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A large-scale study across the avian clade identifies ecological drivers of neophobia. 一项横跨鸟类进化的大规模研究确定了新恐惧症的生态驱动因素。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-14 eCollection Date: 2025-10-01 DOI: 10.1371/journal.pbio.3003394
Rachael Miller, Vedrana Šlipogor, Kai R Caspar, Jimena Lois-Milevicich, Carl Soulsbury, Stephan A Reber, Claudia Mettke-Hofmann, Megan Lambert, Benjamin J Ashton, Alice M I Auersperg, Melissa Bateson, Solenne Belle, Boris Bilčík, Laura M Biondi, Francesco Bonadonna, Desiree Brucks, Michael W Butler, Samuel P Caro, Marion Charrier, Tiffany Chatelin, Johnathan Ching, Nicola S Clayton, Benjamin J Cluver, Ella B Cochran, Francesca Cornero, Emily Danby, Samara Danel, Martina Darwich, James R Davies, Alicia de la Colina, Dominik Fischer, Ondřej Fišer, Florencia Foitzick, Edward C Galluccio, Clara Garcia-Co, Elias Garcia-Pelegrin, Isabelle George, Kai-Philipp Gladow, Raúl O Gómez, Anna Grewer, Katie Grice, Lauren M Guillette, Devon C Hallihan, Katie J Harrington, Frauke Heer, Chloe Henry, Vladimira Hodova, Marisa Hoeschele, Cécilia Houdelier, Paula Ibáñez de Aldecoa, Oluwaseun Serah Iyasere, Yuka Kanemitsu, Mina Khodadadi, Duc Khong, Melanie G Kimball, Ariana N Klappert, Lucy N Koch, Uta U König von Borstel, Lubor Košt'ál, Anastasia Krasheninnikova, Lubica Kubikova, Connor T Lambert, Daan W Laméris, Courtenay G Lampert, Oceane Larousse, Christine R Lattin, Zhongqiu Li, Michael Lindenmeier, Delia A Lister, Julia A Mackenzie, Selina Mainz, Danna Masri, Jorg J M Massen, Laurenz Mohr, Wendt Müller, Paul M Nealen, Andreas Nieder, Aurèle Novac, Nínive Paes Cavalcante, Kristina Pascual, Carla Pascual-Guàrdia, Ayushi Patel, Katarína Pichová, Cristina Pilenga, Laurent Prétôt, John L Quinn, Elena Račevska, Juan C Reboreda, Sam Reynolds, Amanda R Ridley, Theresa Rössler, Francisco Ruiz-Raya, Marina Salas, Beatriz C Saldanha, Sebastián M Santiago, Nikola Schlöglová, Gia Seatriz, Eva Serrano-Davies, Eva G Shair Ali, Janja Sirovnik, Zuzana Skalná, Katie E Slocombe, Masayo Soma, Tiziana Srdoc, Stefan Stanescu, Michaela Syrová, Alex H Taylor, Christopher N Templeton, Karlie Thompson, Sandra Trigo, Camille A Troisi, Utku Urhan, Maurice Valbert, Kees van Oers, Alberto Velando, Frederick Verbruggen, Jorrit W Verkleij, Alizée Vernouillet, Jonas Verspeek, Petr Veselý, Auguste M P von Bayern, Eline Waalders, Benjamin A Whittaker, Ella R Williamson, Vanessa A D Wilson, Michelle A Winfield, Neslihan Wittek, Karen K L Yeung, Jade A Zanutto
{"title":"A large-scale study across the avian clade identifies ecological drivers of neophobia.","authors":"Rachael Miller, Vedrana Šlipogor, Kai R Caspar, Jimena Lois-Milevicich, Carl Soulsbury, Stephan A Reber, Claudia Mettke-Hofmann, Megan Lambert, Benjamin J Ashton, Alice M I Auersperg, Melissa Bateson, Solenne Belle, Boris Bilčík, Laura M Biondi, Francesco Bonadonna, Desiree Brucks, Michael W Butler, Samuel P Caro, Marion Charrier, Tiffany Chatelin, Johnathan Ching, Nicola S Clayton, Benjamin J Cluver, Ella B Cochran, Francesca Cornero, Emily Danby, Samara Danel, Martina Darwich, James R Davies, Alicia de la Colina, Dominik Fischer, Ondřej Fišer, Florencia Foitzick, Edward C Galluccio, Clara Garcia-Co, Elias Garcia-Pelegrin, Isabelle George, Kai-Philipp Gladow, Raúl O Gómez, Anna Grewer, Katie Grice, Lauren M Guillette, Devon C Hallihan, Katie J Harrington, Frauke Heer, Chloe Henry, Vladimira Hodova, Marisa Hoeschele, Cécilia Houdelier, Paula Ibáñez de Aldecoa, Oluwaseun Serah Iyasere, Yuka Kanemitsu, Mina Khodadadi, Duc Khong, Melanie G Kimball, Ariana N Klappert, Lucy N Koch, Uta U König von Borstel, Lubor Košt'ál, Anastasia Krasheninnikova, Lubica Kubikova, Connor T Lambert, Daan W Laméris, Courtenay G Lampert, Oceane Larousse, Christine R Lattin, Zhongqiu Li, Michael Lindenmeier, Delia A Lister, Julia A Mackenzie, Selina Mainz, Danna Masri, Jorg J M Massen, Laurenz Mohr, Wendt Müller, Paul M Nealen, Andreas Nieder, Aurèle Novac, Nínive Paes Cavalcante, Kristina Pascual, Carla Pascual-Guàrdia, Ayushi Patel, Katarína Pichová, Cristina Pilenga, Laurent Prétôt, John L Quinn, Elena Račevska, Juan C Reboreda, Sam Reynolds, Amanda R Ridley, Theresa Rössler, Francisco Ruiz-Raya, Marina Salas, Beatriz C Saldanha, Sebastián M Santiago, Nikola Schlöglová, Gia