Subject: PLOS Biology Volume 16(4) April 2018 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

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New Articles in PLOS Biology

PUBLISHED: April 01, 2018 to April 30, 2018

Research Matters

Meta-research matters: Meta-spin cycles, the blindness of bias, and rebuilding trust

Meta-research may not be as click-worthy as a meta-pug ' a pug dog dressed up in a pug costume ' but it is crucial to understanding research, says Lisa Bero in this Research Matters article.

Perspectives

What exactly is N' in cell culture and animal experiments?

An analysis of published animal research revealed that nearly half of the studies (46%) had an artificially inflated sample size and invalid p-values because pseudoreplication was confused for genuine replication.

The paradoxical extinction of the most charismatic animals

Unbeknown to the public, their most charismatic species are highly threatened. This Perspective suggests that the constant presence of these animals in culture and marketing is deceptive and hinders our support for their conservation.

Biocuration: Distilling data into knowledge

This Perspective article maintains that biocuration plays an essential role in delivering knowledge resources that support and raise the value of life sciences research, providing resource-ready data, implementing standards, and incorporating contributions from the community.

Do non-native species contribute to biodiversity?

Biodiversity indicators focus on native species. Non-native species should also be included to better reflect what is observed in the field and the interests of non-biologists.

Ups and downs in early electron cryo-microscopy

In the early 1980s two young scientists working in the newly born field of electron cryo-microscopy made an apparently significant discovery that others failed to replicate. More than thirty years later, Nobel laureate Jacques Dubochet and his co-worker Erwin Knapek reunite to discuss what went wrong.

How measurement science can improve confidence in research results

While measurement science may seem perfunctory, its principles underpin almost all research. This Perspective article maintains that applying these principles can help ensure reproducibility and confidence in research results, and improve the return on our research investments.

Meta-Research Articles

Preclinical efficacy studies in investigator brochures: Do they enable risk'benefit assessment?

Analysis of data from institutional review boards shows that risk-benefit analysis for early-phase clinical trials is hindered by insufficient and potentially biased information about the supporting preclinical evidence provided in investigator brochures.

Laboratory mouse housing conditions can be improved using common environmental enrichment without compromising data

A large-scale study of two strains of lab mouse shows that the inclusion of nesting material and shelters as environmental enrichment does not impair the scientific assessment of a battery of 164 physiological parameters in mice.

The gender gap in science: How long until women are equally represented?

Text mining of more than 10 million academic papers identifies those fields of science that will retain a highly imbalanced gender ratio for many years to come.

Research Articles

Amino acid starvation sensing dampens IL-1beta production by activating riboclustering and autophagy

Activation of the amino acid deprivation-sensing pathway using Halofuginone effectively inhibits the production of interleukin-1beta , and protects mice from colitis by triggering GCN2-mediated riboclustering and autophagy.

Degenerate time-dependent network dynamics anticipate seizures in human epileptic brain

An intracranial electroencephalography study in human epileptic patients yields novel insights into how normal physiological brain activity undergoes the transition to seizures over a period of hours.

Semantic representation in the white matter pathway

A study using patient neuroimaging and behavioral data reveals novel mechanisms for representing object semantic information by white matter connection patterns between regions of the cortex.

Nitric oxide-mediated posttranslational modifications control neurotransmitter release by modulating complexin farnesylation and enhancing its clamping ability

Nitric oxide regulates synaptic transmission at the Drosophila neuromuscular junction by post-translationally modifying the fusion clamp protein complexin, thereby altering its farnesylation state and clamping ability.

Age is not just a number: Naive T cells increase their ability to persist in the circulation over time

Confronting a set of mathematical models with multiple novel and published datasets reveals that naive T cells slowly increase their ability to persist in the body the longer they survive.

Stable centrosomal roots disentangle to allow interphase centriole independence

A combination of cell fusion, genome editing and live cell imaging provides new insights into how the position and number of centrosomes is regulated in vivo.

The rostromedial tegmental nucleus is essential for non-rapid eye movement sleep

The tail of the ventral tegmental area of the midbrain, which is primarily composed of GABAergic neurons, regulates non-rapid eye movement sleep by modulating dopaminergic systems.

The ecology of immune state in a wild mammal, Mus musculus domesticus

A study of the immune ecology of wild house mice ' the same species as the lab mouse ' shows that their immune state is promoted by individuals' body condition and constrained by their age.

Organic cation transporter 1 (OCT1) modulates multiple cardiometabolic traits through effects on hepatic thiamine content

A study of mice lacking the organic cation transporter OCT1, a model of hepatic thiamine (vitamin B1) deficiency, provides a molecular understanding of how levels of thiamine and OCT1 contribute to metabolic traits observed in humans and mice.

Dectin-1/2'induced autocrine PGE2 signaling licenses dendritic cells to prime Th2 responses

The parasitic helminth Schistosoma mansoni primes T helper 2 responses via an interaction between helminth egg antigens and the host pattern recognition receptors Dectin-1 and Dectin-2, which triggers production of prostaglandin E2.

