Evaluated articles

eLife Assessment

This useful study analyzed 335 Mycobacterium tuberculosis Complex genomes and found that MTBC has a closed pangenome with few accessory genes. The research provides solid evidence for gene presence-absence patterns which support the appending conclusions however, the main criticism regarding the dominance of genome reduction remains.

eLife assessment

This valuable study explores a new strategy of lysin-derived antimicrobial peptide-primed screening to find peptidoglycan hydrolases from bacterial proteomes. Using this strategy, the authors identified five peptidoglycan hydrolases from Acinetobacter baumannii, which they tested on various Gram-positive and Gram-negative pathogens for antimicrobial activity. The revised manuscript addressed most of the prior concerns, and the data presented are solid and will be of interest to microbiologists.

eLife Assessment

This fundamental study substantially advances our understanding of how habitat fragmentation and climate change jointly influence bird community thermophilization in a fragmented island system. The authors provide convincing evidence using appropriate and validated methodologies to examine how island area and isolation affect the colonization of warm-adapted species and the extinction of cold-adapted species. This study is of high interest to ecologists and conservation biologists, as it provides insight into how ecosystems and communities respond to climate change.

eLife assessment

This important study investigates neurobiological mechanisms underlying the maintenance of stable, functionally appropriate rhythmic motor patterns during changing environmental conditions - temperature in this study in the crab Cancer borealis stomatogastric central neural pattern generating circuits producing the rhythmic pyloric motor pattern, which is naturally subjected to temperature perturbations over a substantial range. The authors present compelling evidence that the neuronal hyperpolarization-activated inward current (Ih), known to contribute to rhythm control, plays a vital role in the ability of these circuits to appropriately adjust the frequency of rhythmic neural activity in a smooth monotonic fashion while maintaining the relative timing of different phases of the activity pattern that determines proper functional motor coordination transiently and persistently to temperature perturbations. This study will be of interest to neurobiologists studying rhythmic motor circuits and systems and their physiological adaptations.

eLife assessment

This important study explores how cells maintain subcellular structures in the face of constant protein turnover, focusing on neurons, whose synapses must be kept stable over long periods of time for memory storage. Using proteins from knock-in mice expressing tagged variants of the synaptic scaffold protein PSD95, nanobodies, and multiple imaging methods, there is compelling evidence that PSD95 proteins form complexes at synapses in which single protein copies are sequentially replaced over time. This happens at different rates in different synapse types and is slowest in areas where PSD95 lifetime is the longest and long-term memories are stored. While of general relevance to cell biology, these findings are of particular interest to neuroscientists because they support the hypothesis put forward by Francis Crick that stable synapses, and hence stable long-term memories, can be maintained in the face of short protein lifetimes by sequential replacement of individual subunits in synaptic protein complexes.

eLife Assessment

The authors studied the relationship between structural and functional lateralization in the planum temporale region of the brain, whilst also considering the morphological presentation of a single or duplicated Heschl's gyrus. The analyses are compelling due to a large sample size, inter-rater reliability, and corrections for multiple comparisons. The associations in this important work might serve as a reference for future targeted-studies on brain lateralization.

eLife Assessment

This study used deep neural networks (DNN) to reconstruct voice information (viz., speaker identity), from fMRI responses in the auditory cortex and temporal voice areas, and assessed the representational content in these areas with decoding. A DNN-derived feature space approximated the neural representation of speaker identity-related information. The findings are valuable and the approach solid, yielding insight into how a specific model architecture can be used to relate the latent spaces of neural data and auditory stimuli to each other.

eLife Assessment

Some delayed rectifier currents in neurons are formed by the combination of Kv2 and silent subunits, KvS. However, we lack the tools to identify these heteromeric channels in vivo. In this important study by the Sack group, the authors identify a pharmacological tool that can reveal the presence of KvS subunits as components of the delayed rectifier potassium currents in selected neurons. The experimental evidence presented in the manuscript is compelling and represents a significant advance that should be of interest to a wide community of neuroscientists and channel physiologists.

eLife Assessment

This important study combines EEG, neural networks and multivariate pattern analysis to show that real-world size, retinal size and real-world depth are represented at different latencies. The evidence presented is convincing and the work will be of broader interest to the experimental and computational vision community.

eLife Assessment

In their study, Cummings et al. provide a valuable advance in understanding the hierarchical regulation of tubulin polyglycylation, demonstrating that TTLL8 initiates monoglycylation which is a prerequisite for TTLL10-mediated polyglycylation. The evidence supporting these mechanistic insights is solid, relying on a compelling combination of purified biochemical assays, mass spectrometry, and microscopy. The work is further valued for revealing an unexpected crosstalk between polyglycylation and polyglutamylation that ensures a balanced post-translational modification landscape for proper cilia function.

