación y el diseño de tecnologías transformadoras en la innovación de la IA

Comité intersectorial de stakeholders múltiples.

Puntos de acción

Mapear a los stakeholders clave e invitar representantes, especialmente de grupos marginados, para compartir sus perspectivas.

Incluir académicos, ONG y comunidades técnicas, evaluando su interés en la igualdad sustantiva y la capacidad de los grupos marginados para influir en las decisiones.

Considerar sus necesidades, compensarlos por su tiempo, garantizar accesibilidad y fomentar condiciones que fortalezcan su agencia.

Establecer un comité multiactorial intersectorial que asegure diversidad en la planificación y decisiones, comprendiendo desequilibrios de poder y necesidades de acción.

Reviewer #1 (Public review):

Summary:

Casas-Tinto et al. present convincing data that injury of the adult Drosophila CNS triggers transdifferentiation of glial cell and even the generation of neurons from glial cells. This observation opens up the possibility to get an handle on the molecular basis of neuronal and glial generation in the vertebrate CNS after traumatic injury caused by Stroke or Crush injury. The authors use an array of sophisticated tools to follow the development of glial cells at the injury site in very young and mature adults. The results in mature adults reveal a remarkable plasticity in the fly CNS and dispels the notion that repair after injury may be only possible in nerve cords which are still developing. The observation of so called VC cells which do not express the glial marker repo could point to the generation of neurons by former glial cells.

Conclusion:

The authors present an interesting story which is technically sound and could form the basis for an in depth analysis of the molecular mechanism driving repair after brain injury in Drosophila and vertebrates.

Strengths:

The evidence for transdifferentiation of glial cells is convincing. In addition, the injury to the adult CNS shows an inherent plasticity of the mature ventral nerve cord which is unexpected.

Weaknesses:

Traumatic brain injury in Drosophila has been previously reported to trigger mitosis of glial cells and generation of neural stem cells in the larval CNS and the adult brain hemispheres. Therefore this report adds to but does not significantly change our current understanding. The origin and identity of VC cells is still unclear. The authors show that VC cells are not GABA- or glutamergic. Yet, there are many other neurotransmitter or neuropetides. It would have been nice to see a staining with another general neuronal marker such as anti-Syt1 to confirm the neuronal identity of Syt1.

Reviewer #1 (Public review):

Li et al. investigate Ca2+ signaling in T. gondii and argue that Ca2+ tunnels through the ER to other organelles to fuel multiple aspects of T. gondii biology. They focus in particular on TgSERCA as the presumed primary mechanism for ER Ca2+ filling. Although, when TgSERCA was knocked out there was still a Ca2+ release in response to TG present. Overall the Ca2+ signaling data do not support the conclusion of Ca2+ tunneling through the ER to other organelles in fact they argue for direct Ca2+ uptake from the cytosol into the organelles as outlined in the specific points below. The authors show EM membrane contact sites between the ER and other organelles, so Ca2+ released by the ER could presumably be taken up by other organelles but that is not ER Ca2+ tunneling. They clearly show that SERCA is required for T. gondii function. Overall, the data presented to not fully support the conclusions reached.

Reviewer #1 (Public review):

Summary:

Recordings were made from the dentate nucleus of two monkeys during a decision-making task. Correlates of stimulus position and stimulus information were found to varying degrees in the neuronal activities.

Strengths:

A difficult decision-making task was examined in two monkeys.

Weaknesses:

One of the monkeys had difficulty learning the task. The initial version of the manuscript lacked a coherent hypothesis to be tested, although the revision has improved things. In its current form, the manuscript does not provide data regarding the possibility that this part of the brain may have little to do with the task that was being studied. As noted in the response to the reviewer's comments, future studies could address this issue by providing results of additional inactivation experiments.

Reviewer #1 (Public review):

Summary:

The authors bring together implanted radiofrequency coils, high-field MRI imaging, awake animal imaging, and sensory stimulation methods in a technological demonstration. The results are very detailed descriptions of the sensory systems under investigation.

Strengths:

The maps are qualitatively excellent for rodent whole-brain imaging.<br /> The design of the holder and the coil is pretty clever.

Weaknesses:

Some unexpected regions appear on the whole brain maps, and the discussion of these regions is succinct.<br /> The authors do not make the work and effort to train the animals and average the data from several hundred trials apparent enough. This is important for any reader who would like to consider implementing this technology.<br /> The data is not available. This does not let the readers make their own assessment of the results.

Comments on revisions:

All good, I can but only congratulate the authors on a study well done.

Reviewer #2 (Public review):

Summary:

This manuscript builds on previous work suggesting that the CCK peptide is the releasing hormone for FSH in fishes, which is different than that observed in mammals where both LH and FSH release are under the control of GnRH. Based on data using calcium imaging as a readout for stimulation of the gonadotrophs, the researchers present data supporting the hypothesis that CCK stimulates FSH-containing cells in the pituitary. In contrast LH containing cells show a weak and variable response to CCK, but are highly responsive to GnRH. Data are presented that support the role of CCK in release of FSH. Researchers also state the functional overlap exists in the potency of GnRH to activate FSH cells, thus the two signalling pathways are not separate.<br /> The results are of interest to the field because for many years the assumption has been that fishes use the same signalling mechanism. These data present an intriguing variation where a hormone involved in satiation acts in the control of reproduction.

Strengths:

The strengths of the manuscript are that researchers have shed light on different pathways controlling reproduction in fishes.

Weaknesses:

Weaknesses are that it is not clear if multiple ligand/receptors are involved (more than one CCK and more than one receptor?). The imaging of the CCK terminals and CCK receptors needs to be reinforced.

Comments on revisions:

The authors have responded to the comments with clarity and have made the important requested changes such as clarifying the CCK receptors (their expression and exactly which receptor was targeted), and emphasizing the interactions of CCK, namely that CCK induces LH secretion, but not to the same extent as FSH. All minor comments directed to the layout of the figures and text have been addressed. In summary, comments have been addressed satisfactorily.

Reviewer #2 (Public review):

This work combines a model of two-dimensional dendritic growth with attraction and stabilisation by synaptic activity. The authors find that constraining growth models with competition for synaptic inputs produces artificial dendrites that match some key features of real neurons both over development and in terms of final structure. In particular, incorporating distance-dependent competition between synapses of the same dendrite naturally produces distinct phases of dendritic growth (overshoot, pruning, and stabilisation) that are observed biologically and leads to local synaptic organisation with functional relevance. The approach is elegant and well-explained but makes some significant modelling assumptions that might impact the biological relevance of the results.

The main strength of the work is the general concept of combining morphological models of growth with synaptic plasticity and stabilisation. This is an interesting way to bridge two distinct areas of neuroscience in a manner that leads to findings that could be significant for both. The modelling of both dendritic growth and distance-dependent synaptic competition is carefully done, constrained by reasonable biological mechanisms, and well-described in the text. The paper also links its findings, for example in terms of phases of dendritic growth or final morphological structure, to known data well.

The authors have managed to address my previous comments on the paper well by considering axonal dynamics, spatial correlations, and the effects of changing ratios of BDNF-proBDNF. The modelling has now been validated over a wider range of confounding factors and looks to be a solid basis for future work in this direction.

Reviewer #1 (Public review):

Summary:

This work uses a novel, ethologically relevant behavioral task to explore decision-making paradigms in C. elegans foraging behavior. By rigorously quantifying multiple features of animal behavior as they navigate in a patch food environment, the authors provide strong evidence that worms exhibit one of three qualitatively distinct behavioral responses upon encountering a patch:<br /> (1) "search", in which the encountered patch is below the detection threshold;<br /> (2) "sample", in which animals detect a patch encounter and reduce their motor speed, but do not stay to exploit the resource and are therefore considered to have "rejected" it; and<br /> (3) "exploit", in which animals "accept" the patch and exploit the resource for tens of minutes.<br /> Interestingly, the probability of these outcomes varies with the density of the patch as well as the prior experience of the animal. Together, these experiments provide an interesting new framework for understanding the ability of the C. elegans nervous system to use sensory information and internal state to implement behavioral state decisions.

Strengths:

(1) The work uses a novel, neuroethologically-inspired approach to studying foraging behavior.

(2) The studies are carried out with an exceptional level of quantitative rigor and attention to detail.

(3) Powerful quantitative modeling approaches including GLMs are used to study the behavioral states that worms enter upon encountering food, and the parameters that govern the decision about which state to enter.

(4) The work provides strong evidence that C. elegans can make 'accept-reject' decisions upon encountering a food resource.

(5) Accept-reject decisions depend on the quality of the food resource encountered as well as on internally represented features that provide measurements of multiple dimensions of internal state, including feeding status and time.

Weaknesses:

(1) The authors repeatedly assert that an individual's behavior in the foraging assay depends on its prior history (particularly cultivation conditions). While this seems like a reasonable expectation, it is not fully fleshed out. The work would benefit from studies in which animals are raised on more or less abundant food before the behavioral task.

(2) The authors convincingly show that the probability of particular behavioral outcomes occurring upon patch encounter depends on time-associated parameters (time since last patch encounter, time since last patch exploitation). There are two concerns here. First, it is not clear how these values are initialized - i.e., what values are used for the first occurrence of each behavioral state? More importantly, the authors don't seem to consider the simplest time parameter, the time since the start of the assay (or time since worm transfer). Transferring animals to a new environment can be associated with significant mechanical stimulus, and it seems quite possible that transferring animals causes them to enter a state of arousal. This arousal, which certainly could alter sensory function or decision-making, would likely decay with time. It would be interesting to know how well the model performs using time since assay starts as the only time-dependent parameter.

(3) Similarly, Figures 2L and M clearly show that the probability of a search event occurring upon a patch encounter decreases markedly with time. Because search events are interpreted as a failure to detect a patch, this implies that the detection of (dilute) patches becomes more efficient with time. It would be useful for the authors to consider this possibility as well as potential explanations, which might be related to the point above.

(4) Based on their results with mec-4 and osm-6 mutants, the authors assert that chemosensation, rather than mechanosensation, likely accounts for animals' ability to measure patch density. This argument is not well-supported: mec-4 is required only for the function of the six non-ciliated light-touch neurons (AVM, PVM, ALML/R, PLML/R). In contrast, osm-6 is expected to disrupt the function of the ciliated dopaminergic mechanosensory neurons CEP, ADE, and PDE, which have previously been shown to detect the presence of bacteria (Sawin et al 2000). Thus, the paper's results are entirely consistent with an important role of mechanosensation in detecting bacterial abundance. Along these lines, it would be useful for the authors to speculate on why osm-6 mutants are more, rather than less, likely to "accept" when encountering a patch.

(5) While the evidence for the accept-reject framework is strong, it would be useful for the authors to provide a bit more discussion about the null hypothesis and associated expectations. In other words, what would worm behavior in this assay look like if animals were not able to make accept-reject decisions, relying only on exploit-explore decisions that depend on modulation of food-leaving probability?

Reviewer #1 (Public review):

Summary:

The authors demonstrated that a mouse model of Opitz syndrome induced by Mid1 gene knockout exhibited a significant decrease in α rhythm in HPC and abnormal synchronization of γ rhythm in the prefrontal cortex and hippocampus, showing decreased synaptic plasticity and learning and memory dysfunction. All these effects were attributed to the inhibition of p Creb by PP2Ac.

Strengths:

The authors used Mid1 gene knockout mice as a mouse model of Opitz syndrome. They carried out RNA seq analysis and found cAMP signaling pathway, calcium signaling pathway, and 100 other pathways have changed significantly.

Weaknesses:

(1) A Mid1 supplementation experiment in Mid1 knockout mice was lacking in this study.

(2) Enzymes that regulate Creb phosphorylation include not only phosphatases such as PP2A, but also kinases such as CaMKII, PKA, and ERK1/2. These protein kinases should be detected, especially CaMKII, their bioinformatics data show calcium signaling pathways have significantly changed.

Reviewer #1 (Public review):

Summary:

Cesar, Santos & Cogni use a meta-analysis to report on the direction and magnitude of three fundamental fitness components in defensive symbioses. Specifically, the work focuses on interactions between three arthropod host families (Aphididae, Culicidae, Drosophilidae, and others) and common bacterial endosymbionts (Wolbachia, Serratia, Hamiltonella, Spiroplasma, Rickettsia, Regiella X-type and Arsenophonus). The results of the overall analysis confirm common assumptions and previous work on such fitness components, showing that defensive symbionts provide strong protection to hosts and cause detectable costs to both hosts and the enemy. The analysis provides insight into the extent of the cost/benefit tradeoff for hosts, reporting that the cost is six times lower than the protective effect. The confirmation that natural enemies attacking hosts infected with symbionts have a reduction in their fitness is also an interesting one, as this shows that the majority of defensive symbionts provide protection by resisting enemy infection, as opposed to tolerating it. This finding has important consequences for evolutionary counter-responses in the enemy species. Of course, this result has less relevance for certain types of enemies (such as parasitoids) where successful infection is dependent upon host killing.

Interesting results also emerge from the subgroup analysis. For the full dataset, both natural and introduced symbionts were similarly effective in positively influencing the fitness of hosts. However, in the Wolbachia-specific analysis, the artificially introduced symbionts caused costs to the hosts where the natural strain did not. These findings have potentially important ramifications for schemes that use endosymbionts for biocontrol or vector competence, suggesting that (in some cases) natural strains may be the more stable choice for deploying (as they are associated with lower costs).

The analysis draws from an impressively large dataset, but the interpretation of the full impact of the results would be helped by greater detail on the species/strain level systems included, the data extraction approach, and inclusion criteria. Accounting for phylogenetic nonindependence and alternative coding of one of the moderator variables could also strengthen the biological relevance of the models. Suggestions and thoughts are outlined below.

Strengths & Potential Improvements:

An impressively large number of effect sizes (3000) from only 226 studies is collected, robustly confirming common assumptions on the magnitude of fundamental fitness components. However the paper would benefit from a clear breakdown in the main text of the specificities of each system included (e.g. a table at the host species/symbiont strain level, where it is possible). Currently, there is not enough detail for those who want a deep dive to understand what data was extracted for the analysis from these 226 studies, or those who want to understand the underlying diversity in the dataset.

