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Three Cluster O mycobacteriophages isolated in Philadelphia, PA. 在宾夕法尼亚州费城分离到的三种 O 型嗜分枝杆菌群。
microPublication biology Pub Date : 2024-11-12 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001375
Alexander DiGiacomo, Nicole Bowen, Thientrinh Nguyen, Sophia Borrello, Naomi Brooks, Ella Bubeck, Cole Buker, Lauren Charboneau, Ariana Corapi, Katelyn Derstine, Leah Fries, Olivia Graveley, Isabella Jimenez, Paul Lacour, Ignacio Llorente Fernandez, Madeleine Malesich, Sydney Matusiak, Jacob McNelly, Skyler Reka, Simon Sheppard, Lauren Zile, Ava Smith, Jessalyn Aquilino, Danielle Niblock, Anne Winkler, Leya Givvines, C Nicole Sunnen, Julia Lee-Soety
{"title":"Three Cluster O mycobacteriophages isolated in Philadelphia, PA.","authors":"Alexander DiGiacomo, Nicole Bowen, Thientrinh Nguyen, Sophia Borrello, Naomi Brooks, Ella Bubeck, Cole Buker, Lauren Charboneau, Ariana Corapi, Katelyn Derstine, Leah Fries, Olivia Graveley, Isabella Jimenez, Paul Lacour, Ignacio Llorente Fernandez, Madeleine Malesich, Sydney Matusiak, Jacob McNelly, Skyler Reka, Simon Sheppard, Lauren Zile, Ava Smith, Jessalyn Aquilino, Danielle Niblock, Anne Winkler, Leya Givvines, C Nicole Sunnen, Julia Lee-Soety","doi":"10.17912/micropub.biology.001375","DOIUrl":"10.17912/micropub.biology.001375","url":null,"abstract":"<p><p>We report here the discovery and characterization of three novel bacteriophages infecting <i>Mycobacterium smegmatis</i> . These siphoviruses were isolated from soil collected in urban areas around Saint Joseph's University in Philadelphia. Mycobacteriphages Idergollasper, FoulBall, and Schuy are assigned to actinobacteriophage cluster O based on gene content similarity, and have prolate capsids typical for this cluster.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11600133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741675","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 Thor in Drosophila yakuba. yakuba 果蝇 Thor 同源物的基因模型。
microPublication biology Pub Date : 2024-11-12 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001029
Jhilam Dasgupta, Emile Moura Coelho da Silva, Gregory Sileo, Joyce Stamm, Thomas C Giarla, Chinmay P Rele
{"title":"Gene model for the ortholog of <i>Thor</i> in <i>Drosophila yakuba</i>.","authors":"Jhilam Dasgupta, Emile Moura Coelho da Silva, Gregory Sileo, Joyce Stamm, Thomas C Giarla, Chinmay P Rele","doi":"10.17912/micropub.biology.001029","DOIUrl":"10.17912/micropub.biology.001029","url":null,"abstract":"<p><p>Gene model for the ortholog of Thor ( <i>Thor</i> ) in the <i>D. yakuba</i> May 2011 (WUGSC dyak_caf1/DyakCAF1) Genome Assembly (GenBank Accession: GCA_000005975.1 ) of <i>Drosophila yakuba</i> . 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":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11600134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741670","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
Drosophila melanogaster c306 GAL4 is not specific to ovarian cells. 黑腹果蝇 c306 GAL4 对卵巢细胞没有特异性。
microPublication biology Pub Date : 2024-11-11 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001383
Ashley C Goll, Kaden H Bex, Tina L Tootle
{"title":"<i>Drosophila melanogaster</i> c306 GAL4 is not specific to ovarian cells.","authors":"Ashley C Goll, Kaden H Bex, Tina L Tootle","doi":"10.17912/micropub.biology.001383","DOIUrl":"10.17912/micropub.biology.001383","url":null,"abstract":"<p><p>A widely used genetic tool in <i>Drosophila melanogaster</i> is the GAL4/UAS system. This bipartite system allows for tissue and cell-specific expression and is used for both overexpression and RNA interference (RNAi) knockdown studies. Here we provide evidence that c306 GAL4 expression is not restricted to somatic ovarian cells but is also expressed in cells giving rise to adult bristles. Future work is needed to fully define the cell-specific expression pattern c306 GAL4.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11589785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142735218","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
Transgenerational Sterility of a Transgenic C. elegans : A Cautionary Tale. 转基因 elegans 的跨代不育：一个警世故事。
microPublication biology Pub Date : 2024-11-08 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001343
Zachary Leydig, Judith Yanowitz
