Subject: PLOS Biology Volume 17(11) November 2019 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

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New Articles in PLOS Biology

PUBLISHED: November 01, 2019 to November 29, 2019

Essays

Framing the discussion of microorganisms as a facet of social equity in human health

What do microbes have to do with social equity? This Essay explores the argument that access to beneficial microorganisms is a facet of public health, and that health inequality may be compounded by inequitable microbial exposure.

Language evolution and complexity considerations: The no half-Merge fallacy

This Essay argues that the evolution of language cannot be as simple as prominent linguists Berwick and Chomsky have recently proposed, showing that the jump from the atomicity of Merge to a single-mutation scenario is not valid, and therefore cannot be used as justification for theory of language evolution along those lines.

Perspectives

Host-associated microbiomes drive structure and function of marine ecosystems

The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. This Perspective article outlines research priorities to strengthen our current knowledge of host-microbiome interactions, to help predict responses to anthropogenic stressors and to inform future management strategies.

Neuroimaging-based prediction of mental traits: Road to utopia or Orwell?

Advances in machine learning on neuroimaging data have opened up the possibility of objectively predicting individual traits like intelligence, personality, or clinical risks from brain scans. This Perspective article discusses the methodological and ethical challenges arising from these advances.

Development, environmental degradation, and disease spread in the Brazilian Amazon

This Perspective article maintains that a development model for the Amazon must be bold, creative, carefully planned, and sustainable, explicitly acknowledging the importance of public health in reinforcing economic development, environmental protection, and land use change.

Community Pages

Boosting natural history research via metagenomic clean-up of crowdsourced feces

Natural history research is in crisis and non-charismatic species are increasingly ignored; this Community Page article argues and demonstrates that shotgun sequencing of serendipitously obtained faecal samples could reverse this trend for 1000 mammal species within 10 years.

Building de novo cryo-electron microscopy structures collaboratively with citizen scientists

This Community Page article demonstrates that microscopists can now collaborate with the players of the computer game Foldit to generate thorough high-quality de novo structural models; this development could greatly speed the generation of excellent Cryo-EM structures when used as a complement to current methods.

Meta-Research Article

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias

Analysis of numerous RNA-seq datasets reveals a recurrent sample-specific length bias that causes frequent false positive calls by gene-set enrichment analyses, leading to functional misinterpretation of the data. Its removal requires methods that allow the integration of gene length as sample-specific covariate.

Research Articles

CEH-60/PBX regulates vitellogenesis and cuticle permeability through intestinal interaction with UNC-62/MEIS in Caenorhabditis elegans

The evolutionarily conserved interaction of two Hox cofactors (PBX and MEIS orthologues) in the nematode Caenorhabditis elegans controls the production of yolk and renders the animal's surface coat impermeable to small molecules.

Loss of MYO5B expression deregulates late endosome size which hinders mitotic spindle orientation

Loss of the recycling endosome-associated motor protein myosin Vb causes the formation of giant late endo-lysosomes; these in turn hinder the orientation of the mitotic spindle and chromosome segregation. Deregulated endosome size thus hampers faithful cell division.

The role of selection and evolution in changing parturition date in a red deer population

Adaptive genetic evolution and phenotypic plasticity both contribute to a two-week advancement of birth dates earlier in spring in a deer population subject to temperature warming over four decades.

Hypothalamic miR-30 regulates puberty onset via repression of the puberty-suppressing factor, Mkrn3

The microRNA miR-30 suppresses the expression of Mkrn3 (a known repressor of puberty) in the hypothalamus by binding to a highly conserved region of its 3' untranslated region, representing a novel mechanism for finely modulating the tempo of puberty.

The intragenus and interspecies quorum-sensing autoinducers exert distinct control over Vibrio cholerae biofilm formation and dispersal

The pathogenic bacterium Vibrio cholerae uses both kin and nonkin quorum-sensing autoinducer molecules to control its biofilm life cycle; this study shows that each autoinducer plays a unique role in regulating biofilm formation and dispersal.

Mangroves reduce the vulnerability of coral reef fisheries to habitat degradation

Despite wide-ranging negative effects of coral reef degradation on reef communities, hope might exist for reef-associated predators that use nursery habitats. This study uses size-based ecosystem models of coral reefs to assess the effects of the presence and absence of mangrove nurseries.