Seatriz, Eva Serrano-Davies, Eva G Shair Ali, Janja Sirovnik, Zuzana Skalná, Katie E Slocombe, Masayo Soma, Tiziana Srdoc, Stefan Stanescu, Michaela Syrová, Alex H Taylor, Christopher N Templeton, Karlie Thompson, Sandra Trigo, Camille A Troisi, Utku Urhan, Maurice Valbert, Kees van Oers, Alberto Velando, Frederick Verbruggen, Jorrit W Verkleij, Alizée Vernouillet, Jonas Verspeek, Petr Veselý, Auguste M P von Bayern, Eline Waalders, Benjamin A Whittaker, Ella R Williamson, Vanessa A D Wilson, Michelle A Winfield, Neslihan Wittek, Karen K L Yeung, Jade A Zanutto","doi":"10.1371/journal.pbio.3003394","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003394","url":null,"abstract":"<p><p>Neophobia, or aversion to novelty, is important for adaptability and survival as it influences the ways in which animals navigate risk and interact with their environments. Across individuals, species and other taxonomic levels, neophobia is known to vary considerably, but our understanding of the wider ecological drivers of neophobia is hampered by a lack of comparative multispecies studies using standardized methods. Here, we utilized the ManyBirds Project, a Big Team Science large-scale collaborative open science framework, to pool efforts and resources of 129 collaborators at 77 institutions from 24 countries worldwide across six continents. We examined both difference scores (between novel object test and control conditions) and raw data of latency to touch familiar food in the presence (test) and absence (control) of a novel object among 1,439 subjects from 136 bird species across 25 taxonomic orders incorporating lab, field, and zoo sites. We first demonstrated that consistent differences in neophobia existed among individuals, among species, and among other taxonomic levels in our dataset, rejecting the null hypothesis that neophobia is highly plastic at all taxonomic levels with no evidence for evolutionary divergence. We then tested for effects of ecological factors on neophobia, including diet, sociality, habitat, and range, while accounting for phylogeny. We found that (i) species with more specialist diets were more neophobic than those with more generalist diets, providing support for the Neophobia Threshold Hypothesis; (ii) migratory species were also more neophobic than nonmigratory species, which supports the Dangerous Niche Hypothesis. Our study shows that the evolution of avian neophobia has been shaped by ecological drivers and demonstrates the potential of Big Team Science to advance our understanding of animal behavior.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003394"},"PeriodicalIF":7.2,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145294179","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}
引用次数: 0
Combining gamma neuromodulation and robotic rehabilitation after a stroke restores parvalbumin interneuron dynamics and improves motor recovery in mice. 结合伽马神经调节和机器人康复中风后恢复小白蛋白中间神经元动力学和改善运动恢复小鼠。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-14 eCollection Date: 2025-10-01 DOI: 10.1371/journal.pbio.3002806
Livia Vignozzi, Francesca Macchi, Elena Montagni, Maria Pasquini, Alessandra Martello, Antea Minetti, Éléa Coulomb, Anna Letizia Allegra Mascaro, Silvestro Micera, Matteo Caleo, Cristina Spalletti
{"title":"Combining gamma neuromodulation and robotic rehabilitation after a stroke restores parvalbumin interneuron dynamics and improves motor recovery in mice.","authors":"Livia Vignozzi, Francesca Macchi, Elena Montagni, Maria Pasquini, Alessandra Martello, Antea Minetti, Éléa Coulomb, Anna Letizia Allegra Mascaro, Silvestro Micera, Matteo Caleo, Cristina Spalletti","doi":"10.1371/journal.pbio.3002806","DOIUrl":"https://doi.org/10.1371/journal.pbio.3002806","url":null,"abstract":"<p><p>Stroke is a leading cause of long-term disability, frequently associated with persistent motor deficits. Gamma band oscillations, generated by synchronous discharge of parvalbumin-positive interneurons (PV-INs), are critically affected after stroke in humans and animals. Both gamma band and PV-INs play a key role in motor function, thus representing a promising target for poststroke neurorehabilitation. Noninvasive neuromodulatory approaches are considered a safe intervention and can be used for this purpose. Here, we