PLoS Biology: Archived Table of Contents 
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by S ílvia Vale-Costa, Temitope Akhigbe Etibor, Daniela Brás, Ana Laura Sousa, Mariana Ferreira, Gabriel G. Martins, Victor Hugo Mello, Maria João Amorim
It is now established that many viruses that threaten public health establish condensates via phase transitions to complete their lifecycles, and knowledge on such processes may offer new strategies for antiviral therapy. In the case of influenza A virus (IAV), liquid condensates known as viral inclusions, concentrate the 8 distinct viral ribonucleoproteins (vRNPs) that form IAV genome and are viewed as sites dedicated to the assembly of the 8-partite genomic complex....
Source: PLoS Biology: Archived Table of Contents - November 20, 2023 Category: Biology Authors: S ílvia Vale-Costa Source Type: research
Copy-back viral genomes induce a cellular stress response that interferes with viral protein expression without affecting antiviral immunity
by Lavinia J. Gonz ález Aparicio, Yanling Yang, Matthew Hackbart, Carolina B. López
Antiviral responses are often accompanied by translation inhibition and formation of stress granules (SGs) in infected cells. However, the triggers for these processes and their role during infection remain subjects of active investigation. Copy-back viral genomes (cbVGs) are the primary inducers of the mitochondrial antiviral signaling (MAVS) pathway and antiviral immunity during Sendai virus (SeV) and respiratory syncytial virus (RSV) infections. The relationship between cbVGs and cellular stress during viral infections is unknown. Her...
Source: PLoS Biology: Archived Table of Contents - November 20, 2023 Category: Biology Authors: Lavinia J. Gonz ález Aparicio Source Type: research
Brn3b regulates the formation of fear-related midbrain circuits and defensive responses to visual threat
by Hyoseo Lee, Hannah Weinberg-Wolf, Hae-Lim Lee, Tracy Lee, Joseph Conte, Carlos Godoy-Parejo, Jonathan B. Demb, Andrii Rudenko, In-Jung Kim
Defensive responses to visually threatening stimuli represent an essential fear-related survival instinct, widely detected across species. The neural circuitry mediating visually triggered defensive responses has been delineated in the midbrain. However, the molecular mechanisms regulating the development and function of these circuits remain unresolved. Here, we show that midbrain-specific deletion of the transcription factor Brn3b causes a loss of neurons projecting to the lateral...
Source: PLoS Biology: Archived Table of Contents - November 20, 2023 Category: Biology Authors: Hyoseo Lee Source Type: research
How many species are there on Earth? Progress and problems
by John J. Wiens
How many species exist on Earth? Projections range from millions to trillions. A 2011 paper in PLOS Biology provided a comprehensive estimate of 9 million.
How many species are there on Earth? Projections have ranged from the millions to the trillions. This Perspective looks at how a 2011 PLOS Biology study transformed this field and what is still to be done to find a definitive answer. (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - November 20, 2023 Category: Biology Authors: John J. Wiens Source Type: research
The murine meninges acquire lymphoid tissue properties and harbour autoreactive B cells during chronic < i > Trypanosoma brucei < /i > infection
by Juan F. Quintana, Matthew C. Sinton, Praveena Chandrasegaran, Lalit Kumar Dubey, John Ogunsola, Moumen Al Samman, Michael Haley, Gail McConnell, Nono-Raymond Kuispond Swar, Dieudonn é Mumba Ngoyi, David Bending, Luis de Lecea, Annette MacLeod, Neil A. Mabbott
The meningeal space is a critical brain structure providing immunosurveillance for the central nervous system (CNS), but the impact of infections on the meningeal immune landscape is far from being fully understood. The extracellular protozoan parasiteTrypanosoma brucei, which causes human African trypanosomiasis (HAT) or sleeping sickness, accumulates in the men...
Source: PLoS Biology: Archived Table of Contents - November 20, 2023 Category: Biology Authors: Juan F. Quintana Source Type: research
A simple Turing reaction –diffusion model explains how PLK4 breaks symmetry during centriole duplication and assembly
by Zachary M. Wilmott, Alain Goriely, Jordan W. Raff
Centrioles duplicate when a mother centriole gives birth to a daughter that grows from its side. Polo-like-kinase 4 (PLK4), the master regulator of centriole duplication, is recruited symmetrically around the mother centriole, but it then concentrates at a single focus that defines the daughter centriole assembly site. How PLK4 breaks symmetry is unclear. Here, we propose that phosphorylated and unphosphorylated species of PLK4 form the 2 components of a classical Turing reaction –diffusion system. These 2 components bind to/unbind from the surface of the mother centr...
Source: PLoS Biology: Archived Table of Contents - November 20, 2023 Category: Biology Authors: Zachary M. Wilmott Source Type: research
Item-specific neural representations during human sleep support long-term memory
by Jing Liu, Tao Xia, Danni Chen, Ziqing Yao, Minrui Zhu, James W. Antony, Tatia M. C. Lee, Xiaoqing Hu
Understanding how individual memories are reactivated during sleep is essential in theorizing memory consolidation. Here, we employed the targeted memory reactivation (TMR) paradigm to unobtrusively replaying auditory memory cues during human participants ’ slow-wave sleep (SWS). Using representational similarity analysis (RSA) on cue-elicited electroencephalogram (EEG), we found temporally segregated and functionally distinct item-specific neural representations: the early post-cue EEG activity (within 0 to 2,000 ms)...
