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C. albicans pseudouridine glycosidase is important for growth in hygromycin stress and for filamentation. 白色念珠菌假尿苷糖苷酶对潮霉素胁迫下的生长和丝化很重要。
microPublication biology Pub Date : 2025-08-21 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001713
Rheanna E Walther, Emeline Singh, Douglas A Bernstein
{"title":"<i>C. albicans</i> pseudouridine glycosidase is important for growth in hygromycin stress and for filamentation.","authors":"Rheanna E Walther, Emeline Singh, Douglas A Bernstein","doi":"10.17912/micropub.biology.001713","DOIUrl":"10.17912/micropub.biology.001713","url":null,"abstract":"<p><p>When an RNA is no longer needed or has become damaged, it is degraded to its single base components. Pseudouridine is found in all domains of life and is found in a variety of types of RNA. Pseudouridine has ribose and uracil moieties attached via a C-C bond. Cleavage of this bond is performed by pseudouridine glycosidases. We find deletion of the pseudouridine glycosidase from the human fungal pathogen <i>C. albicans</i> leads to sensitivity to hygromycin and changes to filamentation. In addition, deletion of pseudouridine glycosidase leads to the upregulation of several permeases. Our data suggest pseudouridine glycosidases are important for <i>C. albicans</i> fitness.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol: An absolute egg-to-adult viability assay in Drosophila melanogaster. 实验方案：黑腹果蝇卵到成虫的绝对活力测定。
microPublication biology Pub Date : 2025-08-21 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001656
Cassidy Schneider, Spencer Koury, Laurie S Stevison
{"title":"Protocol: An absolute egg-to-adult viability assay in <i>Drosophila melanogaster</i>.","authors":"Cassidy Schneider, Spencer Koury, Laurie S Stevison","doi":"10.17912/micropub.biology.001656","DOIUrl":"10.17912/micropub.biology.001656","url":null,"abstract":"<p><p>Measures of organismal fitness must take into account reproductive output and survivorship across life-history stages. In <i>Drosophila melanogaster</i> , a laboratory model system, these traits are often quantified with egg-laying assays and egg-to-adult viability. While several protocols for automated egg counting exist, these methods typically preclude directly analyzing phenotypic distributions in resulting adults. Here, we digitally score eggs from photographs taken under standard laboratory culturing conditions (cornmeal media in polystyrene vials) using a method compatible with scoring surviving adults. This absolute measurement of egg-to-adult viability, that also allows investigation of survivorship biases, was applied to three commonly used laboratory strains.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12411937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Tetracycline-Inducible Promoter Replacement System for Schizosaccharomyces pombe. 四环素诱导的pombe裂糖菌启动子替换系统。
microPublication biology Pub Date : 2025-08-21 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001759
Samirul Bashir, Sasirekha Sivakumar, Nicholas Rhind
{"title":"A Tetracycline-Inducible Promoter Replacement System for <i>Schizosaccharomyces pombe</i>.","authors":"Samirul Bashir, Sasirekha Sivakumar, Nicholas Rhind","doi":"10.17912/micropub.biology.001759","DOIUrl":"10.17912/micropub.biology.001759","url":null,"abstract":"<p><p>Inducible promoters are essential tools for regulating gene expression. In fission yeast, various inducible promoter systems have been developed over the years, aiding gene function studies. A key challenge with existing promoters is their high expression in the \"off \" state, with most systems showing only about a 10-fold difference between \"on\" and \"off\" conditions. A recent study introduced the <i>PenotetS</i> tetracycline promoter system, achieving nearly a 100-fold dynamic range. However, it was not designed to replace endogenous promoters. In this work, we have adapted the <i>PenotetS</i> system to enable the replacement of gene promoters directly at their endogenous genomic locations.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Snapshot of Defense Systems in Multidrug Resistant Klebsiella pneumoniae. 多重耐药肺炎克雷伯菌防御系统的研究进展。
microPublication biology Pub Date : 2025-08-20 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001752
Tosin Yetunde Senbadejo, Samuel Ntiamoah Osei, Abiola Isawumi