present a novel, clinically relevant, noninvasive, and well-tolerated sub-acute treatment combining robotic rehabilitation with advanced neuromodulation techniques, validated in a mouse model of ischemic injury. During the sub-acute poststroke phase, we scored profound deficits in motor-related gamma band activity in the perilesional cortex. These deficits were accompanied by reduced PV-IN firing rates and increased functional connectivity, both at the perilesional and at the whole-cortex levels. Therefore, we tested the therapeutic potential of coupling robotic rehabilitation with optogenetic PV-IN-driven gamma band stimulation in a subacute poststroke phase during motor training to reinforce the efficacy of the treatment. Frequency-specific movement-related gamma band stimulation, when combined with physical training, significantly improved forelimb motor function. More importantly, by pairing robotic rehabilitation with a clinical-like noninvasive 40 Hz transcranial Alternating Current Stimulation, we achieved similar motor improvements mediated by the effective restoring of movement-related gamma band power, improvement of PV-IN maladaptive network dynamics, and increased PV-IN connections in premotor cortex. Our research introduces a new understanding of the role of parvalbumin-interneurons in poststroke impairment and recovery. These results highlight the synergistic potential of combining perilesional gamma band stimulation with robotic rehabilitation as a promising and realistic therapeutic approach for stroke patients.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3002806"},"PeriodicalIF":7.2,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145294130","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}
引用次数: 0
The superficial layers of the primary visual cortex create a saliency map that feeds forward to the parietal cortex. 初级视觉皮层的浅层形成了一幅显著性图,并将其传递给顶叶皮层。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-14 DOI: 10.1371/journal.pbio.3003159
Chen Liu, Chengwen Liu, Laurentius Huber, Li Zhaoping, Peng Zhang
{"title":"The superficial layers of the primary visual cortex create a saliency map that feeds forward to the parietal cortex.","authors":"Chen Liu, Chengwen Liu, Laurentius Huber, Li Zhaoping, Peng Zhang","doi":"10.1371/journal.pbio.3003159","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003159","url":null,"abstract":"<p><p>A salient visual object with a distinct feature from the surrounding environment automatically captures attention. While the saliency signals have been found in many brain regions, their source remains highly controversial. Here, we investigated the neural origin of visual saliency using cortical layer-dependent functional magnetic resonance imaging (fMRI) of cerebral blood volume (CBV) at 7 Tesla. Behaviorally, human observers were better at detecting salient foreground bars with a larger orientation contrast from uniformly oriented background bars. Saliency-sensitive signals were strongest in the superficial layers of the primary visual cortex (V1) and in the middle layers of the intraparietal sulcus (IPS) of the parietal cortex. Layer-dependent effective connectivity revealed the transmission of saliency signals along the feedforward pathway from V1 to IPS. Furthermore, behavioral sensitivity to the foreground stimulus correlated significantly with the fMRI response in the superficial layers of V1. Our findings provide mesoscale evidence that a visual saliency map is created by iso-feature suppression through lateral inhibition in the superficial layers of V1, and then feeds forward to attentional control brain regions to guide attention and eye movements.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003159"},"PeriodicalIF":7.2,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145294155","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}
引用次数: 0
Identification and characterization of tumor-associated astrocyte subpopulations and their interactions with the tumor microenvironment in experimental glioblastomas. 实验性胶质母细胞瘤中肿瘤相关星形胶质细胞亚群的鉴定和表征及其与肿瘤微环境的相互作用。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-13 DOI: 10.1371/journal.pbio.3002893
Mitrajit Ghosh, Paulina Pilanc-Kudlek, Szymon Baluszek, Karol Jacek, Katarzyna Poleszak, Paulina Szadkowska, Anna M Lenkiewicz, Bartłomiej Gielniewski, Aleksandra Ellert-Miklaszewska, Maria G Castro, Bozena Kaminska