Currently, when the 'natural enemy group' is tested as a moderator it is coded broadly by type of organism (e.g. virus, bacterium, fungi, parasitoid). But this doesn't adequately capture the mode of killing/fitness reduction by the enemy, which would be the much more biologically relevant categorisation for your questions. For example, parasitoid infection is dependent upon host death (thus host fecundity is not relevant, because the host either survived or did not). Among bacterial and viral pathogens antagonists there is scope for both fecundity and survival to be affected. This in turn may be a very influential factor for the outcome. You could consider recoding this enemy moderator.

The analysis is restricted to arthropod hosts and defensive symbionts that are also classed as endosymbionts. This focus should be made clear early on in the paper, as there are many systems (that are classed by many as defensive symbioses) that are not part of the analysis.

There is fairly minimalistic testing of moderators/sub-groups (which probably has its statistical strengths) but perhaps there are also some missed opportunities for testing other ecological contributors to variance, including coinfection (although perhaps limited by power) and other approaches to coding enemy group (as detail above).

Looking at the overview of systems included, there's likely a high degree of phylogenetic non-independence in the dataset. Where it is possible, using phylogenetically controlled models could strengthen this analysis.

Looking at your included systems (Table S5), you might be able to test the effect of coinfection on the 3 variables of interest. For example, it would be particularly important to see if the effects of two symbionts are additive or not.

No code for the analysis is provided for review at this stage and full details of the dataset are also not available. This slightly limits the ability to assess the full scope and robustness of the study. It would be helpful to have an extensive table in the supplementary detailing (minimum) the reference, study, experiment, host species, symbiont strain, and a description of the exact data extraction source (e.g.table/figure/in text), and method of extraction.

Reviewer #1 (Public review):

Summary:

In this study, Seidenthal et al. investigated the role of the C. elegans Flower protein, FLWR-1, in synaptic transmission, vesicle recycling, and neuronal excitability. They confirmed that FLWR-1 localizes to synaptic vesicles and the plasma membrane and facilitates synaptic vesicle recycling at neuromuscular junctions, albeit in an unexpected manner. The authors observed that hyperstimulation results in endosome accumulation in flwr-1 mutant synapses, suggesting that FLWR-1 facilitates the breakdown of endocytic endosomes, which differs from earlier studies in flies that suggested the Flower protein promotes the formation of bulk endosomes. This is a valuable finding. Using tissue-specific rescue experiments, the authors showed that expressing FLWR-1 in GABAergic neurons restored the aldicarb-resistant phenotype seen in flwr-1 mutants to wild-type levels. In contrast, FLWR-1 expression in cholinergic neurons in flwr-1 mutants did not restore aldicarb sensitivity, yet muscle expression of FLWR-1 partially but significantly recovered the aldicarb-resistant defects. The study also revealed that removing FLWR-1 leads to increased Ca2+ signaling in motor neurons upon photo-stimulation. Further, the authors conclude that FLWR-1 contributes to the maintenance of the excitation/inhibition (E/I) balance by preferentially regulating the excitability of GABAergic neurons. Finally, SNG-1::pHluorin data imply that FLWR-1 removal enhances synaptic transmission, however, the electrophysiological recordings do not corroborate this finding.

Strengths:

This study by Seidenthal et al. offers valuable insights into the role of the Flower protein, FLWR-1, in C. elegans. Their findings suggest that FLWR-1 facilitates the breakdown of endocytic endosomes, which marks a departure from its previously suggested role in forming endosomes through bulk endocytosis. This observation could be important for understanding how Flower proteins function across species. In addition, the study proposes that FLWR-1 plays a role in maintaining the excitation/inhibition balance, which has potential impacts on neuronal activity.

Weaknesses:

One issue is the lack of follow-up tests regarding the relative contributions of muscle and GABAergic FLWR-1 to aldicarb sensitivity. The findings that muscle expression of FLWR-1 can significantly rescue aldicarb sensitivity are intriguing and may influence both experimental design and data interpretation. Have the authors examined aldicarb sensitivity when FLWR-1 is expressed in both muscles and GABAergic neurons, or possibly in muscles and cholinergic neurons? Given that muscles could influence neuronal activity through retrograde signaling, a thorough examination of FLWR-1's role in muscle is necessary, in my opinion.

Would the results from electrophysiological recordings and GCaMP measurements be altered with muscle expression of FLWR-1? Most experiments presented in the manuscript compare wild-type and flwr-1 mutant animals. However, without tissue-specific knockout, knockdown, or rescue experiments, it is difficult to separate cell-autonomous roles from non-cell-autonomous effects, in particular in the context of aldicarb assay results. Also, relying solely on levamisole paralysis experiments is not sufficient to rule out changes in muscle AChRs, particularly due to the presence of levamisole-resistant receptors.

This issue regarding the muscle role of FLWR-1 also complicates the interpretation of results from coelomocyte uptake experiments, where GFP secreted from muscles and coelomocyte fluorescence were used to estimate endocytosis levels. A decrease in coelomocyte GFP could result from either reduced endocytosis in coelomocytes or decreased secretion from muscles. Therefore, coelomocyte-specific rescue experiments seem necessary to distinguish between these possibilities.

The manuscript states that GCaMP was used to estimate Ca2+ levels at presynaptic sites. However, due to the rapid diffusion of both Ca2+ and GCaMP, it is unclear how this assay distinguishes Ca2+ levels specifically at presynaptic sites versus those in axons. What are the relative contributions of VGCCs and ER calcium stores here? This raises a question about whether the authors are measuring the local impact of FLWR-1 specifically at presynaptic sites or more general changes in cytoplasmic calcium levels.

The experiments showing FLWR-1's presynaptic localization need clarification/improvement. For example, data shown in Fig. 3B represent GFP::FLWR-1 is expressed under its own promoter, and TagRFP::ELKS-1 is expressed exclusively in GABAergic neurons. Given that the pflwr-1 drives expression in both cholinergic and GABAergic neurons, and there are more cholinergic synapses outnumbering GABAergic ones in the nerve cord, it would be expected that many green FLWR-1 puncta do not associate with TagRFP::ELKS-1. However, several images in Figure 3B suggest an almost perfect correlation between FLWR-1 and ELKS-1 puncta. It would be helpful for the readers to understand the exact location in the nerve cord where these images were collected to avoid confusion.

The SNG-1::pHluorin data in Figure 5C is significant, as they suggest increased synaptic transmission at flwr-1 mutant synapses. However, to draw conclusions, it is necessary to verify whether the total amount of SNG-1::pHluorin present on synaptic vesicles remains the same between flwr-1 mutant and wild-type synapses. Without this comparison, a conclusion on levels of synaptic vesicle release based on changes in fluorescence might be premature, in particular given the results of electrophysiological recordings.

Finally, the interpretation of the E74Q mutation results needs reconsideration. Figure 8B indicates that the E74Q variant of FLWR-1 partially loses its rescuing ability, which suggests that the E74Q mutation adversely affects the function of FLWR-1. Why did the authors expect that the role of FLWR-1 should have been completely abolished by E74Q? Given that FLWR-1 appears to work in multiple tissues, might FLWR-1's function in neurons requires its calcium channel activity, whereas its role in muscles might be independent of this feature? While I understand there is ongoing debate about whether FLWR-1 is a calcium channel, the experiments in this study do not definitively resolve local Ca2+ dynamics at synapses. Thus, in my opinion, it may be premature to draw firm conclusions about calcium influx through FLWR-1.

Also, the aldicarb data presented in Figures 8B and 8D show notable inconsistencies that require clarification. While Figure 8B indicates that the 50% paralysis time for flwr-1 mutant worms occurs at 3.5-4 hours, Figure 8D shows that 50% paralysis takes approximately 2.5 hours for the same flwr-1 mutants. This discrepancy should be addressed. In addition, the manuscript mentions that the E74Q mutation impairs FLWR-1 folding, which could significantly affect its function. Can the authors show empirical data supporting this claim?

Reviewer #1 (Public review):

Summary:

This work is a continuation of a previous paper from the Arnold group, where they engineered GFE3, which allows to specifically ablate inhibitory synapses. Here, the authors generate 3 different actuators:

(1) An excitatory synapse ablator.

(2) A photoactivatable inhibitory synapse ablator.

(3) A chemically inhibitory synapse ablator.

Following initial engineering, the authors present characterization and optimization data to showcase that these new tools allow one to specifically ablate synapses, without toxicity and with specificity. Furthermore, they showcase that these manipulations are reversible.

Altogether, these new tools would be important for the neuroscience community.

Strengths:

The authors convincingly demonstrate the engineering, optimization, and characterization of these new probes. The main novelty here is the new excitatory synapse ablator, which has not been shown yet and thus could be a valuable tool for neuroscientists.

Weaknesses:

There are a few specific issues with regard to these probes that are unclear to me, which require some explanation or potentially new analysis and experiments.

The biggest concern in this regard is: that almost all the characterization is performed in cultured dissociated neurons. I wonder if, for the typical neuroscience user, it would be trivial to characterize how well these tools express and operate in vivo. This could be substantially different and present some limitations as to the utility of these tools.

Reviewer #1 (Public review):

Summary:

This paper is a relevant overview of the currently published literature on low-intensity focussed ultrasound stimulation (TUS) in humans, with a meta-analysis of this literature that explores which stimulation parameters might predict the directionality of the physiological stimulation effects.

The pool of papers to draw from is small, which is not surprising given the nascent technology. It seems nevertheless relevant to summarize the current field in the way done here, not least to mitigate and prevent some of the mistakes that other non-invasive brain stimulation techniques have suffered from, most notably the theory- and data-free permutation of the parameter space.<br /> The meta-analysis concludes that there are, at best, weak trends toward specific parameters predicting the direction of the stimulation effects. The data have been incorporated into an open database, that will ideally continue to be populated by the community and thereby become a helpful resource as the field moves forward.

Strengths:

The current state of human TUS is concisely and well summarized. The methods of the meta-analysis are appropriate. The database is a valuable resource.

Weaknesses:

These are not so much weaknesses but rather comments and suggestions that the authors may want to consider.

(1) I may have missed this, but how will the database be curated going forward? The resource will only be as useful as the quality of data entry, which, given the complexity of TUS can easily be done incorrectly.

(2) It would be helpful to report the full statistics and effect sizes for all analyses. At times, only p-values are given. The meta-analysis only provides weak evidence (judged by the p-values) for two parameters having a predictive effect on the direction of neuromodulation. This reviewer thinks a stronger statement is warranted that there is currently no good evidence for duty cycle or sonication direction predicting outcome (though I caveat this given the full stats aren't reported). The concern here is that some readers may gallop away with the impression that the evidence is compelling because the p-value is on the correct side of 0.05.

(3) This reviewer thinks the issue of (independent) replication should be more forcefully discussed and highlighted. The overall motivation for the present paper is clearly and thoughtfully articulated, but perhaps the authors agree that the role that replication has to play in a nascent field such as TUS is worth considering.

(4) A related point is that many of the results come from the same groups (the so-called theta-TUS protocol being a clear example). The analysis could factor this in, but it may be helpful to either signpost independent replications, which studies come from the same groups, or both.

(5) The recent study by Bao et al 2024 J Phys might be worth including, not least because it fails to replicate the results on theta TUS that had been limited to the same group so far (by reporting, in essence, the opposite result).

(6) The summary of TUS effects is useful and concise. Two aspects may warrant highlighting, if anything to safeguard against overly simplistic heuristics for the application of TUS from less experienced users. First, could the effects of sonication (enhancing vs suppressing) depend on the targeted structure? Across the cortex, this may be similar, but for subcortical structures such as the basal ganglia, thalamus, etc, the idiosyncratic anatomy, connectivity, and composition of neurons may well lead to different net outcomes. Do the models mentioned in this paper account for that or allow for exploring this? And is it worth highlighting that simple heuristics that assume the effects of a given TUS protocol are uniform across the entire brain risk oversimplification or could be plain wrong? Second, and related, there seems to be the implicit assumption (not necessarily made by the authors) that the effects of a given protocol in a healthy population transfer like for like to a patient population (if TUS protocol X is enhancing in healthy subjects, I can use it for enhancement in patient group Y). This reviewer does not know to which degree this is valid or not, but it seems simplistic or risky. Many neurological and psychiatric disorders alter neurotransmission, and/or lead to morphological and structural changes that would seem capable of influencing the impact of TUS. If the authors agree, this issue might be worth highlighting.

Reviewer #1 (Public review):

Summary:

The authors examine the role of the medial prefrontal cortex (mPFC) in cognitive control, i.e. the ability to use task-relevant information and ignore irrelevant information, in the rat. According to the central-computation hypothesis, cognitive control in the brain is centralized in the mPFC and according to the local hypothesis, cognitive control is performed in task-related local neural circuits. Using the place avoidance task which involves cognitive control, it is predicted that if mPFC lesions affect learning, this would support the central computation hypothesis whereas no effect of lesions would rather support the local hypothesis. The authors thus examine the effect of mPFC lesions in learning and retention of the place avoidance task. They also look at functional interconnectivity within a large network of areas that could be activated during the task by using cytochrome oxydase, a metabolic marker. In addition, electrophysiological unit recordings of CA1 hippocampal cells are made in a subset of (lesioned or intact) animals to evaluate overdispersion, a firing property that reflects cognitive control in the hippocampus. The results indicate that mPFC lesions do not impair place avoidance learning and retention (though flexibility is altered during conflict training), do not affect cognitive control seen in hippocampal place cell activity (alternation of frame-specific firing), a measure of location-specific firing variability, in pretraining. It nevertheless has some effect on functional interconnections. The results overall support the local hypothesis.

Strengths:

(1) Straightforward hypothesis: clarification of the involvement of the mPFC in the brain is expected and achieved. Appropriate use of fully mastered methods (behavioral task, electrophysiological recordings, measure of metabolic marker cytochrome oxidase) and rigorous analysis of the data. The conclusion is strongly supported by the data.

