Subject: PLOS Biology Volume 16(9) September 2018 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

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New Articles in PLOS Biology

PUBLISHED: September 01, 2018 to September 28, 2018

Research Matters

To fight tuberculosis, fund basic research

As the United Nations General Assembly meets for its first high-level meeting on tuberculosis (TB) on September 26, this Research Matters article urges the need to consider basic research as an essential component of any future anti-TB strategy.

Essays

Harnessing positive species interactions as a tool against climate-driven loss of coastal biodiversity

Amelioration of environmental conditions by habitat-forming species can sustain the persistence of stress-sensitive species under increasingly adverse climates. Times are ripe for active use of habitat-forming populations to halt the climate-driven crisis of biodiversity.

The Sacred Ibis debate: The first test of evolution

This Essay describes how early ideas about evolution focused on the remarkable sacred ibis mummies of ancient Egypt; the results of a pre-Darwinian showdown between two giants of biology ' Lamarck and Cuvier ' set back the acceptance of evolution for decades to come.

Perspectives

Science without publication paywalls: cOAlition S for the realisation of full and immediate Open Access

In this Perspective, a group of national funders, joined by the European Commission and the European Research Council, announce plans to make Open Access publishing mandatory for recipients of their agencies' research funding.

Carnivore conservation needs evidence-based livestock protection

Evidence that interventions to protect livestock from large carnivores are effective is lacking, as identified by four independent teams; this Perspective article calls on a coalition of scientists to build such a dataset to facilitate carnivore conservation.

Science in the fight to uphold the rights of children

In this Perspective article, Peter Hotez and Arthur Caplan argue that scientists can have important and new roles in limiting recent declines in the rights of children across America (and in some European countries), especially in the areas of child poverty, low vaccination rates, gun violence, and disease and malnutrition due to climate change.

Haves and have nots must find a better way: The case for open scientific hardware

In 2013 Eve Marder raised concerns about research equipment availability and the divide between well-funded and poorly-funded labs. Five years later, with the issue still present, this Perspective article discusses a possible solution: the wide adoption of Open Source Hardware, not only to reduce the divide, but also to make research and education more robust, reliable and widespread.

Community Page

EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

This Community Page article presents EukRef, which brings together experts in diverse eukaryotic lineages to curate 18S rDNA data using phylogenetic methods with the goal of assembling a reference database spanning the entire eukaryotic tree of life.

Meta-Research Article

Large-scale investigation of the reasons why potentially important genes are ignored

By characterizing the reasons for gene-specific bias in the number of publications (and extent of funding) per gene, this study explains why biomedical research collectively ignores potentially important genes.

Research Articles

Hook length of the bacterial flagellum is optimized for maximal stability of the flagellar bundle

Flagella are the motility organelles of many bacteria. This study shows that bacteria control the optimal length of the flagellar hook structure to nanometer tolerances in order to maximize their motility performance.

Copper-dependent amino oxidase 3 governs selection of metabolic fuels in adipocytes

A study of adipocytes shows that copper is essential for balancing their sugar and lipid utilization; this is mediated by the activation of the copper-dependent amino-oxidase AOC3/SSAO.

Transcriptional outcomes and kinetic patterning of gene expression in response to NF-kappa B activation

The NF-kappa B family of transcription factors regulate cellular responses to a wide variety of environmental cues. This study reveals a time-dependent cascade of NF-kappa B-dependent gene expression in activated B lymphoma cells and identifies mechanisms by which these unique kinetic patterns are established.

Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast

The previously uncharacterized yeast protein Lso2 and its human ortholog CCDC124 bind to a universally conserved region of the ribosome; Lso2 is required in yeast for global translation during recovery from extended starvation.

Protein kinase A negatively regulates Ca2+ signalling in Toxoplasma gondii

The cAMP-dependent protein kinase A enables human parasite Toxoplasma gondii to establish a replicative niche in newly invaded host cells by switching off calcium signaling.

Vocal practice regulates singing activity'dependent genes underlying age-independent vocal learning in songbirds

A vocal learner, the zebra finch, "actively" controls its vocal learning plasticity through self-motivated vocal practice; during the critical period of song learning, vocal practice influences the expression dynamics of activity-dependent, but not age-related genes.

Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones

Host chaperones enable the influenza virus to evade the host's innate immune response by ameliorating the biophysically deleterious consequences of adaptive mutations (such as the nucleoprotein Pro283 variant that strengthened the 1918 pandemic strain).

Jagged1/Notch2 controls kidney fibrosis via Tfam-mediated metabolic reprogramming

Notch pathway activation (and specifically the interaction between Jagged1 ligand and Notch2 receptor) in kidney tubules plays an important role in the development of kidney fibrosis though metabolic reprogramming.

