PLoS Biology Research Articles

Microbiome complexity shapes metabolism.

Equipped with a novel isolator-housed metabolic cage system, a study in PLOS Biology assessed how the metabolism of mice harboring a defined minimal microbial community (OligoMM12) differs from that of germ-free and conventionally colonized mice.

SARS-CoV-2 takes the bait: Exosomes as endogenous decoys.

Writing in PLOS Biology, Ching and colleagues show that ACE2-decorated exosomes are deployed as natural inhibitory decoys against SARS-CoV-2. High decoy levels correlate with improved patient outcomes, suggesting they directly help COVID-19 recovery and supporting the concept of successful future decoy-based therapies.

Searching for serial dependencies in the brain.

Identifying the neural correlates of visual serial dependence has lagged behind the behavioral understanding. A new study in PLOS Biology provides a model of interpreting the complex relationship between physiology and behavior in studies of serial dependence.

Glutamate and clock help bean bugs track seasonal reproductive changes.

Animals adapt their seasonal physiology by measuring photoperiodic changes over the calendar year. A new study in PLOS Biology uncovers changes in glutamate dynamics in the bean bug that are dependent on photoperiod and a clock gene.

The changing influence of host genetics on the leaf fungal microbiome throughout plant development.

Host genetics and the environment influence which fungal microbes colonize a plant. A new study in PLOS Biology finds that the relative influence of these factors changes throughout the development of the biofuel crop switchgrass growing in field settings.

The path of voices in our brain.

Categorising voices is crucial for auditory-based social interactions. A recent study by Rupp and colleagues in PLOS Biology capitalises on human intracranial recordings to describe the spatiotemporal pattern of neural activity leading to voice-selective responses in associative auditory cortex.

Sweet sensors support stressed cell survival.

Gustatory receptors (Grs) are well known for their functions in sensory neurons in detecting food and toxins. An intriguing new study in PLOS Biology provides evidence for a role for Grs in Drosophila epithelia in protecting stressed cells from proteotoxicity.

Expanding the epitranscriptome: Dihydrouridine in mRNA.

Nucleotide modifications can markedly influence mRNA processing and metabolism. New studies, one in PLOS Biology, show that approximately 130 yeast mRNAs contain dihydrouridine, a derivative of uridine. Functional studies show that dihydrouridine, in some cases, can affect mRNA splicing.

Enzymes flying under the radar: Cryptic METTL3 can persist in knockout cells.

The presence of m6A in mRNA of METTL3 knockout cells has long been a point of confusion. In this issue of PLOS Biology, Poh and colleagues reveal alternatively spliced, catalytically active METTL3 isoforms that persist in cells previously thought to lack the enzyme.

How sex chromosomes get trapped into nonrecombination.

Suppression of recombination along the Y chromosome leads to its degeneration, so why does a process with such potentially deleterious consequences arise? In this issue of PLOS Biology, a new model reveals how and why this might be.

Reptile research shows new avenues and old challenges for extinction risk modelling.

In a new PLOS Biology paper, de Oliveira Caetano and colleagues presented an innovative method to estimate extinction risk in reptile species worldwide. The method shows a promising avenue to support Red List assessment, alongside some well-known challenges.

Neurons contribute to pathology in a mouse model of Krabbe disease in a cell-autonomous manner.

In this issue of PLOS Biology, Kreher and colleagues show in a mouse model that in vivo, neurons and not only myelinating glia are primary effectors of disease progression in Krabbe disease. The neuron-specific model generated allows the unprecedented capacity to investigate the neuronal autonomous component of this disorder.

Aligning evidence for the genesis of visual gamma oscillations

New findings in PLOS Biology show that visual gamma oscillations are greatly attenuated by small spatial discontinuities in visual stimuli, suggesting that their genesis occurs in response to predictable regularities in the visual world.

A defective structural zipper in photoreceptors causes inherited blindness.

Being able to see the beauty of this world is a wonderful thing unfortunately unavailable to people with inherited blindness. In this issue of PLOS Biology, Mercey and colleagues present optimized expansion microscopy for retinal tissue, which represents a huge step forward in our ability to study these blinding conditions.

In the Spotlight-Established Researcher.

In the Spotlight-Established Researcher.

Whole-proteome structures shed new light on posttranslational modifications.

Accurate but protein-only AlphaFold models may show structural fingerprints of likely posttranslational modifications (PTMs). In this issue of PLOS Biology, Bludau and colleagues add a functional context to models by combining them with readily available proteomics results.

Preprint citation practice in PLOS

The role of preprints in the scientific production and their part in citations have been growing over the past 10 years. In this paper we study preprint citations in several different aspects: the progression of preprint citations over time, their relative frequencies in relation to the IMRaD structure of articles, their distributions over time, per preprint database and per PLOS journal. We have processed the PLOS corpus that covers 7 journals and a total of about 240,000 articles up to January 2021, and produced a dataset of 8460 preprint citation contexts that cite 12 different preprint databases. Our results show that preprint citations are found with the highest frequency in the Method section of articles, though small variations exist with respect to journals. The PLOS Computational Biology journal stands out as it contains more than three times more preprint citations than any other PLOS journal. The relative parts of the different preprint databases are also examined. While ArXiv and bioRxiv are the most frequent citation sources, bioRxiv’s disciplinary nature can be observed as it is the source of more than 70% of preprint citations in PLOS Biology, PLOS Genetics and PLOS Pathogens. We have also compared the lexical content of preprint citation contexts to the citation content to peer-reviewed publications. Finally, by performing a lexicometric analysis, we have shown that preprint citation contexts differ significantly from citation contexts of peer-reviewed publications. This confirms that authors make use of different lexical content when citing preprints compared to the rest of citations.

Perplexing dynamics of Wolbachia proteins for cytoplasmic incompatibility.

The mechanism of symbiont-induced cytoplasmic incompatibility (CI) has been a long-standing mystery. A new study on Wolbachia's Cif proteins in PLOS Biology provides supportive evidence for the "Host modification model," although the alternative "Toxin-antidote model" is still in the running.

Binucleation ramps up gene expression meeting the physiological demands of an organism.

In this issue of PLOS Biology, van Rijnberk and colleagues show how polyploidy, via binucleation, enables Caenorhabditis elegans intestinal cells to ramp up gene expression supplying the oocytes with the necessary lipids for optimal organismal growth and reproductive fitness.

Inferences regarding oneself and others in the human brain.

The human brain can infer one's own and other individuals' mental states through metacognition and mentalizing, respectively. A new study in PLOS Biology has implicated distinct brain regions of the medial prefrontal cortex (PFC) in metacognition and mentalizing.