PLOS Biology: New Articles

A Peer-Reviewed Open-Access Journal
  1. Metabolic and epigenetic dysfunctions underlie the arrest of in vitro fertilized human embryos in a senescent-like state

    by Yang Yang, Liyang Shi, Xiuling Fu, Gang Ma, Zhongzhou Yang, Yuhao Li, Yibin Zhou, Lihua Yuan, Ye Xia, Xiufang Zhong, Ping Yin, Li Sun, Wuwen Zhang, Isaac A. Babarinde, Yongjun Wang, Xiaoyang Zhao, Andrew P. Hutchins, Guoqing Tong

    Around 60% of in vitro fertilized (IVF) human embryos irreversibly arrest before compaction between the 3- to 8-cell stage, posing a significant clinical problem. The mechanisms behind this arrest are unclear. Here, we show that the arrested embryos enter a senescent-like state, marked by cell cycle arrest, the down-regulation of ribosomes and histones and down-regulation of MYC and p53 activity. The arrested embryos can be divided into 3 types. Type I embryos fail to complete the maternal-zygotic transition, and Type II/III embryos have low levels of glycolysis and either high (Type II) or low (Type III) levels of oxidative phosphorylation. Treatment with the SIRT agonist resveratrol or nicotinamide riboside (NR) can partially rescue the arrested phenotype, which is accompanied by changes in metabolic activity. Overall, our data suggests metabolic and epigenetic dysfunctions underlie the arrest of human embryos.
  2. A versatile new tool derived from a bacterial deubiquitylase to detect and purify ubiquitylated substrates and their interacting proteins

    by Mengwen Zhang, Jason M. Berk, Adrian B. Mehrtash, Jean Kanyo, Mark Hochstrasser

    Protein ubiquitylation is an important posttranslational modification affecting a wide range of cellular processes. Due to the low abundance of ubiquitylated species in biological samples, considerable effort has been spent on methods to purify and detect ubiquitylated proteins. We have developed and characterized a novel tool for ubiquitin detection and purification based on OtUBD, a high-affinity ubiquitin-binding domain (UBD) derived from an Orientia tsutsugamushi deubiquitylase (DUB). We demonstrate that OtUBD can be used to purify both monoubiquitylated and polyubiquitylated substrates from yeast and human tissue culture samples and compare their performance with existing methods. Importantly, we found conditions for either selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins. As proof of principle for these newly developed methods, we profiled the ubiquitylome and ubiquitin-associated proteome of the budding yeast Saccharomyces cerevisiae. Combining OtUBD affinity purification with quantitative proteomics, we identified potential substrates for the E3 ligases Bre1 and Pib1. OtUBD provides a versatile, efficient, and economical tool for ubiquitin research with specific advantages over certain other methods, such as in efficiently detecting monoubiquitylation or ubiquitin linkages to noncanonical sites.
  3. The origin of RNA interference: Adaptive or neutral evolution?

    by Alessandro Torri, Johannes Jaeger, Thomas Pradeu, Maria-Carla Saleh

    The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA (asRNA) gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability.
  4. Aligning evidence for the genesis of visual gamma oscillations

    by Brett L. Foster, Eleonora Bartoli

    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. This Primer explores the implications of a recent PLOS Biology study showing that gamma synchrony in visual cortex is disrupted when small discontinuities are added to visual stimuli. This suggests that gamma synchrony is highly sensitive to regularities in the visual world and potentially play a role in predictive processing.
  5. The machine learning–powered BirdNET App reduces barriers to global bird research by enabling citizen science participation

    by Connor M. Wood, Stefan Kahl, Ashakur Rahaman, Holger Klinck

    The BirdNET App, a free bird sound identification app for Android and iOS that includes over 3,000 bird species, reduces barriers to citizen science while generating tens of millions of bird observations globally that can be used to replicate known patterns in avian ecology. Involving the general public in research through free bird sound identification apps such as BirdNET can generate tens of millions of bird observations globally, helping citizen science to power avian ecology

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