PLoS Biology最新文献

{"title":"Humans and great apes visually track event roles in similar ways.","authors":"Vanessa A D Wilson, Sebastian Sauppe, Sarah Brocard, Erik Ringen, Moritz M Daum, Stephanie Wermelinger, Nianlong Gu, Caroline Andrews, Arrate Isasi-Isasmendi, Balthasar Bickel, Klaus Zuberbühler","doi":"10.1371/journal.pbio.3002857","DOIUrl":"10.1371/journal.pbio.3002857","url":null,"abstract":"<p><p>Human language relies on a rich cognitive machinery, partially shared with other animals. One key mechanism, however, decomposing events into causally linked agent-patient roles, has remained elusive with no known animal equivalent. In humans, agent-patient relations in event cognition drive how languages are processed neurally and expressions structured syntactically. We compared visual event tracking between humans and great apes, using stimuli that would elicit causal processing in humans. After accounting for attention to background information, we found similar gaze patterns to agent-patient relations in all species, mostly alternating attention to agents and patients, presumably in order to learn the nature of the event, and occasionally privileging agents under specific conditions. Six-month-old infants, in contrast, did not follow agent-patient relations and attended mostly to background information. These findings raise the possibility that event role tracking, a cognitive foundation of syntax, has evolved long before language but requires time and experience to become ontogenetically available.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002857"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11593759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733215","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":"Mining biology for antibiotic discovery.","authors":"Cesar de la Fuente-Nunez","doi":"10.1371/journal.pbio.3002946","DOIUrl":"10.1371/journal.pbio.3002946","url":null,"abstract":"<p><p>The rise of antibiotic resistance calls for innovative solutions. The realization that biology can be mined digitally using artificial intelligence has revealed a new paradigm for antibiotic discovery, offering hope in the fight against superbugs.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002946"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620567/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733624","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 strategy to design protein-based antagonists against type I cytokine receptors.","authors":"Timo Ullrich, Olga Klimenkova, Christoph Pollmann, Asma Lasram, Valeriia Hatskovska, Kateryna Maksymenko, Matej Milijaš-Jotić, Lukas Schenk, Claudia Lengerke, Marcus D Hartmann, Jacob Piehler, Julia Skokowa, Mohammad ElGamacy","doi":"10.1371/journal.pbio.3002883","DOIUrl":"10.1371/journal.pbio.3002883","url":null,"abstract":"<p><p>Excessive cytokine signaling resulting from dysregulation of a cytokine or its receptor can be a main driver of cancer, autoimmune, or hematopoietic disorders. Here, we leverage protein design to create tailored cytokine receptor blockers with idealized properties. Specifically, we aimed to tackle the granulocyte-colony stimulating factor receptor (G-CSFR), a mediator of different types of leukemia and autoinflammatory diseases. By modifying designed G-CSFR binders, we engineered hyper-stable proteins that function as nanomolar signaling antagonists. X-ray crystallography showed atomic-level agreement with the experimental structure of an exemplary design. Furthermore, the most potent design blocks G-CSFR in acute myeloid leukemia cells and primary human hematopoietic stem cells. Thus, the resulting designs can be used for inhibiting or homing to G-CSFR-expressing cells. Our results also demonstrate that similarly designed cytokine mimics can be used to derive antagonists to tackle other type I cytokine receptors.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002883"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11596305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733846","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":"Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.","authors":"Lanxiang Wang, Yue Liu, Haoran Ni, Wenlong Zuo, Haimei Shi, Weixin Liao, Hongbin Liu, Jiajia Chen, Yang Bai, Hong Yue, Ancheng Huang, Jonathan Friedman, Tong Si, Yinggao Liu, Moxian Chen, Lei Dai","doi":"10.1371/journal.pbio.3002921","DOIUrl":"10.1371/journal.pbio.3002921","url":null,"abstract":"<p><p>Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002921"},"PeriodicalIF":9.