(2) Weaknesses: No notable weaknesses in the conception, making of the study, and data analysis. The introduction does not mention important aspects of the work, i.e. cytochrome oxidase measure and electrophysiological recordings. The study is actually richer than expected from the introduction.

Reviewer #1 (Public review):

Summary:

This paper shows that the synthetic opioid fentanyl induces respiratory depression in rodents. This effect is revised by the opioid receptor antagonist naloxone, as expected. Unexpectedly, the peripherally restricted opioid receptor antagonist naloxone methiodide also blocks fentanyl-induced respiratory depression.

Strengths:

The paper reports compelling physiology data supporting the induction of respiratory distress in fentanyl-treated animals. Evidence suggesting that naloxone methiodide reverses this respiratory depression is compelling. This is further supported by pharmacokinetic data suggesting that naloxone methiodide does not penetrate into the brain, nor is it metabolized into brain-penetrant naloxone.

Weaknesses:

A weakness of the study is the fact that the functional significance of opioid-induced changes in neural activity in the nTS (as measured by cFos and GcAMP/photometry) is not established. Does the nTS regulate fentanyl-induced respiratory depression, and are changes in nTS activity induced by naloxone and naloxone methiodide relevant to their ability to reverse respiratory depression?

Reviewer #1 (Public review):

Summary:

Aging reduces tissue regeneration capacity, posing challenges for an aging population. In this study, the authors investigate impaired bone healing in aging, focusing on calvarial bones, and introduce a two-part rejuvenation strategy. Aging depletes osteoprogenitor cells and reduces their function, which hinders bone repair. Simply increasing the number of these cells does not restore their regenerative capacity in aged mice, highlighting intrinsic cellular deficits. The authors' strategy combines Wnt-mediated osteoprogenitor expansion with intermittent fasting, which remarkably restores bone healing. Intermittent fasting enhances osteoprogenitor function by targeting NAD+ pathways and gut microbiota, addressing mitochondrial dysfunction - an essential factor in aging. This approach shows promise for rejuvenating tissue repair, not only in bones but potentially across other tissues.

Strengths:

This study is exciting, impressive, and novel. The data presented is robust and supports the findings well.

Weaknesses:

As mentioned above the data is robust and supports the findings well. I have minor comments only.

Reviewer #1 (Public review):

Summary:

The study investigates how uncertainty and heuristic strategies influence reward-based decision-making, using a novel two-armed bandit task combined with computational modeling. It aims to disentangle uncertainty-driven behavior from heuristic strategies such as repetition bias and win-stay-lose-shift tendencies, while also exploring individual differences in these processes.

Strengths:

The paper is methodologically sound, and the inclusion of subjective reports enhances the validity of the model testing. The findings on the use of heuristics under specific uncertainty conditions are particularly intriguing.

Weaknesses:

(1) Unclear how the findings significantly diverge from previous work:

At the start of the introduction, the authors propose a working hypothesis of "heterogeneity in the uncertainty effects." However, this concept is already well-established in the field. Foundational work by Yu and Dayan (2005) and more recent studies by Gershman and colleagues on total and relative uncertainty have provided substantial evidence supporting this idea. Additionally, the notion that such heterogeneity could explain mixed findings has been discussed in studies like Wilson (2014). What specific problem are the authors addressing here, and how does their work significantly differ from previous research?

Later on, however, it seems that the authors' hypothesis is to test the role of multiple factors in driving participants' decisions in the context considered by the authors. First, why is it important to solve such a puzzle? Second, this too has been investigated previously, see for example Dubois (2022), eLife. Therefore, what novel things is this paper bringing to the table? I do see that the task is novel - mostly combining different experimental strategies previously adopted - and that the model includes both heuristics and uncertainty-based strategies, which can account for their shared variance ... but are the authors really answering a novel question? Also, it is not very clear which question the authors are answering see point C below.

(2) The sample size appears to be quite small, and the results would be more convincing if supported by a replication study.

(3) The results section can be somewhat unclear at times, as it introduces novel aspects (e.g., the fMRI session) or questions that were not previously explained within the framework outlined in the introduction. While the findings related to psychopathology are interesting, their relevance to the research question posed in the introduction is not immediately clear. If these findings have significant added value, it would be helpful for the authors to highlight this earlier in the manuscript. Similarly, the results on individual differences in uncertainty (Section 3.6), though intriguing, appear tangential to the primary research question regarding the role of multiple factors in driving participants' decisions. Overall, it would strengthen the manuscript to clarify the main research question and ensure the results are more directly aligned with it.

Reviewer #1 (Public review):

In this manuscript, Chen et al. investigate the role of the membrane estrogen receptor GPR30 in spinal mechanisms of neuropathic pain. Using a wide variety of techniques, they first provide convincing evidence that GPR30 expression is restricted to neurons within the spinal cord, and that GPR30 neurons are well-positioned to receive descending input from the primary sensory cortex (S1). In addition, the authors put their findings in the context of the previous knowledge in the field, presenting evidence demonstrating that GRP30 is expressed in the majority of CCK-expressing spinal neurons. Overall, this manuscript furthers our understanding of neural circuity that underlies neuropathic pain and will be of broad interest to neuroscientists, especially those interested in somatosensation. Nevertheless, the manuscript would be strengthened by additional analyses and clarification of data that is currently presented.

Strengths:

The authors present convincing evidence for the expression of GPR30 in the spinal cord that is specific to spinal neurons. Similarly, complementary approaches including pharmacological inhibition and knockdown of GPR30 are used to demonstrate the role of the receptor in driving nerve injury-induced pain in rodent models.

Weaknesses:

Although steps were taken to put their data into the broader context of what is already known about the spinal circuitry of pain, more considerations and analyses would help the authors better achieve their goal. For instance, to determine whether GPR30 is expressed in excitatory or inhibitory neurons, more selective markers for these subtypes should be used over CamK2. Moreover, quantitative analysis of the extent of overlap between GRP30+ and CCK+ spinal neurons is needed to understand the potential heterogeneity of the GRP30 spinal neuron population, and to interpret experiments characterizing descending SI inputs onto GRP30 and CCK spinal neurons. Filling these gaps in knowledge would make their findings more solid.

Reviewer #1 (Public review):

Summary:

The study by Xu and colleagues provides a useful study of brainstem circuits involved in evoked respiratory reflexes that they define to be cough or cough-like in nature. The study is conducted in mice which has the benefit of allowing for the use of modern transgenic tools, although many of the experiments end up using viral vector-based approaches that could be deployed in any species. The disadvantage of the mouse model is understanding the true identity of the respiratory event that is defined as cough. This limitation requires careful interrogation in order to understand the biology of the circuit under investigation. In this respect, the authors provide an incomplete description of a putative cough pathway linking the caudal spinal trigeminal nucleus with the ventral respiratory group. Neurons assigned as CaMKII+ with putative inputs from the paratrigeminal nucleus are central to this circuit, although the evidence for each of these claims is relatively weak or non-existent. Overall, the study employs interesting methods but limitations in methods and details of methods reduce interpretation of the study outcomes.

Strengths:

The use of modern methods to investigate brainstem circuits involved in an essential respiratory reflex.

Weaknesses:

(1) The most significant issue that needs careful consideration is the exact respiratory response, which is called a cough. The authors show a trace from their plethysmography recordings and superimpose the 3 phases of cough (inspiration, compression, expiration) with confidence, yet the parameters used to delineate these phases are unclear. Of more concern, an identical respiratory trace was reported recently as a sneeze in Jiang et al Cell 2024 (PMID 39243765). Comparing Figure 1 in the Xu study with Figure 5 in the Jiang study, it is impossible to see any difference in the respiratory trace that would allow the assignment of one as cough and the other as sneeze. The audio signals also look remarkably similar and the purported cough signal in the Jiang study is quite different. Gannot et al Nat Neurosci 2024 (PMID 38977887) seems to agree with Xu in the identity of a cough signal, but Li et al Cell 2021 (PMID 34133943) again labels these as sneezes. One of the older studies that tried to classify respiratory signals in mice (Chen et al PlosONE 2013) labeled the Jiang cough trace as a deep inspiration, while sneeze looks different again. To add further confusion, Zhang et al AJP 2017 (PMID 28228416 ) provide yet another respiratory plethysmography trace that they define as a cough, and label responses discussed above as expiration reflexes. This begs the question - who, if anyone, is correct? Interpreting the circuits underlying these peculiar mouse responses depends on accuracy in defining the response in the first instance.

(2) The involvement of the causal nSp5 in cough is an unexpected finding. Some understanding of if and how vagal afferent inputs reach this location would help strengthen the manuscript. The authors claim in the discussion that the nucleus of the solitary tract is not the source of inputs, but rather they may arise from the paratrigeminal nucleus (although no data is presented to support this claim). This could fit with the known jugular vagal afferent pathway, which is embryologically distinct and terminates in trigeminal regions, rather than the NTS. But if this is correct, what does this finding then say about the purported involvement of NTS neurons in cough in mice, for example, the recent study by Gannot et al Nat Neurosci where Tac1-expressing NTS neurons were integral for what they call cough in mice? Xu and colleagues are encouraged to resolve their input circuitry so that we can better understand the pathway under investigation and how it relates to the NTS pathway. Related to this, and the issues differentiating cough-like responses from sneeze, the authors will need to consider how to differentiate their cough-like circuitry from the sneeze pathway from the caudal nSp5 to the cVRG as reported by Li et al Cell 2021. It seems highly possible that the two groups are studying the same circuitry, yet the interpretation is confounded by an inability to agree on the identity of the evoked response.

(3) Injection volumes and titres for AAV transductions are not stated anywhere. The methods (line 484) indicate that different volumes were used for different purposes, but nowhere is this information stated properly. Looking at representative images suggests that volumes were very large, with most of the brainstem often transduced. As single slices are only ever shown it becomes a concern as to how extensive transductions truly are. The authors need to provide complete maps of viral transduction so that readers can understand exactly what regions could contribute to responses, thereby confounding interpretation.

(4) The authors do not provide any data to explore the impacts of manipulations on basal breathing. This is important as impacts on the respiratory patterning will likely have profound effects on evoked responses that are not related to the specific pathway under investigation. For example, in Figure 2b. breathing looks to be severely compromised in the TKO animals and disrupted in the M4 DREADD animals. Figure 3 also shows the effects of optical stimulation on breathing patterns, which appear like apnea with several breakthrough augmented breaths (some labeled as cough?), although hard to see properly in the traces provided. Figure 5, one would expect VRG inhibition to have impacts on breathing, and the traces supplied appear to suggest this is the case. Please include data showing breathing effects and consider how these may confound your study interpretation.

Reviewer #1 (Public review):

Summary:

The authors propose a new model of biologically realistic reinforcement learning in the direct and indirect pathway spiny projection neurons in the striatum. These pathways are widely considered to provide a neural substrate for reinforcement learning in the brain. However, we do not yet have a full understanding of mechanistic learning rules that would allow successful reinforcement learning like computations in these circuits. The authors outline some key limitations of current models and propose an interesting solution by leveraging learning with efferent inputs of selected actions. They show that the model simulations are able to recapitulate experimental findings about the activity profile in these populations of mice during spontaneous behavior. They also show how their model is able to implement off-policy reinforcement learning.

Strengths:

The manuscript has been very clearly written and the results have been presented in a readily digestible manner. The limitations of existing models, that motivate the presented work, have been clearly presented and the proposed solution seems very interesting. The novel contribution of the proposed model is the idea that different patterns of activity drive current action selection and learning. Not only does this allow the model is able to implement reinforcement learning computations well, but this suggestion may have interesting implications regarding why some processes selectively affect ongoing behavior and others affect learning. The model is able to recapitulate some interesting experimental findings about various activity characteristics of dSPN and iSPN pathway neuronal populations in spontaneously behaving mice. The authors also show that their proposed model can implement off-policy reinforcement learning algorithms with biologically realistic learning rules. This is interesting since off-policy learning provides some unique computational benefits and it is very likely that learning in neural circuits may, at least to some extent, implement such computations.

Weaknesses:

A weakness in this work is that it isn't clear how a key component in the model - an efferent copy of selected actions - would be accessible to these striatal populations. The authors propose several plausible candidates, but future work may clarify the feasibility of this proposal.

Reviewer #1 (Public review):

Summary:

This manuscript describes the analysis of fetal MRI and diffusion-weighted images of the fetal brain in utero, which reveals correlations between spatial and temporal patterns in diffusion behavior (associated with tissue microstructure) with local geometry of the brain surface (describing cortical folding). The authors use advanced imaging and image analysis pipelines, notably high angular resolution multi-shell diffusion imaging (HARDI) and multi-shell, multi-tissue constrained spherical deconvolution (MSMT-CSD) analysis of the resulting data to analyze. The key metric of tissue microstructure is "tissue fraction" which describes the relative contribution of organized anisotropic diffusion to overall diffusion, and the key geometry parameter is sulcal depth.

The major observation is that tissue fraction, which generally increases with gestational age, is lower in sulcal fundi, and importantly that the relative difference in tissue fraction emerges *before* folding occurs. The relatively low values of tissue fraction in regions of incipient sulci may be important to the physical mechanism of cortical folding.

Strengths:

Strengths of the manuscript include the application of advanced, highly technical imaging and image analysis methods to extract high-resolution data on both surface geometry and diffusion from a unique fetal cohort. The comparison of local features of surface and microstructure in both age-matched and age-mismatched analyses reveals a clear negative correlation between tissue fraction and sulcal depth.

Weaknesses:

The authors could improve the manuscript by (i) expanding their effort to place their current findings in the context of mechanistic models of folding and (ii) explaining more clearly how the diffusion measurements reflect tissue fraction. The relationship between the tissue fraction metric, the diffusion measurements, and the tissue microstructure is quite opaque.

Reviewer #2 (Public review):

Summary:

The study by Sun et al. introduces a useful system utilizing the proteasomal accessory factor A (PafA) and HaloTag for investigating drug-protein interactions in both in vitro (cell culture) and in vivo (zebrafish) settings. The authors presented the development and optimization of the system, as well as examples of its application and the identification of potential novel drug targets. However, the manuscript requires considerable improvements, particularly in writing and justification of experimental design. There are several inaccuracies in data description and a lack of statistics in some figures, undermining the conclusions drawn in the manuscript. Additionally, the authors introduced variants of the ligands and its cognate substrates, yet their use in different experiments appears random and lacks justification. It is challenging for readers to remember and track the specific properties of each variant, further complicating the interpretation of the results.

