PLoS Biology最新文献

{"title":"Changes in sea floor productivity are crucial to understanding the impact of climate change in temperate coastal ecosystems according to a new size-based model","authors":"A. Audzijonyte, Gustav W. Delius, R. Stuart‐Smith, C. Novaglio, G. Edgar, Neville S. Barrett, Julia L. Blanchard","doi":"10.1371/journal.pbio.3002392","DOIUrl":"https://doi.org/10.1371/journal.pbio.3002392","url":null,"abstract":"The multifaceted effects of climate change on physical and biogeochemical processes are rapidly altering marine ecosystems but often are considered in isolation, leaving our understanding of interactions between these drivers of ecosystem change relatively poor. This is particularly true for shallow coastal ecosystems, which are fuelled by a combination of distinct pelagic and benthic energy pathways that may respond to climate change in fundamentally distinct ways. The fish production supported by these systems is likely to be impacted by climate change differently to those of offshore and shelf ecosystems, which have relatively simpler food webs and mostly lack benthic primary production sources. We developed a novel, multispecies size spectrum model for shallow coastal reefs, specifically designed to simulate potential interactive outcomes of changing benthic and pelagic energy inputs and temperatures and calculate the relative importance of these variables for the fish community. Our model, calibrated using field data from an extensive temperate reef monitoring program, predicts that changes in resource levels will have much stronger impacts on fish biomass and yields than changes driven by physiological responses to temperature. Under increased plankton abundance, species in all fish trophic groups were predicted to increase in biomass, average size, and yields. By contrast, changes in benthic resources produced variable responses across fish trophic groups. Increased benthic resources led to increasing benthivorous and piscivorous fish biomasses, yields, and mean body sizes, but biomass decreases among herbivore and planktivore species. When resource changes were combined with warming seas, physiological responses generally decreased species’ biomass and yields. Our results suggest that understanding changes in benthic production and its implications for coastal fisheries should be a priority research area. Our modified size spectrum model provides a framework for further study of benthic and pelagic energy pathways that can be easily adapted to other ecosystems.","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":" 29","pages":""},"PeriodicalIF":9.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138616183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"It is time to authenticate the Microbiome Sciences with accredited educational programs and departments","authors":"Nichole Ginnan, Seth R. Bordenstein","doi":"10.1371/journal.pbio.3002420","DOIUrl":"https://doi.org/10.1371/journal.pbio.3002420","url":null,"abstract":"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.","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":" 511","pages":""},"PeriodicalIF":9.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138611049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards detailed predictions of coastal ecosystem function under climate change","authors":"Diego R. Barneche, Renato A. Morais","doi":"10.1371/journal.pbio.3002430","DOIUrl":"https://doi.org/10.1371/journal.pbio.3002430","url":null,"abstract":"The complex ways in which ongoing warming will restructure ecosystems remains poorly understood. A new simulation study in PLOS Biology suggests that expected changes in food resources for marine consumers will outpace the direct, pervasive effects of predicted +2.5°C warming.","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"28 3‐4","pages":""},"PeriodicalIF":9.8,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138626264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial Note: The Communication Factor EDF and the Toxin-Antitoxin Module mazEF Determine the Mode of Action of Antibiotics.","authors":"","doi":"10.1371/journal.pbio.3002325","DOIUrl":"10.1371/journal.pbio.3002325","url":null,"abstract":"","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"21 9","pages":"e3002325"},"PeriodicalIF":7.8,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10506701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10655937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SEC14-like condensate phase transitions at plasma membranes regulate root growth in Arabidopsis.","authors":"Chen Liu, Andriani Mentzelopoulou, Fotini Papagavriil, Prashanth Ramachandran, Artemis Perraki, Lucas Claus, Sebastian