PLoS BiologyPub Date : 2025-03-25DOI: 10.1371/journal.pbio.3003127
Daniel Routledge, Nonia Pariente
{"title":"On improving the sustainability of peer review.","authors":"Daniel Routledge, Nonia Pariente","doi":"10.1371/journal.pbio.3003127","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003127","url":null,"abstract":"<p><p>The term \"reviewer fatigue\" has become only too familiar in scientific publishing. How can we ease the burden on reviewers to make the peer review system more sustainable, while streamlining the publication process for authors?</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003127"},"PeriodicalIF":9.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711830","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}
PLoS BiologyPub Date : 2025-03-21DOI: 10.1371/journal.pbio.3003005
Kevin S Chen, Anuj K Sharma, Jonathan W Pillow, Andrew M Leifer
{"title":"Navigation strategies in Caenorhabditis elegans are differentially altered by learning.","authors":"Kevin S Chen, Anuj K Sharma, Jonathan W Pillow, Andrew M Leifer","doi":"10.1371/journal.pbio.3003005","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003005","url":null,"abstract":"<p><p>Learned olfactory-guided navigation is a powerful platform for studying how a brain generates goal-directed behaviors. However, the quantitative changes that occur in sensorimotor transformations and the underlying neural circuit substrates to generate such learning-dependent navigation is still unclear. Here we investigate learned sensorimotor processing for navigation in the nematode Caenorhabditis elegans by measuring and modeling experience-dependent odor and salt chemotaxis. We then explore the neural basis of learned odor navigation through perturbation experiments. We develop a novel statistical model to characterize how the worm employs two behavioral strategies: a biased random walk and weathervaning. We infer weights on these strategies and characterize sensorimotor kernels that govern them by fitting our model to the worm's time-varying navigation trajectories and precise sensory experiences. After olfactory learning, the fitted odor kernels reflect how appetitive and aversive trained worms up- and down-regulate both strategies, respectively. The model predicts an animal's past olfactory learning experience with > 90% accuracy given finite observations, outperforming a classical chemotaxis metric. The model trained on natural odors further predicts the animals' learning-dependent response to optogenetically induced odor perception. Our measurements and model show that behavioral variability is altered by learning-trained worms exhibit less variable navigation than naive ones. Genetically disrupting individual interneuron classes downstream of an odor-sensing neuron reveals that learned navigation strategies are distributed in the network. Together, we present a flexible navigation algorithm that is supported by distributed neural computation in a compact brain.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003005"},"PeriodicalIF":9.8,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674612","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}
PLoS BiologyPub Date : 2025-03-20eCollection Date: 2025-03-01DOI: 10.1371/journal.pbio.3003061
Rory L Cooper, Michel C Milinkovitch
{"title":"In vivo sonic hedgehog pathway antagonism temporarily results in ancestral proto-feather-like structures in the chicken.","authors":"Rory L Cooper, Michel C Milinkovitch","doi":"10.1371/journal.pbio.3003061","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003061","url":null,"abstract":"<p><p>The morphological intricacies of avian feathers make them an ideal model for investigating embryonic patterning and morphogenesis. In particular, the sonic hedgehog (Shh) pathway is an important mediator of feather outgrowth and branching. However, functional in vivo evidence regarding its role during feather development remains limited. Here, we demonstrate that an intravenous injection of sonidegib, a potent Shh pathway inhibitor, at embryonic day 9 (E9) temporarily produces striped domains (instead of spots) of Shh expression in the skin, arrests morphogenesis, and results in unbranched and non-invaginated feather buds-akin to proto-feathers-in embryos until E14. Although feather morphogenesis partially recovers, hatched treated chickens exhibit naked skin regions with perturbed follicles. Remarkably, these follicles are subsequently reactivated by seven weeks post-hatching. Our RNA-sequencing data and rescue experiment using Shh-agonism confirm that sonidegib specifically down-regulates Shh pathway activity. Overall, we provide functional evidence for the role of the Shh pathway in mediating feather morphogenesis and confirm its role in the evolutionary emergence and diversification of feathers.