The conclusions of this paper are mostly backed by data, but certain aspects of data analysis and description require further clarification and expansion.

Comments on revisions:

We would like thank authors for submitting this revised version. We appreciate their inclusion of additional experiments, which convincingly demonstrate the absence of significant toxicity for in vivo applications. All our concerns and questions have been fully addressed. The clarity and quality of the writing have been substantially improved. We believe this innovative proximity labeling tool would be inspiring and valuable for the field.

Reviewer #1 (Public Review):

This work presents a replicable difference in predictive processing between subjects with and without tinnitus. In two independent MEG studies and using a passive listening paradigm, the authors identify an enhanced prediction score in tinnitus subjects compared to control subjects. In the second study, individuals with and without tinnitus were carefully matched for hearing levels (next to age and sex), increasing the probability that the identified differences could truly be attributed to the presence of tinnitus. Results from the first study could successfully be replicated in the second, although the effect size was notably smaller.

Throughout the manuscript, the authors provide a thoughtful interpretation of their key findings and offer several interesting directions for future studies. Their conclusions are fully supported by their findings. Moreover, the authors are sufficiently aware of the inherent limitations of cross-sectional studies.

Strengths:

The robustness of the identified differences in prediction scores between individuals with and without tinnitus is remarkable, especially as successful replication studies are rare in the tinnitus field. Moreover, the authors provide several plausible explanations for the decline of the effect size observed in the second study.

The rigorous matching for hearing loss, in addition to age and sex, in the second study is an important strength. This ensures that the identified differences cannot be attributed to differences in hearing levels between the groups.

The used methodology is explained clearly and in detail, ensuring that the used paradigms may be employed by other researchers in future studies. Moreover, the registering of the data collection and analysis methods for Study 2 as a Registered Report should be commended, as the authors have clearly adhered to the methods as registered.

Reviewer #1 (Public review):

Summary of the work:

In this work Fruchard et. al. study the enzyme Tgt and how it modifies guanine in tRNAs to queuosine (Q), essential for Vibrio cholerae's growth under aminoglycoside stress. Q's role in codon decoding efficiency and its proteomic effects during antibiotic exposure is examined, revealing Q modification impacts tyrosine codon decoding and influences RsxA translation, affecting the SoxR oxidative stress response. The research proposes Q modification's regulation under environmental cues reprograms the translation of genes with tyrosine codon bias, including DNA repair factors, crucial for bacterial antibiotic response.

The experiments are well-designed and conducted and the conclusions, for the most part, are well-supported by the data.

Comments on revisions:

The authors have answered my queries

Joint Public Review:

Based on bioinformatics and expression analysis using mouse and human samples, the authors claim that the adhesion G-protein coupled receptor ADGRA3 may be a valuable target for increasing thermogenic activity and metabolic health. Genetic approaches to deplete ADGRA3 expression in vitro resulted in reduced expression of thermogenic genes including Ucp1, reduced basal respiration and metabolic activity as reflected by reduced glucose uptake and triglyceride accumulation. In line, nanoparticle delivery of shAdgra3 constructs is associated with increased body weight, reduced thermogenic gene expression in white and brown adipose tissue (WAT, BAT), and impaired glucose and insulin tolerance. On the other hand, ADGRA3 overexpression is associated with an improved metabolic profile in vitro and in vivo, which can be explained by increasing the activity of the well-established Gs-PKA-CREB axis. Notably, a computational screen suggested that ADGRA3 is activated by hesperetin. This metabolite is a derivative of the major citrus flavonoid hesperidin and has been described to promote metabolic health. Using appropriate in vitro and in vivo studies, the authors show that hesperitin supplementation is associated with increased thermogenesis, UCP1 levels in WAT and BAT, and improved glucose tolerance, an effect that was attenuated in the absence of ADGRA3 expression.

The revised manuscript fails to address several reviewer concerns, such as the measurement of whole-body energy expenditure through indirect calorimetry and the assessment of food intake.

The previous reviews are here: https://elifesciences.org/reviewed-preprints/100205v2/reviews#tab-content

Reviewer #1 (Public review):

Summary:

This paper presents a data processing pipeline to discover causal interactions from time-lapse imaging data and convincingly illustrates it on a challenging application for the analysis of tumor-on-chip ecosystem data.

The core of the discovery module is the original tMIIC method of the authors, which is shown in supplementary material to compare favourably to two state-of-the-art methods on synthetic temporal data on a 15 nodes network.

Strengths:

This paper tackles the problem of learning causal interactions from temporal data which is an open problem in presence of latent variables.

The core of the method tMIIC of the authors is nicely presented in connection to Granger-Schreiber causality and to the novel graphical conditions used to infer latent variables and based on a theorem about transfer entropy.

tMIIC compares favourably to PC and PCMCI+ methods using different kernels on synthetic datasets generated from a network of 15 nodes.

A full application to tumor-on-chip cellular ecosystems data including cancer cells, immune cells, cancer-associated fibroblasts, endothelial cells and anti cancer drugs, with convincing inference results with respect to both known and novel effects between those components and their contact.

The code and dataset are available online for the reproducibility of the results.

Weaknesses:

The references to "state-of-the-art methods" concerning the inference of causal networks should be more precise by giving citations in the main text, and better discussed in general terms, both in the first section and in the section of presentation of CausalXtract. It is only in the legend of the figures of the supplementary material that we get information.

Of course, comparison on our own synthetic datasets can always be criticized but this is rather due to the absence of a common benchmark in this domain compared to other domains. I recommend the authors to explicitly propose their datasets made accessible in supplementary material as benchmark for the community.

Comments on revisions:

This is a very nice paper.

Reviewer #1 (Public review):

This study presents a novel application of inverted encoding (i.e., decoding) to detect non-linear correlates of crossmodal integration in human neural activity, using EEG (electroencephalography). The method is successfully applied to data from a group of 41 participants, performing a spatial localization task on auditory, visual, and audio-visual events. The analyses clearly show a behavioural superiority for audio-visual localization. Like previous studies, the results when using traditional univariate ERP analyses were inconclusive, showing once more the need for alternative, more sophisticated approaches. The inverted encoding approach of this study, harnessing on the multivariate nature of the signal, captured clear signs of super-additive responses, considered by many as the hallmark of multisensory integration. Despite the removal of eye-movement artefacts from the signal eliminated the significant decoding effect, the author's control analyses showed that decoding is more effective from parietal, compared to frontal electrodes, thereby ruling out ocular contamination as the sole origin of the relevant signal.

This significant finding can bear important advances in the many fields where multisensory integration has been shown to play an important role, by providing a way to bring much needed coherence across levels of analysis, from behaviour to single-cell electrophysiology. To achieve this, it would be ideal to contrast whether the pattern of super-additive effects in other scenarios where clear behavioural signs of multisensory integration are also observed. One could also try to further support the posterior origin of the super-additive effects by source localization.

Comments on revised version:

All my previous concerns have been addressed. I congratulate the authors on a very nice paper.

Reviewer #1 (Public review):

Summary:

The authors aim to elucidate the diversity and gene expression patterns of marine plankton using innovative collection and sequencing methodologies. Their work investigates the taxonomic and functional profiles of planktonic communities, providing insights into their ecological roles and responses to environmental changes.

Strengths:

The methodology utilized in this study, particularly the combination of single-cell sequencing and advanced bioinformatics techniques, represents a significant advancement in the field of plankton research. The application of the Smart-seq2 protocol for cDNA synthesis, followed by rigorous quality control measures, ensures high-quality data generation. This comprehensive approach not only enhances the resolution of the obtained genetic information but also allows for a more detailed exploration of the diversity and functional potential of the phytoplankton community.

One of the major strengths of this study is the rigorous methodological approach, including precise sampling techniques and robust data analysis protocols, which enhance the reliability of the results. The use of advanced sequencing technologies allows for a comprehensive assessment of gene expression, significantly contributing to our understanding of plankton diversity and its implications for marine ecosystems.

Weaknesses:

While the evidence presented is solid, there are areas where the analysis could be expanded. The authors could further explore the ecological interactions within plankton communities, which would provide a more holistic view of their functional roles. Additionally, a broader discussion of the implications of their findings for marine conservation efforts could enhance the manuscript's impact.

The choice of both the plankton net and filter pore size during the plankton collection process is critical, as these factors directly impact the types of phytoplankton collected. The use of a 25 μm filter paper, in particular, may result in the omission of many eukaryotic phytoplankton species. This limitation, combined with the characteristics of the plankton net, could affect the comprehensiveness and accuracy of the results, potentially influencing the study's conclusions regarding phytoplankton diversity.

The timing of fixation is crucial, as it directly affects whether the measured transcriptome accurately represents the organisms' actual transcriptional state in their native water environment. If fixation occurred a significant time after sample collection, the transcriptomic data may not reflect their true in situ transcriptional activity, which greatly reduces the relevance of this method.

Reviewer #1 (Public review):

Summary:

This study by Fuqua et al. studies the emergence of sigma70 promoters in bacterial genomes. While there have been several studies to explore how mutations lead to promoter activity, this is the first to explore this phenomena in a wide variety of backgrounds, which notably contain a diverse assortment of local sigma70 motifs in variable configurations. By exploring how mutations affect promoter activity in such diverse backgrounds, they are able to identify a variety of anecdotal examples of gain/loss of promoter activity and propose several mechanisms for how these mutations are interacting within the local motif landscape. Ultimately, they show how different sequences have different probabilities of gaining/losing promoter activity and may do so through a variety of mechanisms.

Major strengths and weaknesses of the methods and results:

This study uses Sort-Seq to characterize promoter activity, which has been adopted by multiple groups and shown to be robust. Furthermore, they use a slightly altered protocol which allows measurements of bi-directional promoter activity. This combined with their pooling strategy allows them to characterize expression of many different backgrounds in both directions in extremely high-throughput which is impressive! A second key approach this study relies on is the identification of promoter motifs using position weight matrices (PWMs). While these methods are prone to false positives, the authors implement a systematic approach which is standard in the field. However, drawing these types of binary definitions (is this a motif? yes/no) should always come with the caveat that gene expression is quantitative traits that we oversimplify when drawing boundaries.

Their approach to randomly mutagenize promoters allowed them to find many examples of different types of evolutions that may occur to increase or decrease promoter activity. They have supported these with validations in more controlled backgrounds which convincingly support their proposed mechanisms for promoter evolution.

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

The authors express a key finding that the specific landscape of promoter motifs in a sequence affect the likelihood that local mutations create or destroy regulatory elements. The authors have described many examples, including several that are non-obvious, and show convincingly that different sequence backgrounds have different probabilities for gaining or losing promoter activity. This overarching conclusion is supported by trend and mechanistic data which show differences in probabilities of evolving promoters, as well as the mechanisms underlying these evolutions. Furthermore, these mutations are well described and presented, showing the strength of emergent promoter motifs and their specific spacings from existing motifs within the sequence.

Impact of the work on the field, and the utility of the methods and data to the community:

This study enhances our understanding of the diverse mechanisms by which promoters can evolve or devolve, potentially improving models that predict mutational outcomes. While this study reveals complex mutational patterns, modeling them could significantly advance our ability to predict bacterial evolutionary trajectories and interpret genomes, bringing us closer to that goal.

Recent work in the field of bacterial gene regulation has raised interest in bidirectional promoter regions. While the authors do not discuss how mutations that raise expression in one direction may affect another, they have created an expansive dataset which may enable other groups to study this interesting phenomenon. Also, their variation of the Sort-Seq protocol will be a valuable example for other groups who may be interested in studying bidirectional expression. Lastly, this study may be of interests to groups studying eukaryotic regulation as it can inform how the evolution of transcription factor binding sites influences short-range interactions with local regulator elements.

Any additional context to understand the significance of the work:

Predicting whether a sequence drives promoter activity is a challenging task. By learning the types of mutations that create or destroy promoters, this study provides valuable insights for computational models aimed at predicting promoter activity.

Comments on revised version:

I am satisfied with the extensive changes made by the author. This manuscript is excellent.

I very much like the change in figures to incorporate the sequence information. It is great to see clear representations of the emergent sigma70 motifs and their spacing relative to existing motifs. This addition significantly improves the clarity of the findings.

The validation of mutations on a clean background is well-executed, and the results are convincing. I appreciate the effort put into validating their results. The additional analyses that include TGn and UP-element motifs are also well done and highly relevant, as these elements are known to compensate for weaker or absent -35 sequences.

Most or all perceived inconsistencies from the previous version have been resolved. While I don't think the fluorescence threshold of 1.5 a.u. for promoter activity is justified, the authors do acknowledge this shortcoming, and even empirically-derived thresholds are still technically arbitrary.

I particularly enjoyed Figure 1E, thank you for entertaining my analysis request! Also, the H-NS story is a nice addition showing how transcription factors influence this evolution

Overall, this revised manuscript is an excellent contribution to the field, and I have no further recommendations for improvement.

Reviewer #1 (Public review):

Summary:

In this manuscript, Liu et al. present CROWN-seq, a technique that simultaneously identifies transcription-start nucleotides and quantifies N6,2'-O-dimethyladenosine (m6Am) stoichiometry. This method is derived from ReCappable-seq and GLORI, a chemical deamination approach that differentiates A and N6-methylated A. Using ReCappable-seq and CROWN-seq, the authors found that genes frequently utilize multiple transcription start sites, and isoforms beginning with an Am are almost always N6-methylated. These findings are consistently observed across nine cell lines. Unlike prior reports that associated m6Am with mRNA stability and expression, the authors suggest here that m6Am may increase transcription when combined with specific promoter sequences and initiation mechanisms. Additionally, they report intriguing insights on m6Am in snRNA and snoRNA and its regulation by FTO. Overall, the manuscript presents a strong body of work that will significantly advance m6Am research.