Barg, Peter Dörmann, Yvon Jaillais, Philipp Johnen, Eugenia Russinova, Electra Gizeli, Gabriel Schaaf, Panagiotis Nikolaou Moschou","doi":"10.1371/journal.pbio.3002305","DOIUrl":"10.1371/journal.pbio.3002305","url":null,"abstract":"<p><p>Protein function can be modulated by phase transitions in their material properties, which can range from liquid- to solid-like; yet, the mechanisms that drive these transitions and whether they are important for physiology are still unknown. In the model plant Arabidopsis, we show that developmental robustness is reinforced by phase transitions of the plasma membrane-bound lipid-binding protein SEC14-like. Using imaging, genetics, and in vitro reconstitution experiments, we show that SEC14-like undergoes liquid-like phase separation in the root stem cells. Outside the stem cell niche, SEC14-like associates with the caspase-like protease separase and conserved microtubule motors at unique polar plasma membrane interfaces. In these interfaces, SEC14-like undergoes processing by separase, which promotes its liquid-to-solid transition. This transition is important for root development, as lines expressing an uncleavable SEC14-like variant or mutants of separase and associated microtubule motors show similar developmental phenotypes. Furthermore, the processed and solidified but not the liquid form of SEC14-like interacts with and regulates the polarity of the auxin efflux carrier PINFORMED2. This work demonstrates that robust development can involve liquid-to-solid transitions mediated by proteolysis at unique plasma membrane interfaces.</p>","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"21 9","pages":"e3002305"},"PeriodicalIF":7.2,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10307574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selective retention of dysfunctional mitochondria during asymmetric cell division in yeast.","authors":"Xenia Chelius,&nbsp;Veronika Bartosch,&nbsp;Nathalie Rausch,&nbsp;Magdalena Haubner,&nbsp;Jana Schramm,&nbsp;Ralf J Braun,&nbsp;Till Klecker,&nbsp;Benedikt Westermann","doi":"10.1371/journal.pbio.3002310","DOIUrl":"10.1371/journal.pbio.3002310","url":null,"abstract":"<p><p>Decline of mitochondrial function is a hallmark of cellular aging. To counteract this process, some cells inherit mitochondria asymmetrically to rejuvenate daughter cells. The molecular mechanisms that control this process are poorly understood. Here, we made use of matrix-targeted D-amino acid oxidase (Su9-DAO) to selectively trigger oxidative damage in yeast mitochondria. We observed that dysfunctional mitochondria become fusion-incompetent and immotile. Lack of bud-directed movements is caused by defective recruitment of the myosin motor, Myo2. Intriguingly, intact mitochondria that are present in the same cell continue to move into the bud, establishing that quality control occurs directly at the level of the organelle in the mother. The selection of healthy organelles for inheritance no longer works in the absence of the mitochondrial Myo2 adapter protein Mmr1. Together, our data suggest a mechanism in which the combination of blocked fusion and loss of motor protein ensures that damaged mitochondria are retained in the mother cell to ensure rejuvenation of the bud.</p>","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"21 9","pages":"e3002310"},"PeriodicalIF":9.8,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10310579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Asymmetric connections with starburst amacrine cells underlie the upward motion selectivity of J-type retinal ganglion cells.","authors":"Bo Wang, Yifeng Zhang","doi":"10.1371/journal.pbio.3002301","DOIUrl":"10.1371/journal.pbio.3002301","url":null,"abstract":"<p><p>Motion is an important aspect of visual information. The directions of visual motion are encoded in the retina by direction-selective ganglion cells (DSGCs). ON-OFF DSGCs and ON DSGCs co-stratify with starburst amacrine cells (SACs) in the inner plexiform layer and depend on SACs for their direction selectivity. J-type retinal ganglion cells (J-RGCs), a type of OFF DSGCs in the mouse retina, on the other hand, do not co-stratify with SACs, and how direction selectivity in J-RGCs emerges has not been understood. Here, we report that both the excitatory and inhibitory synaptic inputs to J-RGCs are direction-selective (DS), with the inhibitory inputs playing a more important role for direction selectivity. The DS inhibitory inputs come from SACs, and the functional connections between J-RGCs and SACs are spatially asymmetric. Thus, J-RGCs and SACs form functionally important synaptic contacts even though their dendritic arbors show little overlap. These findings underscore the need to look beyond the neurons' stratification patterns in retinal circuit studies. Our results also highlight the critical role of SACs for retinal direction selectivity.