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003061"},"PeriodicalIF":9.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671654","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}
PLoS BiologyPub Date : 2025-03-20eCollection Date: 2025-03-01DOI: 10.1371/journal.pbio.3003076
Sheng Huang, Chengji Piao, Zhiying Zhao, Christine B Beuschel, Oriane Turrel, David Toppe, Stephan J Sigrist
{"title":"Enhanced memory despite severe sleep loss in Drosophila insomniac mutants.","authors":"Sheng Huang, Chengji Piao, Zhiying Zhao, Christine B Beuschel, Oriane Turrel, David Toppe, Stephan J Sigrist","doi":"10.1371/journal.pbio.3003076","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003076","url":null,"abstract":"<p><p>Sleep is crucial for cognitive functions and life span across species. While sleep homeostasis and cognitive processes are linked through cellular and synaptic plasticity, the signaling pathways connecting them remain unclear. Here, we show that Drosophila insomniac (inc) short sleep mutants, which lack an adaptor protein for the autism-associated Cullin-3 ubiquitin ligase, exhibited enhanced Pavlovian aversive olfactory learning and memory, unlike other sleep mutants with normal or reduced memory. Through a genetic modifier screen, we found that a mild reduction of Protein Kinase A (PKA) signaling specifically rescued the sleep and longevity phenotypes of inc mutants. However, this reduction further increased their excessive memory and mushroom body overgrowth. Since inc mutants displayed higher PKA signaling, we propose that inc loss-of-function suppresses sleep via increased PKA activity, which also constrains the excessive memory of inc mutants. Our data identify a signaling cascade for balancing sleep and memory functions, and provide a plausible explanation for the sleep phenotypes of inc mutants, suggesting that memory hyperfunction can provoke sleep deficits.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003076"},"PeriodicalIF":9.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671642","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}
PLoS BiologyPub Date : 2025-03-19eCollection Date: 2025-03-01DOI: 10.1371/journal.pbio.3003070
Andrea J Radtke, Ifeanyichukwu U Anidi, Leanne Arakkal, Armando J Arroyo-Mejias, Rebecca T Beuschel, Katy Börner, Colin J Chu, Beatrice Clark, Menna R Clatworthy, Jake Colautti, Fabian Coscia, Joshua Croteau, Saven Denha, Rose Dever, Walderez O Dutra, Sonja Fritzsche, Spencer Fullam, Michael Y Gerner, Anita Gola, Kenneth J Gollob, Jonathan M Hernandez, Jyh Liang Hor, Hiroshi Ichise, Zhixin Jing, Danny Jonigk, Evelyn Kandov, Wolfgang Kastenmüller, Joshua F E Koenig, Rosa K Kortekaas, Aanandita Kothurkar, Alexandra Y Kreins, Ian T Lamborn, Yuri Lin, Katia Luciano Pereira Morais, Aleksandra Lunich, Jean C S Luz, Ryan B MacDonald, Chen Makranz, Vivien I Maltez, John E McDonough, Ryan V Moriarty, Juan M Ocampo-Godinez, Vitoria M Olyntho, Annette Oxenius, Kartika Padhan, Kirsten Remmert, Nathan Richoz, Edward C Schrom, Wanjing Shang, Lihong Shi, Rochelle M Shih, Emily Speranza, Salome Stierli, Sarah A Teichmann, Tibor Z Veres, Megan Vierhout, Brianna T Wachter, Adam K Wade-Vallance, Margaret Williams, Nathan Zangger, Ronald N Germain, Ziv Yaniv