Strengths:

The technology development part of the work is exceptionally strong, with thoughtful controls and well-supported conclusions.

Weaknesses:

Given the high stoichiometry of m6Am, further association with upstream and downstream sequences (or promoter sequences) does not appear to yield strong signals. As such, transcription initiation regulation by m6Am, suggested by the current work, warrants further investigation.

Reviewer #1 (Public review):

Summary:

In this work, Qiu and colleagues examined the effects of preovulatory (i.e., proestrous or late follicular phase) levels of circulating estradiol on multiple calcium and potassium channel conductances in arcuate nucleus kisspeptin neurons. Although these cells are strongly linked to a role as the "GnRH pulse generator," the goal here was to examine the physiological properties of these cells in a hormonal milieu mimicking late proestrus, the time of the preovulatory GnRH-LH surge. Computational modeling is used to manipulate multiple conductances simultaneously and support a role for certain calcium channels in facilitating a switch in firing mode from tonic to bursting. CRISPR knockdown of the TRPC5 channel reduced overall excitability, but this was only examined in cells from ovariectomized mice without estradiol treatment.

Comments to address most recent author response:

The concern regarding the CRISPR experiments being confined to OVX mice is that the results can only suggest that CRISPR-mediated knockdown of TRPC5 can, at best, phenocopy the OVX+E condition. A reciprocal experiment in the opposite direction (for example, that returning TRPC5 to OVX levels in OVX+E mice prevents the changes in firing activity and pattern typical of the OVX+E2 condition) would strengthen the indication that E2-sensitive changes in TRPC5 expression and function are critically important to surge function. Acknowledging this as a limitation of the studies would help to better contextualize the value of the CRISPR experiments to an understanding of surge mechanisms when done only in OVX conditions.

The nature of the confusion regarding the consideration of OVX+E2 conditions in the computational model primarily arises from the methods description in the supplemental file: "The effect of E2 on ionic currents is modelled as a change in the maximum conductance parameter. For currents IM,IT, ICa and ITRPC5 this change is inferred from the qPCR data assuming that the conductance is directly proportional to the mRNA expression." If these were instead based on the whole-cell recordings as the authors now indicate in their response, then this description needs to be edited and clarified accordingly. Furthermore, the section states, "For ISK, IBK, Ileak, the OVX and OVX+E2 conductances are obtained from current-voltage relationships recorded from Kiss1ARH neurons in the absence/presence of iberiotoxin (BK blocker) and apamin (SK blocker). All other currents were assumed to be unaffected by E2." This section thus does not directly indicate that the recordings in the stated figures were used in the model, and moreover suggests that currents besides ISK, IBK, and Ileak were not different in OVX+E2 conditions.

The prior evidence stated for correlation of mRNA and channel conductance is not explicitly cited in the manuscript. It is well known that post-translational modifications, physiological modulation of individual channel biophysical properties, and many other factors can influence the end output of a membrane conductance. Therefore, the authors should, at minimum, provide a literature citation supporting the assumption used here.

Reviewer #1 (Public review):

Summary:

This study from Abssy et al. aims to determine if different non-invasive peripheral stimulation techniques - such as magnetic and electrical stimulations - may influence pain intensity, unpleasantness, and secondary hyperalgesia using a 4-arm parallel-group study. They observed no effect on pain intensity and unpleasantness. Also, they reported that only the TENS (electrical stimulation) did not impact secondary hyperalgesia. They hypothesized that the effects were probably due to the sound emitted by RPMS (magnetic stimulation). In a follow-up study, they tried to determine if covering the sound of RPMS would abolish the effect on secondary hyperalgesia using a single-arm design. They observed no effect of RPMS.

Strengths:

(1) The research team recruited a relatively large sample size for this type of study.

(2) The phasic heat pain protocol appears rigorous and well-described.

(3) The Figures are helpful in facilitating the understanding of the study design and results.

(4) The statistical analyses appear sound.

Weaknesses:

(1) The proposed design is not sufficient to answer the research question. The rationale of the study proposed in the introduction is that auditory stimulation may explain the analgesic effects of RPMS. To answer this question, the authors should have used a factorial design using 4 groups (active RPMS + sound; active RPMS + no sound; sham RPMS + sound; sham RPMS + no sound). Using this design, it would have been possible to determine if the sound, the afferent stimulation, or both are necessary to produce analgesia. Rather, they tested two types of RPMS (iTBS, cTBS) without real rationale, one electrical stimulation and a placebo.

(2) There are multiple ways that the current design could have introduced biases. The study was not randomized but pseudo-randomised. What does that mean? Was their allocation concealment? Was the assessor and data analyst blinded to group allocation? Did an intention to treat analyses were performed? Did the participants were adequately blinded (was it measured)?

(3) The TENS parameters used were not optimal and are not those commonly used in clinical practice. This could have explained the lack of TENS effects. The lack of TENS effects has not been discussed and it is concerning. If TENS had been effective (as expected), the story about the auditory effects would not have been presented as the primary mechanisms underlying the current results.

(4) No primary outcome has been identified. It is important to mention that the interpretation of results is based on the presence of only one statistically significant result. Pain intensity and pain unpleasantness are not affected. This was not properly addressed in the Discussion. What does that mean that secondary hyperalgesia is affected but not pain?

(5) The use of secondary hyperalgesia as a variable requires further clarification. How is it possible to measure secondary hyperalgesia if there is no lesioned tissue? If heat creates secondary hyperalgesia without lesion, what does that mean physiologically? Is it a valid and reliable "pain" variable?

(6) The follow-up study has been designed to cover the RPMS sound using pink noise. However, the pink noise was also present during the PHP measurement. How can we determine whether the absence of change is due to the pink noise during the RPMS or the presence of pink noise during PHP? I don't think this is possible to discriminate.

Appraisal:

(7) Despite all these potential issues, authors interpret their data with high confidence and with several overstatements in the Title, Abstract, and Discussion. The results do not support their conclusions. The fact that auditory stimulation may produce an analgesic effect is a hypothesis, but the current study cannot ascertain it.

Reviewer #1 (Public Review):

Summary:

Park et al. conducted various analyses attempting to elucidate the biological significance of SARS-CoV-2 mutations. However, the study lacks a clear objective. The specific goals of the analyses in each subsection are unclear, as is how the results from these subsections are interconnected. Compiling results from unrelated analyses into a single paper can be confusing for readers. Clarifying the objective and narrowing down the topics would make the paper's purpose clearer.

The logic of the study is also unclear. For instance, the authors developed an evaluation score, APESS, for analyzing viral sequences. Although they state that the APESS score correlates with viral infectivity, there is no explanation in the results section about why this is the case.

In summary, I recommend reconsidering the structure of the paper.

Reviewer #1 (Public review):

Summary:

This important study by Takano et. al. describes a novel approach for optogenetically evoking seizures in an etiologically relevant mouse model of epilepsy. The authors developed a model that can trigger seizures "on demand" using optogenetic stimulation of CA1 principal cells in mice rendered epileptic by an intra-hippocampal kainate (IHK) injection into CA3. The authors discuss their model in the context of the limitations of current animal models used in epilepsy drug development. In particular, their model addresses concerns regarding existing models where testing typically involves inducing acute seizures in healthy animals or waiting on infrequent, spontaneous seizures in epileptic animals.

Strengths:

A strength of this manuscript is that this approach may facilitate the evaluation of novel therapeutics since these evoked seizures are demonstrated as being sufficiently similar to spontaneous seizures in these same mice which are more laborious to analyze. The data demonstrating the commonality of pharmacology and EEG features between evoked seizures and spontaneous seizures in epileptic mice, while also being different from evoked seizures in naïve mice, are convincing despite concerns regarding the biological significance of the differences in effect sizes of these features. The structural, functional, and behavioral differences between a seizure-naïve and epileptic mouse are complex and important issues. This study positively impacts the wider epilepsy research community by investigating seizure semiology and pharmaceutical responses in these populations.

Weaknesses:

While the data generally supports the authors' conclusions, a weakness of this manuscript lies in their analytical approach where EEG feature-space comparisons used the number of spontaneous or evoked seizures as their replicates as opposed to the number of IHK mice; these large data sets tend to identify relatively small effects of uncertain biological significance as being highly statistically significant. Furthermore, the clinical relevance of similarly small differences in EEG feature space measurements between seizure-naïve and epileptic mice is also uncertain. Finally, the multiple surgeries and long timetable to generate these mice may limit the value compared to existing models in drug-testing paradigms.

Reviewer #2 (Public review):

Summary:

Wilson's disease is a rare genetic disorder caused by mutations in the ATP7B gene. Previous studies have documented that ATP7B mutations can disrupt copper metabolism, affecting brain and liver function. In this paper, the authors performed a retrospective clinical study and found that Wilson's disease has a high incidence of cholecystitis. Single-cell RNA-seq analysis revealed changes in the immune microenvironment, including the activation of immune responses and the exhaustion of natural killer cells.

Strengths:

A key finding of this study is that the predominant ATP7B gene mutation in the Chinese population is the 2333G>T (p. R778L) mutation. The authors reported associations between Wilson's disease and cholecystitis, as well as the exhaustion of natural killer cells.

Weaknesses:

The underlying mechanisms linking ATP7B mutations to cholecystitis and natural killer cell exhaustion remain unclear. Specifically, it is not yet determined whether copper metabolism alterations directly cause cholecystitis and natural killer cell exhaustion, or if these effects are secondary to liver dysfunction.

Comments on revisions:

The authors fully addressed my questions and I don't have further comments.

Reviewer #1 (Public review):

Summary:

The research study under review investigated the relationship between gut and identified potential biomarkers derived from the nasopharyngeal and gut microbiota-based that could aid predicting COVID-19 severity. The study reported significant changes in the richness and Shannon diversity index in nasopharyngeal microbiome associated with severe symptoms.

Strengths:

The study successfully identified differences in the microbiome diversity that could indicate or predict disease severity. Furthermore, the authors demonstrated a link between individual nasopharyngeal organisms and the severity of SARS-CoV-2 infection. The density of the nasopharyngeal organism was shown to be a potential predictors of severity of COVID-19.

Reviewer #1 (Public review):

This manuscript from Schwintek and coworkers describes a system in which gas flow across a small channel (10^-4-10^-3 m scale) enables the accumulation of reactants and convective flow. The authors go on to show that this can be used to perform PCR as a model of prebiotic replication.

Strengths:

The manuscript nicely extends the authors' prior work in thermophoresis and convection to gas flows. The demonstration of nucleic acid replication is an exciting one, and an enzyme-catalyzed proof-of-concept is a great first step towards a novel geochemical scenario for prebiotic replication reactions and other prebiotic chemistry.

The manuscript nicely combines theory and experiment, which generally agree well with one another, and it convincingly shows that accumulation can be achieved with gas flows and that it can also be utilized in the same system for what one hopes is a precursor to a model prebiotic reaction. This continues efforts from Braun and Mast over the last 10-15 years extending a phenomenon that was appreciated by physicists and perhaps underappreciated in prebiotic chemistry to increasingly chemically relevant systems and, here, a pilot experiment with a simple biochemical system as a prebiotic model.

I think this is exciting work and will be of broad interest to the prebiotic chemistry community. The techniques described will be useful to the community as well.

Weaknesses:

This work stands well on its own in advancing the field and is well-supported by the evidence presented. The weaknesses below are thus more hopes for future work than limitations of a study that I find to be a complete and well-executed piece of work.

This paper's use of highly evolved protein enzymes is a potential limitation in its direct relevance to prebiotic chemistry. But this is less a limitation of the manuscript than the state of the field after the authors' advances. It will be of interest to see how these systems function in, e.g., RiboPCR (10.1073/pnas.1610103113) and with non enzymatic systems.

Similarly, some of the artifacts in this work (appreciated and noted by the authors) arising from gas bubbles evolving prevent the simulations from fully describing their results. However, gas-liquid interactions were likely important in prebiotic chemistry and the authors note several areas in which these could be important in future systems.

Reviewer #1 (Public review):

This study provides compelling evidence that RAR, rather than its obligate dimerization partner RXR, is functionally limiting for chromatin binding. This manuscript provides a paradigm for how to dissect the complicated regulatory networks formed by dimerizing transcription factor families.

Dahal and colleagues use advanced SMT techniques to revisit the role of RXR in DNA-binding of the type-2 nuclear receptor (T2NR) RAR. The dominant consensus model for regulated DNA binding of T2NRs poses that they compete for a limited pool of RXR to form an obligate T2NR-RXR dimer. Using advanced SMT and proximity-assisted photoactivation technologies Dahal et al. now test the effect of manipulating the endogenous pool size of RAR and RXR on heterodimerization and DNA-binding in live U2OS cells. Surprisingly, it turns out that RAR, rather than RXR, is functionally limiting for heterodimerization and chromatin binding. By inference, the relative pool size of various T2NRs expressed in a given cell, rather than RXR, is likely determine chromatin binding and transcriptional output.

The conclusions of this study are well supported by the experimental results and provides unexpected novel insights in the functioning of the clinically important class of T2NR TFs. Moreover, the presented results show how the use of novel technologies can put long-standing theories on how transcription factors work upside down. This manuscript provides a paradigm for how to further dissect the complicated regulatory networks formed by T2NRs or other dimerizing TFs. I am convinced by the revised manuscript and have no additional concerns or comments.

Reviewer #1 (Public review):

Summary:

The manuscript by Yao S. and colleagues aims to monitor the potential autosomal regulatory role of the master regulator of X chromosome inactivation, the Xist long non-coding RNA. It has recently become apparent that in the human system, Xist RNA can not only spread in cis on the future inactive X chromosome but also reach some autosomal regions where it recruits transcriptional repression and Polycomb marking. Previous work has also reported that Xist RNA can show a diffused signal in some biological contexts in FISH experiments.

In this study, the authors investigate whether Xist represses autosomal loci in differentiating female mouse embryonic stem cells (ESCs) and somatic mouse embryonic fibroblasts (MEFs). They perform a time course of ESC differentiation followed by Capture Hybridization of Associated RNA Targets (CHART) on both female and male ESCs, as well as pulldowns with sense oligos for Xist. The authors also examine transcriptional activity through RNA-seq and integrate this data with prior ChIP-seq experiments. Additional experiments were conducted in MEFs and Xist-ΔB repeat mutants, the latter fails to recruit Polycomb repressors.

