This article accuses Meta of actively promoting violence against the Rohingya in Myanmar through its algorithms. The article states that despite acknowledging its role, Meta has resisted calls to pay reparations to Rohingya refugees and failed to provide an effective remedy. The report calls for Meta to adopt ongoing human rights due diligence, cease invasive data collection, and provide reparations to affected communities. It also advocates regulators to ban tracking-based targeted advertising and regulate content-shaping algorithms to prevent similar abuses in other regions.

Twitter's design and culture can make it difficult to repair or reconcile after public shaming incidents because since every thing is in real-time and everything has viral potential it means that misinformation or negative narratives can spread rapidly, often before the accused has a chance to respond or clarify. Furthermore, the ability to be anonymous can make it difficult to identify and reach a compromise with the people behind the public humiliation.

acknowledges that tragedies evoke a range of emotions, often simultaneously, within characters, actors performing the roles, and the audience. These emotions can be complex and even contradictory, reflecting the depth and complexity of human experience portrayed in tragic narratives. Hillman further explores the complexity of emotions by highlighting how one emotion can serve as a mask or cover for another underlying emotion. Additionally, he notes that irrationality and confusion in tragic situations can complicate straightforward attributions of emotion, adding layers of depth and ambiguity.

This emotional liberation provides characters with a temporary sense of freedom and autonomy. Hillman notes that while Shakespeare's comedies initially allow for this emotional release and freedom, they ultimately steer characters back towards structured societal norms and communal arrangements. The temporary liberation through emotion is eventually reconciled within a structured framework by the end of the comedic narrative. Hillman contrasts this with Shakespeare's tragedies, which depict the breakdown of formalized societal structures and rituals designed to regulate and channel emotions. In tragedies, these structures often fail to contain or redistribute emotions effectively, leading to chaos, conflict, and tragedy.

intense states of emotion lead to radical transformation could suggest (made by eugene) is the main reason shakespeares lifelong fascination with Ovid

Hillman is pointing out the paradox that despite the intense and sometimes destructive nature of primal emotions (such as passion, desire, and anguish), they often serve as the central driving force that shapes the heroic identity of the protagonist in tragic works. These emotions become the core elements that define the character's sense of self and purpose.He highlights how the protagonist's experience of intense pleasure (jouissance) intertwined with anguish can simultaneously create and destroy their heroic identity. The very emotions that empower the protagonist can also lead to their downfall or unraveling, blurring the lines between creation and destruction.

Shakespeare thoroughly explores and examines the profound and often intense emotions experienced by characters in his tragedies. This includes feelings such as love, jealousy, anger, despair, and ambition, among others. Shakespeare's characters are portrayed in a way that allows the audience to deeply empathize with their emotional experiences.

suggesting that it is particularly challenging to analyze or describe the connections between tragedy (as a literary or dramatic genre) and affect (the emotional impact it has on individuals).

eLife assessment

This valuable study reports a chemogenetic screen for resistance and sensitivity towards three compounds that inhibit cell cycle progression: camptothecin, colchicine, and palbociclib. Following up on the palbociclib results, the authors provide solid evidence that knockdown of the PRC2.1 complex, likely through increasing D-type cyclin expression, confers resistance to palbociclib. The generality of the results would be improved by demonstrating the effect of PRC2.1 on cyclin expression and cell cycle progression in more than one cell line.

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. It is suggested that increased expression of D-type cyclins results in palbociclib resistance.

Strengths:

The results of this study are interesting and contribute 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. The inclusion of these data would significantly improve the paper. However, besides some presentation issues and typos as described below, it is my opinion that the results are robust and of broad interest.

Major questions:

(1) Is the resistance to CDK4/6 inhibition conferred by mutation of MTF2 mediated by Rb?

(2) Are mutations in PRC2.1 found in genetic analyses of tumour samples in patients with acquired resistance?

Reviewer #2 (Public Review):

Summary:

Longhurst et al. assessed cell cycle regulators using a chemogenetic CRISPR-Cas9 screen in haploid human cell line HAP1. Besides known cell cycle regulators they identified the PRC2.1 subcomplex to be specifically involved in G1 progression, given that the absence of members of the complex makes the cells resistant to Palbociclib. They further showed that in HAP1 cells the PRC2.1, but not the PRC2.2 complex is important to repress the cyclins CCND1 and CCND2. This can explain the enhanced resistance to Palbociclib, a CDK4/6-Inhibitor, after PRC2.1 deletion.

Strengths:

The initial CRISPR screen is very interesting because it uses three distinct chemicals that disturb the cell cycle at various stages. This screen mostly identified known cell cycle regulators, which demonstrates the validity of the approach. The results can be used as a resource for future research.

The most interesting outcome of the experiment is the finding that knockouts of the PRC2.1 complex make the cell resistant to Palbociclib. In a further experiment, the authors focused on MTF2 and JARID2 as the main components of PRC2.1 and PRC2.2, respectively. Via extensive analyses, including genome-wide experiments, they confirmed that MTF2 is particularly important to repress the cyclins CCND1 and CCND2. The absence of MTF2 therefore leads to increased expression of these genes, sufficient to make the cell resistant to palociclib. This result will likely be of wide interest to the community.

Weaknesses:

The main weakness of the manuscript is that the experiments were performed in only one cell line. To draw more general conclusions, it would be essential to confirm some of the results in other cell lines.<br /> In addition, some of the findings, such as the results from the CRISPR screen as well as the stronger impact of the MTF2 KO on H3K27me3 and gene expression (compared to JARID2 KO), are not unexpected, given that similar results were already obtained before by other labs.

Reviewer #3 (Public Review):

This study begins with a chemogenetic screen to discover previously unrecognized regulators of the cell cycle. Using a CRISPR-Cas9 library in HAP1 cells and an assay that scores cell fitness, the authors identify genes that sensitize or desensitize cells to the presence of palbociclib, colchicine, and camptothecin. These three drugs inhibit proliferation through different mechanisms, and with each treatment, expected and unexpected pathways were found to affect drug sensitivity. The authors focus the rest of the experiments and analysis on the polycomb complex PRC2, as the deletion of several of its subunits in the screen conferred palbociclib resistance. The authors find that PRC2, specifically a complex dependent on the MTF2 subunit, methylates histone 3 lysine 27 (H3K27) in promoters of genes associated with various processes including cell-cycle control. Further experiments demonstrate that Cyclin D expression increases upon loss of PRC2 subunits, providing a potential mechanism for palbociclib resistance.

The strengths of the paper are the design and execution of the chemogenetic screen, which provides a wealth of potentially useful information. The data convincingly demonstrate in the HAP1 cell line that the MTF2-PRC2 complex sustains the effects of palbociclib (Figure 4), methylates H3K27 in CpG-rich promoters (Figure 5), and represses Cyclin D expression (Figure 6). These results could be of great interest to those studying cell-cycle control, resistance mechanisms to therapeutic cell-cycle inhibitors, and chromatin regulation and gene expression.

There are several weaknesses that limit the overall quality and potential impact of the study. First, none of the results from the colchicine and camptothecin screens (Figures 1 and 2) are experimentally validated, which lessens the rigor of those data and conclusions. Second, all experiments validating and further exploring results from the palbociclib screen are restricted to the Hap1 cell line, so the reproducibility and generality of the results are not established. While it is reasonable to perform the initial screen to generate hypotheses in the Hap1 line, other cancer and non-transformed lines should be used to test further the validity of conclusions from data in Figures 4-6. Third, conclusions drawn from data in Figures 3D and 4D are not fully supported by the experimental design or results. Finally, there have been other similar chemogenetic screens performed with palbociclib, most notably the study described by Chaikovsky et al. (PMID: 33854239). Results here should be compared and contrasted to other similar studies.

eLife assessment

The authors explore ER stress signalling mediated by ATF6 using a genome-wide gene depletion screen. They find that the ER chaperone Calreticulin binds and directly represses ATF6; this proposed function for Calreticulin is intriguing and constitutes an important finding. The evidence presented is based on CHO genetic evidence and biochemical results and is convincing.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Tung and colleagues identify Calreticulin as a repressor of ATF6 signaling using a CRISPR screen and characterize the functional interaction between ATF6 and CALR.

Strengths:

The manuscript is well written and interesting with an innovative experimental design that provides some new mechanistic insight into ATF6 regulation as well as crosstalk with the IRE1 pathway. The methods used were fit for purpose and reasonable conclusions were drawn from the data presented. Findings are novel and bring together glycoprotein quality control and activation of one sensor of the UPR. This is a novel perspective on how the integration of ER homeostasis signals could be sensed in the ER.

Weaknesses:

Several points remain to be documented to support the authors' model.

Reviewer #2 (Public Review):

Summary:

In this study, the authors set out to use an unbiased CRISPR/Cas9 screen in CHO cells to identify genes encoding proteins that either increase or repress ATF6 signaling in CHO cells.

Strengths:

The strengths of the paper include the thoroughness of the screens, the use of a novel, double ATF6/IRE1 UPR reporter cell line, and follow-up detailed experiments on two of the findings in the screens, i.e. FURIN and CRT, to test the validity of involvement of each as direct regulators of ATF6 signaling. Additional strengths are the control experiments that validate the ATF6 specificity of the screens, as well as, for CRT, the finding of focus, determining roles for the glycosylation and cysteines in ATF6 as mechanistically involved in how CRT represses ATF6, at least in CHO cells.

Weaknesses:

The weaknesses of the paper are that the authors did not describe why they focused only on the top 100 proteins in each list of ATF6 activators and repressors. Additionally, there were a few methodology items missing, such as the nature of where the insertion site in the CHO cell genome of the XBP1::mCherry reporter. Since the authors go to great lengths to insert the other reporter for ATF6 activation in a "safe harbor" location, it leads to questions about whether the XBP1::mCherry reporter insertion is truly innocuous. An additional weakness is that the evidence for the physical interaction between ATF6LD and CRT is not strong, being dependent mainly on a single IP/IB experiment in Figure 4C that comprises only 1 lane on the gel for each of the test cases. Moreover, while that figure suggests that the interaction between CRT and ATF6 is decreased by mutating out the glycosylation sites in the ATF6LD, the BLI experiment in the same figure, 4B, suggests that there are no differences in the affinities of CRT for ATF6LD WT, deltaGly and deltaCys. An additional detail is that I found Figure 6A to be difficult to interpret, and that 6B was required in order for me to best evaluate the points being made by the authors in this figure.

