PLoS Biology最新文献_第6页

CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data. CellTracksColab 是一个可对细胞追踪数据进行编译、分析和探索的平台。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-08-08 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002740

Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet

{"title":"CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data.","authors":"Estibaliz Gómez-de-Mariscal, Hanna Grobe, Joanna W Pylvänäinen, Laura Xénard, Ricardo Henriques, Jean-Yves Tinevez, Guillaume Jacquemet","doi":"10.1371/journal.pbio.3002740","DOIUrl":"10.1371/journal.pbio.3002740","url":null,"abstract":"In life sciences, tracking objects from movies enables researchers to quantify the behavior of single particles, organelles, bacteria, cells, and even whole animals. While numerous tools now allow automated tracking from video, a significant challenge persists in compiling, analyzing, and exploring the large datasets generated by these approaches. Here, we introduce CellTracksColab, a platform tailored to simplify the exploration and analysis of cell tracking data. CellTracksColab facilitates the compiling and analysis of results across multiple fields of view, conditions, and repeats, ensuring a holistic dataset overview. CellTracksColab also harnesses the power of high-dimensional data reduction and clustering, enabling researchers to identify distinct behavioral patterns and trends without bias. Finally, CellTracksColab also includes specialized analysis modules enabling spatial analyses (clustering, proximity to specific regions of interest). We demonstrate CellTracksColab capabilities with 3 use cases, including T cells and cancer cell migration, as well as filopodia dynamics. CellTracksColab is available for the broader scientific community at https://github.com/CellMigrationLab/CellTracksColab.","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11335138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908029","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

Diatom abundance in the polar oceans is predicted by genome size. 根据基因组大小预测极地海洋中硅藻的丰度。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-08-08 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002733

Wade R Roberts, Adam M Siepielski, Andrew J Alverson

{"title":"Diatom abundance in the polar oceans is predicted by genome size.","authors":"Wade R Roberts, Adam M Siepielski, Andrew J Alverson","doi":"10.1371/journal.pbio.3002733","DOIUrl":"10.1371/journal.pbio.3002733","url":null,"abstract":"A principal goal in ecology is to identify the determinants of species abundances in nature. Body size has emerged as a fundamental and repeatable predictor of abundance, with smaller organisms occurring in greater numbers than larger ones. A biogeographic component, known as Bergmann's rule, describes the preponderance, across taxonomic groups, of larger-bodied organisms in colder areas. Although undeniably important, the extent to which body size is the key trait underlying these patterns is unclear. We explored these questions in diatoms, unicellular algae of global importance for their roles in carbon fixation and energy flow through marine food webs. Using a phylogenomic dataset from a single lineage with worldwide distribution, we found that body size (cell volume) was strongly correlated with genome size, which varied by 50-fold across species and was driven by differences in the amount of repetitive DNA. However, directional models identified temperature and genome size, not cell size, as having the greatest influence on maximum population growth rate. A global metabarcoding dataset further identified genome size as a strong predictor of species abundance in the ocean, but only in colder regions at high and low latitudes where diatoms with large genomes dominated, a pattern consistent with Bergmann's rule. Although species abundances are shaped by myriad interacting abiotic and biotic factors, genome size alone was a remarkably strong predictor of abundance. Taken together, these results highlight the cascading cellular and ecological consequences of macroevolutionary changes in an emergent trait, genome size, one of the most fundamental and irreducible properties of an organism.","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11309476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908030","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

Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes. 沙门氏菌基因组可塑性的综合蓝图确定了致病基因的热点。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-08-07 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002746

Simran Krishnakant Kushwaha, Yi Wu, Hugo Leonardo Avila, Abhirath Anand, Thomas Sicheritz-Pontén, Andrew Millard, Sandhya Amol Marathe, Franklin L Nobrega

{"title":"Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes.","authors":"Simran Krishnakant Kushwaha, Yi Wu, Hugo Leonardo Avila, Abhirath Anand, Thomas Sicheritz-Pontén, Andrew Millard, Sandhya Amol Marathe, Franklin L Nobrega","doi":"10.1371/journal.pbio.3002746","DOIUrl":"10.1371/journal.pbio.3002746","url":null,"abstract":"Understanding the dynamic evolution of Salmonella is vital for effective bacterial infection management. This study explores the role of the flexible genome, organised in regions of genomic plasticity (RGP), in shaping the pathogenicity of Salmonella lineages. Through comprehensive genomic analysis of 12,244 Salmonella spp. genomes covering 2 species, 6 subspecies, and 46 serovars, we uncover distinct integration patterns of pathogenicity-related gene clusters into RGP, challenging traditional views of gene distribution. These RGP exhibit distinct preferences for specific genomic spots, and the presence or absence of such spots across Salmonella lineages profoundly shapes strain pathogenicity. RGP preferences are guided by conserved flanking genes surrounding integration spots, implicating their involvement in regulatory networks and functional synergies with integrated gene clusters. Additionally, we emphasise the multifaceted contributions of plasmids and prophages to the pathogenicity of diverse Salmonella lineages. Overall, this study provides a comprehensive blueprint of the pathogenicity potential of Salmonella. This unique insight identifies genomic spots in nonpathogenic lineages that hold the potential for harbouring pathogenicity genes, providing a foundation for predicting future adaptations and developing targeted strategies against emerging human pathogenic strains.","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11305592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903346","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