{"title":"Snapshot of Defense Systems in Multidrug Resistant <i>Klebsiella pneumoniae</i>.","authors":"Tosin Yetunde Senbadejo, Samuel Ntiamoah Osei, Abiola Isawumi","doi":"10.17912/micropub.biology.001752","DOIUrl":"10.17912/micropub.biology.001752","url":null,"abstract":"<p><p>Bacterial defense mechanisms protect pathogens from host immunity, bacteriophages, and harsh environments. This study investigates defense systems in multidrug-resistant <i>Klebsiella pneumoniae</i> from Ghanaian hospital ICUs, focusing on CRISPR-Cas, restriction-modification (R-M), and toxin-antitoxin (TA) systems. Genomes of environmental (NS2) and clinical (PS4) strains were sequenced and analyzed using PADLOC, defensefinder, and TADB3.0. NS2 carries 12 defense systems, including CRISPR-Cas, while PS4 has five. Both possess diverse RM and TA systems. These strains, resistant to six antibiotic classes, encode clinically significant defense systems, suggesting microbial exchange between fomites and humans, potentially increasing infection risks in ICU environments requiring targeted surveillance.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12409485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145016834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane. Dnm1是线粒体外膜上Fis1聚集的必要条件。
microPublication biology Pub Date : 2025-08-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001780
Miyu Sasahara, Shunsuke Matsumoto, Yasushi Tamura
{"title":"Dnm1 Is Required for the Focal Clustering of Fis1 on the Mitochondrial Outer Membrane.","authors":"Miyu Sasahara, Shunsuke Matsumoto, Yasushi Tamura","doi":"10.17912/micropub.biology.001780","DOIUrl":"10.17912/micropub.biology.001780","url":null,"abstract":"<p><p>In yeast, mitochondrial fission is mediated by the dynamin-like GTPase Dnm1, which is recruited to the mitochondrial outer membrane by its receptor, Fis1. To investigate the spatial distribution of Fis1, we used the CRISPR-Cas9 system to insert the gene fragment encoding mNeonGreen into the <i>FIS1</i> gene for its N-terminal tagging. Fluorescence microscopy revealed that mNeonGreen-Fis1 appeared as discrete puncta on mitochondria, in addition to a diffuse signal. Here, we show that the focal clustering of Fis1 is dependent on Dnm1. Our findings provide insight into the spatial organization of membrane proteins, highlighting a mechanism by which a downstream effector can influence the distribution of its upstream receptor.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12406049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145002097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sequence Analysis and Modeling of the Repetitive Region of the Long Isoform of Clarinet/CLA-1. 单簧管/CLA-1长异构体重复区序列分析与建模
microPublication biology Pub Date : 2025-08-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001712
Benjamin Hunt, Timothy Hunt, Zhao Xuan
{"title":"Sequence Analysis and Modeling of the Repetitive Region of the Long Isoform of Clarinet/CLA-1.","authors":"Benjamin Hunt, Timothy Hunt, Zhao Xuan","doi":"10.17912/micropub.biology.001712","DOIUrl":"10.17912/micropub.biology.001712","url":null,"abstract":"<p><p>The <i>C. elegans</i> active zone gene <i>cla-1</i> encodes three main isoforms. The long isoform, CLA-1 L, functions beyond regulating synaptic vesicle exocytosis, including synaptic vesicle clustering and endocytic sorting of a transmembrane autophagy protein. CLA-1 L contains a large N-terminal repetitive region. Sequence analysis indicates that this region is enriched with acidic residues and displays disordered structures interspersed with helical sections. While modeling a portion of the repetitive region revealed dynamic transitions between compact and less compact conformations, modeling the entire region suggests a predominantly extended structure. This study sheds light on how CLA-1 L carries out its diverse functions.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12402934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gene model for the ortholog of lin-28 in Drosophila mojavensis. 莫氏果蝇同源基因lin-28的基因模型。
microPublication biology Pub Date : 2025-08-18 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001096
Megan E Lawson, Jessica Cooper, Brian Schwartz, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>lin-28</i> in <i>Drosophila mojavensis</i>.","authors":"Megan E Lawson, Jessica Cooper, Brian Schwartz, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.001096","DOIUrl":"10.17912/micropub.biology.001096","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>lin-28</i> in the <i>Drosophila mojavensis</i> May 2011 (Agencourt dmoj_caf1/DmojCAF1) Genome Assembly (GenBank Accession: GCA_000005175.1 ). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus <i>Drosophila</i> using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12402932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of SARS1 as a Prognostic Biomarker in Invasive Lobular Carcinoma Using Lasso-Logistic Regression. 利用套索-逻辑回归鉴定SARS1作为侵袭性小叶癌预后的生物标志物。