Based on this experimental design, the authors make several bold claims:

(1) Xist binds to about a hundred specific autosomal regions.<br /> (2) This binding is specific to promoter regions rather than broad spreading.<br /> (3) Xist autosomal signal is inversely correlated with PRC1/2 marks but positively correlated with transcription.<br /> (4) Xist targeting results in the attenuation of transcription at autosomal regions.<br /> (5) The B-repeat region is important for autosomal Xist binding and gene repression.<br /> (6) Xist binding to autosomal regions also occurs in somatic cells but does not lead to gene repression.

Together, these claims suggest that Xist might play a role in modulating the expression of autosomal genes in specific developmental and cellular contexts in mice.

Strengths:

This paper deals with an interesting hypothesis that Xist ncRNA can also function at autosomal loci.

Weaknesses:

The revised manuscript now includes many additional bioinformatic analyses to support the premise that Xist RNA targets a specific set of about 100 promoters and attenuates their expression in the early stages of differentiation. I have previously raised significant concerns about the bioinformatic analyses and the robustness of the data, especially those linked to CHART-seq datasets. Despite some improvements, fundamental problems with the analysis remain, precluding a conclusion on whether Xist RNA binds specific autosomal promoters. The main concerns include:

(1) The authors nicely explain the use of biological replicates; however, they still fail to provide the sufficient analysis I requested on d0 and sense probes. While some quantification is presented in Figures 1E and 1F, the peak calling I asked for has still not been performed. In the response document, the authors report that about 600 peaks were identified in d0 female ESCs compared to about 100 in differentiated conditions. They explain this by the well-known phenomenon of having a background of differentiated cells in d0. In my opinion, this reasoning is flawed. With 98% of cells not inducing Xist in the culture, it is unimaginable why 600 peaks would be detected in the peak calling analysis. Rather, this demonstrates a high background in the CHART peak calling. To assess this further, I have reanalyzed d7 CHART datasets and found robust enrichment of the sense probe on promoters of genes, even stronger than the antisense probe. MACS peak calling also identifies a robust number of peaks on the sense probe. Indeed, even though Figure 1F shows low sense probe enrichment, this is because it focuses on the anti-sense peaks only. An opposite effect is observed when focusing on all genes or on sense-peaks. Thefore it is tough to decide which of the signal is truelly due to Xist binding and what is an inherent problem with the CHART signal. These results cast serious doubts on the biological conclusions of this work and point to a very high background level of promoter signal in both sense and antisense samples.

(2) The authors do not address the conundrum of their results: how is it possible to have a genome-wide autosomal accumulation of Xist signal at promoters (see Figures 1A and 1B), while simultaneously specifically affecting only 100 promoters in the genome? The signal is either general (as Figures 1A and 1B suggest) or specific (as implied by the peak calling), but it cannot be both. Current data points to the fact that CHART has a bias for the most open parts of the chromatin.

(3) The text is still very confusing when it comes to Polycomb. Some experiments point to the fact that there are few PRC1/2 marks at putative Xist autosomal binding sites (Figure 3C), while the use of X1 induces the loss of PRC2 marks. I still find this internally contradictory. The authors sadly do not address my concerns with additional analysis. Their current data indicate that upon Xist upregulation, Xist-RNA binds to autosomal regions that are highly expressed and devoid of Polycomb. These loci then become transcriptionally attenuated and gain some (but low) level of PRC2 in a Xist-dependent fashion. If this model is true, then all these regions should not have Xist in d0 of differentiation and should also have slightly lower levels of PRC2. The argument that there is a low level of Xist in 2-5% of cells should not be a problem because most of the signal will come from the 98% of cells not expressing Xist (as seen in Figure 1A). Without timepoint 0, the whole premise of the paper is difficult to interpret. Either the d0 samples are good enough, or the system is so leaky that it is nearly impossible to identify Xist-specific effects. Males are a useful control but are obviously a genetically very different line with distinct epigenetic and signaling statuses. It is crucial to compare the timing of repression/PRC accumulation to conclude if and how Xist is functional on these loci.

(4) The authors did not address my concerns about the transcriptional analysis. I belive that the control genes are not selected properly. This analysis should not have been performed on just 100 randomly selected regions/genes. Instead, bootstrapping of 100 randomly selected regions/genes should be done, e.g., 1000 times. Additionally, one should only sample from expressed genes to have a comparable control gene set. For example, in Figures 4D and 4E, the distribution of control regions is entirely different. To stress again, relying on a set of 100 randomly selected genes/regions is not statistically robust; controls have to be matched, and bootstrapping has to be performed. Finally, each timepoint uses a different set of autosomal targets. There is a need to visualize the same set of genes across all timepoints (including d0). For example, are genes bound by Xist at d7 highly expressed at d0 and then attenuated only at d7? What happens to them at d14 (see points from 3)? The arguments about d0 heterogeneity are again not convincing (nor is Figure 3H, which shows a different set of genes).

(5) Transcriptional analysis is often shown only as tracks however the reads for key example genes have to be quantified properly and not just visualized or amalgamated in a violin plot.

Reviewer #1 (Public review):

The study by Longhurst et al. investigates the mechanisms of chemoresistance and chemosensitivity towards three compounds that inhibit cell cycle progression: camptothecin, colchicine, and palbociclib. Genome-wide genetic screens were conducted using the HAP1 Cas9 cell line, revealing compound-specific and shared pathways of resistance and sensitivity. The researchers then focused on novel mechanisms that confer resistance to palbociclib, identifying PRC2.1. Genetic and pharmacological disruption of PRC2.1 function, but not related PRC2.2, leads to resistance to palbociclib. The researchers then show that disruption of PRC2.1 function (for example, by MTF2 deletion), results in locus-specific changes in H3K27 methylation and increases in D-type cyclin expression. The study shows that increased expression of D-type cyclins results in palbociclib resistance.

Strengths:

The results of this study are interesting, and the study contributes insights into the molecular mechanisms of CDK4/6 inhibitors. Importantly, while CDK4/6 inhibitors are effective in the clinic, tumour recurrence is very high due to acquired resistance.

Weaknesses:

A key resistance mechanism is Rb loss, so it is important to understand if resistance conferred by PRC2.1 loss is mediated by Rb, and whether restoration of PRC2.1 function in Rb-deplete cells results in renewed palbociclib sensitivity. It is also important to understand the clinical implications of the results presented. Inclusion of these data would significantly improve the paper. At present, it is unclear if mutations in PRC2.1 are found in genetic analyses of tumour samples in patients with acquired resistance.

Reviewer #1 (Public review):

The authors aim to investigate the relationship between low estrogen levels, postmenopausal hypertension, and the potential role of the molecule L-AABA as a biomarker for hypertension. By employing metabolomic analysis and various statistical methods, the study seeks to understand how estrogen deficiency affects blood pressure and identify key metabolites involved in this process, with a particular focus on L-AABA.

Strengths:

The study addresses a relevant and understudied area: the role of estrogen and metabolites in postmenopausal hypertension. It presents a novel hypothesis that L-AABA may serve as a protective factor against hypertension, which could have significant clinical implications if proven.

Weaknesses:

The evidence linking L-AABA to hypertension is largely correlative, lacking experimental validation or mechanistic proof. Key limitations, such as the inadequacy of the ovariectomy model in replicating human menopause, are acknowledged but not addressed with alternative approaches. In summary, while the study offers an intriguing hypothesis, its conclusions are premature and require further experimental validation and human data to substantiate the claims.

Reviewer #1 (Public review):

Summary:

Kan et al. report the serendipitous discovery of a Bacillus amyloliquefaciens strain that kills N. gonorrhoeae. They use TnSeq to identify that the anti-gonococcal agent is oxydifficidin and show that it acts at the ribosome and that one of the dedA gene products in N. gonorrhoeae MS11 is important for moving the oxydifficidin across the membrane.

Strengths:

- This is an impressive amount of work, moving from a serendipitous observation through TnSeq to characterize the mechanism by which Oxydifficidin works.

Weaknesses:

- The genetic diversity of dedA and rplL in N. gonorrhoeae is still not clear, as the authors looked at diversity of these genes in only 220 isolates (of unclear relationship to each other).

It's not so much a weakness as a source of confusion: how did the authors choose to screen a tiny transposon library of 50 mutants? Since they were surprised to find 4 transposon insertions (if I'm reading it correctly), what was the motivation for even looking at this small library? And since the mutation that led them to the biosynthetic gene cluster wasn't even a transposon insertion but a frameshift, it seems they had another huge episode of serendipity.

Reviewer #1 (Public Review):

In this manuscript, Yong and colleagues link perturbations in lysosomal lipid metabolism with the generation of protein aggregates resulting from proteosome inhibition. The main tool used is the ProteoStat stain to assess protein aggregate burden in native cells (i.e. cells under no exogenous or endogenous stress). They initially use CRISPR-based genome-wide screens to identify several genes that affect this aggregate burden. Interestingly, knockdown of genes involved in lysosomal acidification was a major signature which led to identification of other culprit lysosome-associated genes that included ones involved in lipid metabolism. Subsequent CRISPR screen focused on lipidomic analysis led to identification of sphingolipid and cholesterol esters as lipid classes with effects on proteostasis.

Comments on revised version:

They did a decent job addressing most of my comments and the new data (including LysoIP) makes for much more plausible conclusions.

They propose the idea that microautophagy is mediating the delivery of these aggregates to lysosomes.

It appears there are enough experiments and support now for their premise.

The lysosomal lipid metabolism link to proteostasis is still a lingering question in this work but they addressed each of the points I raised regarding it and revised the manuscript accordingly with pertinent discussion.

It is difficult to truly address the lipid link and I think we have to acknowledge that. But overall, looking at the effort and conclusions, this has been improved enough to be a valuable contribution to the field.

Reviewer #1 (Public review):

Summary:

This manuscript constitutes further analysis of a dataset generated for a previously-published study from the same group. The experiments in the previous work use an RNA-DNA proximity assay to capture RNAs that interact with chromatin, especially beyond their site of transcription, by crosslinking-and proximity ligation. The previous work added one novel feature to this treatment, compared to other studies by the same group, where they treated the nuclei with RNase A prior to crosslinking. The initial study concluded that long-range chromatin interaction via chromatin looping is affected by RNase treatment. In the current manuscript, the group analyze the data from this experiment in more detail. They describe some notable features of RNAs that remain after RNase treatment and where they are associated within the genome. Overall, the further analyses are somewhat useful, with some exceptions for specific analyses that are not clear in the current manuscript. The work is very complementary to the previously published original study, to the point that it is surprising it was not included in that study.

Strengths:

(1) The analyses are a useful complement that fill in gaps from the Calandrelli et al paper. Some of the findings are suggestive of RNA-protein networks that operate at long distances to regulate promoters.

Weaknesses:

(1) The beginning of the Results section, and elsewhere, describes steps that likely were performed in the previous publication from which the data are being further analyzed and possibly partially reanalyzed. The current manuscript should more clearly describe if there are any aspects of the pipeline that have been modified from the Calandrelli study (which does not have much detail regarding iMARGI parameters in the published paper) for the further analysis in this manuscript.

(2) The RNase treatment approach is similar to that addressed in recent papers from the Jenner and Davidovich groups (https://doi.org/10.1016/j.celrep.2024.113856; https://doi.org/10.1016/j.celrep.2024.113858) where these groups found RNase treatment significantly affected solubility of chromatin, causing aggregation. The authors should address this work and place it in light of their current study.

(3) Figure 1f: it is not clear what it means for genes to be "non-differentially expressed" in this context. Isn't this also RNase-insensitive? And how is the "Ctrl specific" RNA set determined? This is confusing, since RNase is assumed to degrade most of the RNA in these samples.

(4) Figure 2a: The results are somewhat surprising, given that protein-coding genes are depleted more in the RNase treatment. Is the Ctrl set the same as in 1f? This emphasizes the importance of defining that population better.

(5) Figure 3a: The text references this figure in ways that do not match the figure, referencing at least nine column clusters when there are only six. Heatmaps of certain TFs and "RAH explained" percentages don't seem to match the Results section description, either. The authors claim EZH2 binding sites are the top TF overlap with RAHs and yet do not include EZH2 in Figure 3a. Suz12 (EZH2 binding partner) and H3K27me3 (EZH2 product) are also referenced in the text for this figure, but not included in the figure itself.

(6) The manuscript uses the term "non-diffusive RNA-chromatin interactome" which is not directly supported by data. The authors use the term initially to describe the RNase-resistant species in their previous work, but through the current study, they support a model where the RNase resistance is simply due to protection by protein binding, not by any constraints on diffusion in particular chromatin environments.

Reviewer #1 (Public review):

Summary:

This work examines the binding of several phosphonate compounds to a membrane-bound pyrophosphatase using several different approaches, including crystallography, electron paramagnetic resonance spectroscopy, and functional measurements of ion pumping and pyrophosphatase activity. The work attempts to synthesize these different approaches into a model of inhibition by phosphonates in which the two subunits of the functional dimer interact differently with the phosphonate.

Strengths:

This study integrates a variety of approaches, including structural biology, spectroscopic measurements of protein dynamics, and functional measurements. Overall, data analysis was thoughtful, with careful analysis of the substrate binding sites (for example calculation of POLDOR omit maps).

Weaknesses:

Unfortunately, the protein did not crystallize with the more potent phosphonate inhibitors. Instead, structures were solved with two compounds with weak inhibitory constants >200 micromolar, which limits the molecular insight into compounds that could possibly be developed into small molecule inhibitors. Likewise, the authors choose to focus the spectroscopy experiments on these weaker binders, missing an opportunity to provide insight into the interaction between more potent binders and the protein.

In general, the manuscript falls short of providing any major new insight into membrane-bound pyrophosphatases, which are a very well-studied system. Subtle changes in the structures and ensemble distance distributions suggest that the molecular conformations might change a little bit under different conditions, but this isn't a very surprising outcome. It's not clear whether these changes are functionally important, or just part of the normal experimental/protein ensemble variation.