Overall, I believe that this work will positively impact the field as it provides a list of potential regulators of ATF6 activation and repression that others will be able to use as a launch point for discovering such interactions in cells and tissues or interest beyond CHO cells. However, I agree with the authors that these findings were in CHO cell lines and that it is possible, if not likely, that some of the interactions they found will be cell type/line specific.

eLife assessment

This fundamental paper reports a new biosensor to study G protein-coupled receptor activation by the pituitary adenylyl cyclase-activating polypeptide (PACAP) in cell culture, ex vivo (mouse brain slices), and in vivo (zebrafish). Convincing data are presented that show the new sensor works, albeit at very high (non-physiological) concentrations of exogenous PACAP. The sensor has not yet been used to detect endogenously released PACAP, raising questions about whether the sensor can be used for its intended purpose. While further work must be pursued to achieve broad in vivo applications under physiological conditions, the new tool will be of interest to cell biologists, especially those studying the large and important GPCR family.

Reviewer #1 (Public Review):

Summary:

The manuscript "Engineering of PAClight1P78A: A High-Performance Class-B1 GPCR-Based Sensor for PACAP1-38" by Cola et al. presents the development of a novel genetically encoded sensor, PAClight1P78A, based on the human PAC1 receptor. The authors provide a thorough in vitro and in vivo characterization of this sensor, demonstrating its potential utility across various applications in life sciences, including drug development and basic research.

The diverse methods to validate PAClight1P78A demonstrate a comprehensive approach to sensor engineering by combining biochemical characterization with in vivo studies in rodent brains and zebrafish. This establishes the sensor's biophysical properties (e.g., sensitivity, specificity, kinetics, and spectral properties) and demonstrates its functionality in physiologically relevant settings. Importantly, the inclusion of control sensors and the testing of potential intracellular downstream effects such as G-protein activation underscore a careful consideration of specificity and biological impact.

Strengths:

The fundamental development of PAClight1P78A addresses a significant gap in sensors for Class-B1 GPCRs. The iterative design process -starting from PAClight0.1 to the final PAClight1P78A variant - demonstrates compelling optimization. The innovative engineering results in a sensor with a high apparent dynamic range and excellent ligand selectivity, representing a significant advancement in the field. The rigorous in vitro characterization, including dynamic range, ligand specificity, and activation kinetics, provides a critical understanding of the sensor's utility. Including in vivo experiments in mice and zebrafish larvae demonstrates the sensor's applicability in complex biological systems.

Weaknesses:

The manuscript shows that the sensor fundamentally works in vivo, albeit in a limited capacity. The titration curves show sensitivity in the nmol range at which endogenous detection might be possible. However, perhaps the sensor is not sensitive enough or there are not any known robust paradigms for PACAP release. A more detailed discussion of the sensors's limitations, particularly regarding in vivo applications and the potential for detecting endogenous PACAP release, would be helpful.

There are several experiments with an n=1 and other low single-digit numbers. I assume that refers to biological replicates such as mice or culture wells, but it is not well defined. n=1 in experimental contexts, particularly in Figure 1, raises significant concerns about the exact dynamic range of the sensor, data reproducibility, and the robustness of conclusions drawn from these experiments. Also, ROI for cell cultures, like in Figure 1, is not well defined. The methods mentioned ROIs were manually selected, which appears very selective, and the values in Figure 1c become unnecessarily questionable. The lack of definition for "ROI" is confusing. Do ROIs refer to cells, specific locations on the cell membrane, or groups of cells? It would be best if the authors could use unbiased methods for image analysis that include the majority of responsive areas or an explanation of why certain ROIs are included or excluded.

Reviewer #2 (Public Review):

Summary:

The PAClight1 sensor was developed using an approach successful for the development of other fluorescence-based GPCR sensors, which is the complete replacement of the third intracellular loop of the receptor with a circularly-permuted green fluorescent protein. When expressed in HEK cells, this sensor showed good expression and a weak but measurable response to the extracellular presence of PACAP1-38 (a F/Fo of 43%). Additional mutation near the site of insertion of the linearized GPF, at the C-terminus of the receptor, and within the second intracellular loop produced a final optimized sensor with F/Fo of >1000%. Finally, screening of mutational libraries that also included alterations in the extracellular ligand-binding domain of the receptor yielded a molecule, PAClight1P78A, that exhibited a high ligand-dependent fluorescence response combined with a high differential sensitivity to PACAP (EC50 30 nM based on cytometric sorting of stably transfected HEK293 cells) compared to its congener VIP, (with which PACAP shares two highly related receptors, VPAC1 and VPAC2) as well as several unrelated neuropeptides, and significantly slowed activation kinetics by PACAP in the presence of a 10-fold molar excess of the PAC1 antagonist PACAP6-38. A structurally highly similar control construct, PAClight1P78Actl, showed correspondingly similar basal expression in HEK293 cells, but no PACAP-dependent enhancement in fluorescent properties.

PAClight1P78A was expressed in neurons of the mouse cortex via AAV9.hSyn-mediated gene transduction. Slices taken from PAClight1P78A-transfected cortex, but not slices taken from PAClight1P78Actl-transfected cortex exhibited prompt and persistent elevation of F/Fo after 2 minutes of perfusion with PACAP1-38 which persisted for up to 14 minutes and was statistically significant after perfusion with 3000, but not 300 or 30 nM, of peptide. Likewise, microinfusion of 200 nL of 300 uM PACAP1-38 into the cortex of optical fiber-implanted freely moving mice elicited a F/Fo (%) of greater than 15, and significantly higher than that elicited by application of similar concentrations of VIP, CRF, or enkephalin, or vehicle alone. In vivo experiments were carried out in zebrafish larvae by the introduction of PAClight1P78A into single-cell stage Danio rerio embryos using a Tol2 transposase-based plasmid with a UAS promoter via injection (of plasmid and transposase mRNA), and sorting of post-fertilization embryos using a marker for transgenesis carried in the UAS : PAClight1P78A construct. Expression of PAClight1P78A was directed to cells in the olfactory bulb which express the fish paralog of the human PAC1 receptor by using the Tg(GnRH3:gal4ff) line, and fluorescent signals were elicited by intracerebroventricular administration of PACAP1-38 at a single concentration (1 mM), which were specific to PACAP and to the presence of PAClight1P78A per se, as controlled by parallel experiments in which PAClight1P78Actl instead of PAClight1P78A was contained in the transgenic plasmid.

Major strengths and weaknesses of the methods and results:

The report represents a rigorous demonstration of the elicitation of fluorescent signals upon pharmacological exposure to PACAP in nervous system tissue expressing PAClight1P78A in both mammals (mice) and fish (zebrafish larvae). Figure 4d shows a change in GFP fluorescence activation by PACAP occurring several seconds after the cessation of PACAP perfusion over a two-minute period, and its persistence for several minutes following. One wonders if one is apprehending the graphical presentation of the data incorrectly, or if the activation of fluorescence efficiency by ligand presentation is irreversible in this context, in which case the utility of the probe as a real-time indicator, in vivo, of released peptide might be diminished.

Appraisal of achievement of aims, and data support of conclusions:

Small cavils with controls are omitted for clarity; the larger issue of appraisal of results based on the scope of the designed experiments is discussed in the section below. An interesting question related to the time dependence of the PACAP-elicited activation of PAClight1P87A is its onset and reversibility, and additional data related to this would be welcome.

Discussion of the impact of the work, and utility of the methods and data:

Increasingly, neurotransmitter function may be observed in vivo, rather than by inferring in vivo function from in vitro, in cellular, or ex vivo experimentation. This very valuable report discloses the invention of a genetically encoded sensor for the class B1 GPCR PAC1. PAC1 is the major receptor for the neuropeptide PACAP, which in turn is a major neurotransmitter involved in brain response to psychogenic stress, or threat, in vertebrates as diverse as mammals and fishes. If this sensor possesses the sensitivity to detect endogenously released PACAP in vivo it will indeed be an impactful tool for understanding PACAP neurotransmission (and indeed PACAP action in general, in immune and endocrine compartments as well) in future experiments.

However, the sensor has not yet been used to detect endogenously released PACAP. Until this has been done, one cannot answer the question as to whether the levels of exogenously perfused/administered PACAP used here merely to calibrate the sensor's sensitivity are indeed unphysiologically high. If endogenous PACAP levels don't get that high, then the sensor will not be useful for its intended purpose. The authors should address this issue and allude to what kind of experiments would need to be done in order to detect endogenous PACAP release in living tissue in intact animals. The authors could comment upon the success of other GPCR sensors that have been used to observe endogenous ligand release, and where along the pathway to becoming a truly useful reagent this particular sensor is.

Reviewer #3 (Public Review):

Summary:

The manuscript introduces PAClight1P78A, a novel genetically encoded sensor designed to facilitate the study of class-B1 G protein-coupled receptors (GPCRs), focusing on the human PAC1 receptor. Addressing the significant challenge of investigating these clinically relevant drug targets, the sensor demonstrates a high dynamic range, excellent ligand selectivity, and rapid activation kinetics. It is validated across a variety of experimental contexts including in vitro, ex vivo, and in vivo models in mice and zebrafish, showcasing its utility for high-throughput screening, basic research, and drug development efforts related to GPCR dynamics and pharmacology.

Strengths:

The innovative design of PAClight1P78A successfully bridges a crucial gap in GPCR research by enabling real-time monitoring of receptor activation with high specificity and sensitivity. The extensive validation across multiple models emphasizes the sensor's reliability and versatility, promising significant contributions to both the scientific understanding of GPCR mechanisms and the development of novel therapeutics. Furthermore, by providing the research community with detailed methodologies and access to the necessary viral vectors and plasmids, the authors ensure the sensor's broad applicability and ease of adoption for a wide range of studies focused on GPCR biology and drug targeting.

Weaknesses<br /> To further strengthen the manuscript and validate the efficacy of PAClight1P78A as a selective PACAP sensor, it is crucial to demonstrate the sensor's ability to detect endogenous PACAP release in vivo under physiological conditions. While the current data from artificial PACAP application in mouse brain slices and microinfusion in behaving mice provide foundational insights into the sensor's functionality, these approaches predominantly simulate conditions with potentially higher concentrations of PACAP than naturally occurring levels.