{"title":"Identification and characterization of tumor-associated astrocyte subpopulations and their interactions with the tumor microenvironment in experimental glioblastomas.","authors":"Mitrajit Ghosh, Paulina Pilanc-Kudlek, Szymon Baluszek, Karol Jacek, Katarzyna Poleszak, Paulina Szadkowska, Anna M Lenkiewicz, Bartłomiej Gielniewski, Aleksandra Ellert-Miklaszewska, Maria G Castro, Bozena Kaminska","doi":"10.1371/journal.pbio.3002893","DOIUrl":"https://doi.org/10.1371/journal.pbio.3002893","url":null,"abstract":"<p><p>Astrocytes comprise ~50% of all brain cells and present distinct morphological, molecular and functional properties in different brain regions. In glioblastoma (GBM), an aggressive primary brain tumor, astrocytes become activated and tumor-associated astrocytes (TAAs) exhibit different transcriptomic profiles, morphology, and functions supporting disease progression. Heterogeneity and specific roles of TAAs within various regions of tumors are poorly known. Advancements of single-cell and spatial transcriptomics allow to profile tumors at unprecedented resolution revealing cell phenotypes, hidden functionalities, and spatial architecture in disease-specific context. We combined spatial transcriptomics and multiple immunofluorescent staining to visualize TAAs heterogeneity and location of various subpopulations in three intracranial murine glioma models. Using distinct gene expression profiles, we identified subtypes of TAAs with distinct localization and inferred their specialized functionalities. Gene signatures associated with TAAs reflected their reprograming in the tumor microenvironment (TME), revealed their multiple roles and potential contributing factors shaping the local milieu. Using spatial correlation analysis of the spots, we inferred the interactome of Slc1a2 (encoding a glutamate transporter) with the other markers of TAAs based on segregated areas of the tumor. The designer RGD peptide that blocked tumor-microglia communications, altered the spatial distribution of TAAs in GL261 gliomas providing new insights into cell-to-cell communication. Spatial transcriptomics combined with multiple staining unveils multiple functional phenotypes of TAAs and interactions within TME. We demonstrate distinct morphology of TAAs and different roles in various regions of the tumor. Glioma-induced heterogeneity of TAAs allows adaptation to the pharmacologically induced modification of the immunosuppressive TME.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3002893"},"PeriodicalIF":7.2,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287455","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}
引用次数: 0
Simple scaling laws control the genetic architectures of human complex traits. 简单的标度定律控制着人类复杂性状的遗传结构。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-13 eCollection Date: 2025-10-01 DOI: 10.1371/journal.pbio.3003402
Yuval B Simons, Hakhamanesh Mostafavi, Huisheng Zhu, Courtney J Smith, Jonathan K Pritchard, Guy Sella
{"title":"Simple scaling laws control the genetic architectures of human complex traits.","authors":"Yuval B Simons, Hakhamanesh Mostafavi, Huisheng Zhu, Courtney J Smith, Jonathan K Pritchard, Guy Sella","doi":"10.1371/journal.pbio.3003402","DOIUrl":"10.1371/journal.pbio.3003402","url":null,"abstract":"<p><p>Genome-wide association studies have revealed that the genetic architectures of complex traits vary widely, including in terms of the numbers, effect sizes, and allele frequencies of significant hits. However, at present we lack a principled way of understanding the similarities and differences among traits. Here, we describe a probabilistic model that combines the effects of mutation, drift, and stabilizing selection at individual sites with a genome-scale model of phenotypic variation. In this model, the architecture of a trait arises from the distribution of selection coefficients of mutations and from two scaling parameters. We fit this model for 95 highly polygenic quantitative traits of different kinds from the UK Biobank. Notably, we infer that all these traits have fairly similar, though not identical, distributions of selection coefficients. This similarity suggests that differences in architectures of highly polygenic traits arise mainly from the two scaling parameters: the mutational target size and heritability per site, which vary by orders of magnitude among traits. When these two scale factors are accounted for, we find that the architectures of all 95 traits are very similar.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003402"},"PeriodicalIF":7.2,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12517483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287456","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}