The ZLD-bound crystal structure doesn't predict the DEER distances, and the conformation of Na+ binding site sidechains in the ZLD structure doesn't predict whether sodium currents occur. This might suggest that the ZLD structure captures a conformation that does not recapitulate what is happening in solution/ a membrane.

Reviewer #1 (Public review):

Summary:

This study used whole genome data to investigate Beefalo ancestry for the first time, filling the gap in the field of Beefalo ancestry. The authors used preserved semen samples to generate genomic data on 47 registered Beefalo and 3 bison hybrids, further questioning the ABA's stated goal of ⅜ bison ancestry. In addition, the authors also show that ancestry profiles of Beefalo and bison hybrid genomes are consistent with repeated backcrossing to either parental species, demonstrating the value of genomic information in examining gene flow between species in the genus Bison. This is an interesting study that still has some major weaknesses that exist, but overall, the work demonstrates the utility of genomic information in validating specific breeding claims for a more complete understanding of gene flow and genetic variation among bovine species.

Strengths:

Numerous genetic analysis methods such as PCA, ADMIXTURE, F4 ratios, and local ancestry inference techniques revealed that no single Beefalo set meets the ancestry requirements set by the American Beefalo Association (ABA) and some beefalo had detectable indicine cattle ancestry.

Weaknesses:

While this study contributes to our knowledge of Beefalo ancestry, there are some key issues that need to be addressed in terms of analysing the specific results as well as writing the article.

Reviewer #1 (Public review):

In this paper, the authors reveal that the MK2 inhibitor CMPD1 can inhibit the growth, migration, and invasion of breast cancer cells both in vitro and in vivo by inducing microtubule depolymerization, preferentially at the microtubule plus-end, leading to cell division arrest, mitotic defects, and apoptotic cell death. They also showed that CMPD1 treatment upregulates genes associated with cell migration and cell death, and downregulates genes related to mitosis and chromosome segregation in breast cancer cells, suggesting a potential mechanism of CMPD1 inhibition in breast cancer. Besides, they used the combination of an MK2-specific inhibitor, MK2-IN-3, with the microtubule depolymerizer vinblastine to simultaneously disrupt both the MK2 signaling pathway and microtubule dynamics, and they claim that inhibiting the p38-MK2 pathway may help to enhance the efficacy of MTAs in the treatment of breast cancer. However, there are a few concerns, including:

(1) What is the effect of CMPD1 on breast cancer metastasis?

(2) The mechanism is lacking as to how MK2 inhibitors enhance the efficacy of MTAs.

Reviewer #1 (Public review):

Summary:

By using an established NAFLD model, choline-deficient high-fat diet, Barros et al show that LPS challenge causes excessive IFN-γ production by hepatic NK cells which further induces recruitment and polarization of a PD-L1 positive neutrophil subset leading to massive TNFα production and increased host mortality. Genetic inhibition of IFN-γ or pharmacological blockade of PD-L1 decreases recruitment of these neutrophils and TNFα release, consequently preventing liver damage and decreasing host death.

Since NAFLD is often accompanied by chronic, low-grade inflammation, it can lead to an overactive but dysfunctional immune response and increase the body's overall susceptibility to infections, therefore this is a very important research question.

Weaknesses:

I have quite a lot of concerns with this manuscript. One of those is that the authors did not indeed show that the seen effect is really due to NAFLD itself. The role of choline is already known in the context of sepsis since its deficiency (which can be observed in about two weeks through deterioration of liver structure and function) leads to body organ dysfunction both in humans and animals. Nolan and Vilayat in 1968 showed that the hepatic injury and mortality due to endotoxinaemic shock induced by intraperitoneal injection of LPS was significantly increased in adult female Holtzman rats fed on a choline-deficient diet. Therefore, in order to really show that the effect is mediated due to NAFLD some other diet model must be used (e.g. high-fat, high-fructose, and high-cholesterol diet).

Reviewer #1 (Public review):

Summary:

The authors are trying to determine if SFN treatment results in dephosphorylation of TFEB, subsequent activation of autophagy-related genes, exocytosis of lysosomes, and reduction in lysosomal cholesterol levels in models of NPC disease.

Strengths:

(1) Clear evidence that SFN results in translocation of TFEB to the nucleus.

(2) In vivo data demonstrating that SFN can rescue Purkinje neuron number and weight in NPC1-/- animals.

Weaknesses:

(1) Lack of molecular details regarding how SFN results in dephosphorylation of TFEB leading to activation of the aforementioned pathways. Currently, datasets represent correlations.

(2) Based on the manuscript narrative, discussion, and data it is unclear exactly how steady-state cholesterol would change in models of NPC disease following SFN treatment. Yes, there is good evidence that lysosomal flux to (and presumably across) the plasma membrane increases with SFN. However, lysosomal biogenesis genes also seem to be increasing. Given that NPC inhibition, NPC1 knockout, or NPC1 disease mutations are constitutively present and the cell models of NPC disease contain lysosomes (even with SFN) how could a simple increase in lysosomal flux decrease cholesterol levels? It would seem important to quantify the number of lysosomes per cell in each condition to begin to disentangle differences in steady state number of lysosomes, number of new lysosomes, and number of lysosomes being exocytosed.

(3) Lack of evidence supporting the authors' premise that "SFN could be a good therapeutic candidate for neuropathology in NPC disease".

Reviewer #1 (Public Review):

Summary:

The work from Petazzi et al. aimed at identifying novel factors supporting the differentiation of human hematopoietic progenitors from induced-pluripotent stem cells (iPSCs). The authors developed an inducible CRISPR-mediated activation strategy (iCRISPRa) to test the impact of newly identified candidate factors on the generation of hematopoietic progenitors in vitro. They first compared previously published transcriptomic data of iPSC-derived hemato-endothelial populations with cells isolated ex vivo from the aorta-gonad-mesonephros (AGM) region of the human embryo and they identified 9 transcription factors expressed in the aortic hemogenic endothelium that were poorly expressed in the in vitro differentiated cells. They then tested the activation of these candidate factors in an iPSC-based culture system supporting the differentiation of hematopoietic progenitors in vitro. They found that the IGF binding protein 2 (IGFBP2) was the most upregulated gene in arterial endothelium after activation and they demonstrated that IGFBP2 promotes the generation of functional hematopoietic progenitors in vitro.

Strengths:

The authors developed a very useful doxycycline-inducible system to activate the expression of specific candidate genes in human iPSC. This approach allows us to simultaneously test the impact of 9 different transcription factors on in vitro differentiation of hematopoietic cells, and the system appears to be very versatile and applicable to a broad variety of studies. Using this approach, the authors exhaustively demonstrated the role of IGFBP2 in promoting the generation of functional hematopoietic progenitors in vitro from iPSCs.

Weaknesses:

The authors performed a very thorough characterization of the system in proof-of-principle experiments activating a single transcription factor. However, when 9 independent factors were used, it is not always clear whether the observed results were the consequence of the simultaneous activation of all 9 TF or just a subset of them.

Reviewer #3 (Public review):

Summary:

Machhua et al. in their work focused on unravelling the molecular mechanism of daptomycin binding and interaction with bacterial cell membranes. Daptomycin (Dap) is an acidic, cyclic lipopeptide composed of 13 amino acids, known for preferential binding to anionic lipids, particularly phosphatidylglycerol (PG), which are prevalent components in the membranes of Gram-positive bacteria. The process of binding and antimicrobial efficacy of Dap are significantly influenced by the ionic composition of the surrounding environment, especially the presence of Ca2+ ions. The authors underscore the presence of significant knowledge gaps in our understanding of daptomycin's mode of action. Several critical questions remain unanswered, including the basis for selective recognition and accumulation in membranes of Gram-positive strains, the specific role of Ca2+ ions in this process, and the mechanisms by which daptomycin binds to and inserts into the cell membrane.

Dap is intrinsically fluorescent due to its kynurenine residue (Kyn-13) and this property allows direct imaging of Dap binding to model cell membranes without the need of additional labeling. Taking advantage of this Dap autofluorescence, authors monitored the emission intensity of micelles, composed of varying DMPG content upon their exposure to Dap and compared it with the kinetics of fluorescence observed for zwitterionic DMPC and other negatively charged lipids such as cardiolipin (CA), POPA and POPS. The authors noted that the linear relationship between DMPG content and Dap fluorescence is strongly lipid-specific, as it was not observed for other anionic lipids. The manuscript sheds light on the specificity of Dap's interaction with CA and DMPG lipids. Through Ca2+ sequestration with EGTA, the authors demonstrated that the binding of Dap with CA is reversible, while its interaction with DMPG results in the irreversible insertion of Dap into the lipid membrane structure, caused by the significant conformational change of this lipopeptide. The formation of a stable DMPG-Dap complex was also verified in bacterial cells isolated from Gram-positive bacteria B. subtilis, where Dap exhibited a permanent binding to PG lipids.

Altogether, the authors endeavored to illuminate novel insights into the molecular basis of Dap binding, interaction, and the mechanism of insertion into bacterial cell membranes. Such understanding holds promise for the development of innovative strategies in combating drug resistance and the emerging of the so-called superbugs.

Strengths:

- The manuscript by Machhua et al. provides a comprehensive analysis of the Dap mechanism of binding and interaction with the membrane. It discusses various aspects of this, only apparently trivial interaction such as the importance of PG presence in the membrane, the impact of Ca2+ ions, and different mechanisms of Dap binding with other negatively charged lipids.<br /> - The authors focused not only on model membranes (micelles) but also extended their research to bacterial cell membranes obtained from B. subtilis<br /> - The research is not only a report of the experimental findings but tries to give potential hypotheses explaining the molecular mechanisms behind the observed results

Weaknesses:

- The authors overestimate their findings, stating that they propose a novel mechanism of Dap interaction with bacterial cell membranes. This research is the extension of the hypotheses that have already been reported.<br /> - The literature study and overall discussion about the mechanism of action of Ca2+ ions or conformational changes of daptomycin could be improved.

Reviewer #1 (Public review):

Summary:

This work used a comprehensive dataset to compare the effects of species diversity and genetic diversity within each trophic level and across three trophic levels. The results stated that species diversity had negative effects on ecosystem functions, while genetic diversity had positive effects. Additionally, these effects were observed only within each trophic level and not across the three trophic levels studied. Although the effects of biodiversity, especially genetic diversity across multi-trophic levels, have been shown to be important, there are still very few empirical studies on this topic due to the complex relationships and difficulty in obtaining data. This study collected an excellent dataset to address this question, enhancing our understanding of genetic diversity effects in aquatic ecosystems.

Strengths:

The study collected an extensive dataset that includes species diversity of primary producers (riparian trees), primary consumers (macroinvertebrate shredders), and secondary consumers (fish). It also includes genetic diversity of the dominant species in each trophic level, biomass production, decomposition rates, and environmental data. The writing is logical and easy to follow.

Weaknesses:

The two main conclusions-(1) species diversity had negative effects on ecosystem functions, while genetic diversity had positive effects, and (2) these effects were observed only within each trophic level, not across the three levels-are overly generalized. Analysis of the raw data shows that species and genetic diversity have different effects depending on the ecosystem function. For example, neither affected invertebrate biomass, but species diversity positively influenced fish biomass, while genetic diversity had no effect. Furthermore, Table S2 reveals that only four effect sizes were significant (P < 0.05): one positive genetic effect, one negative genetic effect, and two negative species effects, with two effects within a trophic level and two across trophic levels. Additionally, using a P < 0.2 threshold to omit lines in the SEMs is uncommon and was not adequately justified. A more cautious interpretation of the results, with acknowledgment of the variability observed in the raw data, would strengthen the manuscript.

Reviewer #1 (Public review):

Summary:

This manuscript reports the substrate-bound structure of SiaQM from F. nucleatum, which is the membrane component of a Neu5Ac-specific Tripartite ATP-dependent Periplasmic (TRAP) transporter. Until recently, there was no experimentally derived structural information regarding the membrane components of TRAP transporter, limiting our understanding of the transport mechanism. Since 2022, there have been 3 different studies reporting the structures of the membrane components of Neu5Ac-specific TRAP transporters. While it was possible to narrow down the binding site location by comparing the structures to proteins of the same fold, a structure with substrate bound has been missing. In this work, the authors report the Na+-bound state and the Na+ plus Neu5Ac state of FnSiaQM, revealing information regarding substrate coordination. In previous studies, 2 Na+ ion sites were identified. Here, the authors also tentatively assign a 3rd Na+ site. The authors reconstitute the transporter to assess the effects of mutating the binding site residues they identified in their structures. Of the 2 positions tested, only one of them appears to be critical to substrate binding.

Strengths:

The main strength of this work is the capture of the substrate bound state of SiaQM, which provides insight into an important part of the transport cycle.

Weaknesses:

The main weakness is the lack of experimental validation of the structural findings. The authors identified the Neu5Ac binding site, but only test 2 residues for their involvement in substrate interactions, which is quite limited. However, comparison with previous mutagenesis studies on homologues supports the location of the Neu5Ac binding site. The authors tentatively identified a 3rd Na+ binding site, which if true would be an impactful finding, but this site was not sufficiently experimentally tested for its contribution to Na+ dependent transport. This lack of experimental validation prevents the authors from unequivocally assigning this site as a Na+ binding site. However, the reporting of these new data is important as it will facilitate follow up studies by the authors or other researchers.

Comments on revisions:

Overall, the authors have done a good job of addressing the reviewers' comments. It's good to know that the authors are working on the characterisation of the potential metal binding site mutants - characterising just a few of these will provide much needed experimental support for this potential Na+ site.<br /> The new MD simulations provide some additional support for the new Na+ site and could be included. However, as the authors know, direct experimental characterisation of mutants is the ideal evidence of the Na+ site.