{"title":"The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques.","authors":"Andrea J Radtke, Ifeanyichukwu U Anidi, Leanne Arakkal, Armando J Arroyo-Mejias, Rebecca T Beuschel, Katy Börner, Colin J Chu, Beatrice Clark, Menna R Clatworthy, Jake Colautti, Fabian Coscia, Joshua Croteau, Saven Denha, Rose Dever, Walderez O Dutra, Sonja Fritzsche, Spencer Fullam, Michael Y Gerner, Anita Gola, Kenneth J Gollob, Jonathan M Hernandez, Jyh Liang Hor, Hiroshi Ichise, Zhixin Jing, Danny Jonigk, Evelyn Kandov, Wolfgang Kastenmüller, Joshua F E Koenig, Rosa K Kortekaas, Aanandita Kothurkar, Alexandra Y Kreins, Ian T Lamborn, Yuri Lin, Katia Luciano Pereira Morais, Aleksandra Lunich, Jean C S Luz, Ryan B MacDonald, Chen Makranz, Vivien I Maltez, John E McDonough, Ryan V Moriarty, Juan M Ocampo-Godinez, Vitoria M Olyntho, Annette Oxenius, Kartika Padhan, Kirsten Remmert, Nathan Richoz, Edward C Schrom, Wanjing Shang, Lihong Shi, Rochelle M Shih, Emily Speranza, Salome Stierli, Sarah A Teichmann, Tibor Z Veres, Megan Vierhout, Brianna T Wachter, Adam K Wade-Vallance, Margaret Williams, Nathan Zangger, Ronald N Germain, Ziv Yaniv","doi":"10.1371/journal.pbio.3003070","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003070","url":null,"abstract":"<p><p>Multiplexed imaging is a powerful approach in spatial biology, although it is complex, expensive and labor-intensive. Here, we present the IBEX Knowledge-Base, a central resource for reagents, protocols and more, to enhance knowledge sharing, optimization and innovation of spatial proteomics techniques.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003070"},"PeriodicalIF":9.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665097","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}
PLoS BiologyPub Date : 2025-03-18eCollection Date: 2025-03-01DOI: 10.1371/journal.pbio.3003051
Ashley T Simkins, William J Sutherland, Lynn V Dicks, Craig Hilton-Taylor, Molly K Grace, Stuart H M Butchart, Rebecca A Senior, Silviu O Petrovan
{"title":"Past conservation efforts reveal which actions lead to positive outcomes for species.","authors":"Ashley T Simkins, William J Sutherland, Lynn V Dicks, Craig Hilton-Taylor, Molly K Grace, Stuart H M Butchart, Rebecca A Senior, Silviu O Petrovan","doi":"10.1371/journal.pbio.3003051","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003051","url":null,"abstract":"<p><p>Understanding the consequences of past conservation efforts is essential to inform the means of maintaining and restoring species. Data from the IUCN Red List for 67,217 animal species were reviewed and analyzed to determine (i) which conservation actions have been implemented for different species, (ii) which types of species have improved in status and (iii) which actions are likely to have driven the improvements. At least 51.8% (34,847) of assessed species have actions reported, mostly comprising protected areas (82.7%). Proportionately more actions were reported for tetrapods and warm-water reef-building corals, and fewer for fish, dragonflies and damselflies and crustaceans. Species at greater risk of extinction have a wider range of species-targeted actions reported compared with less threatened species, reflecting differences in documentation and conservation efforts. Six times more species have deteriorated than improved in status, as reflected in their IUCN Red List category. Almost all species that improved have conservation actions in place, and typically were previously at high risk of extinction, have smaller ranges and were less likely to be documented as threatened by hunting and habitat loss or degradation. Improvements in status were driven by a wide range of actions, especially reintroductions; for amphibians and birds, area management was also important. While conservation interventions have reduced the extinction risk of some of the most threatened species, in very few cases has full recovery been achieved. Scaling up the extent and intensity of conservation interventions, particularly landscape-scale actions that benefit broadly distributed species, is urgently needed to assist the recovery of biodiversity.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003051"},"PeriodicalIF":9.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659438","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}
PLoS BiologyPub Date : 2025-03-18eCollection Date: 2025-03-01DOI: 10.1371/journal.pbio.3003078
Miguel Medina Muñoz, Holly L Nichols, Kerri L Coon