Although the sensor's specificity for the PAC1 receptor and its primary ligand is a pivotal achievement, exploring its potential application to other GPCRs within the class-B1 family or broader categories could enhance the manuscript's impact, suggesting ways to adapt this technology for a wider array of receptor studies. Additionally, while the sensor's performance is convincingly demonstrated in short-term experiments, insights into its long-term stability and reusability in more prolonged or repeated measures scenarios would be valuable for researchers interested in chronic studies or longitudinal behavioral analyses. Addressing these aspects could broaden the understanding of the sensor's practical utility over extended research timelines.

Furthermore, the current in vivo experiments involving microinfusion of PACAP near sensor-expressing areas in behaving mice are based on a relatively small sample size (n=2), which might limit the generalizability of the findings. Increasing the number of subjects in these experimental groups would enhance the statistical power of the results and provide a more robust assessment of the sensor's in vivo functionality. Expanding the sample size will not only validate the findings but also address potential variability within the population, thereby reinforcing the conclusions drawn from these crucial experiments.

Stand by this articulation. The chosen technologies did not quite deliver what is needed

indylab

Transformers give Clojurists some of the benefits of "Object Orientation" without many of the downsides Clojurists dislike about objects.

1. Objects couple behaviors required from multiple callers into a single class, while transformers do not change existing behaviors for existing callers by default
2. Objects push inheritance first design, whereas transformer inheritance is a function of shared structure between Clojure data structures derived from one another and design is driven by concrete implementation needs, like regular Clojure
3. Objects couple state and methods in spaghetti ways and transformers are just immutable maps. And just like how Clojure lets you stash stateful things like atoms in functions, transformers allow you to build stateful transformers, but like Clojure the default convention is to do everything immutably
4. Objects try to provide data hiding as a function of encapsulation whereas transformers are doing the opposite, exposing data otherwise hidden by a closure

There are many strategies for reusing code in the software industry. In Clojure, we use what some call a "lego" method of building small, single purpose functions that just can be used in a million different contexts, because of a tasteful use of simplicity in the right places. This works tremendously well for 95% of use cases. In certain use-cases, like for building hierarchies of functions that are highly self-similar, like with UI toolkits, transformers provide a better alternative.Transformers allow you to build a UI toolkit with 25% the code of normal function composition and 25% of the code required for evolution over time for the widgets in that hierarchy. The lego method is great for vertically composing things together, but when you want to make lateral changes for only certain callers in the tree, you have to defensively copy code between duplicative implementation trees and just call them "grandpa-function-1" and "grandpa-function-2" and then make versions 1 and 2 for all functions that wrapped the grandpa-functions afterwards. Transformers provide a solution for that situation, in the rare cases we end up in them in Clojure, without the downsides of a traditional object system.

eLife assessment

This important study investigates the relationship between transcription factor condensate formation, transcription, and 3D gene clustering of the MET regulon in the model organism S. cerevisiae. The authors provide solid experimental evidence that transcription factor condensates enhance transcription of MET-regulated genes, but the evidence that nuclear condensates per se drive MET gene clustering is incomplete and would benefit from further experimental analyses. This paper will be of interest to molecular biologists working on chromatin and transcription, although its impact would be strengthened by revising the literature citations and including additional experimental work.

Reviewer #1 (Public Review):

Summary:

In this study, James Lee, Lu Bai, and colleagues use a multifaceted approach to investigate the relationship between transcription factor condensate formation, transcription, and 3D gene clustering of the MET regulon in the model organism S. cerevisiae. This study represents a second clear example of inducible transcriptional condensates in budding yeast, as most evidence for transcriptional condensates arises from studies of mammalian systems. In addition, this study links the genomic location of transcriptional condensates to the potency of transcription of a reporter gene regulated by the master transcription factor contained in the condensate. The strength of evidence supporting these two conclusions is strong. Less strong is evidence supporting the claim that Met4-containing condensates mediate the clustering of genes in the MET regulon.

Strengths:

The manuscript is for the most part clearly written, with the overriding model and specific hypothesis being tested clearly explained. Figure legends are particularly well written. An additional strength of the manuscript is that most of the main conclusions are supported by the data. This includes the propensity of Met4 and Met32 to form puncta-like structures under inducing conditions, formation of Met32-containing LLPS-like droplets in vitro (within which Met4 can colocalize), colocalization of Met4-GFP with Met4-target genes under inducing conditions, enhanced transcription of a Met3pr-GFP reporter when targeted within 1.5 - 5 kb of select Met4 target genes, and most impressively, evidence that several MET genes appear to reposition under transcriptionally inducing conditions. The latter is based on a recently reported novel in vivo methylation assay, MTAC, developed by the Bai lab.

Weaknesses:

My principal concern is that the authors fail to show convincing evidence for a key conclusion, highlighted in the title, that nuclear condensates per se drive MET gene clustering. Figure 4E demonstrates that Met4 molecules, not condensates per se, are necessary for fostering distant cis and trans interactions between MET6 and three other Met4 targets under -met inducing conditions. In addition, the paper would be strengthened by discussing a recent study conducted in yeast that comes to many of the same conclusions reported here, including the role of inducible TF condensates in driving 3D genome reorganization (Chowdhary et al, Mol. Cell 2022).

Other concerns:

(1) A central premise of the study is that the inducible formation of condensates underpins the induction of MET gene transcription and MET gene clustering. Yet, Figure 1 suggests (and the authors acknowledge) that puncta-like Met4-containing structures pre-exist in the nuclei of non-induced cells. Thus, the transcription and gene reorganization observed is due to a relatively modest increase in condensate-like structures. Are we dealing with two different types of Met4 condensates? (For example, different combinations of Met4 with its partners; Mediator- or Pol II-lacking vs. Mediator- or Pol II-containing; etc.?) At the very least, a comment to this effect is necessary.

(2) Using an in vitro assay, the authors demonstrate that Met4 colocalizes with Met32 LLPS droplets (Figure 2F). Is the same true in vivo - that is, is Met32 required for Met4 condensation? This could be readily tested using auxin-induced degradation of Met32. Along similar lines, the claim that Met32 is required for MET gene clustering (line 250) requires auxin-induced degradation of this protein.

(3) The authors use a single time point during -met induction (2 h) to evaluate TF clustering, transcription (mRNA abundance), and 3D restructuring. It would be informative to perform a kinetic analysis since such an analysis could reveal whether TF clustering precedes transcriptional induction or MET gene repositioning. Do the latter two phenomena occur concurrently or does one precede the other?

(4) Based on the MTAC assay, MET13 does not appear to engage in trans interactions with other Met4 targets, whereas MET6 does (Figures 4C and 4E). Does this difference stem from the greater occupancy of Met4 at MET6 vs. MET13, greater association of another Met co-factor with the chromatin of MET6 vs. MET13, or something else?

Reviewer #2 (Public Review):

Summary:

This manuscript combines live yeast cell imaging and other genomic approaches to study how transcription factor (TF) condensates might help organize and enhance the transcription of the target genes in the methionine starvation response pathway. The authors show that the TFs in this response can form phase-separated condensates through their intrinsically disordered regions (IDRs), and mediate the spatial clustering of the related endogenous genes as well as reporter inserted near the endogenous target loci.

Strengths:

This work uses rigorous experimental approaches, such as imaging of endogenously labeled TFs, determining expression and clustering of endogenous target genes, and reporter integration near the endogenous target loci. The importance of TFs is shown by rapid degradation. Single-cell data are combined with genomic sequencing-based assays. Control loci engineered in the same way are usually included. Some of these controls are very helpful in showing the pathway-specific effect of the TF condensates in enhancing transcription.

Weaknesses:

Perhaps the biggest weakness of this work is that the role of IDR and phase separation in mediating the target gene clustering is unclear. This is an important question. TF IDRs may have many functions including mediating phase separation and binding to other transcriptional molecules (not limited to proteins and may even include RNAs). The effect of IDR deletion on reduced Fano number in cells could come from reduced binding with other molecules. This should be tested on phase separation of the purified protein after IDR deletion. Also, the authors have not shown IDR deletion affects the clustering of the target genes, so IDR deletion may affect the binding of other molecules (not the general transcription machinery) that are specifically important for target gene transcription. If the self-association of the IDR is the main driving force of the clustering and target gene transcription enhancement, can one replace this IDR with totally unrelated IDRs that have been shown to mediate phase separation in non-transcription systems and still see the gene clustering and transcription enhancement effects? This work has all the setup to test this hypothesis.

The Met4 protein was tagged with MBP but Met 32 was not. MBP tag is well known to enhance protein solubility and prevent phase separation. This made the comparison of their in vitro phase behavior very different and led the authors to think that maybe Met32 is the scaffold in the co-condensates. If MBP was necessary to increase yield and solubility during expression and purification, it should be cleaved (a protease cleavage site should be engineered) to allow phase separation in vitro.

Are ATG36 and LDS2 also supposed to be induced by -met? This should be explained clearly. The signals are high at -met.

Figure 6B, the Met4-GFP seems to form condensates at all three loci without a very obvious difference, though 6C shows a difference. 6C is from only one picture each. The authors should probably quantify the signals from a large number of randomly selected pictures (cells) and do statistics.

Reviewer #3 (Public Review):

Summary:

In this study, the authors probe the connections between clustering of the Met4/32 transcription factors (TFs), clustering of their regulatory targets, and transcriptional regulation. While there is an increasing number of studies on TF clustering in vitro and in vivo, there is an important need to probe whether clustering plays a functional role in gene expression. Another important question is whether TF clustering leads to the clustering of relevant gene targets in vivo. Here the authors provide several lines of evidence to make a compelling case that Met4/32 and their target genes cluster and that this leads to an increase in transcription of these genes in the induced state. First, they found that, in the induced state, Met4/32 forms co-localized puncta in vivo. This is supported by in vitro studies showing that these TFs can form condensates in vitro with Med32 being the driver of these condensates. They found that two target genes, MET6 and MET13 have a higher probability of being co-localized with Met4 puncta compared with non-target loci. Using a targeted DNA methylation assay, they found that MET13 and MET6 show Met4-dependent long-range interactions with other Met4-regulated loci, consistent with the clustering of at least some target genes under induced conditions. Finally, by inserting a Met4-regulated reporter gene at variable distances from MET6, they provide evidence that insertion near this gene is a modest hotspot for activity.

