Evaluated articles

Evaluation Summary:

Calcium-calmodulin (CaM) signaling plays an essential role within and outside of the nervous system. Moreover, it is conserved from plants to humans. While a lot is known about the mechanisms of cellular calcium level fluctuations, how CaM levels are regulated is less clear. In this manuscript, Vuong-Brender and colleagues characterize a, likely, conserved role of the transcription factor CAMT-1 in the homeostatic regulation of CaM levels and show how it impacts animal behavior and nervous system function. The paper is a tour-de-force across multiple techniques and model systems. The data is of a very high quality and supports most of the authors' claims strongly and convincingly.

(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:

The question investigated - to understand the computational significance of different types of local interneurons in neural circuits - is an important and significant problem. Here authors elucidate the role of the two types of LNs, by combining whole-cell patch clamp recordings with calcium imaging via single cell dye injection. This method enables them to monitor calcium dynamics of the different axons and branches of single LNs in identified glomeruli of the antennal lobe, while the membrane potential can be recorded at the same time. They conclude that non-spiking LNs with graded responses show glomerular restricted responses to odorants and spiking LNs show similar responses across glomeruli.

(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 work, which will be of value to evolutionary and clinical microbiologists, uses a well-designed experimental evolution strategy to tease apart contributions of history, chance, and selection on the evolution of antibiotic resistance in A. baumannii, an important microbial pathogen. While relevant, the work will benefit from further clarification regarding some of the concepts and procedures used and revision of some of the interpretations.

(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:

This paper examines the visual-ocular response in participants when exposed to the static magnetic field of a 3T MRI system. Historically, this problem has been approached from a safety perspective. In the present study, the authors ask about the behavioral consequences of this field given that it induces a response in the vestibular system, hypothesized to mimic that of a caloric vestibular stimulation event. As such, one should anticipate a biased vestibulo-ocular reflex in the static field as well as biases in spatial attention. These predictions were confirmed, with the attentional bias manifest in eye movements during a visual search task. This is an important finding because it reveals functional "artifacts" that may arise during fMRI studies, effects that may need to be considered by those conducting research in the MR environment (especially functional 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. Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Evaluation Summary:

In this manuscript the authors use a combination of transcriptomics, metabolomics, and quantitative measurements of growth to characterize the temporal and spatial distribution of cells with different metabolic states within colony of biofilms of the model bacterium Escherichia coli. They show that within the biofilm cells performing different metabolic functions are distributed in different regions of the colonies, and propose a model where nutrient cross-feeding through the amino acid alanine explains the phenotypic heterogeneity observed within the biofilm. The findings reported have potential broad implications for thinking about the spatial structure of communities of all bacterial species.

(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 the study presented here, the authors used the fruitfly Drosophila melanogaster to identify a new molecular regulator - the E3 ubiquitin ligase Thin - of presynaptic homeostatic plasticity (PHP), a process where synaptic signaling between motorneurons and muscle cells is dynamically adapted to compensate exogenously imposed changes in synapse strength. Based on a very substantial set of high quality data, the authors propose that Thin functions presynaptically during PHP, that presynaptic thin negatively regulates neurotransmitter release under baseline conditions by limiting the number of release-ready synaptic vesicles, and that Thin controls transmitter release by regulating Dysbindin, a schizophrenia-susceptibility gene required for PHP. The authors' conclusion is that Thin links protein-degradation-dependent proteostasis of Dysbindin to homeostatic regulation of neurotransmitter release. The major claims of the paper are well supported by the data, but alternative hypotheses cannot yet be unequivocally excluded.

(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 names with the authors.)

Evaluation Summary:

This manuscript describes a framework for rapidly quantifying relative extracellular vesicle (EV) yield and purity across isolation methods, with a focus on using size exclusion chromatography (SEC) for EV isolation from small volumes of pooled plasma and cerebrospinal fluid (CSF) samples. The authors used single molecule array (Simoa) assays for the quantification of EVs using three tetraspanins (CD9, CD63, and CD81), and report the outcomes of assessing EV yields and purity with respect to albumin by various SEC parameters (Sepharose size, column length, fractions collected). This is the first demonstration of the use of Simoa with three commonly used tetraspanins to measure EVs from small volumes of CSF, of great relevance to human CSF biomarker studies, but these methods could also be applied to compare EV isolation methods from other fluids such as cell culture media.

(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 names with the authors.)

Evaluation Summary:

Kaplan and colleagues build upon their earlier work using genetic phenotypes to find and analyze mutations that determine how mRNA start sites are chosen. Here they provide convincing genetic evidence supporting a model in which the Transcription Factor II H (TFIIH) protein complex pushes downstream DNA back into the RNA polymerase active site, creating a window within which the polymerase can choose particular start sites. This will primarily interest those in the transcription field who are thinking about initiation mechanisms.

(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 work, Minh Nguyen and colleagues performed single nuclear RNAseq of human dorsal root ganglion (DRG) neurons and classified them into 15 clusters. A bioinformatic comparison to mouse lumbar DRG single nucleus sequencing results is also described. The importance of reporting the single nucleus or single cell molecular profiles of human DRG cannot be overstated. Proper molecular targeting of therapeutics requires knowing this information. Given that the field is just starting to understand the human specific molecular signature of primary somatosensory neurons using single cell/nuclear RNAseq, this study is important and timely, providing one of the first gene expression databases of individual human DRG neurons.