Transcriptional regulatory divergence underpinning species-specific learned vocalization in songbirds

In two closely related songbird species with distinct species-specific songs, divergence in transcriptional regulation (via both cis- and trans-regulatory changes) alters the expression of approximately 10% of the genes transcribed in specific brain regions involved in learned vocal production.

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

This study shows that plants' response to phosphate starvation has more influence on plant microbiota than does the phosphate concentration itself; these changes are not necessarily beneficial for the plant, and can even exacerbate the phosphate starvation.

Type I interferon limits mast cell'mediated anaphylaxis by controlling secretory granule homeostasis

This study reveals a novel role for type I interferon in mast cell homeostasis; spontaneous type I interferon signaling regulates the biogenesis of secretory granules and maturation of mast cells via STAT1 and STAT3, and limits the onset of systemic anaphylaxis.

Local vulnerability and global connectivity jointly shape neurodegenerative disease propagation

Many neurodegenerative diseases, including Parkinson's disease, may be prion illnesses characterized by propagation of abnormal proteins through the brain. An agent-based model informed by infectious disease epidemiology recapitulates the distribution of atrophy in Parkinson's disease, suggesting that connectomics and local gene expression interact to shape the spatial progression of the disease in the brain.

Parental breeding age effects on descendants' longevity interact over 2 generations in matrilines and patrilines

Why do individuals within populations vary enormously in mortality risk and longevity? A study of neriid flies shows that paternal age can affect offspring longevity as strongly as maternal age does, and that breeding age effects can interact over two generations in both matrilines and patrilines.

Loss of adenomatous polyposis coli function renders intestinal epithelial cells resistant to the cytokine IL-22

The adenomatous polyposis coli (APC) gene is mutated in 85% of colorectal cancers. This study shows that when APC is mutated in murine intestinal epithelial cells, they no longer respond to IL-22, a cytokine that is considered important for colorectal cancer progression; this has implications for IL-22 as a therapeutic target for cancer treatment.

Tissue tropism and transmission ecology predict virulence of human RNA viruses

Comparative analysis using machine learning shows that specificity of tissue tropism and transmission biology can act as predictive risk factors for the virulence of human RNA viruses.

A specific type of insulin-like peptide regulates the conditional growth of a beetle weapon

Animals can evolve sexually selected weapons and ornaments as the exaggerations of specific body parts, often linked to nutritional status. This study shows that in the broad-horned flour beetle, one insulin-like peptide (among the five encoded by their genome) was found to specifically regulate weapon growth. Functional diversification of ligand peptides may account for the ecological divergence of sexually selected exaggerated traits.

Short Reports

Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics

A simple mathematical framework that defines the rates of sampling and phenotypic testing necessary to efficiently detect novel resistance variants and thus maintain the sensitivity of genotype-based antimicrobial resistance diagnostics.

Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity

A single-cell transcriptomic study of the immune system of the cancer-resistant naked mole-rat reveals that this animal lacks natural killer (NK) cells, thought to be crucial for cancer resistance. In contrast to dramatically expanded NK cell receptor and MHC-I gene families in human and mouse genomes, the naked mole-rat genome lacks the expansion of NK cell receptor genes and only has two MHC-I genes.

Resolving noise'control conflict by gene duplication

Gene expression tuning is limited by a conflict between expression plasticity and expression noise. This study shows that duplicated genes can resolve this conflict by functioning as one unit with expression control that is both environmentally responsive and low-noise, revealing a new adaptive benefit of duplication.

Methods and Resources

Data-driven analyses of motor impairments in animal models of neurological disorders

This study demonstrates that a state-of-the-art neural network can provide automated scoring of motor deficits with an accuracy equivalent to that of human experts and has the potential to teach us to develop more-sensitive behavioral tests.

GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors

G protein-coupled receptors (GPCRs) are the most commonly used family of drug targets in most disease settings other than cancer. This work reveals that GPCRs (including many which are already targets of approved drugs) show elevated expression in solid tumors. Expression of certain GPCRs appears to have prognostic relevance, and many GPCRs undergo widespread mutation and copy number variation.

Formal Comment

All or nothing: No half-Merge and the evolution of syntax

In response to an Essay by Martins and Boeckx, this Formal Comment by Berwick and Chomsky argues that a crucial step in the evolution of human language can now be pinpointed to the appearance of a single new, but simple, computational operation.

Corrections

Correction: ADAMTS5 Is a Critical Regulator of Virus-Specific T Cell Immunity

Correction: Song playbacks demonstrate slower evolution of song discrimination in birds from Amazonia than from temperate North America

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