Weaknesses:

(1) Please provide more information on the assay for puncta formation (Figure 1). It's unclear to me from the description provided how this assay was able to quantitate the number of puncta in cells.

2) How does the number of puncta in cells correspond with the number of Met-regulated genes? What are the implications of this calculation?

3) A control for chromosomal insertion of the Met-regulated reporter was a GAL4 promoter derivative reporter. However, this control promoter seems 5-10 fold more active than the Met-regulated promoter (Figure 6). It's possible that the high activity from the control promoter overcomes some other limiting step such that chromosomal location isn't important. It would be ideal if the authors used a promoter with comparable activity to the Met-reporter as a control.

(4) It seems like transcription from a very large number of genes is altered in the Met4 IDR mutant (Figure 7F). Why is this and could this variability affect the conclusions from this experiment?

eLife assessment

Wounds are commonly infected, which can lead to delayed or poor wound healing, thereby significantly impacting morbidity and overall quality of life for patients. This manuscript uses single cell RNA sequencing to try to understand the impact of infection on various cell types during wound healing in a mouse model. The methodology is solid and the results provide a valuable 'atlas' of the cellular changes associated with infected and uninfected wounds which will be of interest to the field.

Reviewer #2 (Public Review):

Summary:

The authors have performed a detailed analysis of the complex transcriptional status of numerous cell types present in wounded tissue, including keratinocytes, fibroblasts, macrophages, neutrophils, and endothelial cells. The comparison between infected and uninfected wounds is interesting and the analysis suggests possible explanations for why infected wounds are delayed in their healing response.

Strengths:

The paper presents a thorough and detailed analysis of the scRNAseq data. The paper is clearly written and the conclusions drawn from the analysis are appropriately cautious. The results provide an important foundation for future work on the healing of infected and uninfected wounds.

Weaknesses:

The analysis is purely descriptive and no attempt is made to validate whether any of the factors identified are playing functional roles in wound healing. Such experiments would be appropriate for followup work. The experimental setup is analyzing a single time point and does not include a comparison to unwounded skin. Nevertheless, the present data do provide a useful point of comparison for the field.

eLife assessment

The current manuscript re-examines an established claim in the literature that human PANX-1 is regulated by Src kinase phosphorylation at two tyrosine residues, Y199 and Y309. This issue is important for our understanding of Pannexin channel regulation. The authors present an extensive series of experiments that fail to detect PANX-1 phosphorylation at these sites. Although the authors' approach is more rigorous than the previous studies, this work relies primarily on negative results that are not unambiguously definitive; the work nonetheless provides a compelling reason for the field to reexamine conclusions drawn in earlier studies.

Reviewer #2 (Public Review):

The widely distributed pannexin 1 (PANX1) is an ATP-permeable channel that plays an important role in intercellular communication and has been implicated in various pathophysiological processes and diseases. Previous studies have demonstrated that PANX1 can be phosphorylated at two molecular sites via the non-receptor kinase Src, thereby leading to channel opening and ATP release. In this paper, the authors used a variety of methods to detect tyrosine phosphorylation modification of PANX1 channel protein, however, their results showed that commercially available antibodies against the two phosphorylation sites used in previous studies did not work well, in other words, phosphorylation changes in PANX1 could not be detected by those antibodies. Therefore, the authors call for the re-examination and evaluation of previous research results.

In general, this is a meticulous study, using different detection methods and different expression systems.

Reviewer #3 (Public Review):

The manuscript by Ruan et al. addresses an important issue in Panx1 research, i.e. the activation of the channel formed by Panx1 via protein phosphorylation. If the authors' conclusions are correct, the previous claims for Panx1 phosphorylation on the basis of the commercial anti-phospho-Panx1 antibodies would be in question.

This is a very detailed and comprehensive analysis making use of state-of-the-art techniques, including mass spectrometry and phos-tag gel electrophoresis.

In general, the study is well-controlled as relating to negative controls.

The value of this manuscript is, that it could spawn new, more function-oriented studies on the activation of Panx1 channels.

The weaknesses identified previously are reproduced below:

Weaknesses:

Although the manuscript addresses an important issue, the activation of the ATP-release channel Panx1 by protein phosphorylation, the data provided do not support the firm conclusion that such activation does not exist. The failure to reproduce published data obtained with commercial anti-phospho Panx1 antibodies can only be of limited interest for a subfield.

(1) The title claiming that "Panx1 is NOT phosphorylated..." is not justified by the failure to reproduce previously published data obtained with these antibodies. If, as claimed, the antibodies do not recognize Panx1, their failure cannot be used to exclude tyrosine phosphorylation of the Panx1 protein. There is no positive control for the antibodies.

(2) The authors claim that exogenous SRC expression does not phosphorylate Y198. DeLalio et al. 2019 show that Panx1 is constitutively phosphorylated at Y198, so an effect of exogenous SRC expression is not necessarily expected.

(3) The authors argue that the GFP tag of Panx1at the COOH terminus does not interfere with folding since the COOH modified (thrombin cleavage site) Panx1 folds properly, forming an amorphous glob in the cryo-EM structure. However, they do not show that the COOH-modified Panx1 folds properly. It may not, because functional data strongly suggest that the terminal cysteine dives deep into the pore. For example, the terminal cysteine, C426, can form a disulfide bond with an engineered cysteine at position F54 (Sandilos et al. 2012).

(4) The authors dismiss the additional arguments for tyrosine phosphorylation of Panx1 given by the various previous studies on Panx1 phosphorylation. These studies did not, as implied, solely rely on the commercial anti-phospho-Panx1 antibodies, but also presented a wealth of independent supporting data. Contrary to the authors' assertion, in the previous papers the pY198 and pY308 antibodies recognized two protein bands in the size range of glycosylated and partial glycosylated Panx1.

(5) A phosphorylation step triggering channel activity of Panx1 would be expected to occur exclusively on proteins embedded in the plasma membrane. The membrane-bound fraction is small in relation to the total protein, which is particularly true for exogenously expressed proteins. Thus, any phosphorylated protein may escape detection when total protein is analyzed. Furthermore, to be of functional consequence, only a small fraction of the channels present in the plasma membrane need to be in the open state. Consequently, only a fraction of the Panx1 protein in the plasma membrane may need to be phosphorylated. Even the high resolution of mass spectroscopy may not be sufficient to detect phosphorylated Panx1 in the absence of enrichment processes.

(6) In the electrophysiology experiments described in Figure 7, there is no evidence that the GFP-tagged Panx1 is in the plasma membrane. Instead, the image in Figure 7a shows prominent fluorescence in the cytoplasm. In addition, there is no evidence that the CBX-sensitive currents in 7b are mediated by Panx1-GFP and are not endogenous Panx1. Previous literature suggests that the hPanx1 protein needs to be cleaved (Chiu et al. 2014) or mutated at the amino terminus (Michalski et al 2018) to see voltage-activated currents, so it is not clear that the currents represent hPANX1 voltage-activated currents.

Note from the editors: The authors provided a rebuttal to the latest review, but no additional data, so we encourage readers to read the concerns and the author responses.

The bad thing about the social media community is that initailly man who can not attract woman may not consider themselves as incel, but when they find a community share the same experience, it's easy to feel included and start the toxic actions.

eLife assessment

The authors present an important study of a multi-cellular platform involving co-culturing of various hiPSC-derived hepatocyte like cells, cholangiocytes, stellate cells and macrophages to mimic the liver microenvironment. The aggregates are then treated with fatty acids and examined through transcriptomic and functional assays. The techniques and methodologically are sound, and the evidence supporting the conclusion is convincing, although more clinically relevant data demonstrating the effect of some potential pharmacological agents on the platform would serve to strengthen the study.

Reviewer #1 (Public Review):

There is an undisputable need for better in vitro models recapitulating steatotic liver diseases. This article is from a group of well-known stem cell experts that use human induced pluripotent stem cells (hiPSCs) to build a multicellular steatosis model in vitro. While the model is strong for testing hepatocytes responses, it falls short on translational aspects as well as on non-parenchymal liver cells.

(1) The authors should use the new nomenclature for the disease, MASLD / MASH, as proposed by the scientific societies (Rinella ME, et al. J Hepatol. 2023; 79(6):1542-1556. PMID: 37364790).

(2) There has been a similar approach by the Takebe group (Ouchi R, et al., Cell Metab. 2019; 30(2):374-384, PMID: 31155493). What is different in this model?

(3) The work is very technical and does neither provide any new mechanistic insights nor does it test any new interventions. I do see the clear technical advance in the long-term culture. However, I do not see that this system would allow modelling true "chronic" changes in MASLD, e.g. steatohepatitis and/or fibrosis.

(4) While I am very convinced about the validity of the "hepatocyte" component in this system, the NPC compartment is insufficient. The 3D model does certainly not contain Kupffer cells (which have very distinct characteristics from "M0" macrophages) and does not contain true HSCs (LX-2 is a very insufficient model). Also, the model lacks flow conditions, which does not allow to factor in pathogenic signals from the circulation / portal vein (e.g. gut-liver axis). This will only allow very limited insights into the crosstalk between hepatocytes and NPCs.

(5) The translational value of this model remains unclear to me. The scRNA-seq data should be meticulously compared to sc/snRNA-seq data from human MASLD livers at different stages to understand, what this system is able to model (maybe very early stages of steatosis?).

(6) The study lacks a "use case" to study interventions, e.g. testing resmetirom or any other of the new MASLD drugs in this system.

Reviewer #2 (Public Review):

Summary:

The authors developed a 3D multi-cellular platform mimicking the complex interplays involved in the pathogenesis of NAFLD/NASH by employing hiPSCs-derived parenchymal and non-parenchymal cells in combination of organoids obtained from primary human cholangiocytes and the human hepatic stellate cell line LX2. They show that hiPSC-derived hepatocyte are able to accumulate intracellular lipids in fashion similar to human NAFLD and that prolonged accumulation leads to activation of inflammatory and fibrogenic pathways.