{"title":"Microbiota isolate collections: A key to global vector-borne disease control.","authors":"Miguel Medina Muñoz, Holly L Nichols, Kerri L Coon","doi":"10.1371/journal.pbio.3003078","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003078","url":null,"abstract":"<p><p>Insect vector microbiomes are essential for insect function, making them promising targets for controlling vector-borne diseases. Microbial isolate collections aid in identifying microbial targets, but expanding these collections must rely on coordinated efforts that are ethical and ensure equitable benefit sharing.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003078"},"PeriodicalIF":9.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659436","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}
PLoS BiologyPub Date : 2025-03-18eCollection Date: 2025-03-01DOI: 10.1371/journal.pbio.3003052
Sui Huang, Ana M Soto, Carlos Sonnenschein
{"title":"The end of the genetic paradigm of cancer.","authors":"Sui Huang, Ana M Soto, Carlos Sonnenschein","doi":"10.1371/journal.pbio.3003052","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003052","url":null,"abstract":"<p><p>Genome sequencing of cancer and normal tissues, alongside single-cell transcriptomics, continues to produce findings that challenge the idea that cancer is a 'genetic disease', as posited by the somatic mutation theory (SMT). In this prevailing paradigm, tumorigenesis is caused by cancer-driving somatic mutations and clonal expansion. However, results from tumor sequencing, motivated by the genetic paradigm itself, create apparent 'paradoxes' that are not conducive to a pure SMT. But beyond genetic causation, the new results lend credence to old ideas from organismal biology. To resolve inconsistencies between the genetic paradigm of cancer and biological reality, we must complement deep sequencing with deep thinking: embrace formal theory and historicity of biological entities, and (re)consider non-genetic plasticity of cells and tissues. In this Essay, we discuss the concepts of cell state dynamics and tissue fields that emerge from the collective action of genes and of cells in their morphogenetic context, respectively, and how they help explain inconsistencies in the data in the context of SMT.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003052"},"PeriodicalIF":9.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659440","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}
PLoS BiologyPub Date : 2025-03-17DOI: 10.1371/journal.pbio.3003053
Chaya Mushka Fridman, Kinga Keppel, Vladislav Rudenko, Jon Altuna-Alvarez, David Albesa-Jové, Eran Bosis, Dor Salomon
{"title":"A new class of type VI secretion system effectors can carry two toxic domains and are recognized through the WHIX motif for export.","authors":"Chaya Mushka Fridman, Kinga Keppel, Vladislav Rudenko, Jon Altuna-Alvarez, David Albesa-Jové, Eran Bosis, Dor Salomon","doi":"10.1371/journal.pbio.3003053","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003053","url":null,"abstract":"<p><p>Gram-negative bacteria employ the type VI secretion system (T6SS) to deliver toxic effectors into neighboring cells and outcompete rivals. Although many effectors have been identified, their secretion mechanism often remains unknown. Here, we describe WHIX, a domain sufficient to mediate the secretion of effectors via the T6SS. Remarkably, we find WHIX in T6SS effectors that contain a single toxic domain, as well as in effectors that contain two distinct toxic domains fused to either side of WHIX. We demonstrate that the latter, which we name double-blade effectors, require two cognate immunity proteins to antagonize their toxicity. Furthermore, we show that WHIX can be used as a chassis for T6SS-mediated secretion of multiple domains. Our findings reveal a new class of polymorphic T6SS cargo effectors with a unique secretion domain that can deploy two toxic domains in one shot, possibly reducing recipients' ability to defend themselves.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 3","pages":"e3003053"},"PeriodicalIF":9.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651499","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}
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