{"title":"Transgenerational Sterility of a Transgenic <i>C. elegans</i> : A Cautionary Tale.","authors":"Zachary Leydig, Judith Yanowitz","doi":"10.17912/micropub.biology.001343","DOIUrl":"10.17912/micropub.biology.001343","url":null,"abstract":"<p><p>The integration of fluorescent protein tags (GFP, mScarlet, mNeon, etc) by CRISPR is often inefficient due to the size of the tags (hundreds of base pairs). To facilitate fluorescent tagging, the split-GFP and split-Scarlet systems have been optimized for use in <i>C. elegans</i> (Goudeau et al., 2021). In <i>C. elegans</i> , <i>glh-1 ::T2A::wrmScarlet(1-10)</i> allows germline gene expression of red fusion proteins. While initial studies reported wild-type broods at both permissive and non-permissive temperatures, we report here that at least one such transgene confers sterility after continuous culturing at 25.5 °C. This serves as a cautionary tale for use of the <i>glh-1</i> driver and/or T2A::mScarlet fusions to this protein.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11584908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711823","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
Conserved region of human TDP-43 is structurally similar to membrane binding protein FARP1 and protein chaperons BAG6 and CYP33. 人类 TDP-43 的保守区在结构上与膜结合蛋白 FARP1 以及蛋白伴侣 BAG6 和 CYP33 相似。
microPublication biology Pub Date : 2024-11-07 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001388
Ljiljana Sjekloća, Emanuele Buratti
{"title":"Conserved region of human TDP-43 is structurally similar to membrane binding protein FARP1 and protein chaperons BAG6 and CYP33.","authors":"Ljiljana Sjekloća, Emanuele Buratti","doi":"10.17912/micropub.biology.001388","DOIUrl":"10.17912/micropub.biology.001388","url":null,"abstract":"<p><p>Transactive response DNA-binding protein of 43 KDa (TDP-43) is important for RNA metabolism in all animals and in humans is involved in neuromuscular diseases. Full-length TDP-43 is prone to oligomerization and misfolding what renders difficult its characterization. We report that TDP-43 domains are structurally similar to lipid binding protein FARP1 and protein chaperons BAG6 and CYP33. Sequence analysis suggests putative lipid binding sites throughout TDP-43 and in vitro thioflavin T fluorescence assays show that cholesterol and phosphatidylcholine affect fibrillation of recombinant TDP-43 fragments. Our findings suggest that TDP-43 can bind lipids directly and it may contribute to its own chaperoning.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712071","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
Generation of an endogenous auxin inducible degron-tagged SPAS-1/spastin to investigate its targeted depletion in C. elegans neurons. 生成内源性辅酶诱导性脱粒子标记的 SPAS-1/spastin，以研究其在秀丽隐杆线虫神经元中的定向消耗。
microPublication biology Pub Date : 2024-11-07 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001328
Emily Brown, Samantha Kuszynski, Faith Akoachere, James Feduccia, Lili Malatinszky, Eric S Luth
{"title":"Generation of an endogenous auxin inducible degron-tagged SPAS-1/spastin to investigate its targeted depletion in <i>C. elegans</i> neurons.","authors":"Emily Brown, Samantha Kuszynski, Faith Akoachere, James Feduccia, Lili Malatinszky, Eric S Luth","doi":"10.17912/micropub.biology.001328","DOIUrl":"10.17912/micropub.biology.001328","url":null,"abstract":"<p><p>To facilitate investigations of the microtubule severing protein spastin and its specific role in neurons, we aimed to create a <i>C. elegans</i> strain in which the spastin homolog SPAS-1 is visible and can be degraded with spatial and temporal precision. We used CRISPR-Cas9 to fuse an auxin-inducible degron and mScarlet to the endogenous SPAS-1 protein, enabling degradation of SPAS-1 in neurons during desired life stages. DNA sequencing confirmed in-frame insertion with the SPAS-1 N-terminus and fluorescence microscopy revealed endogenous SPAS-1 throughout the CRISPR-edited worms. Auxin treatment in <i>rgef-1::TIR1; mScarlet::AID*::3xFLAG::spas-1</i> animals reduced mScarlet::SPAS-1 fluorescence in neuronal ganglia.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711199","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
Examining hydrogen peroxide-containing organelles in seaweeds. 研究海藻中含有过氧化氢的细胞器。
microPublication biology Pub Date : 2024-11-07 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001217
Joseph S Ramahi, Keiko L Hokeness, John Gonzales, Jadi Allen, Roman D P Marquez, Robin A A Rojas, Sergey Ingram, Sara Capponi, Jennifer E Smith, Brian von Herzen, John Dueber, Zheng-Hui He
