Subject: PLOS Biology Volume 16(7) July 2018 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

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New Articles in PLOS Biology

PUBLISHED: July 01, 2018 to July 31, 2018

Research Matters

Species in ecosystems and all that jazz

This Research Matters article suggests that studying how species produce ecological functions can be like watching jazz musicians improvise as they respond and adapt to one another to create their music.

Perspectives

Sometimes you're the scooper, and sometimes you get scooped: How to turn both into something good

PLOS Biology has a new complementary research policy that leverages "scooped" papers to address the reproducibility crisis. This Perspective article presents the experience of the scooper and scoopee for the first paper published under this policy.

The next generation of natural history collections

This Perspective article proposes that new approaches to collecting, digitizing, processing and analyzing natural history specimens can open new research opportunities and collaboration across disciplinary boundaries.

Community Pages

Strength in numbers: Collaborative science for new experimental model systems

The lack of diverse model microorganisms restricts our capacity to explore and understand cellular life. This Community Page article maintains that through coordinated, collaborative effort significant advancements can be made to this and other large challenges in biology.

Digital open science'Teaching digital tools for reproducible and transparent research

This Community Page article describes a new graduate course that highlights essential methods for transparent and reproducible research and provides adaptable open educational resources for integration into graduate curricula.

Research Articles

Nonmonotonic recruitment of ventromedial prefrontal cortex during remote memory recall

A neuroimaging study reveals that the human ventromedial prefrontal cortex (vmPFC) has an unexpected time-dependent temporal profile of engagement during the recall of remote autobiographical memories, whereby vmPFC engagement subsides after one year but returns for memories older than two years.

A revised understanding of Tribolium morphogenesis further reconciles short and long germ development

Fluorescent live imaging of embryogenesis in the beetle Tribolium castaneum shows that many cells previously thought to be extraembryonic actually form large parts of the embryo.

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria

The identification of gut-colonizing bacteria from wild Drosophila melanogaster helps us to understand interactions between fruit flies and their gut microbiota in an ecological context and enables the study of microbial gut colonization in this key model organism.

p38alpha blocks brown adipose tissue thermogenesis through p38delta inhibition

A new study unexpectedly reveals that the protein kinase p38alpha controls brown fat thermogenesis by inhibiting the related kinase p38delta ; lack of adipose p38alpha increases thermogenesis, while lack of p38delta reduces thermogenic capacity.

Cholinergic-mediated coordination of rhythmic sympathetic and motor activities in the newborn rat spinal cord

How does the somatic motor system mobilize the autonomic nervous system so that muscle oxygenation can match the physiological demand? A study of rat spinal cord reveals intraspinal cholinergic coupling of somatic motoneurons and sympathetic preganglionic neurons.

Molecular mechanism of the tree shrew's insensitivity to spiciness

A point mutation in the TRPV1 channel of tree shrews enables them to eat chili peppers with impunity; the authors speculate that this may represent an adaptation to consuming the pepper plant Piper boehmeriaefolium, which grows in their native range and produces a capsaicin analogue.

The noisy basis of morphogenesis: Mechanisms and mechanics of cell sheet folding inferred from developmental variability

Analysis of the variability in the geometry of cell sheet folding during embryonic inversion in the green alga Volvox globator reveals details of the underlying processes driven by cell shape changes.

Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii

The mitochondrial F-type ATP synthase from the human pathogen Toxoplasma gondii consists of many novel subunits, evolutionarily conserved in related parasitic and free-living apicomplexan, chromerid and dinoflagellate species.

Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments

Particular regions on the actin monomer are responsible for the divergent actin dynamics of Plasmodium, which affect both actin filament incorporation and parasite motility.

Hair cell identity establishes labeled lines of directional mechanosensation

Mechanosensory neurons become directionally tuned via selective innervation of hair cells with unique planar polarizations. High-resolution videomicroscopy and experimentation on the zebrafish lateral line reveal a robust cellular algorithm that generates and maintains labeled lines of directional mechanosensation.

Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development

Ribosome profiling and evolutionary analysis suggest that upstream open reading frames (uORFs) evolve adaptively and modulate coding sequence translation during development of Drosophila fruit flies.

A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis

Fruit fly muscle can systemically control aging in distal tissues through the secretion of the cytokine Diedel; this cytokine, hijacked by viruses to influence host-virus interactions, dictates tissue aging by attenuating cell death responses.

Roles of fibronectin isoforms in neonatal vascular development and matrix integrity

The plasma form of fibronectin (pFN) exerts a critical role in safeguarding vascular function and organization; both pFN and vascular smooth muscle-derived fibronectin (cFN) guide postnatal vascular matrix organization.