A noncanonical role for dynamin-1 in regulating early stages of clathrin-mediated endocytosis in non-neuronal cells

Live cell imaging reveals a non-canonical and isoform-specific role for dynamin-1, the fission GTPase, in regulating the assembly and maturation of clathrin-coated pits, and functioning as a nexus between signaling and endocytosis.

Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity

A study of the development of the nervous system of the nematode Caenorhabditis elegans reveals a novel function for a member of the basic helix-loop-helix family of transcription factors in controlling terminal neuron differentiation (rather than initial commitment to a neural fate).

Elasticity-based boosting of neuroepithelial nucleokinesis via indirect energy transfer from mother to daughter

During development of the cerebral cortex, when neural progenitor cells round up for mitosis, this mechanically triggers a spring-like recoiling mechanism that squeezes out daughter cell nuclei from the narrow cell-production space.

In vivo clonal analysis reveals spatiotemporal regulation of thalamic nucleogenesis

The thalamus is organized into many cellular aggregates called nuclei. Quantitative in vivo clonal analysis of thalamic progenitor cells reveals novel principles of stem cell division and differentiation that lead to the formation of this complex nuclear architecture.

The neural system of metacognition accompanying decision-making in the prefrontal cortex

The process of considering the outcome of a decision and whether a decision should be adjusted is known as metacognition. This study supports a construct for the functional architecture of the metacognition neural system in the prefrontal cortex, distinct from the neural system of decision-making itself.

Activation of temperature-sensitive TRPV1-like receptors in ARC POMC neurons reduces food intake

Intense exercise is known to transiently decrease appetite. A neurophysiological study reveals that this is because temperature-sensitive TRPV1-like receptors in the hypothalamus mediate.

Agent-specific learning signals for self'other distinction during mentalising

Computational neuroimaging shows that the human brain can distinguish beliefs attributed to "self" from those attributed to "other" by encoding fundamental learning variables in agent-specific (i.e. self versus other) activity patterns.

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

A comparative genomic analysis of bdelloid rotifers provides insights into the evolution of the structure and content of their genomes, revealing that they may be less unusual than previously thought.

Assessing the stability of polio eradication after the withdrawal of oral polio vaccine

Oral polio vaccine has been a highly effective tool for interrupting polio outbreaks. This study uses mathematical modelling of infection and transmission to ask whether the vaccine will remain effective long after polio eradication.

Polarization-resolved microscopy reveals a muscle myosin motor-independent mechanism of molecular actin ordering during sarcomere maturation

A novel imaging technique allows quantification of the growing molecular order of actin during assembly and maturation of sarcomeres in developing Drosophila flight muscles.

Mib1 prevents Notch Cis-inhibition to defer differentiation and preserve neuroepithelial integrity during neural delamination

The transient maintenance of Notch signaling in prospective neurons allows them to constrict their apical domain and seamlessly delaminate from the ventricular wall as they commit to differentiation.

Antibiotic combination efficacy (ACE) networks for a Pseudomonas aeruginosa model

The efficacy of antibiotic combinations against Pseudomonas aeruginosa is determined by two complementary factors; synergistic interactions between drugs enhance bacterial extinction, while trade-offs like collateral sensitivity limit the potential of the bacteria to adapt.

Short Reports

Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation

How does mitochondrial function influence nuclear epigenetics? This study shows that the observed effect of mitochondrial dysfunction on DNA hypermethylation is mediated by changes in the metabolism of methionine and polyamines.

Dissecting the null model for biological invasions: A meta-analysis of the propagule pressure effect

What determines whether or not an alien species will successfully establish in a novel environment? A quantitative meta-analysis reveals that increasing propagule pressure has a positive mean effect on establishment success across every dataset and hypothesis tested.

Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly

The evolution of a gravity-sensing crystal in eukaryotic pin molds is likely to have originated with the acquisition of a high-order protein assembly from bacteria.

Dependence of innate lymphoid cell 1 development on NKp46

An essential role of NKp46 in regulating innate lymphoid cell 1 (ILC1) homeostasis and development is demonstrated using an NKp46-deficient mouse model.

Methods and Resources

Ultrastructural localisation of protein interactions using conditionally stable nanobodies

A new toolkit comprising conditionally-stable GFP and mCherry-binding nanobodies fused to ascorbate peroxidase allows high-resolution detection of proteins and (via an ultrastructural split-GFP' system) protein-protein interactions by electron microscopy.

In vivo insertion pool sequencing identifies virulence factors in a complex fungal'host interaction

This study presents iPool-seq ' a method of selective sequencing from complex genomic samples to assess the frequencies of insertion mutants within a mutant pool ' and illustrates its utility by identifying genes in the fungal pathogen Ustilago maydis that influence virulence in maize.

Corrections

Correction: The Economics of Reproducibility in Preclinical Research

Correction: Late Maastrichtian pterosaurs from North Africa and mass extinction of Pterosauria at the Cretaceous-Paleogene boundary

Correction: Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain

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

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