Source: PLoS Biology: Archived Table of Contents - November 20, 2023 Category: Biology Authors: Jing Liu Source Type: research
No assembly required: Time for stronger, simpler publishing standards for DNA sequences
by B W. Thuronyi, Erika A. DeBenedictis, Jeffrey E. Barrick
Uniformly accessible DNA sequences are needed to improve experimental reproducibility and automation. Rather than descriptions of how engineered DNA is assembled, publishers should require complete and empirically validated sequences.
Describing how DNA constructs were assembled is no longer necessary when it is possible to fully sequence the final results to validate them. In this Perspective, the authors suggest that outdated methods narratives should be replaced with DNA sequence files when publishing life sciences research. (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - November 16, 2023 Category: Biology Authors: B W. Thuronyi Source Type: research
Correction: Sleep loss leads to the withdrawal of human helping across individuals, groups, and large-scale societies
by Eti Ben Simon, Raphael Vallat, Aubrey Rossi, Matthew P. Walker (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - November 15, 2023 Category: Biology Authors: Eti Ben Simon Source Type: research
Correction: Farnesyl pyrophosphate is a new danger signal inducing acute cell death
by Jing Chen, Xiaochen Zhang, Liping Li, Xianqiang Ma, Chunxiao Yang, Zhaodi Liu, Chenyang Li, Maria J. Fernandez-Cabezudo, Basel K. al-Ramadi, Chuan Wu, Weishan Huang, Yong Zhang, Yonghui Zhang, Wanli Liu (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - November 15, 2023 Category: Biology Authors: Jing Chen Source Type: research
Carbon dioxide regulates cholesterol levels through SREBP2
by Nityanand Bolshette, Saar Ezagouri, Vaishnavi Dandavate, Iuliia Karavaeva, Marina Golik, Hu Wang, Peter J. Espenshade, Timothy F. Osborne, Xianlin Han, Gad Asher
In mammals, O2 and CO2 levels are tightly regulated and are altered under various pathological conditions. While the molecular mechanisms that participate in O2 sensing are well characterized, little is known regarding the signaling pathways that participate in CO2 signaling and adaptation. Here, we show that CO2 levels control a distinct cellular transcriptional response that differs from mere pH changes. Unexpectedly, we discovered that CO2 regulates the exp...
Source: PLoS Biology: Archived Table of Contents - November 15, 2023 Category: Biology Authors: Nityanand Bolshette Source Type: research
Global terrestrial invasions: Where naturalised birds, mammals, and plants might spread next and what affects this process
by Henry H äkkinen, Dave Hodgson, Regan Early
More species live outside their native range than at any point in human history. Yet, there is little understanding of the geographic regions that will be threatened if these species continue to spread, nor of whether they will spread. We predict the world ’s terrestrial regions to which 833 naturalised plants, birds, and mammals are most imminently likely to spread, and investigate what factors have hastened or slowed their spread to date. There is huge potential for further spread of naturalised birds in North America, mammals in Eastern Europe, a nd plants in North Ameri...
Source: PLoS Biology: Archived Table of Contents - November 14, 2023 Category: Biology Authors: Henry H äkkinen Source Type: research
How can we reduce biomedical research ’s carbon footprint?
by Frank J. Kelly
Biomedical research is a significant contributor to the global carbon footprint. Practices are available that could make a difference; however, there are significant obstacles ahead, including a lack of specialist expertise in sustainable research practices.
It isn ’t easy being green in biomedical research. This Perspective looks at what changes in practice can make a difference now, and what challenges will need to be overcome to truly make a difference in the long run. (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - November 13, 2023 Category: Biology Authors: Frank J. Kelly Source Type: research
scapGNN: A graph neural network –based framework for active pathway and gene module inference from single-cell multi-omics data
by Xudong Han, Bing Wang, Chenghao Situ, Yaling Qi, Hui Zhu, Yan Li, Xuejiang Guo
Although advances in single-cell technologies have enabled the characterization of multiple omics profiles in individual cells, extracting functional and mechanistic insights from such information remains a major challenge. Here, we present scapGNN, a graph neural network (GNN)-based framework that creatively transforms sparse single-cell profile data into the stable gene –cell association network for inferring single-cell pathway activity scores and identifying cell phenotype–associated gene modules from single-cell multi-omics data. Sy...
Source: PLoS Biology: Archived Table of Contents - November 13, 2023 Category: Biology Authors: Xudong Han Source Type: research
Correction: DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program
by Yuelong Yan, Chao Zhang, Jing Hao, Xue-Lian Wang, Jia Ming, Li Mi, Jie Na, Xinli Hu, Yangming Wang (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - November 9, 2023 Category: Biology Authors: Yuelong Yan Source Type: research