Glucotypes reveal new patterns of glucose dysregulation

This study presents a method for "glucotype" classification from continuous glucose-monitoring data, enabling a more comprehensive assessment of an individual's glucose regulation, with the potential for early identification of those at risk of type 2 diabetes and/or cardiovascular disease.

Blindsight relies on a functional connection between hMT+ and the lateral geniculate nucleus, not the pulvinar

A neuroimaging study reveals the functional pathway that allows us to see' and respond to movement in the absence of conscious vision, after damage to the primary visual cortex.

Deconstructing the principles of ductal network formation in the pancreas

A combination of computational modelling and experimental study of the pancreas shows that glands do secretion "test-runs" during development, enabling the evolution of a ductal meshwork into a tree optimized for the delivery of secretory products.

Auditory midbrain coding of statistical learning that results from discontinuous sensory stimulation

How do we learn to recognize the person approaching us from the sound of their footsteps? A subcortical structure, the auditory midbrain, can remember sound regularities across temporally spread windows.

HIV induces synaptic hyperexcitation via cGMP-dependent protein kinase II activation in the FIV infection model

Over half of human immunodeficiency virus (HIV)-infected individuals suffer from HIV-associated neurocognitive disorders. This study shows that HIV and feline immunodeficiency virus (FIV) share a core mechanism for inducing synaptic hyperexcitation via aberrant activation of neuronal cGMP-dependent protein kinase II.

CCL20 triggered by chemotherapy hinders the therapeutic efficacy of breast cancer

Production of the chemokine CCL20 is triggered by taxane chemotherapy of "triple-negative" breast cancer, reducing its efficacy. CCL20 thereby acts as a biomarker to predict the efficacy of chemotherapy and as a therapeutic target to improve taxane-sensitivity.

Short Reports

The actin remodeling protein cofilin is crucial for thymic alpha beta but not gamma delta T-cell development

A study using knock-in mice expressing a non-functional form of the actin remodeling protein cofilin reveals that cofilin is differentially involved in the development of alpha beta versus gamma delta T cells.

A bidirectional relationship between sleep and oxidative stress in Drosophila

What is the function of sleep? In the case of fruit flies, this study identifies defense against oxidative stress as a function of sleep, and implicates oxidative stress in regulation of sleep.

In vitro'transcribed guide RNAs trigger an innate immune response via the RIG-I pathway

The introduction of in vitro transcribed guide RNAs, which are a necessary component of the CRISPR/Cas genome editing system, triggers an innate immune response in mammalian cells.

Mechanotransduction in talin through the interaction of the R8 domain with DLC1

A new talin-mediated mechanotransduction mechanism that involves a tumor suppressor protein regulates cellular processes downstream RhoA.

Differential aging of growth plate cartilage underlies differences in bone length and thus helps determine skeletal proportions

Bones at different anatomical locations vary dramatically in size and length. This study reveals that these differences in length are achieved in part by modulating the progression of aging in the cartilaginous growth plates.

Bile diversion, a bariatric surgery, and bile acid signaling reduce central cocaine reward

This study reveals that a new gut-based bariatric surgery chronically elevates systemic bile acid levels and reduces cocaine reward. These findings highlight the importance of determining whether bile acid analogs represent a viable pharmacological treatment for cocaine abuse.

Comparative genomics and the nature of placozoan species

Based on morphology alone, the phylum Placozoa appears to contain the single animal species Trichoplax adhaerens. Comparative genomics now tears apart this "species," allowing the description of the new Placozoan genus and species Hoilungia hongkongensis.

Maternal care boosted by paternal imprinting in mammals

A study of the imprinted gene Phlda2 in mice suggests that the father's genes can influence "motherly love" (nursing and grooming of pups) by manipulating signals from the placenta.

Methods and Resources

CellProfiler 3.0: Next-generation image processing for biology

The release of CellProfiler version 3.0 adds the ability to analyze images in three dimensions; this article describes the technological improvements that will make you want to upgrade.

Decoding the chromatin proteome of a single genomic locus by DNA sequencing

This paper describes Epi-Decoder; a barcode-based strategy to identify and quantify in an unbiased and systematic manner the proteome of individual genomic loci by DNA sequencing.

De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture

This study creates a genome assembly of unprecedented quality and contiguity for the fruit fly Drosophila miranda, a model for sex chromosome research; the assembly recovers notoriously difficult regions to assemble, including entire centromeres, and >100 Mb of the heterochromatic Y chromosome.

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