Aside from the characterisation of mutants, which seems to be held up by technical issues, the only remaining issue is the comparison of the Na+- and Na+/Neu5Ac-bound states with ASCT2.<br /> It still does not make sense to me why the authors are not directly comparing their Na+ only and Na+/Neu5Ac states with the structures of VcINDY in the Na+-only and Na+/succinate bound states. These VcINDY structures also revealed no conformational changes in the HP loops upon binding succinate, as the authors see for SiaQM. Therefore, this comparison is very supportive. It is understood that the similarity to the DASS structure is mentioned on p.17, but it is also interesting and useful to note that TRAP and DASS transporters also share a lack of substrate-induced local conformational changes, to the extent these things have been measured.

Reviewer #1 (Public review):

Summary:

The authors analyzed the bacterial colonization of human sperm using 16S rRNA profiling. Patterns of microbiota colonization were subsequently correlated with clinical data, such as spermiogram analysis, presence of reactive oxygen species (ROS), and DNA fragmentation. The authors identified three main clusters dominated by Streptococcus, Prevotella, and Lactobacillus & Gardnerella, respectively, which aligns with previous observations. Specific associations were observed for certain bacterial genera, such as Flavobacterium and semen quality. Overall, it is a well-conducted study that further supports the importance of the seminal microbiota.

Strengths:

- The authors performed the analysis on 223 samples, which is the largest dataset in semen microbiota analysis so far<br /> - Inclusion of negative controls to control contaminations.<br /> - Inclusion of a positive control group consisting of men with proven fertility.

Weaknesses:

- The manuscript needs comprehensive proofreading for language and formatting. In many instances spaces are missing or not required.<br /> - Could the authors explore correlation network analyses to get additional insights in the structure of different clusters?<br /> - The github link is not correct.<br /> - It is not possible to access the dataset on ENA.<br /> - Add the graphs obtained with decontam analysis as a supplementary figure.<br /> - There is nothing about the RPL group in the results section, while the authors discuss this issue in the introduction. What about the controls with proven fertility?<br /> - While correctly stated in the title, the term microbiota should be used throughout the manuscript instead of "microbiome"

Comments on revised version:

Discussion: Could the authors discuss more the findings about Flavobacterium? Has it ever been associated with the urogenital tract? What is the relative abundance in the present study: this type of bacterium has been previously associated with contaminations (PMID: 25387460, 30497919).

Figure 1: Increase the size of panel A.

Figure 3: Can the authors indicate the relative abundance of each genus/species by the size of the node?

Supplementary data: I don't see anywhere the decontam plots.

Reviewer #1 (Public review):

Summary:

In the manuscript entitled "Magnesium modulates phospholipid metabolism to promote bacterial phenotypic resistance to antibiotics", Li et al demonstrated the role of magnesium in promoting phenotypic resistance in V. alginolyticus. Using standard microbiological and metabolomic techniques, the authors have shown the significance of fatty acid biosynthesis pathway behind the resistance mechanism. This study is significant as it sheds light on the role of an exogenous factor in altering membrane composition, polarization and fluidity which ultimately leads to antimicrobial resistance.

Strengths:

Authors have used different approaches to demonstrate the effect of Mg+2 on drug resistance in Vibrio alginolyticus. The revised version of the manuscript is much improved, with a very informative introduction and a variety of methodologies with clear explanation of the experiments performed. Also, additional experiments were performed as suggested by the reviewers which certainly enhanced the quality of the paper. I believe the findings of this study will be of high impact in the bacterial community.

Weaknesses:

There are a few grammatical mistakes.

Comments on revisions:

The authors have done a comprehensive job of addressing all my concerns in their revised version.

Reviewer #1 (Public review):

Summary:

In this paper Homan et al used mouse models of Metabolic Dysfunction-Associated Steatotic Liver Disease and different specific target deletions in cells to rule out the role of Complement 3a Receptor 1 in the pathogenesis of disease. They provided limited evidence and only descriptive results that despite C3aR being relevant in different contexts of inflammation, however, these tenets did not hold true.

Comments on revisions:

The revised version fulfilled my queries.

Reviewer #2 (Public review):

Summary:

The manuscript by Bock and colleagues describes generation of an AAV-delivered adenine base editing strategy to knockdown PTBP1 and the behavioral and neurorestorative effects of specifically knocking down striatal or nigral PTBP1 in astrocytes or neurons in a mouse model of Parkinson disease. The authors found that knocking down PTBP1 in neurons, but not astrocytes, and in striatum, but not nigra, results in the phenotypic reorganization of neurons to TH+ cells sufficient to rescue motor phenotypes, though insufficient to normalize responses to dopaminomimetic drugs.

Strengths:

The manuscript is well-written and adds to the growing literature challenging previous findings by Qian et al., 2020 and Zhou et al., 2020 indicating that astrocytic downregulation of PTBP1 can induce conversion to dopaminergic neurons in the midbrain and improve parkinsonian symptoms. The base editing approach is interesting and potentially more therapeutically relevant than previous approaches.

Weaknesses:

The animal model utilized, the 6-OHDA model, though useful to examine dopaminergic cell loss, exhibits accelerated neurodegeneration and none of the typical pathological hallmarks (synucleinopathy, Lewy bodies, etc.) compared to the typical etiology of Parkinson disease, limiting its translational interpretation. The identity of the converted neurons is unclear. Though the immunohistochemical methodology indicates they may be MSNs and/or interneurons, a more comprehensive identity is still lacking. There remains no real evidence that these cells actually release dopamine. Since striatal dopamine was assessed by whole-tissue analysis, which is not necessarily reflective of synaptic dopamine availability, it is difficult to assess whether the ~10% increase in TH+ cells in the striatum was sufficient to improve dopamine function. However, the improvement in motor activity suggests that it was.

Reviewer #2 (Public review):

Summary:

The authors aimed to investigate the functionality of the GnRH (gonadotropin-releasing hormone) pulse generator in different mouse models to understand its role in reproductive physiology and its implications for conditions like polycystic ovary syndrome (PCOS). They compared the GnRH pulse generator activity in control mice, peripubertal androgen (PPA) treated mice, and prenatal androgen (PNA) exposed mice. The study sought to elucidate how androgen exposure affects the GnRH pulse generator and subsequent LH (luteinizing hormone) secretion, contributing to the pathophysiology of PCOS.

Strengths:

(1) Comprehensive Model Selection: The use of both PPA and PNA mouse models allows for a comparative analysis that can distinguish the effects of different timings of androgen exposure.

(2) Detailed Methodology: The methods employed, such as photometry recordings and serial blood sampling, are robust and allow for precise measurement of GnRH pulse generator activity and LH secretion.

(3) Clear Results Presentation: The experimental results are well-documented with appropriate statistical analyses, ensuring the findings are reliable and reproducible.

(4) Relevance to PCOS: The study addresses a significant gap in understanding the neuroendocrine mechanisms underlying PCOS, making the findings relevant to both basic science and potentially clinical research.

Weaknesses

(1) Model Limitations: While the PNA mouse model is suggested as the most appropriate for studying PCOS, the authors acknowledge that it does not completely replicate the human condition, particularly the elevated LH response seen in women with PCOS.

(2) Complex Data Interpretation: The reduced progesterone feedback and its effects on the GnRH pulse generator in PNA mice add complexity to data interpretation, making it challenging to draw straightforward conclusions.

(3) Machine Learning (ML) Selection and Validation: While k-means clustering is a useful tool for pattern recognition, the manuscript lacks detailed justification for choosing this specific algorithm over other potential methods. The robustness of clustering results has not been validated.

(4) Biological Interpretability: Although the machine learning approach identified cyclical patterns, the biological interpretation of these clusters in the context of PCOS is not thoroughly discussed. A deeper exploration of how these clusters correlate with physiological and pathological states could enhance the study's impact.

(5) Sample Size: The study uses a relatively small number of animals (n=4-7 per group), which may limit the generalisability of the findings. Larger sample sizes could provide more robust and statistically significant results.

(6) Scope of Application: The findings, while interesting, are primarily applicable to mouse models. The translation to human physiology requires cautious interpretation and further validation.

Comments on revised version:

I did not find the response to my main concerns regarding justification for the choice of the number of clusters (k) and providing evidence of cluster robustness satisfactory at all. It sounds contradictory to me to state that the authors have used unsupervised ML approach when at the same time had clear understanding of the data and the features they wanted to capture. Unsupervised approaches are meant to reveal features that are not apparent by eye... however in their response the authors state, "...our aim was to develop an unsupervised approach that would automatically detect the onset and existence of the key features of pulse generator cyclicity that were apparent by eye...". This sounds like a rather supervised ML approach to me.<br /> Furthermore, I am still unsure why did the authors choose k=5, i.e. assumed there are 5 clusters in the data, and did they explore other possible values for k?<br /> - If not why not? How does this fit with the claims that their ML approach is unsupervised, in other words purely data-driven without making any assumptions?<br /> - If yes did they compare the robustness of their clustering results obtained for different values of k?

Reviewer #1 (Public Review):

Summary:

This paper presents an innovative decoding approach for brain-computer interfaces (BCIs), introducing a new method named MINT. The authors develop a trajectory-centric approach to decode behaviors across several different datasets, including eight empirical datasets from the Neural Latents Benchmark. Overall, the paper is well written and their method shows impressive performance compared to more traditional decoding approaches that use a simpler approach. While there are some concerns (see below), the paper's strengths, particularly its emphasis on a trajectory-centric approach and the simplicity of MINT, provide a compelling contribution to the field.

Strengths:

The adoption of a trajectory-centric approach that utilizes statistical constraints presents a substantial shift in methodology, potentially revolutionizing the way BCIs interpret and predict neural behaviour. This is one of the strongest aspects of the paper.

The thorough evaluation of the method across various datasets serves as an assurance that the superior performance of MINT is not a result of overfitting. The comparative simplicity of the method in contrast to many neural network approaches is refreshing and should facilitate broader applicability.

Weaknesses:

Scope: Despite the impressive performance of MINT across multiple datasets, it seems predominantly applicable to M1/S1 data. Only one of the eight empirical datasets comes from an area outside the motor/somatosensory cortex. It would be beneficial if the authors could expand further on how the method might perform with other brain regions that do not exhibit low tangling or do not have a clear trial structure (e.g. decoding of position or head direction from hippocampus)

When comparing methods, the neural trajectories of MINT are based on averaged trials, while the comparison methods are trained on single trials. An additional analysis might help in disentangling the effect of the trial averaging. For this, the authors could average the input across trials for all decoders, establishing a baseline for averaged trials. Note that inference should still be done on single trials. Performance can then be visualized across different values of N, which denotes the number of averaged trials used for training.

Comments on revisions:

I have looked at the responses and they are thorough and answer all of my questions.

Reviewer #2 (Public review):

Summary:

This work proposes a synaptic plasticity rule which explains the generation of learned stochastic dynamics during spontaneous activity. The proposed plasticity rule assumes that excitatory synapses seek to minimize the difference between the internal predicted activity and stimulus-evoked activity, and inhibitory synapses tries to maintain the E-I balance by matching the excitatory activity. By implementing this plasticity rule in a spiking recurrent neural network, the authors show that the state-transition statistics of spontaneous excitatory activity agrees with that of the learned stimulus patterns, which is reflected in the learned excitatory synaptic weights. The authors further demonstrate that inhibitory connections contribute to well-defined state-transitions matching the transition patterns evoked by the stimulus. Finally, they show that this mechanism can be expanded to more complex state-transition structures including songbird neural data.

Strengths:

This study makes an important contribution to computational neuroscience, by proposing a possible synaptic plasticity mechanism underlying spontaneous generations of learned stochastic state-switching dynamics that are experimentally observed in the visual cortex and hippocampus. This work is also very clearly presented and well-written, and the authors conducted comprehensive simulations testing multiple hypotheses. Overall, I believe this is a well-conducted study providing interesting and novel aspects on the capacity of recurrent spiking neural networks with local synaptic plasticity.

Weaknesses:

This study is very well-thought out and theoretically valuable to the neuroscience community, and I think the main weaknesses are in regard to how much biological realism is taken into account. For example, the proposed model assumes that only synapses targeting excitatory neurons are plastic, and uses an equal number of excitatory and inhibitory neurons.<br /> The model also assumes Markovian state dynamics while biological systems can depend more on history. This limitation, however, is acknowledged in the Discussion.<br /> Finally, to simulate spontaneous activity, the authors use a constant input of 0.3 throughout the study. Different amplitudes of constant input may correspond to different internal states, so it will be more convincing if the authors test the model with varying amplitudes of constant inputs.

Comments on revisions:

The authors have addressed all of the previously raised concerns satisfactorily, by running extra simulations with a biologically plausible composition of excitatory and inhibitory neurons, plasticity assumed for all synapses, and varied amounts of constant inputs representing internal states or background activities. While in some of these cases the stochastic dynamics during spontaneous activity change or do not replicate those of the learned stimulus patterns as well as before, these extended studies provide thorough evaluations of the strengths and limitations of the proposed plasticity rule as the underlying mechanism of stochastic dynamics during spontaneous activity. Overall, the revision has strengthened the paper significantly.

Reviewer #1 (Public review):

Summary:

The authors aimed to quantify feral pig interactions in eastern Australia to inform disease transmission networks. They used GPS tracking data from 146 feral pigs across multiple locations to construct proximity-based social networks and analyze contact rates within and between pig social units.

Strengths:

(1) Addresses a critical knowledge gap in feral pig social dynamics in Australia.

(2) Uses robust methodology combining GPS tracking and network analysis.

(3) Provides valuable insights into sex-based and seasonal variations in contact rates.

(4) Effectively contextualizes findings for disease transmission modeling and management.

(5) Includes comprehensive ethical approval for animal research.

(6) Utilizes data from multiple locations across eastern Australia, enhancing generalizability.

Weaknesses:

(1) Limited discussion of potential biases from varying sample sizes across populations

(2) Some key figures are in supplementary materials rather than the main text.

(3) Economic impact figures are from the US rather than Australia-specific data.

(4) Rationale for spatial and temporal thresholds for defining contacts could be clearer.

(5) Limited discussion of ethical considerations beyond basic animal ethics approval.

The authors largely achieved their aims, with the results supporting their conclusions about the importance of sex and seasonality in feral pig contact networks. This work is likely to have a significant impact on feral pig management and disease control strategies in Australia, providing crucial data for refining disease transmission models.