microPublication biology Pub Date : 2025-08-18 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001688
Tyrel Porter, Isaí Soto-Colón, Emir Rinaldi-Pérez, David Rivera-Aponte
{"title":"Identification of SARS1 as a Prognostic Biomarker in Invasive Lobular Carcinoma Using Lasso-Logistic Regression.","authors":"Tyrel Porter, Isaí Soto-Colón, Emir Rinaldi-Pérez, David Rivera-Aponte","doi":"10.17912/micropub.biology.001688","DOIUrl":"10.17912/micropub.biology.001688","url":null,"abstract":"<p><p>Aminoacyl-tRNA synthetases (ARSs) have emerging roles in cancer biology. Specifically, <i>TARS1</i> has been linked to immunosuppressive microenvironments and poor prognosis in breast cancer. To identify other ARS genes with prognostic relevance in invasive lobular carcinoma (ILC), we applied lasso-logistic regression to 41 ARS genes using TCGA RNA-seq data and using patient vital status as the binary outcome. Survival analysis showed <i>SARS1</i> expression was associated with significantly reduced survival across 5 and 10 years, while <i>CARS2</i> showed significance at 5 years only. These findings support <i>SARS1</i> as a candidate prognostic biomarker in ILC and suggest broader relevance for ARS genes in breast cancer outcomes.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12402930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The v 24 Allele is a Missense Mutation Within the Predicted Tryptophan 2,3-dioxygenase Protein Domain of vermilion. v24等位基因是预测的朱砂色氨酸2,3-双加氧酶蛋白结构域内的错义突变。
microPublication biology Pub Date : 2025-08-18 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001760
Lorielle M Raab, Steve Kucera, Brian Oliver, Leif Benner
{"title":"The <i>v <sup>24</sup></i> Allele is a Missense Mutation Within the Predicted Tryptophan 2,3-dioxygenase Protein Domain of <i>vermilion</i>.","authors":"Lorielle M Raab, Steve Kucera, Brian Oliver, Leif Benner","doi":"10.17912/micropub.biology.001760","DOIUrl":"10.17912/micropub.biology.001760","url":null,"abstract":"<p><p>Many loss-of-function mutations in the <i>Drosophila</i> <i>vermilion</i> ( <i>v</i> ) gene have been described. However, the causal mutation in the common <i>v <sup>24</sup></i> allele is unknown. We sequenced different <i>v</i> alleles ( <i>v <sup>24</sup></i> , <i>v <sup>+</sup></i> , and <i>v <sup>1</sup></i> ) to identify candidate <i>v <sup>24</sup> </i> mutations. We identified a single T>A missense mutation shared among the three <i>v <sup>24</sup></i> chromosomes, resulting in a Phe>Ile amino acid change within the predicted tryptophan 2,3-dioxygenase protein domain. This same T>A missense mutation has been independently shown to result in a <i>v <sup>-</sup></i> phenotype by Nivard et al., 1993 and is therefore strong corroborating evidence that this mutation is causal for the <i>v <sup>-</sup></i> phenotype in the <i>v <sup>24</sup></i> allele.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12402933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Determination of minimum inhibitory and lethal concentrations of two lactic acid bacteria Lactiplantibacillus plantarum reveals strain-specific antibiotic resistance. 测定两种乳酸菌的最低抑菌浓度和致死浓度揭示菌株特异性抗生素耐药性。
microPublication biology Pub Date : 2025-08-16 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001615
Maria V Mendoza-Dasilva, Lorraine Rodriguez-Rivera, Imilce A Rodriguez-Fernandez
{"title":"Determination of minimum inhibitory and lethal concentrations of two lactic acid bacteria <i>Lactiplantibacillus plantarum</i> reveals strain-specific antibiotic resistance.","authors":"Maria V Mendoza-Dasilva, Lorraine Rodriguez-Rivera, Imilce A Rodriguez-Fernandez","doi":"10.17912/micropub.biology.001615","DOIUrl":"10.17912/micropub.biology.001615","url":null,"abstract":"<p><p>Lactic acid bacteria (LAB) are widely used as probiotics and in fermented foods, yet their antibiotic resistance profiles remain under-characterized. This study evaluates the antibiotic resistance profiles of two <i>Lactiplantibacillus plantarum</i> ( <i>L. plantarum</i> ) strains, LpWF (isolated from <i>Drosophila melanogaster</i> ) and Lp39 (from cabbage), using broth microdilution methods. Minimum inhibitory concentrations (MICs) and minimum lethal concentrations (MLCs) were determined for six antibiotics. Strain-specific differences were found in MICs for kanamycin, neomycin, and geneticin, while ampicillin and chloramphenicol MICs were similar. Both strains exhibited intrinsic resistance to vancomycin. These findings contribute to efforts to characterize the LAB resistome and inform probiotic strain selection.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12398696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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