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142733614","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":"Biofilm dispersal patterns revealed using far-red fluorogenic probes.","authors":"Jojo A Prentice, Sandhya Kasivisweswaran, Robert van de Weerd, Andrew A Bridges","doi":"10.1371/journal.pbio.3002928","DOIUrl":"10.1371/journal.pbio.3002928","url":null,"abstract":"<p><p>Bacteria frequently colonize niches by forming multicellular communities called biofilms. To explore new territories, cells exit biofilms through an active process called dispersal. Biofilm dispersal is essential for bacteria to spread between infection sites, yet how the process is executed at the single-cell level remains mysterious due to the limitations of traditional fluorescent proteins, which lose functionality in large, oxygen-deprived biofilms. To overcome this challenge, we developed a cell-labeling strategy utilizing fluorogen-activating proteins (FAPs) and cognate far-red dyes, which remain functional throughout biofilm development, enabling long-term imaging. Using this approach, we characterize dispersal at unprecedented resolution for the global pathogen Vibrio cholerae. We reveal that dispersal initiates at the biofilm periphery and approximately 25% of cells never disperse. We define novel micro-scale patterns that occur during dispersal, including biofilm compression during cell departure and regional heterogeneity in cell motions. These patterns are attenuated in mutants that reduce overall dispersal or that increase dispersal at the cost of homogenizing local mechanical properties. Collectively, our findings provide fundamental insights into the mechanisms of biofilm dispersal, advancing our understanding of how pathogens disseminate. Moreover, we demonstrate the broad applicability of FAPs as a powerful tool for high-resolution studies of microbial dynamics in complex environments.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002928"},"PeriodicalIF":9.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11627390/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717502","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":"Reconstructing the last common ancestor of all eukaryotes.","authors":"Thomas A Richards, Laura Eme, John M Archibald, Guy Leonard, Susana M Coelho, Alex de Mendoza, Christophe Dessimoz, Pavel Dolezal, Lillian K Fritz-Laylin, Toni Gabaldón, Vladimír Hampl, Geert J P L Kops, Michelle M Leger, Purificacion Lopez-Garcia, James O McInerney, David Moreira, Sergio A Muñoz-Gómez, Daniel J Richter, Iñaki Ruiz-Trillo, Alyson E Santoro, Arnau Sebé-Pedrós, Berend Snel, Courtney W Stairs, Eelco C Tromer, Jolien J E van Hooff, Bill Wickstead, Tom A Williams, Andrew J Roger, Joel B Dacks, Jeremy G Wideman","doi":"10.1371/journal.pbio.3002917","DOIUrl":"10.1371/journal.pbio.3002917","url":null,"abstract":"<p><p>Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002917"},"PeriodicalIF":9.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11627563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717506","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":"Queer- and trans-inclusive faculty hiring-A call for change.","authors":"J L Weissman, Callie R Chappell, Bruno Francesco Rodrigues de Oliveira, Natalya Evans, Anna C Fagre, Desiree Forsythe, Steven A Frese, Rachel Gregor, Suzanne L Ishaq, Juliet Johnston, Bittu K R, Shayle B Matsuda, Sam McCarren, Melanie Ortiz Alvarez de la Campa, Troy A Roepke, Nasa Sinnott-Armstrong, Cora S Stobie, Lauren Talluto, José M Vargas-Muñiz","doi":"10.1371/journal.pbio.3002919","DOIUrl":"10.1371/journal.pbio.3002919","url":null,"abstract":"<p><p>As queer and trans scientists, we face varied and systemic barriers to our professional success, resulting in our relative absence from faculty ranks at many institutions. In this Perspective, we call for a change in faculty hiring practices and present concrete guidance to make it a more inclusive process.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002919"},"PeriodicalIF":9.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11620581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693862","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":"CD74 promotes the formation of an immunosuppressive tumor microenvironment in triple-negative breast cancer in mice by inducing the expansion of tolerogenic dendritic cells and regulatory B cells.","authors":"Bianca Pellegrino, Keren David, Stav Rabani, Bar Lampert, Thuy Tran, Edward Doherty, Marta Piecychna, Roberto Meza-Romero, Lin Leng, Dov Hershkovitz, Arthur A Vandenbark, Richard Bucala, Shirly Becker-Herman, Idit Shachar","doi":"10.1371/journal.pbio.3002905","DOIUrl":"10.1371/journal.pbio.3002905","url":null,"abstract":"<p><p>CD74 is a cell-surface receptor for the cytokine