引用次数: 0
Hippocampal pyramidal cells of the CA1 region are not a major target of the thalamic nucleus reuniens. CA1区的海马锥体细胞不是丘脑核重组的主要目标。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-13 DOI: 10.1371/journal.pbio.3003419
Lilya Andrianova, Paul J Banks, Clair A Booth, Erica S Brady, Gabriella Margetts-Smith, Shivali Kohli, Jonathan Cavanagh, Zafar I Bashir, Chris J McBain, Michael T Craig
{"title":"Hippocampal pyramidal cells of the CA1 region are not a major target of the thalamic nucleus reuniens.","authors":"Lilya Andrianova, Paul J Banks, Clair A Booth, Erica S Brady, Gabriella Margetts-Smith, Shivali Kohli, Jonathan Cavanagh, Zafar I Bashir, Chris J McBain, Michael T Craig","doi":"10.1371/journal.pbio.3003419","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003419","url":null,"abstract":"<p><p>The prefrontal-hippocampal-entorhinal system is perhaps the most widely-studied circuit in cognitive and systems neuroscience, due to its role in supporting cognitive functions such as working memory and decision-making. Disrupted communication within this circuit is a key feature of disorders such as schizophrenia and dementia. Nucleus reuniens (NRe) is a midline thalamic nucleus that sits at the nexus of this circuit, linking these regions together. As there are no direct projections from prefrontal cortex to hippocampus (HPC), the accepted model is that the NRe mediates prefrontal drive of hippocampal activity, although these connections are poorly defined at the cellular and synaptic level. Using ex vivo optogenetics and electrophysiology in both mice and rats, alongside monosynaptic circuit-tracing, we sought to test the mechanisms through which NRe could drive hippocampal activity. Unexpectedly, we found no evidence that pyramidal cells in CA1 receive input from NRe, with midline thalamic input to HPC proper appearing selective for GABAergic interneurons. In other regions targeted by NRe, we found that pyramidal cells in prosubiculum and subiculum received synaptic inputs from NRe that were at least an order of magnitude weaker than those in prefrontal or entorhinal cortices. We conclude that, contrary to widely-held assumptions in the field, the hippocampal pyramidal cells are not a major target of NRe.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003419"},"PeriodicalIF":7.2,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287454","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}
引用次数: 0
FAIR-SMART expands access to supplementary materials for research transparency. FAIR-SMART扩大了对研究透明度补充材料的获取。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-09 DOI: 10.1371/journal.pbio.3003428
Chih-Hsuan Wei, Robert Leaman, Po-Ting Lai, Don Comeau, Shubo Tian, Zhiyong Lu
{"title":"FAIR-SMART expands access to supplementary materials for research transparency.","authors":"Chih-Hsuan Wei, Robert Leaman, Po-Ting Lai, Don Comeau, Shubo Tian, Zhiyong Lu","doi":"10.1371/journal.pbio.3003428","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003428","url":null,"abstract":"<p><p>Supplementary materials accompanying scientific articles are critical components of biomedical research, offering detailed datasets, experimental protocols, and extended analyses that complement the main text. These materials play an important role in enhancing transparency, reproducibility, and scientific impact by providing in depth analyses and the details necessary for reproducing experiments. However, the lack of consistent and standard formats has limited the access to supplementary materials in scientific investigations. In response, we propose a novel system aimed to enhance FAIR access to Supplementary MAterials for Research Transparency (FAIR-SMART). Specifically, we first aggregate supplementary files in