(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:

The manuscript introduces a new molecular screen, MassTitr, to screen for long (36-mer) peptides derived from the human proteome that can bind a specific target. The method is demonstrated using the EVH1 domain of the actin-associated ENAH protein as target. About 100 peptides were isolated, and further analysis identified sequence features that contribute to the binding of the EVH1 domain by these peptides. The human proteome contains many short linear motifs of 4-6 residues that are critical for protein-protein interactions. The work here helps to better understand how the sequence surrounding such motifs contributes to protein-protein interactions.

(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:

Local recycling of synaptic vesicles is required to maintain neurotransmission via clathrin-mediated endocytosis and clathrin-independent ultrafast endocytosis. Clathrin also plays a role in ultrafast endocytosis to regenerate vesicles from a recycling endosome. Here the authors have further tested the role of clathrin and clathrin adaptors in synaptic vesicle endocytosis. This paper raises the interesting possibility that adaptor protein AP-2 but not clathrin contributes to the endocytosis of synaptic vesicle proteins. There are some concerns about differential knockdown of clathrin and AP-2 but if the authors can resolve these, this would be an important result.

(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:

The pleiotropic effects of beneficial mutations have been characterized in various settings, but it is less clear whether and how these pleiotropic patterns change over the course of evolution. Using a technically innovative and intensive experimental design with evolving yeast populations, the authors show that patterns of pleiotropy depend on the evolution environment and can change and vary substantially over relatively short timescales. They also find a surprising amount of variation among replicate populations that increases over time, so generalism or specialism is not deterministic. These technical and conceptual strengths were diminished by insufficient focus on the details of certain treatments that are demonstrative of these broader findings, making the take-home message somewhat unclear.

(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 names with the authors.)

Evaluation Summary:

The authors demonstrate deficits in perceptual tests related to fine-time perception in non-speech and speech sounds in a group of patients with stroke aphasia compared to a control group without a lesion. An area in left auditory cortex is defined that is essential for fine-time perception that is shown in a separate group of normal subjects to other areas including the cerebellum. The work in interesting in suggesting an anatomical basis for interaction between cortical and cerebellar system for perceptual timing.

(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:

These are pressing times for nature, standing alone the impact of multiple (human-based) ecological stressors. Wildlife trade is one of these stressors. And, although it is an acute one, it is the easiest solvable global ecological problem. The authors increase dramatically our understanding of legal and illegal trade of amphibians, and offer a wider methodology (however, and importantly, not necessarily a more complex one) to gain a deeper understanding of the causes and consequences) of amphibians' trade. The work will inspire in conservation biologists similar approaches to learn about the trade of other taxa.

(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 manuscript reveals new molecular details about the human calcium sensing receptor (CaSR), a G protein-coupled receptor that maintains calcium homeostasis and is involved in pathological states. This study, together with other recent structural work on this molecule, will have important implications for the design of molecules that control CaSR activity and treat human disease.

(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 manuscript describes follow-up studies on a hit from a proteome-wide screen for peptides that can bind to the EVH1 domain of the ENAH protein, one of three highly similar Ena/VASP actin regulators. The hit investigated is from a protein called PCARE, which selectively binds to ENAH but not the other two members of the Ena/VASP family, EVL and VASP. The authors provide a good explanation for how this selectivity is achieved and develop a peptide, PCARE-Dual, that specifically binds ENAH more tightly, setting out the stage for developing potent and selective inhibitors of ENAH activity.

(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 primary interest to readers in the field of infectious diseases especially the ones involved in COVID-19 research. The identification of immunological signatures caused by SARS-CoV-2 in HIV-infected individuals is important not only to better predict disease outcomes but also to predict vaccine efficacy and to potentially identify sources of viral variants. In here, the authors leverage a combination of clinical parameters, limited virologic information and extensive flow cytometry data to reach descriptive 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. The reviewers remained anonymous to the authors.)

Evaluation Summary:

This paper claims to identify a long-sought ligand for the receptor protein tyrosine phosphatase Lar that mediates its functions in neuromuscular junction development, mushroom body development, and photoreceptor axon targeting. If correct, this would be of interest to many developmental neurobiologists, However, further evidence is needed to strongly support this claim.

(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:

The manuscript by Lee and co-workers describes the development of 21 unique transgenic mouse lines that express optogenetic sensors and effectors in a cell lineage-specific fashion. The knock-in approach allows the sensors and effectors to be rapidly combined or moved to different backgrounds, such as genetic disease models. Such manipulations are often impractical when using a Cre-based system. This constitutes a vital advantage for many studies. The new mice described here will be very powerful tools to study physiology and alteration in disease models.

(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 shows how astrocytic MCL1 can contribute to postnatal maturation of the brain vascular system. Since the development and physiological roles of perivascular astrocyte coverage are not well understood, this manuscript provides potentially important frame works and should be of interest to the broad fields of neuroscientists.

(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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)