Evaluated articles

Evaluation Summary:

This paper presents a single-molecule, multi-color microscopy study of the real-time assembly of perfringolysin O, a member of the membrane attack complex perforin cholesterol-dependent cytolysin superfamily. With the ability to resolve different states of the species in the reaction, simultaneously with membrane leakage, this work informs on key aspects of the mechanism including identifying potential assemblies involved in membrane lysis, and how membrane binding, oligomerization, and pore transitioning depends on concentration and pH. While some additional controls are needed to clarify the interpretation of the results, this study will be of interest to many, including those studying cytolysin mechanisms, but also the broader field of single-molecule studies of membrane binding proteins.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

In Drosophila neural progenitors (neuroblasts), sequentially-expressed transcription factors (known as temporal transcription factors) ensure the generation of various types of neurons and glia as they divide. However, the mechanisms regulating and finetuning the speed of temporal factor transitions has remained unclear and under-investigated. Here the authors concentrate on a specific temporal transition occurring in medulla neuroblasts and demonstrate that lineage-intrinsic Notch signaling facilitates this transition via at least two identified enhancers. This work provides important insights on the signals and mechanisms that promote temporal transitions in neural progenitors, and therefore regulate cellular diversity in the brain.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript is of broad interest for evolutionary biologists who seek to understand the dynamics of strongly advantageous mutations across time and space. It presents an elegant framework for inferring the strength of natural selection and spread of adaptive variants that accounts for spatially and temporal patterns of genetic variation. The authors extend a previously developed statistical inference method, performs some tests of the performance of their method on simulated data and apply the method to two well-known targets of selection. The development of the method is timely given the growing availability of ancient DNA collections, which have the power to largely increase the accuracy of selection inferences and parameter estimates.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Conway and colleagues use a combination of experiments and theory to test models for how kinetochore-fibers are born in mammalian spindles. Their work is consistent with a model where kinetochore-fibers primarily nucleate de novo at kinetochores, rather than arise from search-and-capture of microtubules. This work should be of interest to experimentalists and theorists broadly interested in self-organization, and in cell division.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

Kiewisz and colleagues performed sophisticated reconstructions of kinetochore-fibers within human spindles using electron tomography, and then analyzed the ultrastructure and organization of their microtubules. This work will not only serve as an incredible resource for the field, but has clear implications for models of kinetochore-fiber and spindle self-organization.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

In this manuscript by Kissiov et al. the authors show that enhancers can play an instructive role in controlling stable random monoallelic expression (RME). In order to do so, they initially focus on a limited set of natural killer (NK) receptor genes that are subject to RME, which they investigate using several in vivo genetic models. Furthermore, they also show that RME can be considerably more prevalent than previously thought and that enhancer strength and/or number might influence the extent of RME for different genes. One remaining question may be whether this model may apply to other gene types than hematopoietic-related genes. Overall, this is a highly relevant manuscript with major implications in gene regulation and enhancer biology and, thus, of broad scientific interest.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Evaluation Summary:

This theoretical study describes the interaction of a planar brush or film of the resident unstructured components of the nuclear pore complex (NPC) called nucleoporins (FG-nups) and different nuclear transport receptors (NTRs). The authors describe impacts of competitive binding that give rise to enrichment of the NTRs, NTF2 and importin-beta, at different depths of the FG-nup film, which could relate to experimental observations in other studies, as well as evidence that crowding could promote the rate of nuclear transport by modulating FG-NTR binding/unbinding. The conclusions were found to be generally supported by the data, relevant to the field of nuclear transport, and able to make specific predictions that can be experimentally tested in the future, although previous studies in the field and the novelty could be better described.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper is of interest for neuroscientists studying neocortical neural activity related to social behavior, with a connection to mouse models of neuropsychiatric disorders. The work provides new data on how loss-of-function of postsynaptic scaffolding and adaptor protein IRSp53 (encoded by the BAIAP2 gene) impacts prefrontal cortex activity and social interaction in mice. Overall, the experiments are properly controlled, although further analysis and interpretations are needed.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This work reports on a mathematical modeling system and associated software implementation for compound eye vision. A critical advance reported here is the ability to model each ommatidium with independent properties and on a software implementation that runs in real time, with tantalizing applications in both modeling biological systems such as insect compound eyes, and the exploration of the possible applications of compound eye vision in robotics.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript is of potential interest to a large audience in the fields of stem cells, developmental biology and neural regeneration. The authors assess the roles of extrinsic versus intrinsic signalling on differentiation of human neural cells by comparing their differentiation rates across different environments (in vitro, in the human embryo and grafted into a chicken embryo). While the experimental design tests the role of environment on differentiation, some aspects of data analysis need to be clarified and extended to support the conclusions.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript provides insight into the zone-specific regulation of inflammatory gene expression in the fetal membranes prior to labor at term. Specifically, the authors demonstrate distinct epigenetic and mi-RNA control of TLR4 signaling in the amnion and chorion, highlighting the role of this pattern recognition receptor in physiological labor. Overall, the experimental design and data analysis are suitable, though the study would benefit from the inclusion of the analysis of fetal membrane tissues from pregnancy complications and/or in vivo studies.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Evaluation Summary:

