Evaluated articles

Evaluation Summary:

This study reports on the inference of the evolutionary trajectory of two specialist species that evolved from one generalist species. The process of speciation is explained as an adaptive process and the changing genetic architecture of the process is analyzed in great detail. The genomic dataset is big and the inference from it solid. The authors reach the conclusion that introgression and de novo mutations, but not standing genetic variation, are the main players in this adaptive process.

(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 will be of interest to theorists in microbial systems biology. It shows that taking protein degradation into account improves theoretical predictions of bacterial growth laws at low growth rates. The theoretical aspects of this work are solid. Some underlying assumptions of the model and key predictions remain to be validated experimentally.

(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 manuscript, the authors discovered a new function of Rai14, an F-actin binding protein, in dendritic spine dynamics. They showed that Rai14 is localized at the spine neck and regulate spine density and function. Heterozygous Rai14 knockout mice showed impaired learning and memory and depressive-like behavior. Overall, this study provides novel insights into the molecular mechanisms underlying spine dynamics and depressive-like behavior. The main conclusions are supported by the data.

(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 will be of interest to researchers studying how spoken language is processed in the brain. The results add to our understanding of how brain oscillations track language information at the syllable, word, and sentence level. The analyses are thoughtful and the key claims of the manuscript are largely supported by the data, although some conclusions may require additional support.

(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 paper is of interest to scientists who study neuroanatomy or the many behavioural phenotypes that have been proposed to be associated with left-right asymmetry of the human brain. The authors' new tool appears to provide clues to identify individuals based on shape asymmetry.

(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:

Krasniewski and colleagues leveraged single-cell transcriptomics to identify subpopulations of macrophages in the skeletal muscle of aging male mice. They identify several new resident subpopulations of skeletal muscle macrophages, spanning a range of polarization states using novel markers, and they identify a shift in relative abundances of these subpopulations with age, leading to a functional shift in inflammatory marker expression and phagocytic capacity. The study overall is an interesting and timely investigation of skeletal muscle macrophage populations and transcriptomics in both healthy young and old mice, and should be a valuable resource for the inflammaging and muscle biology field.

(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 manuscript by Nakane et al investigates phototaxis of the rod shaped bacteria Thermosynechococcus vulcanus. This is important because most our knowledge on phototaxis is only emerging on round-shaped cyanobacteria. In the study, the authors demonstrate that T. vulcanus can chemotax positively or negatively to light depending on the light source. They identify a photoreceptor complex that drives negative phototaxis and propose that it impacts motility by increasing cdiGMP levels, which in turn would regulate the motility complex, formed by bi-polar Type-IV pili. Provided that the link between light induced cdi-GMP and spatial TFP activity is established, the work would provide a new mechanistic framework to explain TFP-driven phototaxis. This is an important topic because TFPs are emerging as spatially-regulated motility machineries in a large number of bacterial systems and linking their activity to receptors and secondary messengers is a current unresolved question.

(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:

Medley et al. study A. mexicanus, an extreme-adapted organism with important connections to human health. The authors test metabolic responses in this natural model of elevated blood glucose and extensive body fat deposits, conditions generally expected to predispose to higher risk for metabolic syndrome and higher frailty. The work is rigorous and will provide a reference for future studies aimed at dissecting the mechanistic basis underlying metabolic shifts in this uniquely attractive model. The authors also provide an open and accessible window into their data and analyses by sharing a Shiny app.

(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:

Analyzing the long-distance migration of centrioles to the dendrite tip of multicilated olfactory neurons in mice, Ching et al. use expansion microscopy to show that centrioles migrate as clusters, which mature as they reach the apical surface. The super-resolution data are impressive and the claims are generally supported by the data. Although the manuscript is largely descriptive, it is an important addition to the field, and will be of broad interest to cell 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 reviewers remained anonymous to the authors.)

eLife assessment

This is an exciting and important study that constitutes a major advance in the molecular understanding of resurgent Na current. Reproducing resurgent current by expression of two proteins has never been done. Here, the authors have for the first time molecularly reconstituted Na channels that produce resurgent Na current. Not only do these experiments satisfactorily and convincingly address a long-standing question in the field, but they also open the door to molecular manipulation of this current, potentially of significant practical use given the proposed role of the current in several disorders and disease states, including pain. The work will be of interest to many neuroscientists.

