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New Articles in PLOS Biology

PUBLISHED: October 01, 2021 to October 31, 2021

Perspective

Wildlife must be protected from crime and trade for the sake of public and planetary health

This Perspective article argues that as we struggle to combat climate change, with the potential loss of a million species and increasing exposure to thousands of new viruses that could spill over from wildlife to humans (as SARS-CoV-2 likely did), it is time to change course.

Primer

AI delivers Michaelis constants as fuel for genome-scale metabolic models

Michaelis constants (Km) are essential to predict the catalytic rate of enzymes but are not widely available. This Primer explores a new study which uses artificial intelligence (AI) to accurately predict Km proteome-wide, potentially paving the way for dynamic, genome-wide modelling of metabolism.

Essays

A field guide to cultivating computational biology

Do you want to attract computational biologists to your project or to your department? Despite the major contributions of computational biology, those attempting to bridge the interdisciplinary gap often languish in career advancement, publication, and grant review. Here, sixteen computational biologists around the globe present "A field guide to cultivating computational biology," focusing on solutions.

Essays

The microbiome impacts host hybridization and speciation

Microbial symbiosis and speciation profoundly shape the composition of life's biodiversity, but how do endosymbionts and microbial communities affect animal hybridization and vice versa? This essay on studies of the microbiome and postmating isolation argues for a long-lasting, intense phase of study on merging microbiology and host hybridization.

Meta-Research Article

Tapping into non-English-language science for the conservation of global biodiversity

A survey of 419,680 peer-reviewed papers in 16 languages reveals that non-English-language studies can expand geographical (by 12-25%) and taxonomic (by 5-32%) coverage of English-language evidence on the effectiveness of biodiversity conservation interventions, especially in biodiverse regions.

Research Articles

Corollary discharge enables proprioception from lateral line sensory feedback

Animals modulate sensory processing in concert with motor actions. A study of the corollary discharge in zebrafish reveals that it modulates the sensitivity of the lateral line during swimming to prevent sensor adaptation and maintain the high-quality feedback necessary for kinematic control.

Research Articles

Dynamic large-scale connectivity of intrinsic cortical oscillations supports adaptive listening in challenging conditions

This study investigates how intrinsic neural oscillations, acting in concert, tune into attentive listening. Using electroencephalography signals collected from people in a dual-talker listening task, the authors find that network connectivity of frontoparietal beta and posterior alpha oscillations is regulated according to the listener's goal.

Research Articles

SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA

The packaging of the SARS-CoV-2 genome is mediated by the nucleocapsid (N) protein; this study shows that the N protein forms liquid condensates with viral genomic RNA and identifies small molecules that alter these condensates.

Research Articles

Individual bacteria in structured environments rely on phenotypic resistance to phage

Bacteriophages represent a promising avenue to overcome the current antibiotic resistance crisis, but evolution of phage resistance remains a concern. This study shows that in the presence of spatial refuges, genetic resistance to phage is less of a problem than commonly assumed, but the persistence of genetically susceptible bacteria suggests that eradicating bacterial pathogens from structured environments may require combined phage-antibiotic therapies.

Research Articles

Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation

Plasmids impose fitness costs on their hosts, but the underlying mechanisms have been unclear. This study shows that specific gene interactions, rather than general properties of plasmids such as their size, are principally responsible for the burden plasmids impose. The propensity of such conflicts to be ameliorated by single compensatory mutations may help to explain why plasmids are so widespread.

Research Articles

The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity

Derived from phages of the gut microbiome, this study describes a CRISPR-Cas9 inhibitor with an unexpected mechanism; instead of binding Cas9 itself, this "anti-CRISPR" relaxes plasmid DNA and enables Cas9 evasion, suggesting that DNA topology is an underappreciated battleground in phage-bacterial conflicts.

Research Articles

Understanding degraded speech leads to perceptual gating of a brain stem reflex in human listeners

Understanding speech in background noise is critical to human communication. This study highlights a critical role for neural feedback circuits that modulate the activity of the inner ear, enabling effective listening to degraded speech.