In this study, Tang and colleagues report that the deletion of the fructose-2,6-phosphatase TIGAR leads resistance to cold-induce hypothermia. Using different complementary approaches, they found that this phenotype originates from alteration in cholinergic neurons. In particular, they found that deleting TIGAR in ChAT-expressing neurons recapitulates the phenotype of the global knock-out. Overall, this is a well-performed study that provides evidence for a role of TIGAR in regulating the neuromuscular junction.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

In this manuscript, the authors present at interesting strategy for directing simultaneous induction of both mesoderm-derived cardiac and endoderm-derived lung epithelial lineages from human induced pluripotent stem cells (hiPSC). All reviewers found the work to be of interest, but concerns were raised regarding the efficiency of the differentiation process (including % of differentiated cells in the final cultures) . In addition, it is noted that experiments presented are based on analysis of a single hiPSC cell line, and only part of the differentiation was repeated in another cell line, and thus the broader applicability of the presented protocol remains to be established. However, the interesting data support the conclusions presented. It is likely that the presented methods will be very useful for researchers focusing on heart and lung development, and may inspire others to take similar approaches for studying development of other organs.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This manuscript examines the role of Nephronectin-Integrin a8 signaling in early stages in the avian corneal development. This is an understudied system with numerous gaps in our comprehension how neural crest derived cells migrate into the "open" space between the corneal epithelium and lens and form the corneal endothelium and stroma. Novel insights are generated on the cellular and molecular mechanisms of this critical process of anterior segment morphogenesis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

The study investigates obesity and adipose distribution on hematopoiesis. It shows that genetically determined adiposity plays a previously underappreciated role in determining blood cell formation and function. The authors performed all the relevant and available MR analyses in the "toolbox". The results support the conclusions. The study will help understand the pathogenesis for clonal hematopoiesis.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

Evaluation Summary:

This study employs a novel bioluminescence-based technique to analyze the import of precursor proteins into the mitochondrial matrix in real time. This is an innovative technical advance that can provide mechanistic detail on the kinetic steps of mitochondrial protein import. It has potential applications in other membrane protein transport systems and it could be applicable to studies in applied science such as screening for drugs targeting the mitochondrial import apparatus.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

The authors used phage display deep mutational scanning of SARS-CoV-2 Spike protein to profile antibody epitopes outside of the RBD that were recognized in two cohorts of subjects, which together included mRNA vaccinated, SARS-CoV-2 infected with mild or severe COVID-19 and vaccinated with prior infection. Key findings of the study are that severe COVID-19 and vaccinated individuals had higher binding to Spike protein regions NTD, CTD, and SH-H compared to individuals with mild COVID-19, while mild COVID-19 infections had higher binding to FP than vaccinated or severe COVID-19 individuals. They also reported that vaccinated individuals with or without prior infection were not different and that covariates did not appear to impact the antibody recognition profiles. The authors identified potential escape pathways in these epitope regions, some of which differed between vaccination and infection or drifted over time. The authors acknowledge that this approach is limited to linear epitopes and does not include RBD epitopes. However, the study provides novel insight into the major epitope regions targeted by polyclonal antibodies elicited by vaccination vs. infection, as well as potential pathways for the virus to escape recognition.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

Evaluation Summary:

Karasawa and colleagues examine two gain-of-function mutations in NLRP3, which are known to cause cryopyrin-associated periodic syndromes (auto-inflammatory diseases with different manifestations), and demonstrate that both mutations appear to result in cryo-sensitive aggregated foci when expressed in cells. This is a very impactful and extensive body of work that is of broad interest to the fields of inflammasomes and autoinflammatory diseases. Data presented support the conclusions, and the findings are translational for patients and applicable to our general understanding of inflammasome function. However, specific issues raised by the Reviewers should be addressed.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

Evaluation Summary:

This preclinical study reports on a novel strategy for sepsis. Sepsis induced by Group A Streptococcus (GAS) in mice leads to depletion of bone marrow HSPCs and mortality and infusion of naive donor HSPCs lower mortality but has no effect on bacterial burden. This supports that HSPCs infusion might attenuate the detrimental immune response in sepsis warranting further investigation of this novel concept.

Evaluation Summary:

This study provides a sound and novel algorithm to analyze the massive cancer data and its findings greatly help inform novel cancer immunotherapy across various cancer types. Moreover, a 3-gene signature was established based upon Tc1, Tc17, and immune cold tumors to estimate the abundance of monocytic infiltrates that could potentially impact on the overall survival of cancer patients. It might be of great interest to the general audience of cancer biologists, immunologists and computational biologists.

(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewer remained anonymous to the authors.)