Evaluation Summary:

This paper will be of interest to the structural biology community and people working on cryogenic fluorescence microscopy. This paper is a clear step forward in the use of single-molecule localization microscopy at angstrom resolution, thanks to low-temperature polarized super-resolution imaging and advanced data processing algorithms.

(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 paper is of interest to scientists within the field of apicomplexans cytoskeleton and malaria parasite proliferation. A series of compelling experimental manipulations identify potential new pellicle proteins and dissect the role of a protein acyl-transferase for the development of the intraerythrocytic stages of Plasmodiun yoelii and the palmitoylation status of two potential substrates.

(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 paper, the authors identify topological metrics in gene-regulatory networks that potentially predict the kinds of phenotypic steady-states that the network allows. In particular, they apply their results to the epithelial-mesenchymal plasticity, showing that the relevant gene regulatory networks are structured as ‘teams' that may be 'strong', yielding stable phenotypes, or 'weak', yielding unstable phenotypes prone to plasticity. The work would be of interest to researchers interested in systems biology and the nonlinear dynamics of biological systems, as well as biologists interested in gene regulatory networks and their (mis)functioning in cancer cells.

(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 focus follows this group's previous work on EROS and NOX2. In this current study the authors examine neutrophil EROS in the generation of superoxide by the NADPH oxidase. They demonstrate how EROS is involved in the maturation of gp91phox and expand our knowledge on the role of EROS in regulating expression of the P2x7 ion channel.

(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:

The authors have systematically examined relationships between muscle length and force potentiation in young adults using very carefully conducted and controlled measurements by dynamometry and estimated using patellar tendon shear wave speed. The paper should be of interest to those who study human performance.

(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:

The paper addresses the highly timely questions of how to quantify aperiodic and periodic neural activity. This was done by extending previous work by embracing time-resolved parametrization of both simulated, noninvasive EEG and intracranial data. The new approach is termed Spectral Parametrization Resolved in Time (SPRiNT) and the paper shows that the slope of aperiodic activity is linked with both behaviour and age. The method thus demonstrates the importance of evaluating the state-dependence of aperiodic activity and dynamic properties of oscillatory components in a time-resolved manner.

(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:

Synaptotagmins are Ca2+ sensors for synchronous neurotransmitter release. However, despite intense study it remains unclear exactly how the binding of 5 Ca2+ ions to Synaptotagmin's two C2 domains leads to the observed Ca2+ dependence of vesicle fusion. This study puts forward a novel mechanistic model of neurotransmitter vesicle fusion (vesicle exocytosis) which is relatively simple but significantly more detailed than the widely used phenomenological models of calcium-dependent fast exocytosis.

(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:

The observations from high quality in vivo and in vitro recordings of tagged CHR neurons are supported by a computational model that suggests feedback inhibition may regulate the activity patterns of CRH neurons in distinct states, and represent an important contribution. The authors also present an unexpected observation that uncovers interesting neural dynamics that will provide the impetus for new studies exploring firing characteristics in discrete physiological and emotional states. Previous work reaching an opposite conclusion and likely effects of urethane on in vivo recordings are not discussed.

(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 manuscript provides a comprehensive unbiased analysis of the fucosylation secretome and correlates with drug response in cancer. It uses a combination of bioinformatic based analyses of multiple datasets and cell based data to identify changes in the secretome and correlates this to drug responses to several targeted therapies.

(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 is of interest to protein biochemists, protein engineers, and those interested in molecular evolution. The computation and experiments presented in this paper are very logical and rigorously performed. The results provide an example of how protein interaction specificity can be rewired using a small number of mutations, in the context of ancestral sequence reconstruction.

(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.)