</p>","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"21 9","pages":"e3002301"},"PeriodicalIF":6.9,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10300937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A TOX-ic axis of epigenetic stem cell maintenance and chemoresistance in colon cancer.","authors":"Christopher G Hubert,&nbsp;Shaun R Stauffer,&nbsp;Justin D Lathia","doi":"10.1371/journal.pbio.3002295","DOIUrl":"10.1371/journal.pbio.3002295","url":null,"abstract":"<p><p>Cancer stem cells drive tumor growth and survival via self-renewal and therapeutic resistance, but the upstream mechanisms are not well defined. In this issue of PLOS Biology, a study in colon cancer reveals a new signalling network that links epigenetic regulation to these phenotypes.</p>","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"21 9","pages":"e3002295"},"PeriodicalIF":9.8,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10503703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10287738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"azyx-1 is a new gene that overlaps with zyxin and affects its translation in C. elegans, impacting muscular integrity and locomotion.","authors":"Bhavesh S Parmar, Amanda Kieswetter, Ellen Geens, Elke Vandewyer, Christina Ludwig, Liesbet Temmerman","doi":"10.1371/journal.pbio.3002300","DOIUrl":"10.1371/journal.pbio.3002300","url":null,"abstract":"<p><p>Overlapping genes are widely prevalent; however, their expression and consequences are poorly understood. Here, we describe and functionally characterize a novel zyx-1 overlapping gene, azyx-1, with distinct regulatory functions in Caenorhabditis elegans. We observed conservation of alternative open reading frames (ORFs) overlapping the 5' region of zyxin family members in several animal species, and find shared sites of azyx-1 and zyxin proteoform expression in C. elegans. In line with a standard ribosome scanning model, our results support cis regulation of zyx-1 long isoform(s) by upstream initiating azyx-1a. Moreover, we report on a rare observation of trans regulation of zyx-1 by azyx-1, with evidence of increased ZYX-1 upon azyx-1 overexpression. Our results suggest a dual role for azyx-1 in influencing zyx-1 proteoform heterogeneity and highlight its impact on C. elegans muscular integrity and locomotion.</p>","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"21 9","pages":"e3002300"},"PeriodicalIF":9.8,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10575671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10265085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new polymodal gating model of the proton-activated chloride channel.","authors":"Piao Zhao, Cheng Tang, Yuqin Yang, Zhen Xiao, Samantha Perez-Miller, Heng Zhang, Guoqing Luo, Hao Liu, Yaqi Li, Qingyi Liao, Fan Yang, Hao Dong, Rajesh Khanna, Zhonghua Liu","doi":"10.1371/journal.pbio.3002309","DOIUrl":"10.1371/journal.pbio.3002309","url":null,"abstract":"<p><p>The proton-activated chloride (PAC) channel plays critical roles in ischemic neuron death, but its activation mechanisms remain elusive. Here, we investigated the gating of PAC channels using its novel bifunctional modulator C77304. C77304 acted as a weak activator of the PAC channel, causing moderate activation by acting on its proton gating. However, at higher concentrations, C77304 acted as a weak inhibitor, suppressing channel activity. This dual function was achieved by interacting with 2 modulatory sites of the channel, each with different affinities and dependencies on the channel's state. Moreover, we discovered a protonation-independent voltage activation of the PAC channel that appears to operate through an ion-flux gating mechanism. Through scanning-mutagenesis and molecular dynamics simulation, we confirmed that E181, E257, and E261 in the human PAC channel serve as primary proton sensors, as their alanine mutations eliminated the channel's proton gating while sparing the voltage-dependent gating. This proton-sensing mechanism was conserved among orthologous PAC channels from different species. Collectively, our data unveils the polymodal gating and proton-sensing mechanisms in the PAC channel that may inspire potential drug development.</p>","PeriodicalId":20240,"journal":{"name":"PLoS Biology","volume":"21 9","pages":"e3002309"},"PeriodicalIF":6.9,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10529583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10265086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}