a single location, standardize them into structured and machine-readable format, and make them accessible via web APIs. Next, we employ advanced large language models to automatically categorize the tabular data, which represents over 90% of the textual content in supplementary materials, enabling precise and efficient data retrieval. By bridging the gap between diverse file types and automated workflows, this work not only advances biomedical research but also highlights the transformative potential of accessible supplementary materials in shaping the behaviors and decision-making processes of the scientific community. FAIR-SMART is freely available for supplementary materials data retrieval via its APIs: https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/FAIR-SMART/.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003428"},"PeriodicalIF":7.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145259873","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}
引用次数: 0
Persistent viral infections impact key biological traits in Drosophila melanogaster. 持续的病毒感染影响黑腹果蝇的关键生物学性状。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-09 DOI: 10.1371/journal.pbio.3003437
Mauro Castelló-Sanjuán, Rubén González, Ottavia Romoli, Hervé Blanc, Jared C Nigg, Maria-Carla Saleh
{"title":"Persistent viral infections impact key biological traits in Drosophila melanogaster.","authors":"Mauro Castelló-Sanjuán, Rubén González, Ottavia Romoli, Hervé Blanc, Jared C Nigg, Maria-Carla Saleh","doi":"10.1371/journal.pbio.3003437","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003437","url":null,"abstract":"<p><p>Persistent viral infections have been assumed to impose minimal fitness costs for insects. We established persistent mono-infections of Drosophila melanogaster with four different enteric RNA viruses: Drosophila A virus (DAV), Drosophila C virus (DCV), Bloomfield virus, and Nora virus. We observed that these infections significantly reduce fly survival, alter the number of viable offspring per female, modulate microbiome composition, impact locomotor abilities, and change activity patterns. These results demonstrate the significant impact of persistent viral infections on key biological traits and expand our understanding of the fitness costs of persistent viral infections for the host. In addition, the four viruses displayed different accumulation kinetics and elicited unique transcriptional profiles with no common core responses. The transcriptional changes triggered by DCV infection persisted even after viral clearance. This comprehensive comparative dataset represents a valuable resource for researchers studying host-pathogen interactions, providing detailed transcriptional profiles, and behavioral measurements across different viral infections and time points. Our findings reveal that persistent viral infections modulate critical aspects of insect biology, affecting host physiology and behavior.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003437"},"PeriodicalIF":7.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145259840","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}
引用次数: 0
Malaria parasites can optimize transmission investment by sensing two within-host cues. 疟疾寄生虫可以通过感知宿主内的两种信号来优化传播投资。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-09 DOI: 10.1371/journal.pbio.3003081
Avril Wang, Megan Ann Greischar, Nicole Mideo
{"title":"Malaria parasites can optimize transmission investment by sensing two within-host cues.","authors":"Avril Wang, Megan Ann Greischar, Nicole Mideo","doi":"10.1371/journal.pbio.3003081","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003081","url":null,"abstract":"<p><p>The timing of investment into reproduction is a key determinant of lifetime reproductive success (fitness). Many organisms exhibit plastic, i.e., environmentally-responsive, investment strategies, raising the questions of what environmental cues trigger responses and why organisms have evolved to respond to those particular cues. For malaria parasites (Plasmodium spp.), investment into the production of specialized transmission stages (versus stages that replicate asexually within the host) is synonymous with reproductive investment and also plastic, responding to host- and parasite-derived factors. Previous theory