Subject: PLOS Biology Volume 16(12) December 2018 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

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New Articles in PLOS Biology

PUBLISHED: December 01, 2018 to December 31, 2018

Essay

Analysis validation has been neglected in the Age of Reproducibility

Just as we do controls for experiments we should all do controls for data analysis ' this is easy to say but requires dedication to implement. This Essay explains the need for analysis validation and provides specific suggestions for how to get started.

Community Page

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

This Community Page article presents a communication standard for the provenance of high-throughput sequencing data; a BioCompute Object (BCO) can serve as a history of what was computed, be used as part of a validation process, or provide clarity and transparency of an experimental process to collaborators.

Research Articles

Neural responses to natural and model-matched stimuli reveal distinct computations in primary and nonprimary auditory cortex

Synthetic sounds engineered to produce the same response as natural sounds in a computational model of auditory cortex provide evidence of hierarchical computation.

Gut microbiota diversity across ethnicities in the United States

Abundance and taxonomic composition of members of the gut microbiome are consistently different between ethnicities in American adults; these differences are reproducible across study populations, and could result from sociocultural, dietary and genetic factors, potentially mediating health disparities.

Widespread winners and narrow-ranged losers: Land use homogenizes biodiversity in local assemblages worldwide

Narrow-ranged species decline while widespread species increase in human-disturbed land uses; all else being equal, this will lead to more homogeneous ecological communities in disturbed land uses, with potential implications for conservation and ecosystem functioning.

Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration

A study of bacterial adaptation to the vertebrate gut challenges assumptions about the primary importance of the intra-host environment, instead highlighting the significance of bacterial immigration and transmission in persistent host-microbe interactions.

Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver

A genome-wide study identifies those gene regulatory regions which in the liver are controlled by feeding, and reveals that glucocorticoid and insulin signaling pathways cooperatively regulate post-prandial repression of gene expression.

Sex-specific dominance reversal of genetic variation for fitness

Experiments with seed beetles show that opposite alleles at polymorphic loci encoding fitness are dominant in heterozygous males versus females; this enables sexually antagonistic selection to maintain genetic variation for fitness.

Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to Pseudomonas syringae

Network-centric integrative analyses of immunity-associated signal transduction, using tomato plants infected with the bacterium Pseudomonas syringae, reveal rules of molecular communication between plants and pathogens governing resistance and susceptibility phenotypes.

Genome-wide functional analyses of plant coiled'coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity

Once a pathogen is detected, plants use the N-terminal coiled-coil domains of nucleotide-binding leucine rich receptors (NLRs) to trans-activate other immune receptors and form heteromeric complexes that initiate defense.

Parental neural responsivity to infants' visual attention: How mature brains influence immature brains during social interaction

This study examines how information is shared between infants and parents by using dual EEG recording during joint play. The results suggest that where the parent is more neurally responsive, the infant is more attentive.

CD71+VISTA+ erythroid cells promote the development and function of regulatory T cells through TGF-beta

This study reveals how a class of immature red blood cells ' erythroid cells expressing the markers CD71 and VISTA ' promote the production of regulatory T cells in the newborn.

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

A fluorescent reporter system reveals that copy number variants (CNVs) are repeatedly generated and selected during the early stages of adaptive evolution, resulting in initially predictable dynamics with thousands of independent CNV-containing lineages competing within populations.

Non-proteolytic ubiquitin modification of PPARgamma by Smurf1 protects the liver from steatosis

Non-proteolytic ubiquitination of peroxisome proliferator-activated receptor ? (PPAR?) by the E3 ligase Smurf1 suppresses its transcriptional activity and plays a critical role in preventing abnormal accumulation of fatty acid in the liver.

MEKK3 coordinates with FBW7 to regulate WDR62 stability and neurogenesis

The protein WDR62, genetic defects in which cause microcephaly in humans, interacts with the kinase MEKK3 and E3 ubiquitin ligase FBW7 to regulate JNK signaling and maintenance of neural progenitor cells in the developing brain.

Lrrk promotes tau neurotoxicity through dysregulation of actin and mitochondrial dynamics

The Parkinson's disease-associated protein LRRK2 controls actin dynamics by directly severing actin filaments and thereby promoting mitochondrial fission. Altering LRRK2 levels enhances tau toxicity via its effect on F-actin and Drp1 localisation.

An opposing function of paralogs in balancing developmental synapse maturation

A balance between the opposing functions of PSD-93 and PSD-95 sets the proper pace for silent synapse maturation, which governs the duration of critical periods and the refinement of perception in the developing visual cortex.

Podoplanin+ tumor lymphatics are rate limiting for breast cancer metastasis

Identification of proliferating lymphatic endothelial cells and their depletion using genetically engineered podoplanin-deficient mice shows that lymphangiogenesis is rate-limiting for breast cancer metastasis.

Catalytic mechanism of the tyrosinase reaction toward the Tyr98 residue in the caddie protein

The cryo-trapped crystal structures of tyrosinase in a complex with its "caddie" protein reveal structural insight into the catalytic mechanism of tyrosinase, the rate-limiting enzyme in the production of melanin.

Short Reports

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

The chromatin environment of CRISPR-Cas9 target sites affects the rate at which mutations accumulate, but not the types of mutation that arise or their frequency following prolonged exposure to Cas9.

Errors as a primary cause of late-life mortality deceleration and plateaus

Late-life mortality deceleration and plateaus have variously been explained through evolution, selection, heterogeneity and even the ending of ageing. However, this study shows that observed errors predict and simulated errors generate these patterns.

Methods and Resources

Direct visualization of single-molecule membrane protein interactions in living cells

A co-immunoimmobilization assay allows direct visualization of transient protein-protein interactions at the single-molecule level in the membranes of living cells on the basis of the protein's intrinsic diffusivity.

Formal Comments

Reply to "Far away from the lamppost"

In this Formal Comment, the authors of the recent publication "Large-scale investigation of the reasons why potentially important genes are ignored" maintain that it can be read as an opportunity to explore the unknown.

Far away from the lamppost

This Formal Comment responds to a recent Meta-Research Article by identifying initiatives that are already in place for funding risky exploratory research that illuminate mysteries of the dark genome.

Plane inclinations: A critique of hypothesis and model choice in Barbi et al

This Formal Comment raises fundamental issues regarding the apparent late-life mortality plateau proposed in Science by Barbi et al. 2018, and on the nature of documentary birth and death certificate evidence in general.

Hypothetical errors and plateaus: A response to Newman

This Formal Comment responds to an article by Saul Newman, and maintains that data errors do not explain mortality plateaus.

Correction

Correction: Brain-Computer Interface-Based Communication in the Completely Locked-In State

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