eLife Assessment

Bowler et al. present a software/hardware system for behavioral control of navigation-based virtual reality experiments, particularly suited for pairing with 2-photon imaging but applicable to a variety of techniques. This system represents a valuable contribution to the field of behavioral and systems neuroscience, as it provides a standardized, easy to implement, and flexible system that could be adopted across multiple laboratories. The authors provide compelling evidence of the functionality of their system by reporting benchmark tests and demonstrating hippocampal activity patterns consistent with standards in the field. This work will be of interest to systems neuroscientists looking to integrate flexible head-fixed behavioral control with neural data acquisition.

eLife Assessment

This important study combines convincing evolution experiments with molecular and genetic techniques to study how a genetic lesion in MreB that causes rod-shaped cells to become spherical, with concomitant deleterious fitness effects, can be rescued by natural selection. The detailed mechanistic investigation increases our understanding of how mreB contributes to cell wall synthesis and shows how compensatory mutations may reestablish its homogeneity.

eLife Assessment

This study presents a method for expressing single-stranded DNA fluorescent aptamers in E. coli using a retron-based strategy. The evidence supporting the successful expression and folding of DNA aptamers is solid, with clear demonstration of fluorescence after extraction, though the aptamers do not function in living cells. The method represents an important technical advance that will likely become standard for DNA aptamer expression in bacterial systems.

eLife Assessment

In this valuable study, Huffer et al posit that non-cold sensing members of the TRPM subfamily of ion channels (e.g., TRPM2, TRPM4, TRPM5) contain a binding pocket for icilin that overlaps with the one found in the cold-activated TRPM8 channel. After examining a body of TRP channel cryo-EM structures to identify the conserved site, this study presents convincing electrophysiological evidence supporting the presence of an icilin binding pocket within TRPM4. This study shows that icilin has modulatory effects on the TRPM4 channel and will be of direct interest to those working in the TRP-channel field, but it also has implications for studies of somatosensation, taste, as well as pharmacological targeting of the TRPM subfamily.

eLife Assessment

This fundamental research conducted a molecular comparison between smooth muscle cells and adjacent fibroblast cells within lung blood vessels affected by pulmonary arterial hypertension. The study identified distinct disease-related states in each cell type and provided deeper insights into their interactions and communication. While certain conclusions should be interpreted with caution due to inherent methodological limitations, the study's findings remain convincing and robust. This is supported by the use of advanced and complementary techniques, as well as the rare isolation of diseased lung blood vessel cells from the same donor, enabling direct comparison.

eLife Assessment

The authors have developed a valuable approach that employs cell-free expression to reconstitute ion channels into giant unilamellar vesicles for biophysical characterisation. The work is convincing and will be of particular interest to those studying ion channels that primarily occur in organelles and are therefore not amenable to be studied by more traditional methods.

eLife Assessment

This important work substantially advances our understanding of RNA structure analysis by introducing an innovative method that extends DMS probing to include guanosine residues, thereby enhancing our ability to detect complex tertiary interactions. The evidence supporting the conclusions is compelling, with detailed analyses demonstrating the method's capacity to differentiate structural contexts and improve RNA structure predictions. This work will be of broad interest to RNA structural biology, biochemistry, and biophysics researchers.

eLife Assessment

This study presents valuable findings, based on solid methods, to link metabolic dysfunction in Wilson's disease to immune cell dysregulation and poor cholecystitis outcomes. The integration of clinical data and single-cell analyses highlights NK cell exhaustion as a key factor, offering insights with potential therapeutic implications. The work will be of interest to colleagues in inflammatory and metabolic diseases.

eLife Assessment

This fundamental work provides new mechanistic insight in regulation of PDGF signaling through splicing controls. The evidence is compelling to demonstrate functional involvement of Srsf3, an RNA binding protein to this new and interesting mechanism. The work will be of broad interest to developmental biologists in general and molecular biologists/biochemists in the field of growth factor signaling and RNA processing.

eLife assessment

The authors combined molecular dynamics simulations and experiments to study the role of ATP as a hydrotrope of protein aggregates. The topic is of major current interest and thus the study potentially makes an important contribution to the community. With the revised version, the level of evidence is considered generally solid, although there remains concern regarding the unusually high ATP concentration used in the simulation.