Strengths:

This is an original attempt to create a 3D all-human multicellular cellular platform recapitulating human NAFLD/NASH. The results are very encouraging. It is of particular note the fact that fibrogenic markers in the 3D system are not extremely (artificially) activated as in the classic 2D system. This makes the proposed platform more realistic.

Weaknesses:

The mixture of hiPSC-derived cells and primary or cell-line cells is understandable although potentially adding some variability to the system. The only unclear aspect is the characteristic of the collagen used to create the 3D system. Which type of collagen? Human? Which stiffness?

ABA therapy for autism is a controversial topic. It's praised by many therapists and families for helping autistic children develop essential life skills. However, some autistic adults who experienced ABA as children criticize it as abusive, comparing it to discredited practices like gay conversion therapy. This debate highlights the divides, and state why ABA is invisible abuse.

“People can take a photo of themselves and, in an instant, manipulate it." I found this to be very interesting because as technology is advancing, it is easier for people to do deep fakes, filters to make you look younger, older, etc. I feel like these filter creates a false image of someones persona which can be very problematic in many ways.

Anya Kamenetz's article on Facebook's teen mental health data raises important concerns about the interpretation and use of the data. The findings from Facebook and its subsidiary Instagram may not be as clear-cut or as clear-cut as initially thought. This suggests that many teens are being influenced by social media. This ambiguity suggests that more comprehensive and independent research is needed to assess the true impact of social media on teen mental health. The article points out the complexity of drawing conclusions from internal data, emphasizing the importance of considering a range of factors that influence teen mental health. This includes the specific ways in which different individuals interact with social media, the context of use, and external influences.

eLife assessment

This fundamental study for the first time defines genetically the role of the Clock gene in basal metazoa, using the cnidarian Nematostella vectensis. With convincing evidence, the study provides insight into the early evolution of circadian clocks. Clock in this species is necessary for daily rhythms under constant conditions, but not under a rhythmic light/dark cycle, suggesting that the major role of the circadian oscillator in this species could be a stabilizing function under non-rhythmic environmental conditions.

eLife assessment

The work by Lewis and co-workers presents important findings on the role of myosin structure/energetics on the molecular mechanisms of hibernation by comparing muscle samples from small and large hibernating mammals. The solid methodological approaches have revealed insights into the mechanisms of non-shivering thermogenesis and energy expenditure.

Reviewer #1 (Public Review):

Summary:

The evolution of non-shivering thermogenesis is of fundamental importance to understand. Here, in small mammals the contractile apparatus of the muscle are shown to increase energy expenditure upon a drop in ambient temperature. Additionally, in the state of torpor, small hibernators did not show an increase in energy expenditure under the same challenge.

Strengths:

The authors have conducted a very well-planned study that has sampled the muscle of large and small hibernators from two continents. Multiple approaches were then used to identify the state of the contractile apparatus, and its energy expenditure under torpor or otherwise.

Weaknesses:

There was only one site of biopsy from the animals used (leg). As the authors state, it would be interesting to know if non-shivering thermogenesis is something that is regionally different in the animal, given the core body and distal limbs have different temperatures.

Reviewer #2 (Public Review):

Summary:

The authors utilized (permeabilized) fibers from muscle samples obtained from brown and black bears, squirrels, and Garden dormice, to provide interesting and valuable data regarding changes in myosin conformational states and energetics during hibernation and different types of activity in summer and winter. Assuming that myosin structure is similar between species then its role as a regulator of metabolism would be similar and not different, yet the data reveal some interesting and perplexing differences between the selected hibernating species.

Strengths:

The experiments on the permeabilized fibers are complementary, sophisticated, and well-performed, providing new information regarding the characteristics of skeletal muscle fibers between selected hibernating mammalian species under different conditions (summer, interarousal, and winter).

The studies involve complementary assessments of muscle fiber biochemistry, sarcomeric structure using X-ray diffraction, and proteomic analyses of posttranslational modifications.

Weaknesses:

It would be helpful to put these findings on permeabilized fibers into context with the other anatomical/metabolic differences between the species to determine the relative contribution of myosin energetics (with these other contributors) to overall metabolism in these different species, including factors such as fat volume/distribution.

Reviewer #3 (Public Review):

Summary and Strengths:

The manuscript by Lewis et al, investigates whether myosin ATP activity may differ between states of hibernation and activity in both large and small mammals. The study interrogates (primarily) permeabilized muscle strips or myofibrils using several state-of-the-art assays, including the mant-ATP assay to investigate ATP utilization of myosin, X-ray diffraction of muscles, proteomics studies, metabolic tests, and computational simulations. The overall data suggests that ATP utilization of myosin during hibernation is different than in active conditions.

A clear strength of this study is the use of multiple animals that utilize two different states of hibernation or torpor. Two large animal hibernators (Eurasian Brown Bear, American Black Bear) represent large animal hibernators that typically undergo a prolonged hibernation. Two small animal hibernators (Garden Dormouse, 13 Lined Ground Squirrel) undergo torpor with more substantial reductions in heart rate and body temperature, but whose torpor bouts are interrupted by short arousals that bring the animals back to near-summer like metabolic conditions.

Especially interesting, the investigators analyze the impact that body temperature may have on myosin ATP utilization by performing assays at two different temperatures (8 and 20 degrees C, in 13 Lined Ground Squirrels).

The multiple assays utilized provide a more comprehensive set of methods with which to test their hypothesis that muscle myosins change their metabolic efficiency during hibernation.

Suggestions and potential Weaknesses:

The following highlight comments from the first Public Review that this reviewer acknowledges authors may not be able to address in the current study but may merit carrying to the revised article of record.

(1) Statistical Analysis<br /> The revised manuscript addresses the substantial issues. The two remaining questions may be noted for future experimental design(s): 1.c. That myosin isoforms may be considered a main effect and 1.e. The importance of biological vs statistical significance, especially for the mant-ATP chase data from the American Black Bear, where there appear to be shifts between the summer and winter data.

(2). Consistency of DRX/SRX data.<br /> The responses to the first Public Review on the prior version of this manuscript highlight that a potential disconnect between the mant-ATP-predicted SRX:DRX proportions and x-ray diffraction studies measuring the position of the myosin heads (Mohran et al PMID 38103642) may be outside of the scope of the current manuscript. The reviewer accepts that a substantial discussion is outside of this article, but considers a brief mention possible differences between ATP kinetics and structural movements of value.

Overall, the manuscript represents a valuable data set comparing myosin properties of skeletal muscles multiple species exhibiting different forms of hibernation/torpor.

I wonder what was stated in those articles that made it so bad

• you're going to be able to modify the top story title to try to make it about the problem
• the other thing you're going to do is you're going to now add another thing to that top story you had the title description now you're going to have that problem statement

Covers the transition from identifying and understanding design problems to formulating solutions, emphasizing the necessity of a clear, succinct problem statement in this process.

Describes the 'top story' as a pivotal part of project management in design, which synthesizes understanding and outlines the plan forward. "you need to have a ticket that says this is what the overarching plan is."

Explains the concept of reflective inquiry where questioning one's own thoughts helps advance understanding in design. "reflective inquiry... helps you think it also helps agendaize your background thinking."

Introduces the Socratic method as a tool for probing and understanding through structured inquiry, which helps uncover underlying truths about design challenges.

Discusses the strategic use of questions to clarify goals and intentions in the design process, promoting a deeper exploration of problems

Recommends creating a glossary to consistently define and use terms, enhancing understanding within teams

Advocates for precise use of language to avoid ambiguity and ensure that design intentions are clearly communicated and understood.

• Be percise about the meaning
  • Builds better understanding (of differences and similarities)
• Keeps everyone on the same page => better collaboration

Stresses the role of writing in design, not for documentation, but as a tool to visualize and refine ideas collaboratively: * Forces us to concrete thoughts * Allow us to not lose threads * Allow us to share our thoughts

Emphasizes that design is not a magical skill but involves concrete, learnable practices that enhance team-based software development.

eLife assessment

This valuable study reports a potential connection between the seminal microbiome and sperm quality/male fertility. The data are generally convincing, but the statistical methods employed need further justification. This study will be of interest to clinicians and biomedical researchers who work on microbiome and male fertility.

Reviewer #2 (Public Review):

Summary:

The study by Mowla et al analysed seminal microbiome together with semen quality parameters in fertile men and men from infertile couples with different infertility diagnoses. The study is of potential interest, with solid study design and methodology, nevertheless, the statistical analysis approach is not fully justified.

-The patient groups have different diagnoses and should be handled as different groups, and not fused into one 'patient' group in analyses.<br /> Why are the data in tables presented as controls and cases? I would consider men from couples with recurrent pregnancy loss, unexplained infertility, and male factor infertility to have different seminal parameters (not to fuse them into one group). This means, that the statistical analyses should be performed considering each group separately, and not to fuse 3 different infertility diagnoses into one patient group.

-Were any covariables included in the statistical analyses, e.g. age, BMI, smoking, time of sexual abstinence, etc?

-Furthermore, it is known that 16S rRNA gene analysis does not provide sensitive enough detection of bacteria on the species level. How much do the authors trust their results on the species level?

-Were the analyses of bacterial genera and species abundances with seminal quality parameters controlled for diagnosis and other confounders?

Strengths:

The cohort of participants seems to be homogenous in the sense of ethnicity and location.

The authors stress that their study is the biggest on the microbiome in semen. However, when considering that the study consists of 4 groups (with n=46-63), it does not stand out from previous studies.

Weaknesses:

There is a lack of paired seminal/urinal samples.

attention à porter au mineurs détenus et aux parents détenus

certainement en sous détection

28% de l'activité

peut ête parce que la FCPE fait aussi office de facilitateur

Reviewer #2 (Public Review):

Summary:

In this study, the authors performed a screening for PDXP inhibitors to identify compounds that could increase levels of pyridoxal 5'- phosphate (PLP), the co-enzymatically active form of vitamin B6. For the screening of inhibitors, they first evaluated a library of about 42,000 compounds for activators and inhibitors of PDXP and secondly, they validated the inhibitor compounds with a counter-screening against PGP, a close PDXP relative. The final narrowing down to 7,8-DHF was done using PLP as a substrate and confirmed the efficacy of this flavonoid as an inhibitor of PDXP function. Physiologically, the authors show that, by acutely treating isolated wild-type hippocampal neurons with 7,8-DHF they could detect an increase in the ratio of PLP/PL compared to control cultures. This effect was not seen in PDXP KO neurons.