Salmonella Typhimurium exploits host polyamines for assembly of the type 3 secretion machinery. 鼠伤寒沙门氏菌利用宿主多胺组装 3 型分泌机制。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-08-05 eCollection Date: 2024-08-01 DOI: 10.1371/journal.pbio.3002731

Tsuyoshi Miki, Takeshi Uemura, Miki Kinoshita, Yuta Ami, Masahiro Ito, Nobuhiko Okada, Takemitsu Furuchi, Shin Kurihara, Takeshi Haneda, Tohru Minamino, Yun-Gi Kim

{"title":"Salmonella Typhimurium exploits host polyamines for assembly of the type 3 secretion machinery.","authors":"Tsuyoshi Miki, Takeshi Uemura, Miki Kinoshita, Yuta Ami, Masahiro Ito, Nobuhiko Okada, Takemitsu Furuchi, Shin Kurihara, Takeshi Haneda, Tohru Minamino, Yun-Gi Kim","doi":"10.1371/journal.pbio.3002731","DOIUrl":"10.1371/journal.pbio.3002731","url":null,"abstract":"Bacterial pathogens utilize the factors of their hosts to infect them, but which factors they exploit remain poorly defined. Here, we show that a pathogenic Salmonella enterica serovar Typhimurium (STm) exploits host polyamines for the functional expression of virulence factors. An STm mutant strain lacking principal genes required for polyamine synthesis and transport exhibited impaired infectivity in mice. A polyamine uptake-impaired strain of STm was unable to inject effectors of the type 3 secretion system into host cells due to a failure of needle assembly. STm infection stimulated host polyamine production by increasing arginase expression. The decline in polyamine levels caused by difluoromethylornithine, which inhibits host polyamine production, attenuated STm colonization, whereas polyamine supplementation augmented STm pathogenesis. Our work reveals that host polyamines are a key factor promoting STm infection, and therefore a promising therapeutic target for bacterial infection.","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11299824/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141894684","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

Cholesterol-dependent dynamic changes in the conformation of the type 1 cholecystokinin receptor affect ligand binding and G protein coupling. 胆固醇依赖性 1 型胆囊收缩素受体构象的动态变化会影响配体结合和 G 蛋白耦合。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-07-31 eCollection Date: 2024-07-01 DOI: 10.1371/journal.pbio.3002673

Kaleeckal G Harikumar, Peishen Zhao, Brian P Cary, Xiaomeng Xu, Aditya J Desai, Maoqing Dong, Jesse I Mobbs, Chirine Toufaily, Sebastian G B Furness, Arthur Christopoulos, Matthew J Belousoff, Denise Wootten, Patrick M Sexton, Laurence J Miller

{"title":"Cholesterol-dependent dynamic changes in the conformation of the type 1 cholecystokinin receptor affect ligand binding and G protein coupling.","authors":"Kaleeckal G Harikumar, Peishen Zhao, Brian P Cary, Xiaomeng Xu, Aditya J Desai, Maoqing Dong, Jesse I Mobbs, Chirine Toufaily, Sebastian G B Furness, Arthur Christopoulos, Matthew J Belousoff, Denise Wootten, Patrick M Sexton, Laurence J Miller","doi":"10.1371/journal.pbio.3002673","DOIUrl":"10.1371/journal.pbio.3002673","url":null,"abstract":"Development of optimal therapeutics for disease states that can be associated with increased membrane cholesterol requires better molecular understanding of lipid modulation of the drug target. Type 1 cholecystokinin receptor (CCK1R) agonist actions are affected by increased membrane cholesterol, enhancing ligand binding and reducing calcium signaling, while agonist actions of the closely related CCK2R are not. In this work, we identified a set of chimeric human CCK1R/CCK2R mutations that exchange the cholesterol sensitivity of these 2 receptors, providing powerful tools when expressed in CHO and HEK-293 model cell lines to explore mechanisms. Static, low energy, high-resolution structures of the mutant CCK1R constructs, stabilized in complex with G protein, were not substantially different, suggesting that alterations to receptor dynamics were key to altered function. We reveal that cholesterol-dependent dynamic changes in the conformation of the helical bundle of CCK receptors affects both ligand binding at the extracellular surface and G protein coupling at the cytosolic surface, as well as their interrelationships involved in stimulus-response coupling. This provides an ideal setting for potential allosteric modulators to correct the negative impact of membrane cholesterol on CCK1R.","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11290853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861362","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

Hyphae of the fungus Aspergillus nidulans demonstrate chemotropism to nutrients and pH. 黑曲霉菌丝对营养物质和 pH 值具有趋化性。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-07-30 eCollection Date: 2024-07-01 DOI: 10.1371/journal.pbio.3002726