macrophage migration inhibitory factor (MIF). MIF binding to CD74 induces a signaling cascade resulting in the release of its cytosolic intracellular domain (CD74-ICD), which regulates transcription in naïve B and chronic lymphocytic leukemia (CLL) cells. In the current study, we investigated the role of CD74 in the regulation of the immunosuppressive tumor microenvironment (TME) in triple-negative breast cancer (TNBC). TNBC is the most aggressive breast cancer subtype and is characterized by massive infiltration of immune cells to the tumor microenvironment, making this tumor a good candidate for immunotherapy. The tumor and immune cells in TNBC express high levels of CD74; however, the function of this receptor in the tumor environment has not been extensively characterized. Regulatory B cells (Bregs) and tolerogenic dendritic cells (tol-DCs) were previously shown to attenuate the antitumor immune response in TNBC. Here, we demonstrate that CD74 enhances tumor growth by inducing the expansion of tumor-infiltrating tol-DCs and Bregs. Utilizing CD74-KO mice, Cre-flox mice lacking CD74 in CD23+ mature B cells, mice lacking CD74 in the CD11c+ population, and a CD74 inhibitor (DRQ), we elucidate the mechanism by which CD74 inhibits antitumor immunity. MIF secreted from the tumor cells activates CD74 expressed on DCs. This activation induces the binding of CD74-ICD to the SP1 promotor, resulting in the up-regulation of SP1 expression. SP1 binds the IL-1β promotor, leading to the down-regulation of its transcription. The reduced levels of IL-1β lead to decreased antitumor activity by allowing expansion of the tol-DC, which induces the expansion of the Breg population, supporting the cross-talk between these 2 populations. Taken together, these results suggest that CD74+ CD11c+ DCs are the dominant cell type involved in the regulation of TNBC progression. These findings indicate that CD74 might serve as a novel therapeutic target in TNBC.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002905"},"PeriodicalIF":9.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693858","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 call for research to address the threat of paper mills.","authors":"Jennifer A Byrne, Anna Abalkina, Olufolake Akinduro-Aje, Jana Christopher, Sarah E Eaton, Nitin Joshi, Ulf Scheffler, Nick H Wise, Jennifer Wright","doi":"10.1371/journal.pbio.3002931","DOIUrl":"10.1371/journal.pbio.3002931","url":null,"abstract":"<p><p>Research paper mills are covert organizations that provide low-quality or fabricated manuscripts to paying clients. As members of the United2Act Research Working Group, we propose 5 key research questions on paper mills that require resourcing and support.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002931"},"PeriodicalIF":9.8,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602203/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142693856","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":"How do mammals convert dynamic odor information into neural maps for landscape navigation?","authors":"Anantu Sunil, Olivia Pedroncini, Andreas T Schaefer, Tobias Ackels","doi":"10.1371/journal.pbio.3002908","DOIUrl":"10.1371/journal.pbio.3002908","url":null,"abstract":"<p><p>Odors are transported by seemingly chaotic plumes, whose spatiotemporal structure contains rich information about space, with olfaction serving as a gateway for obtaining and processing this spatial information. Beyond tracking odors, olfaction provides localization and chemical communication cues for detecting conspecifics and predators, and linking external environments to internal cognitive maps. In this Essay, we discuss recent physiological, behavioral, and methodological advancements in mammalian olfactory research to present our current understanding of how olfaction can be used to navigate the environment. We also examine potential neural mechanisms that might convert dynamic olfactory inputs into environmental maps along this axis. Finally, we consider technological applications of odor dynamics for developing bio-inspired sensor technologies, robotics, and computational models. By shedding light on the principles underlying the processing of odor dynamics, olfactory research will pave the way for innovative solutions that bridge the gap between biology and technology, enriching our understanding of the natural world.</p>","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":"22 11","pages":"e3002908"},"PeriodicalIF":9.8,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11581409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689338","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}