Strengths:

The screening and validation of the PDXP inhibitors have been done very well because the authors have performed crystallographic analysis, a counter screening, and mutation analysis. This is very important because such rigor has not been applied to the original report of 7,8 DHF as an agonist for TrkB. Which is why there is so much controversy on this finding.

Weaknesses:

As mentioned in the summary report the study may benefit from some in vivo analysis of PLP levels following 7,8-DHF treatment, although I acknowledge that it may be challenging because of the working out of the dosage and timing of the procedure.

Reviewer #3 (Public Review):

This is interesting biology. Vitamin B6 deficiency has been linked to cognitive impairment. It is not clear whether supplements are effective in restoring functional B6 levels. Vitamin B6 is composed of pyridoxal compounds and their phosphorylated forms, with pyridoxal 5-phosphate (PLP) being of particular importance. The levels of PLP are determined by the balance between pyridoxal kinase and phosphatase activities. The authors are testing the hypothesis that inhibition of pyridoxal phosphatase (PDXP) would arrest the age-dependent decline in PLP, offering an alternative therapeutic strategy to supplements. Published data illustrating that ablation of the Pdxp gene in mice led to increases in PLP levels and improvement in learning and memory trials are consistent with this hypothesis.

In this report, the authors conduct a screen of a library of ~40k small molecules and identify 7,8-dihydroxyflavone (DHF) as a candidate PDXP inhibitor. They present an initial characterization of this micromolar inhibitor, including a co-crystal structure of PDXP and 7,8-DHF. In addition, they demonstrate that treatment of cells with 7,8 DHP increases PLP levels. Overall, this study provides further validation of PDXP as a therapeutic target for the treatment of disorders associated with vitamin B6 deficiency and provides proof-of-concept for inhibition of the target with small-molecule drug candidates.

Strengths include the biological context, the focus on an interesting and under-studied class of protein phosphatases that includes several potential therapeutic targets, and the identification of a small molecule inhibitor that provides proof-of-concept for a new therapeutic strategy. Overall, the study has the potential to be an important development for the phosphatase field in general.

Weaknesses include the fact that the compound is very much an early-stage screening hit. It is an inhibitor with micromolar potency for which mechanisms of action other than inhibition of PDXP have been reported. Extensive further development will be required to demonstrate convincingly the extent to which its effects in cells are due to on-target inhibition of PDXP.

eLife assessment

This study provides fundamental new knowledge into the role of reversible cysteine oxidation and reduction in protein kinase regulation. The data provide convincing evidence that intra-molecular disulfide bonds serve a repressive regulatory role in the Brain Selective Kinases (BRSK) 1 & 2; part of the as yet understudied 'dark kinome'. The findings will be of broad interest to biochemists, structural biologists, and those interested in the rational design and development of next-generation kinase inhibitors.

Reviewer #3 (Public Review):

Summary:

This manuscript reports the novel observation of alterations in the nuclear pore (NUP) components and the function of the nuclear envelope in knock-in models of APP and presenilin mutations. The data show that loss of NUP immunoreactivity (IR) and pore density are observed at times prior to plaque deposition in this model. The loss of NUP IR is correlated with an increase in intraneuronal Abeta IR with two monoclonal antibodies that react with the N-terminus of Abeta. Similar results are observed in cultured neurons from APP-KI and Wt mice where further results with cultured neurons indicate that Abeta "drives" this process: incubation of neurons with oligomeric, but not monomeric or fibrillar Abeta causes loss of NUP IR, incubation with conditioned media from KI cells but not wt cells also causes loss of NUP IR and treatment with the gamma secretase inhibitor, NAPT partially blocks the loss of NUP IR. Further data show that nuclear envelope function is altered in KI cells and KI cells are more sensitive to TNFalpha-induced necroptosis. This is potentially an important and significant report, but how this fits within the larger picture of what is known about amyloid aggregation and accumulation and pathogenesis in neurons needs to be clarified. The results from mouse brains are strong, while the results from cultured cells are in some instances are of a lower magnitude, less convincing, ambiguous, and sometimes over-interpreted.

Comments on revised version:

I am disappointed in the responses submitted in the revised manuscript. Although there are two new supplemental figures shown, there is no new data that would be needed to address the points raised by myself and the other reviewers. For example, I asked the authors to provide data to place their observations on lower levels of NUPs and mislocalization of nuclear proteins in the context of previously published reports of nuclear amyloid pathology in APP mouse models reported by Pensalfini et al 2014 and Lee et al, 2022 who report amyloid fibrils in some neuronal nuclei along with rosettes of perinuclear autophagic vacuoles containing Abeta immunoreactive material that also stains with amyloid fibril-specific antibodies. In response the authors state: "We have devoted a section of the discussion to highlight some of these findings in the context of Pensalfini et al. 2014 and Lee et al. 2022. Lee et al. tested multiple animal strains to observe the Panthos structures but did not use the App KI mouse model. Since none of our experiments directly tested their observations (e.g. perinuclear fibrils or acidity of autophagic vesicles) in App KI, we decided to take a more conservative approach in our interpretations by framing the NPC deficits without specifying the nature of the intracellular Aβ. We note in discussion that it is entirely possible that App KI animals also show the same Panthos phenotypes and the perinuclear accumulation of Aβ which results in damaged NUPs. To do that, the Panthos phenotype must first be established in App KI mice. "

But the "discussion" is just a couple of sentences that misrepresents the findings of the previous publications and excuses for not doing experiments that the authors should do, like examining whether neurons with intranuclear amyloid and perinuclear autophagic vacuoles occur in the mouse model they use. They are experiments that they should do, and it would be easy to do. Is not an imposition to ask for this data because they presumably have the mouse brain tissue, so they could cut more brain sections and co-stain them with NUP antibodies and the antibodies against fibrillar Abeta and autophagic vesicle markers.

This is just one of many comments where new data is needed but not provided. Disappointing that the revised manuscript is not significantly improved.

On May 25, 2020, in Central Park, New York, there was an incident involving Amy Cooper, a white woman, and Christian Cooper, a black man (they aren't related). Christian asked Amy to put her dog on a leash, which is required in that part of the park. Instead, Amy called the police and falsely said an African American man was threatening her. The video of this encounter went viral, raising serious concerns about racial profiling.

Aja Romano's article in Vox analyzes why jokes about plums are popular on Twitter. I think the article reveals how internet memes develop and spread on social platforms.

I've seen many pictures of ancient animals and even humans. The revolution is mind-blowing and interesting. People evolved to be more intelligent. Animals evolved to be more adapted to their environment or habitat. I believe that evolution is unstoppable and that one day we will eventually be more intelligent.

eLife assessment

In this interesting study, Drożdżyk and colleagues analyze the ability of placental CALHM orthologs to form stable complexes, identifying that CALHM2 and CALHM4 form heterooligomeric channels. The authors then determine cryo-EM structures of heterooligomeric CALHM2 and CALHM4 that reveal a distinct arrangement in which the two orthologs can interact, but preferentially segregate in the channel. This is an important study; the data provide compelling support for the interpretations and overall, the work is clearly described.

Reviewer #1 (Public Review):

The Calcium Homeostasis Modulators (CALHM) are a family of large pore channels, of which the physiological role of CALHM1 and 3 is well understood, in particular their key role in taste sensation via the release of the neurotransmitter ATP. The activation mechanism of CALHM1 involves membrane depolarization and a decrease in extracellular Ca concentration, allowing the passage of large cellular metabolites. However, the activation mechanism and physiological roles of other family members are much less well understood. Many structures of homomeric CALHM proteins have been determined, revealing distinct oligomeric assemblies despite a common transmembrane domain topology. CALHM1 and 3 have been shown functionally to form heteromeric assemblies with properties distinct from those of homomeric CALHM1. However, the structural basis of heteromeric CALHM1 and 3 remains unexplored.

In this paper, Drozdzyk et al. present an important study on the structures of heteromeric channels composed of CALHM2 and CALHM4, extending the structural understanding of the CALHM family beyond homomeric channels. The study relies primarily on cryo-EM. Despite the inherent challenges of structural determination due to the similar structural features of CALHM2 and CALHM4, the authors innovatively use synthetic nanobodies to distinguish between the subunits. Their results show a broad distribution of different heteromeric assemblies, with CALHM4 conformation similar to its homomeric form and CALHM2 conformation influenced by its proximity to CALHM4, and provide detailed insights into the interaction between CALHM2 and CALHM4.

The manuscript is well-structured and presents clear results that support the conclusions drawn. The discovery of heteromeric CALHM channels, although currently limited to an overexpressed system, represents a significant advance in the field of large-pore channels and will certainly encourage further investigation into the physiological relevance and roles of heteromeric CALHM channels.

Comments on the revised version:

I appreciate the authors' efforts to try the alternative data processing strategy. Congratulations to the authors for this interesting and important work!

Reviewer #2 (Public Review):

Summary:

The authors identified that two of the placental CALHM orthologs, CALHM2 and CALHM4 can form heterooligomeric channels that are stable following detergent solubilization. By adding fiducial markers that specifically recognize either CALHM2 or CALHM4, the authors determine a cryo-EM density map of heterooligomeric CALHM2/CALHM4 from which they can determine how the channel in assembled. Surprisingly, the two orthologs segregate into two distinct segments of the channel. This segregation enables the interfacial subunits to ease the transition between the preferred conformations of each ortholog, which are similar to the confirmation that each ortholog adopts in homooligomeric channels.

Strengths:

Through the use of fiducial markers, the authors can clearly distinguish between the CALHM2 and CALHM4 promoters in the heterooligomeric channels, strengthening their assignment of most of the promoters. The authors take appropriate caution in identifying two subunits that are likely a mix of the two orthologs in the channel.

Weaknesses:

Despite the authors' efforts, no currents could be observed that corresponded to CALHM2/CALHM4 channels and thus the functional effect of their interaction is not known.

It strikes me that this mechanism functions similarly to natural selection in ecosystems, where certain traits are favored based on environmental conditions. I wonder how these platforms balance their algorithmic influence with the need to provide a fair and equitable digital space.

I sometimes duplicate certain popular content by creating reaction videos. Furthermore, people often respond to my reaction videos. Additionally, when I come across interesting content, I forward videos to my friends. I believe that as long as it is legal and logical, it should be allowed.

