PLoS Biology: Archived Table of Contents This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Global change ecology: Science to heal a damaged planet
by Andrew J. Tanentzap, Olesya Kolmakova Humanity has drastically altered the biophysical systems that sustain life on Earth. We summarize progress and chart future directions in the emerging field of global change ecology, which studies interactions between organisms and their changing environment. Addressing problems like climate change and food security required the advent of a new global-scale science. This Perspective reflects on the past 20 years of research in the field of global change ecology and looks at where the next 20 years might take us. (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - December 11, 2023 Category: Biology Authors: Andrew J. Tanentzap Source Type: research

Sensory processing in humans and mice fluctuates between external and internal modes
by Veith Weilnhammer, Heiner Stuke, Kai Standvoss, Philipp Sterzer Perception is known to cycle through periods of enhanced and reduced sensitivity to external information. Here, we asked whether such slow fluctuations arise as a noise-related epiphenomenon of limited processing capacity or, alternatively, represent a structured mechanism of perceptual inference. Using 2 large-scale datasets, we found that humans and mice alternate between externally and internally oriented modes of sensory analysis. During external mode, perception aligns more closely with the external sensory information, whereas internal mode is charac...
Source: PLoS Biology: Archived Table of Contents - December 8, 2023 Category: Biology Authors: Veith Weilnhammer Source Type: research

Cas9 degradation in human cells using phage anti-CRISPR proteins
by Zuriah Meacham, Luisa Arake de Tacca, Joseph Bondy-Denomy, David Rabuka, Michael Schelle Bacteriophages encode anti-CRISPR (Acr) proteins that inactivate CRISPR-Cas bacterial immune systems, allowing successful invasion, replication, and prophage integration. Acr proteins inhibit CRISPR-Cas systems using a wide variety of mechanisms. AcrIIA1 is encoded by numerous phages and plasmids, binds specifically to the Cas9 HNH domain, and was the first Acr discovered to inhibit SpyCas9. Here, we report the observation of AcrIIA1-induced degradation of SpyCas9 and SauCas9 in human cell culture, the first example of Acr-induced ...
Source: PLoS Biology: Archived Table of Contents - December 8, 2023 Category: Biology Authors: Zuriah Meacham Source Type: research

Eukaryotic CD-NTase, STING, and viperin proteins evolved via domain shuffling, horizontal transfer, and ancient inheritance from prokaryotes
by Edward M. Culbertson, Tera C. Levin Animals use a variety of cell-autonomous innate immune proteins to detect viral infections and prevent replication. Recent studies have discovered that a subset of mammalian antiviral proteins have homology to antiphage defense proteins in bacteria, implying that there are aspects of innate immunity that are shared across the Tree of Life. While the majority of these studies have focused on characterizing the diversity and biochemical functions of the bacterial proteins, the evolutionary relationships between animal and bacterial proteins are less clear. This ambiguity is partly due ...
Source: PLoS Biology: Archived Table of Contents - December 8, 2023 Category: Biology Authors: Edward M. Culbertson Source Type: research

It is time to authenticate the Microbiome Sciences with accredited educational programs and departments
by Nichole Ginnan, Seth R. Bordenstein The Microbiome Sciences are at a crucial maturation stage. Scientists and educators should now view the Microbiome Sciences as a flourishing and autonomous discipline, creating degree programs and departments that are conducive to cohesive growth. The Microbiome Sciences are at a crucial maturation stage. This Perspective argues that the Microbiome Sciences should now be seen as a flourishing and autonomous discipline and that specialist degree programs and departments should be created to foster continued growth. (Source: PLoS Biology: Archived Table of Contents)
Source: PLoS Biology: Archived Table of Contents - December 7, 2023 Category: Biology Authors: Nichole Ginnan Source Type: research