Riho Yamamoto, Hinata Miki, Ayaka Itani, Norio Takeshita

{"title":"Hyphae of the fungus Aspergillus nidulans demonstrate chemotropism to nutrients and pH.","authors":"Riho Yamamoto, Hinata Miki, Ayaka Itani, Norio Takeshita","doi":"10.1371/journal.pbio.3002726","DOIUrl":"10.1371/journal.pbio.3002726","url":null,"abstract":"The importance of fungi in ecological systems and pathogenicity hinges on their ability to search for nutrients, substrates, and hosts. Despite this, the question of whether fungal hyphae exhibit chemotropism toward them remains largely unresolved and requires close examination at the cellular level. Here, we designed a microfluidic device to assess hyphal chemotropism of Aspergillus nidulans in response to carbon and nitrogen sources, as well as pH. Within this device, hyphae could determine their growth direction in a two-layer flow with distinct compositions that were adjacent but non-mixing. Under conditions with and without a carbon source, hyphae changed growth direction to remain in the presence of a carbon source, but it was still difficult to distinguish between differences in growth and chemotropism. Although nitrogen sources such as ammonia and nitrate are important for growth, the hyphae indicated negative chemotropism to avoid them depending on the specific transporters. This fungus grows equally well at the colony level in the pH range of 4 to 9, but the hyphae exhibited chemotropism to acidic pH. The proton pump PmaA is vital for the chemotropism to acid pH, while the master regulatory for pH adaptation PacC is not involved, suggesting that chemotropism and adaptive growth via gene expression regulation are distinct regulatory mechanisms. Despite various plasma membrane transporters are distributed across membranes except at the hyphal tip, the control of growth direction occurs at the tip. Finally, we explored the mechanisms linking these two phenomena, tip growth and chemotropism.","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11288418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141856912","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

FURNA: A database for functional annotations of RNA structures. FURNA：RNA 结构功能注释数据库。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-07-29 eCollection Date: 2024-07-01 DOI: 10.1371/journal.pbio.3002476

Chengxin Zhang, Lydia Freddolino

引用次数: 0

Correction: GABAergic regulation of striatal spiny projection neurons depends upon their activity state. 更正：纹状体棘突投射神经元的 GABA 能调节取决于其活动状态。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-07-26 eCollection Date: 2024-07-01 DOI: 10.1371/journal.pbio.3002752

Michelle Day, Marziyeh Belal, William C Surmeier, Alexandria Melendez, David Wokosin, Tatiana Tkatch, Vernon R J Clarke, D James Surmeier

引用次数: 0

Prophage induction can facilitate the in vitro dispersal of multicellular Streptomyces structures. 噬菌体诱导可促进多细胞链霉菌结构的体外扩散。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-07-25 eCollection Date: 2024-07-01 DOI: 10.1371/journal.pbio.3002725

Hoda Jaffal, Mounia Kortebi, Pauline Misson, Paulo Tavares, Malika Ouldali, Hervé Leh, Sylvie Lautru, Virginia S Lioy, François Lecointe, Stéphanie G Bury-Moné

引用次数: 0

Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1. 在隐球菌真菌中，交替 TSS 的使用非常普遍，它是对环境线索的反应，并受转录因子 Tur1 的全基因组调控。

IF 9.8 1区生物学

PLoS Biology Pub Date : 2024-07-25 eCollection Date: 2024-07-01 DOI: 10.1371/journal.pbio.3002724

Thi Tuong Vi Dang, Corinne Maufrais, Jessie Colin, Frédérique Moyrand, Isabelle Mouyna, Jean-Yves Coppée, Chinaemerem U Onyishi, Joanna Lipecka, Ida Chiara Guerrera, Robin C May, Guilhem Janbon

{"title":"Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.","authors":"Thi Tuong Vi Dang, Corinne Maufrais, Jessie Colin, Frédérique Moyrand, Isabelle Mouyna, Jean-Yves Coppée, Chinaemerem U Onyishi, Joanna Lipecka, Ida Chiara Guerrera, Robin C May, Guilhem Janbon","doi":"10.1371/journal.pbio.3002724","DOIUrl":"10.1371/journal.pbio.3002724","url":null,"abstract":"Alternative transcription start site (TSS) usage regulation has been identified as a major means of gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. Here, we first re-analyzed TSS-seq data to define genuine TSS clusters in 2 species of pathogenic Cryptococcus. We identified 2 types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates alternative TSS (altTSS) usage genome-wide when cells switch from exponential phase to stationary phase. ChiP-Seq and DamID-Seq analyses suggest that at some loci, the role of Tur1 might be direct. Tur1 has been previously shown to be essential for virulence in C. neoformans. We demonstrated here that a tur1Δ mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the wild-type (WT) strain.","PeriodicalId":49001,"journal":{"name":"PLoS Biology","volume":null,"pages":null},"PeriodicalIF":9.8,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11302930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762032","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