Aging alters the epigenetic asymmetry of HSC division

Epigenetic, transcriptomic and functional assays of paired daughter cells reveal a change in the asymmetry of hematopoietic stem cell division upon aging and a link between cellular and epigenetic polarity in determining the outcome of division.

Evolutionary emergence of infectious diseases in heterogeneous host populations

A combination of new theoretical predictions and experiments using CRISPR-resistant bacteria and their lytic phages shows that the composition of the host population can limit the evolutionary emergence of pathogens.

Midgut-derived neuropeptide F controls germline stem cell proliferation in a mating-dependent manner

A study using the fruit fly Drosophila melanogaster reveals novel insights into how a gut-derived systemic factor, neuropeptide F, couples mating stimulus to germline stem cell behavior through interorgan communication.

The neurodevelopmental precursors of altruistic behavior in infancy

A study of infants provides novel insights into the early development of human altruism by showing that responsiveness to seeing others in distress at 7 months of age predicts altruistic helping behavior at 14 months.

mDia1/3 generate cortical F-actin meshwork in Sertoli cells that is continuous with contractile F-actin bundles and indispensable for spermatogenesis and male fertility

The interaction between developing sperm and somatic Sertoli cells is regulated by an mDia1/3-dependent cortical F-actin meshwork and actomyosin bundles in Sertoli cells, and is indispensable for sperm morphogenesis and male fertility.

EpCAM ectodomain EpEX is a ligand of EGFR that counteracts EGF-mediated epithelial-mesenchymal transition through modulation of phospho-ERK1/2 in head and neck cancers

A clinical and molecular study uncovers a novel signaling crosstalk between EGFR and EpCAM that determines the strong disparities in clinical outcome among head and neck carcinoma patients.

Multiple origins and modularity in the spatiotemporal emergence of cerebellar astrocyte heterogeneity

Clonal and proliferation analyses performed in vivo explain the developmental rules through which the different types of astrocytes are generated in the cerebellum.

Short Reports

The human lymph node microenvironment unilaterally regulates T-cell activation and differentiation

Human T cells show restricted activation in the presence of fibroblastic reticular cells from secondary lymphoid organs, showing an important role for the lymph node microenvironment. This suppression could be reversed in live tissue slices by using a cocktail of specific inhibitors.

Morphology of mitochondria in spatially restricted axons revealed by cryo-electron tomography

Cryo-electron tomography and 3D reconstructions reveal unprecedented constriction and possible membrane remodeling of mitochondria in the extremely restricted space (~80 nm) afforded by axonal processes.

Anthropoid primate'specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length

The expression of a placental protein associated with human birth timing is uniquely regulated in anthropoid primates by the insertion of a THE1B endogenous retroviral element; transgenic mice bearing the human insertion have prolonged gestation.

Manipulating the revision of reward value during the intertrial interval increases sign tracking and dopamine release

Simply lengthening the time between trials to allow for additional value revision increases both the attractiveness of conditioned stimuli that predict reward and the associated dopamine prediction error signals.

Methods and Resources

Refined RIP-seq protocol for epitranscriptome analysis with low input materials

This paper describes refined version of the MeRIP-seq protocol, allowing the detection of the N6-methyladenosine RNA modification (epitranscriptome profiling) in samples where limited material is available, such as patient tumors.

Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites

A combination of proximity biotinylation-based proteomics and machine learning improves the accuracy of the apicoplast proteome in the malaria parasite Plasmodium, identifying proteins of potential biological and therapeutic interest.

Formal Comments

A cautionary note for claims about the microbiome's impact on the "self"

This Formal Comment questions a claim made in a recent Essay that the microbiome affects our concept of 'self,' and challenges the resulting call for 'microbial humanities.'

The microbiome and the human: A reply to Parke and colleagues

This response to Parke et al. reasserts that microbiome research can open new research opportunities and collaboration across disciplinary boundaries such as the natural sciences and the humanities.

The slings and arrows of comparative linguistics

In this Formal Comment the authors respond to objections to their previous Essay, reiterating that comparative linguistics is not an easy undertaking.

Corrections

Correction: Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Correction: Comparative genomics and the nature of placozoan species

Correction: WRAP53 Is Essential for Cajal Body Formation and for Targeting the Survival of Motor Neuron Complex to Cajal Bodies

Correction: LKB1 Regulates Mitochondria-Dependent Presynaptic Calcium Clearance and Neurotransmitter Release Properties at Excitatory Synapses along Cortical Axons

Correction: Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock

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