Collective production of hydrogen sulfide gas enables budding yeast lacking < i > MET17 < /i > to overcome their metabolic defect
by Sonal, Alex E. Yuan, Xueqin Yang, Wenying Shou Assimilation of sulfur is vital to all organisms. InS.cerevisiae, inorganic sulfate is first reduced to sulfide, which is then affixed to an organic carbon backbone by the Met17 enzyme. The resulting homocysteine can then be converted to all other essential organosulfurs such as methionine, cysteine, and glutathione. This pathway has been known for nearly half a century, andmet17 mutants have long been classified as organosulfur auxotrophs, which are unable to grow on sulfate as their sole sulfur source. Surprisingly, we found thatmet17Δ could grow on sulfate, albeit only...
Source: PLoS Biology: Archived Table of Contents - December 7, 2023 Category: Biology Authors: Sonal Source Type: research

Structural basis of G protein –Coupled receptor CMKLR1 activation and signaling induced by a chemerin-derived agonist
by Xuan Zhang, Tina Wei ß, Mary Hongying Cheng, Siqi Chen, Carla Katharina Ambrosius, Anne Sophie Czerniak, Kunpeng Li, Mingye Feng, Ivet Bahar, Annette G. Beck-Sickinger, Cheng Zhang Chemokine-like receptor 1 (CMKLR1), also known as chemerin receptor 23 (ChemR23) or chemerin receptor 1, is a chemoattractant G protein –coupled receptor (GPCR) that responds to the adipokine chemerin and is highly expressed in innate immune cells, including macrophages and neutrophils. The signaling pathways of CMKLR1 can lead to both pro- and anti-inflammatory effects depending on the ligands and physiological contexts. To under stand t...
Source: PLoS Biology: Archived Table of Contents - December 6, 2023 Category: Biology Authors: Xuan Zhang Source Type: research

Adaptive β-lactam resistance from an inducible efflux pump that is post-translationally regulated by the DjlA co-chaperone
by Jordan Costafrolaz, Ga ël Panis, Bastien Casu, Silvia Ardissone, Laurence Degeorges, Martin Pilhofer, Patrick H. Viollier The acquisition of multidrug resistance (MDR) determinants jeopardizes treatment of bacterial infections with antibiotics. The tripartite efflux pump AcrAB-NodT confers adaptive MDR in the polarized α-proteobacteriumCaulobacter crescentus via transcriptional induction by first-generation quinolone antibiotics. We discovered that overexpression of AcrAB-NodT by mutation or exogenous inducers confers resistance to cephalosporin and penicillin ( β-lactam) antibiotics. Combining 2-step mutagenesis-se...
Source: PLoS Biology: Archived Table of Contents - December 5, 2023 Category: Biology Authors: Jordan Costafrolaz Source Type: research

Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants
by Sourabh Palande, Joshua A. M. Kaste, Miles D. Roberts, Kenia Segura Ab á, Carly Claucherty, Jamell Dacon, Rei Doko, Thilani B. Jayakody, Hannah R. Jeffery, Nathan Kelly, Andriana Manousidaki, Hannah M. Parks, Emily M. Roggenkamp, Ally M. Schumacher, Jiaxin Yang, Sarah Percival, Jeremy Pardo, Aman Y. Husbands, Arjun Krishnan, Beronda L Montgomery, Elizabeth Munch, Addi e M. Thompson, Alejandra Rougon-Cardoso, Daniel H. Chitwood, Robert VanBuren Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on ...
Source: PLoS Biology: Archived Table of Contents - December 5, 2023 Category: Biology Authors: Sourabh Palande Source Type: research

Teneurin-3 regulates the generation of non-image-forming visual circuitry and responsiveness to light in the suprachiasmatic nucleus
by John L. Hunyara, K. M. Daly, Katherine Torres, Maria E. Yurgel, Ruchi Komal, Samer Hattar, Alex L. Kolodkin Visual system function depends upon the elaboration of precise connections between retinal ganglion cell (RGC) axons and their central targets in the brain. Though some progress has been made in defining the molecules that regulate RGC connectivity required for the assembly and function of image-forming circuitry, surprisingly little is known about factors required for intrinsically photosensitive RGCs (ipRGCs) to target a principal component of the non-image-forming circuitry: the suprachiasmatic nucleus (SCN). ...
Source: PLoS Biology: Archived Table of Contents - December 4, 2023 Category: Biology Authors: John L. Hunyara Source Type: research