Research Articles

The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis

Male germ cell production is a metabolically-driven and apoptosis-prone process. This study shows that MLX, a nutrient-sensing transcription factor and member of the MYC network, is not required for embryonic development but is necessary for male murine fertility and male germ cell tumor survival; loss of MLX results in altered metabolism, activation of stress pathways and germ cell apoptosis in the testes.

Research Articles

The Plasmodium NOT1-G paralogue is an essential regulator of sexual stage maturation and parasite transmission

Malaria parasites face two bottlenecks in their life cycle: their two transmission events. This study shows that Plasmodium has taken the unorthodox approach of duplicating the gene for the NOT1 RNA regulatory scaffold protein, allowing it to dedicate one paralog to functions that are essential for transmission from mammalian hosts to the mosquito vector.

Research Articles

Inhibition of protein N-myristoylation blocks Plasmodium falciparum intraerythrocytic development, egress and invasion

Understanding the essential factors needed for malaria parasite development could help us find new therapeutic targets. This study reveals that N-myristoylation is a posttranslational modification of proteins essential for the parasites' growth and their invasion of red blood cells.

Research Articles

On the optimality of the enzyme'substrate relationship in bacteria

This study shows that in E. coli, the cellular mass of each metabolite approximately equals the combined mass of the free enzymes waiting to consume it; this simple relationship arises from the optimal utilization of cellular dry mass, and quantitatively describes available experimental data.

Short Reports

Dopamine, sleep, and neuronal excitability modulate amyloid-beta 'mediated forgetting in Drosophila

One of the early hallmarks in Alzheimer's disease is increased forgetting. This study shows that restricted expression of amyloid beta in the memory center of fruit flies causes enhanced forgetting without affecting the ability to learn; forgetting is caused by increased excitability and can be restored with drugs, increased sleep or modulation of dopamine signalling.

Short Reports

Spatial gene expression maps of the intestinal lymphoid follicle and associated epithelium identify zonated expression programs

The intestine is lined with isolated lymphoid follicles that facilitate sampling of luminal antigens to elicit immune responses. This study combines spatial transcriptomics and single molecule transcript imaging to identify spatially localized cellular states in intestinal follicles and their associated epithelium.

Short Reports

Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction

The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs and long-term physiographic changes. This phylogenetic natural history study offers new insights into the evolution of snake ecological diversity after the end-Cretaceous mass extinction, as they took advantage of these new opportunities.

Short Reports

Photophysiological cycles in Arctic krill are entrained by weak midday twilight during the Polar Night

This study shows that ambient light cycles set an internal rhythm that controls visual sensitivity of Arctic krill during the Polar Night ' the darkest part of the year, when the sun remains below the horizon all day. This demonstrates that biologically relevant photoperiods can be achieved during this time of "midday twilight".

Short Reports

Pinging the brain with visual impulses reveals electrically active, not activity-silent, working memories

Visual pinging of the brain triggers EEG responses selective to unattended memories by enhancing active neural signals, not by reactivating activity-silent traces as previously proposed. This finding questions key evidence for the activity-silent theory of working memory.

Methods and Resources

Deep learning allows genome-scale prediction of Michaelis constants from structural features

To understand the action of an enzyme, we need to know its affinity for its substrates, quantified by Michaelis constants, but these are difficult to measure experimentally. This study shows that a deep learning model that can predict them from structural features of the enzyme and substrate, providing KM predictions for all enzymes across 47 model organisms.

Methods and Resources

RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family

Reference datasets help to define canonical biological features and are essential for benchmarking studies. This study presents RefPlantNLR, a comprehensive reference dataset of 481 experimentally validated NLR immune receptors from 31 genera of flowering plants.

Methods and Resources

A phylogenomic framework for charting the diversity and evolution of giant viruses

Giant viruses have transformed our understanding of viral complexity, but we lack a framework for examining their diversity in the biosphere. This study presents a phylogenomic resource for charting the diversity, ecology, and evolution of giant viruses.

Corrections

Correction: Social Opportunity Produces Brain Changes in Fish

Corrections

Correction: Dilp-2'mediated PI3-kinase activation coordinates reactivation of quiescent neuroblasts with growth of their glial stem cell niche

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