Schooling plays a particularly important role for immigrant youth, as it is the key interaction that brings them into contact with their new society, and it plays a key role in their socialization and adaptation to their new cultural environment. Today immigrant children spend the majority of their day in school, more than at any other time in U.S. history, so schooling is critical.

I believe that the need for educational institutions to adapt and evolve is emphasized here, and that schools must work harder to develop students' cognitive skills, competencies and interpersonal skills. The goal is to prepare young people to respond effectively to the complexities and variations of society and life. Schools can ensure that students are equipped not only with academic knowledge, but also with the competencies and skills needed to adapt to the fast-changing world in today's fast-paced changing society.

These questions question the impact of the lives of young newcomers. The question of whether there are differences in the experience of migration between genders is raised, suggesting that boys and girls can have different ideas and understandings of the journey.

The representation of immigrants in the U.S. is discussed here through a variety of cultural and academic mediums, emphasizing that too little attention has been paid to our understanding of adolescent immigrants, and that immigrant children, who currently make up about 15 percent of the total U.S. population, are the fastest-growing segment of the youth population. It is projected that by 2040, one-third of U.S. children will grow up in immigrant families.

Discussed here are the ways in which the story of immigrants in the United States has been presented in various forms of media and scholarly works, including family narratives, legends, poems, folk songs, novels, memoirs, films, history and civics textbooks, and academic studies.

The passage provides an overview of the history of immigration to the United States, emphasizing four key stages: the initial migration of Native Americans from Asia, the arrival of European colonists in the 17th century, the forced migration of African slaves prior to the Civil War, and the migration of mass slavery. From the end of the Napoleonic Wars through the Great Depression, there was a massive influx of European immigrants.

Richard Dawkins defines memes in culture as similar to genes in biology, applying evolutionary theory to culture. Through this comparison, I can explore how cultural ideas spread and change. I believe this is important for understanding human social behavior.

bottom

b is a tip

Teenagers do not have a complete and thorough outlook on life, life and values, so they are easily influenced by the Internet. They see Internet celebrities or stars doing breast augmentation or plastic surgery to make themselves more beautiful and confident, so they blindly follow them. There are also popular posts on the Internet, which may be fake news, but teenagers will believe or forward them. Teenagers should not be exposed to a lot of information from social media, but unfortunately we are in the information age. Information can benefit us or destroy us. Teenagers are often full of curiosity and do not have a strong core, so they are easily influenced by the Internet. They will have psychological problems such as body anxiety, suicidal tendencies, etc. If they are attacked by anonymous netizens, it will cause teenagers to have great emotional fluctuations and distract their attention.

Cop-E-Eez Metal Typists Copy Holder by [[Analogue Papa]]

an

This paragraph stuck out the most to me because it gives us many reasons on why the cost and commitments happen. Missing work especially to be enrolled in a clinical trial is devastating and frustrating. We need to focus on ways to make clinical trials both cost free, and also time free moving onto the future. A couple months ago when I used to go to the chiropractor, I had to skip work almost every other day just to go to a clinical trial. the process starts to get frustrating and ruins employee's payrolls, takes the time, and also ruins their financial side.

扼要

Testing comments.

This is definitely a typo. Question is, which one is the correct one?

meaning: if they were struggling so hard to survive, they wouldn't have devoted so much time creating intricate artefacts and performing elaborate rituals and ceremonies

The transformative potential of translanguaging pedagogy is evident in Yamaira's newfound engagement with history, highlighting the importance of creating inclusive spaces for multilingual learners to leverage their full linguistic repertoire.

Ms. López's approach with Yamaira illustrates how embracing translanguaging practices can empower Latinx bilingual readers to engage deeply with academic texts, transcending linguistic boundaries.

Arturo's experience in a dual-language classroom underscores the disparities faced by Latinx bilingual students in accessing their full linguistic repertoire for reading.

Paco's "reading" of Curious George/Jorge el curioso exemplifies how young bilingual children engage in translanguaging practices when interacting with texts, going beyond the confines of named languages.

Paco's bedtime routine highlights the fluid translanguaging dynamics present in bilingual homes, where language choice is dynamic and responsive to communicative needs.

This article talks about the importance of blocking features in social media platforms and their potential for improvement. It highlights the rise of platforms like Block Party and the unique blocking mechanics of Clubhouse. It raises the question about the effectiveness and inclusivity of existing blocking tools. The author gives a good understanding of the complexities surrounding online interactions and the need for innovative solutions to address harassment and promote healthier online environments.

After taking psychology and reading about the recent global news on mental health I started thinking about the relationship between mental health and people with neurodiverse conditions.This article helped me learn that some mental health issues can be symptoms of neurodiversity in an individual. For example Arash E.Zaghi's, depression and anxiety contributed to his ADHD diagnosis. I chose to annotate this sentence because it suggests that even people with mental health issues or people with neurodiversity are smart people who are capable of achieving standards that neurotypical people can. This sentence goes to show that society has to come together to overcome stereotypes in order to represent the whole population of different types of people working in the stem field or in any field. I am interested in the healthcare field and it is important to represent all types of people and for people in healthcare to help neurodiverse people be confident in expressing their abilities.Furthermore it is important for healthcare providers to be aware of stereotypes and different biases that individuals encounter to ensure the best treatment and care for different types of patients.

why is circulation reduced?

I strongly believe that crowd harassment is never justified. Regardless of the circumstances or disagreements involved, I don't think that targeting someone in a harmful way is ever justified. Crowd Harassment disregards the well-being and dignity of the person or group being targeted and can have effects on their mental health that can last forever.

I agree with the author that ignoring negative or hateful comments is the best way to deal with them. However, this encourages even more extreme comments, as people who want to comment something truthful or meaningful start skipping the comment section and not commenting at all. Commenting and interacting with a community can spread positivity. Even though the comments are full of toxicity and negativity, we must do something about it instead of leaving it as it is.

想知道什么事 RTE 开发者，最好的办法就是找到并关注在公共场域从事 RTE 工作的人，关注他们的产出、技能和责任。

In an unmoderated online spaces, I believe people with lot of followers, such as celebrities, politicians, etc., have the most power to be heard. If the internet allows any speech, people with great influence can say anything they want and will not face any consequences. In contrast, people with little followers, even though they are speaking the truth, are hard to be heard. Therefore, there are many policies or cancel we have built "cancel culture" to prevent people with great influences from great riots on the internet and in real life.

This dataset has been reused with the “archeoViz” application, allowing to visually and statistically explore its variables: https://analytics.huma-num.fr/archeoviz/synecdemus-novus

This reuse is referenced on the “archeoViz Portal” https://analytics.huma-num.fr/archeoviz/home

The statement describes a city in the Rust Belt that is losing population and industry but is trying to turn things around. Although it is currently on the decline, it still shows traits of the much larger, busier city it used to be. There are efforts to rebuild and bring back some of its old glory. The mix of old strengths and new hopes is key to understanding and helping the city.

Hipótesis: Transferencia de conocimientos de Ingles a nuevo lenguaje

DOI: 10.1016/j.celrep.2021.108889

Resource: (Thermo Fisher Scientific Cat# 14-6525-80, RRID:AB_10670424)

Curator: @Naa003

SciCrunch record: RRID:AB_10670424

What is this?

DOI: 10.1016/j.celrep.2021.108883

Resource: (Atlas Antibodies Cat# AMAb91124, RRID:AB_2665809)

Curator: @Naa003

SciCrunch record: RRID:AB_2665809

What is this?

DOI: 10.1186/s13287-024-03734-z

Resource: (IMSR Cat# JAX_000664,RRID:IMSR_JAX:000664)

Curator: @evieth

SciCrunch record: RRID:IMSR_JAX:000664

What is this?

DOI: 10.1186/s13287-024-03734-z

Resource: Fiji (RRID:SCR_002285)

Curator: @evieth

SciCrunch record: RRID:SCR_002285

What is this?

DOI: 10.1111/jcmm.18328

Resource: (ATCC Cat# PTA-5077, RRID:CVCL_6911)

Curator: @evieth

SciCrunch record: RRID:CVCL_6911

What is this?

DOI: 10.1158/2767-9764.CRC-23-0411

Resource: European Bioinformatics Institute (RRID:SCR_004727)

Curator: @evieth

SciCrunch record: RRID:SCR_004727

What is this?

DOI: 10.1158/2767-9764.CRC-23-0411

Resource: Gene Expression Omnibus (GEO) (RRID:SCR_005012)

Curator: @evieth

SciCrunch record: RRID:SCR_005012

What is this?

DOI: 10.1016/j.celrep.2024.114177

Resource: RRID:Addgene_12260

Curator: @abever99

SciCrunch record: RRID:Addgene_12260

What is this?

DOI: 10.1016/j.celrep.2024.114177

Resource: RRID:IMSR_JAX:037456

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:037456

What is this?

DOI: 10.1016/j.celrep.2024.114177

Resource: (IMSR Cat# JAX_017763,RRID:IMSR_JAX:017763)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:017763

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: RRID:Addgene_71782

Curator: @abever99

SciCrunch record: RRID:Addgene_71782

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: RRID:Addgene_52961

Curator: @abever99

SciCrunch record: RRID:Addgene_52961

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: (IMSR Cat# JAX_001303,RRID:IMSR_JAX:001303)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:001303

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: (IMSR Cat# CRL_027,RRID:IMSR_CRL:027)

Curator: @abever99

SciCrunch record: RRID:IMSR_CRL:027

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: (ATCC Cat# CRL-1997, RRID:CVCL_0313)

Curator: @abever99

SciCrunch record: RRID:CVCL_0313

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: (CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)

Curator: @abever99

SciCrunch record: RRID:CVCL_0063

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: (ECACC Cat# 85062806, RRID:CVCL_0428)

Curator: @abever99

SciCrunch record: RRID:CVCL_0428

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: (NCBI_Iran Cat# C558, RRID:CVCL_0152)

Curator: @abever99

SciCrunch record: RRID:CVCL_0152

What is this?

DOI: 10.1016/j.celrep.2024.114176

Resource: (ECACC Cat# 87092802, RRID:CVCL_0480)

Curator: @abever99

SciCrunch record: RRID:CVCL_0480

What is this?