Neurons in the primary visual cortex of freely moving rats encode both sensory and non-sensory task variables
by Anqi Zhang, Anthony M. Zador Neurons in primary visual cortex (area V1) are strongly driven by both sensory stimuli and non-sensory events. However, although the representation of sensory stimuli has been well characterized, much less is known about the representation of non-sensory events. Here, we characterize the specificity and organization of non-sensory representations in rat V1 during a freely moving visual decision task. We find that single neurons encode diverse combinations of task features simultaneously and across task epochs. Despite heterogeneity at the level of single neuron response patterns, both visua...
Source: PLoS Biology: Archived Table of Contents - December 4, 2023 Category: Biology Authors: Anqi Zhang Source Type: research

Structural basis for ligand recognition and signaling of the lysophosphatidylserine receptors GPR34 and GPR174
by Guibing Liu, Xiu Li, Yujing Wang, Xuan Zhang, Weimin Gong Lysophosphatidylserine (LysoPS) is a naturally occurring lipid mediator involved in various physiological and pathological processes especially those related to the immune system. GPR34, GPR174, and P2Y10 have been identified as the receptors for LysoPS, and its analogues have been developed as agonists or antagonists for these receptors. However, the lack of structural information hinders the drug development with novel characteristics, such as nonlipid ligands and allosteric modulators. Here, we determined the structures of human GPR34 and GPR174 in complex wi...
Source: PLoS Biology: Archived Table of Contents - December 4, 2023 Category: Biology Authors: Guibing Liu Source Type: research

Deletion of IFT20 exclusively in the RPE ablates primary cilia and leads to retinal degeneration
by Viola Kretschmer, Sandra Schneider, Peter Andreas Matthiessen, Dominik Reichert, Nathan Hotaling, Gunnar Glas ßer, Ingo Lieberwirth, Kapil Bharti, Rossella De Cegli, Ivan Conte, Emeline F. Nandrot, Helen Louise May-Simera Vision impairment places a serious burden on the aging society, affecting the lives of millions of people. Many retinal diseases are of genetic origin, of which over 50% are due to mutations in cilia-associated genes. Most research on retinal degeneration has focused on the ciliated photoreceptor cells of the retina. However, the contribution of primary cilia in other ocular cell types has largely be...
Source: PLoS Biology: Archived Table of Contents - December 4, 2023 Category: Biology Authors: Viola Kretschmer Source Type: research

In defense of quantitative metrics in researcher assessments
by John P. A. Ioannidis, Zacharias Maniadis Qualitative assessments of researchers are resource-intensive, untenable in nonmeritocratic settings, and error-prone. Although often derided, quantitative metrics could help improve research practices if they are rigorous, field-adjusted, and centralized. Using quantitative metrics to assess researchers is often seen as a poor choice compared with using qualitative assessments. In this Perspective, the authors argue in favor of using rigorous, field-adjusted, centralized, quantitative metrics in a bid to help improve research practices as a low-cost public good. (Source: PLoS ...
Source: PLoS Biology: Archived Table of Contents - December 4, 2023 Category: Biology Authors: John P. A. Ioannidis Source Type: research

Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry
by Aaron Wacholder, Anne-Ruxandra Carvunis Ribosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside of annotated protein-coding genes. However, shotgun mass spectrometry (MS) experiments typically detect only a small fraction of the predicted protein products of this noncanonical translation. The rarity of detection could indicate that most predicted noncanonical proteins are rapidly degraded and not present in the cell; alternatively, it could reflect technical limitations. Here, we leveraged recent advances in ribosome profiling and MS to investigate the factors limiting ...
Source: PLoS Biology: Archived Table of Contents - December 4, 2023 Category: Biology Authors: Aaron Wacholder Source Type: research