has identified optimal plastic transmission investment strategies for the rodent malaria parasite, Plasmodium chabaudi, as a function of the time since infection, implicitly assuming that parasites have perfect information about the within-host environment and how it is changing. We extend that theory to ask which cue(s) should parasites use? Put another way, which cue(s) maximize parasite fitness, quantified as host infectiousness during acute infection? Our results show that sensing a parasite-associated cue, e.g., the abundance of infected red blood cells or transmission stages, allows parasites to achieve fitness approaching that of the optimal time-varying strategy, but only when parasites perceive the cue non-linearly, responding more sensitively to changes at low densities. However, no single cue can recreate the best time-varying strategy or allow parasites to adopt terminal investment as the infection ends, a classic expectation for reproductive investment. Sensing two cues-log-transformed infected and uninfected red blood cell abundance-enables parasites to accurately track the progression of the infection, permits terminal investment, and recovers the fitness of the optimal time-varying investment strategy. Importantly, parasites that detect two cues more efficiently exploit hosts, resulting in higher virulence compared with those sensing only one cue. However, parasites sensing two cues also experience larger fitness declines in the face of environmental and developmental fluctuations. Collectively, our results suggest that sensing non-redundant cues enables more optimal transmission investment but trades off against robustness in the face of environmental and developmental noise.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003081"},"PeriodicalIF":7.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145259828","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}
引用次数: 0
Visualization of Trypanosoma brucei flagellar pocket collar biogenesis identifies two new cytoskeletal structures. 布鲁氏锥虫鞭毛袋领生物发生的可视化发现了两个新的细胞骨架结构。
IF 7.2 1区 生物学
PLoS Biology Pub Date : 2025-10-09 DOI: 10.1371/journal.pbio.3003429
Marie Zelená, Elina Casas, Chloé Lambert, Nicolas Landrein, Denis Dacheux, Eloïse Bertiaux, Kim Ivan Abesamis, Gang Dong, Vladimir Varga, Derrick Roy Robinson, Mélanie Bonhivers
{"title":"Visualization of Trypanosoma brucei flagellar pocket collar biogenesis identifies two new cytoskeletal structures.","authors":"Marie Zelená, Elina Casas, Chloé Lambert, Nicolas Landrein, Denis Dacheux, Eloïse Bertiaux, Kim Ivan Abesamis, Gang Dong, Vladimir Varga, Derrick Roy Robinson, Mélanie Bonhivers","doi":"10.1371/journal.pbio.3003429","DOIUrl":"https://doi.org/10.1371/journal.pbio.3003429","url":null,"abstract":"<p><p>Understanding how cells assemble internal structures is central to cell biology. In Trypanosoma brucei, the flagellar pocket (FP) is essential for nutrient uptake, and immune evasion, and its formation depends on a cytoskeletal structure called the flagellar pocket collar (FPC). However, the mechanisms underlying FPC assembly remain poorly understood. In this study, we used cutting-edge ultrastructure expansion microscopy (U-ExM) to investigate FPC biogenesis in T. brucei. We mapped the formation of the proximal part of the new microtubule quartet (nMtQ) alongside flagellum growth, providing new insights into its assembly. Additionally, we tracked the localization dynamics of key structural proteins-BILBO1, MORN1, and BILBO2-during the biogenesis of the FPC and the hook complex (HC). Notably, we identified two previously undetected structures: the proFPC and the transient FPC-interconnecting fiber (FPC-IF), both of which appear to play crucial roles in linking and organizing cellular components during cell division. By uncovering these novel aspects of FPC biogenesis, our study significantly advances the understanding of cytoskeletal organization in trypanosomes and opens new avenues for exploring the functional significance of these structures.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"23 10","pages":"e3003429"},"PeriodicalIF":7.2,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145259931","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}
引用次数: 0
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