DOI: 10.1016/j.celrep.2024.114175

Resource: (BCRC Cat# 60250, RRID:CVCL_0553)

Curator: @abever99

SciCrunch record: RRID:CVCL_0553

What is this?

DOI: 10.1016/j.celrep.2024.114175

Resource: (KCB Cat# KCB 200732YJ, RRID:CVCL_1379)

Curator: @abever99

SciCrunch record: RRID:CVCL_1379

What is this?

DOI: 10.1016/j.celrep.2024.114175

Resource: (RRID:CVCL_0950)

Curator: @abever99

SciCrunch record: RRID:CVCL_0950

What is this?

DOI: 10.1016/j.celrep.2024.114175

Resource: (KCLB Cat# 00761, RRID:CVCL_5089)

Curator: @abever99

SciCrunch record: RRID:CVCL_5089

What is this?

DOI: 10.1016/j.celrep.2024.114175

Resource: (ATCC Cat# CRL-5914, RRID:CVCL_1517)

Curator: @abever99

SciCrunch record: RRID:CVCL_1517

What is this?

DOI: 10.1016/j.stem.2024.04.002

Resource: (R and D Systems Cat# MAB4605, RRID:AB_3076456)

Curator: @abever99

SciCrunch record: RRID:AB_3076456

What is this?

DOI: 10.1016/j.devcel.2024.04.011

Resource: RRID:BDSC_78371

Curator: @abever99

SciCrunch record: RRID:BDSC_78371

What is this?

DOI: 10.1016/j.devcel.2024.04.011

Resource: RRID:BDSC_31430

Curator: @abever99

SciCrunch record: RRID:BDSC_31430

What is this?

DOI: 10.1016/j.devcel.2024.04.011

Resource: (BDSC Cat# 58362,RRID:BDSC_58362)

Curator: @abever99

SciCrunch record: RRID:BDSC_58362

What is this?

DOI: 10.1016/j.devcel.2024.04.011

Resource: (BDSC Cat# 35544,RRID:BDSC_35544)

Curator: @abever99

SciCrunch record: RRID:BDSC_35544

What is this?

DOI: 10.1016/j.devcel.2024.04.011

Resource: (BDSC Cat# 31417,RRID:BDSC_31417)

Curator: @abever99

SciCrunch record: RRID:BDSC_31417

What is this?

DOI: 10.1016/j.devcel.2024.04.011

Resource: (BDSC Cat# 5137,RRID:BDSC_5137)

Curator: @abever99

SciCrunch record: RRID:BDSC_5137

What is this?

DOI: 10.1016/j.immuni.2024.04.002

Resource: (IMSR Cat# JAX_011081,RRID:IMSR_JAX:011081)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:011081

What is this?

DOI: 10.1016/j.immuni.2024.04.002

Resource: (IMSR Cat# JAX_028020,RRID:IMSR_JAX:028020)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:028020

What is this?

DOI: 10.1016/j.immuni.2024.04.002

Resource: (IMSR Cat# JAX_013148,RRID:IMSR_JAX:013148)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:013148

What is this?

DOI: 10.1016/j.immuni.2024.04.002

Resource: (IMSR Cat# JAX_016959,RRID:IMSR_JAX:016959)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:016959

What is this?

DOI: 10.1016/j.cub.2024.04.035

Resource: (Beyotime Cat# A0208, RRID:AB_2892644)

Curator: @abever99

SciCrunch record: RRID:AB_2892644

What is this?

DOI: 10.1016/j.cub.2024.04.035

Resource: (Thermo Fisher Scientific Cat# A31632, RRID:AB_2813889)

Curator: @abever99

SciCrunch record: RRID:AB_2813889

What is this?

DOI: 10.1242/dmm.050223

Resource: Bloomington Drosophila Stock Center (RRID:SCR_006457)

Curator: @maulamb

SciCrunch record: RRID:SCR_006457

What is this?

DOI: 10.1038/s41598-023-50272-4

Resource: Bloomington Drosophila Stock Center (RRID:SCR_006457)

Curator: @maulamb

SciCrunch record: RRID:SCR_006457

What is this?

DOI: 10.3389/fcell.2023.1293420

Resource: Bloomington Drosophila Stock Center (RRID:SCR_006457)

Curator: @maulamb

SciCrunch record: RRID:SCR_006457

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (Vector Laboratories Cat# PI-1000-1, RRID:AB_2916034)

Curator: @abever99

SciCrunch record: RRID:AB_2916034

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (Cell Signaling Technology Cat# 2729, RRID:AB_1031062)

Curator: @abever99

SciCrunch record: RRID:AB_1031062

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (Cell Signaling Technology Cat# 9172, RRID:AB_2198300)

Curator: @abever99

SciCrunch record: RRID:AB_2198300

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (Cell Signaling Technology Cat# 8457, RRID:AB_10950489)

Curator: @abever99

SciCrunch record: RRID:AB_10950489

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (Abcam Cat# ab118347, RRID:AB_10900748)

Curator: @abever99

SciCrunch record: RRID:AB_10900748

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 340688, RRID:AB_400091)

Curator: @abever99

SciCrunch record: RRID:AB_400091

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 564105, RRID:AB_2744405)

Curator: @abever99

SciCrunch record: RRID:AB_2744405

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 562691, RRID:AB_2737725)

Curator: @abever99

SciCrunch record: RRID:AB_2737725

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 557979, RRID:AB_396971)

Curator: @abever99

SciCrunch record: RRID:AB_396971

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (R and D Systems Cat# AF3365, RRID:AB_562564)

Curator: @abever99

SciCrunch record: RRID:AB_562564

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 566776, RRID:AB_2869859)

Curator: @abever99

SciCrunch record: RRID:AB_2869859

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 561142, RRID:AB_10561690)

Curator: @abever99

SciCrunch record: RRID:AB_10561690

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 565613, RRID:AB_2734770)

Curator: @abever99

SciCrunch record: RRID:AB_2734770

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 553312, RRID:AB_398535)

Curator: @abever99

SciCrunch record: RRID:AB_398535

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (Thermo Fisher Scientific Cat# 25-0114-82, RRID:AB_469590)

Curator: @abever99

SciCrunch record: RRID:AB_469590

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 563687, RRID:AB_2738376)

Curator: @abever99

SciCrunch record: RRID:AB_2738376

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 563687, RRID:AB_2738376)

Curator: @abever99

SciCrunch record: RRID:AB_2738376

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 557644, RRID:AB_396761)

Curator: @abever99

SciCrunch record: RRID:AB_396761

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 554429, RRID:AB_398555)

Curator: @abever99

SciCrunch record: RRID:AB_398555

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 563773, RRID:AB_2738419)

Curator: @abever99

SciCrunch record: RRID:AB_2738419

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 564983, RRID:AB_2739032)

Curator: @abever99

SciCrunch record: RRID:AB_2739032

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 553051, RRID:AB_398528)

Curator: @abever99

SciCrunch record: RRID:AB_398528

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (BD Biosciences Cat# 553013, RRID:AB_394551)

Curator: @abever99

SciCrunch record: RRID:AB_394551

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (IMSR Cat# JAX_022071,RRID:IMSR_JAX:022071)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:022071

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (IMSR Cat# JAX_004781,RRID:IMSR_JAX:004781)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:004781

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (IMSR Cat# JAX_026708,RRID:IMSR_JAX:026708)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:026708

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (IMSR Cat# JAX_004194,RRID:IMSR_JAX:004194)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:004194

What is this?

DOI: 10.1016/j.celrep.2024.113942

Resource: (IMSR Cat# JAX_000664,RRID:IMSR_JAX:000664)

Curator: @abever99

SciCrunch record: RRID:IMSR_JAX:000664

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (SouthernBiotech Cat# 3030-05, RRID:AB_2716837)

Curator: @evieth

SciCrunch record: RRID:AB_2716837

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (SouthernBiotech Cat# 4010-05, RRID:AB_2632593)

Curator: @evieth

SciCrunch record: RRID:AB_2632593

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (SouthernBiotech Cat# 1030-05, RRID:AB_2619742)

Curator: @evieth

SciCrunch record: RRID:AB_2619742

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Cell Signaling Technology Cat# 4691, RRID:AB_915783)

Curator: @evieth

SciCrunch record: RRID:AB_915783

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Cell Signaling Technology Cat# 2840, RRID:AB_2167691)

Curator: @evieth

SciCrunch record: RRID:AB_2167691

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Cell Signaling Technology Cat# 5670, RRID:AB_10828378)

Curator: @evieth

SciCrunch record: RRID:AB_10828378

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Cell Signaling Technology Cat# 2983, RRID:AB_2105622)

Curator: @evieth

SciCrunch record: RRID:AB_2105622

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Cell Signaling Technology Cat# 9122, RRID:AB_823567)

Curator: @evieth

SciCrunch record: RRID:AB_823567

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Abcam Cat# ab2928, RRID:AB_303423)

Curator: @evieth

SciCrunch record: RRID:AB_303423

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Enzo Life Sciences Cat# ADI-SRA-1500, RRID:AB_10618972)

Curator: @evieth

SciCrunch record: RRID:AB_10618972

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Enzo Life Sciences Cat# ADI-SPA-815, RRID:AB_10617277)

Curator: @evieth

SciCrunch record: RRID:AB_10617277

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (StressMarq Biosciences Cat# SPC-195, RRID:AB_2119373)

Curator: @evieth

SciCrunch record: RRID:AB_2119373

What is this?

DOI: 10.21203/rs.3.rs-4114038/v1

Resource: (Cell Signaling Technology Cat# 5670, RRID:AB_10828378)

Curator: @evieth

SciCrunch record: RRID:AB_10828378

What is this?

DOI: 10.1016/j.isci.2024.109062

Resource: (KCLB Cat# 80008, RRID:CVCL_0159)

Curator: @evieth

SciCrunch record: RRID:CVCL_0159

What is this?

DOI: 10.1016/j.isci.2024.109062

Resource: (ATCC Cat# CRL-2638, RRID:CVCL_7256)

Curator: @evieth

SciCrunch record: RRID:CVCL_7256

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DOI: 10.1016/j.isci.2024.109062

Resource: (ATCC Cat# CRL-2539, RRID:CVCL_0125)

Curator: @evieth

SciCrunch record: RRID:CVCL_0125

What is this?