{"title":"Examining hydrogen peroxide-containing organelles in seaweeds.","authors":"Joseph S Ramahi, Keiko L Hokeness, John Gonzales, Jadi Allen, Roman D P Marquez, Robin A A Rojas, Sergey Ingram, Sara Capponi, Jennifer E Smith, Brian von Herzen, John Dueber, Zheng-Hui He","doi":"10.17912/micropub.biology.001217","DOIUrl":"10.17912/micropub.biology.001217","url":null,"abstract":"<p><p>Seaweeds, particularly the red seaweed <i>Asparagopsis taxiformis</i> , produce and sequester bromomethanes, which are known for mitigating methane emissions in ruminants when used as a feed supplement. Bromomethane synthesis requires hydrogen peroxide (H <sub>2</sub> O <sub>2</sub> ). We developed a staining assay utilizing 3,3'-diaminobenzidine (DAB) for identifying H <sub>2</sub> O <sub>2</sub> in three groups of seaweeds (red, brown, and green), including intensely pigmented species. Our findings indicate the previously identified \"gland cell\" in <i>Asparagopsis taxiformis</i> , responsible for bromoform synthesis and retention, is a specialized large organelle rich in H <sub>2</sub> O <sub>2</sub> . Our study introduces an effective survey tool to identify promising seaweed species abundant in bromoform from diverse marine habitats.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712084","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
Mutation of GLP-1/Notch RAM domain results in a strong Glp-1 phenotype. GLP-1/Notch RAM 结构域的突变会导致强烈的 Glp-1 表型。
microPublication biology Pub Date : 2024-11-07 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001391
Sarah L Crittenden, Stephany J Costa Dos Santos, Sindhu Battula, Judith Kimble
{"title":"Mutation of GLP-1/Notch RAM domain results in a strong Glp-1 phenotype.","authors":"Sarah L Crittenden, Stephany J Costa Dos Santos, Sindhu Battula, Judith Kimble","doi":"10.17912/micropub.biology.001391","DOIUrl":"10.17912/micropub.biology.001391","url":null,"abstract":"<p><p>The distal tip cell niche uses GLP-1 /Notch signaling to maintain <i>C. elegans</i> germline stem cells. The RAM domain, which resides within the intracellular portion of the GLP-1 /Notch receptor, is integral to formation of a signaling-dependent transcription activation complex. Here we report the generation of a mutation in the GLP-1 RAM domain, created in a GLP-1 /Notch receptor with a C-terminal V5 tag. The phenotype of <i>glp-1 (RAM <sup>mut</sup> ) <sup>V5</sup></i> homozygotes is similar to that of <i>glp-1</i> null mutants, but expression of the GLP-1 (RAM <sup>mut</sup> ) <sup>V5</sup> protein was normal in the <i>glp-1 (RAM <sup>mut</sup> ) <sup>V5</sup> </i> heterozygotes. We conclude that the RAM mutation abolishes receptor activity.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711561","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
Genome Sequence of Arthrobacter globiformis B-2979 Phage JanetJ. 球形节杆菌 B-2979 噬菌体 JanetJ 的基因组序列。
microPublication biology Pub Date : 2024-11-07 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001351
Arib Ahsan, Ruby S Crosthwait, Josephine J Crosthwait, Srilekha Davuluri, Omoye N Ehimare, Yihao Fan, Tiarra Nikitha Joseph Philomen Raju, Jamie Kim, Alexander Y Lee, Nicholas K Odani, Mugil V Shanmugam, Anmol Singhal, Alana J Snyder, Jessica W Sy, Grace Y Wang, George W Zhou, Christa T Bancroft
{"title":"Genome Sequence of <i>Arthrobacter globiformis B-2979</i> Phage <i>JanetJ</i>.","authors":"Arib Ahsan, Ruby S Crosthwait, Josephine J Crosthwait, Srilekha Davuluri, Omoye N Ehimare, Yihao Fan, Tiarra Nikitha Joseph Philomen Raju, Jamie Kim, Alexander Y Lee, Nicholas K Odani, Mugil V Shanmugam, Anmol Singhal, Alana J Snyder, Jessica W Sy, Grace Y Wang, George W Zhou, Christa T Bancroft","doi":"10.17912/micropub.biology.001351","DOIUrl":"10.17912/micropub.biology.001351","url":null,"abstract":"<p><p>Phage JanetJ was isolated on <i>Arthrobacter globiformis B-2979</i> and has siphovirus morphology. JanetJ's genome consists of 36,986 base pairs, encoding 52 putative protein-coding genes. JanetJ adds to the small number of previously isolated cluster FO phages, none of which encode identifiable immunity repressor or integrase functions, with the exception of phage Maja.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711339","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
Separation of function mutants underline multiple roles of the Srs2 helicase/translocase in break-induced replication in Saccharomyces cerevisiae. 功能分离突变体强调了 Srs2 螺旋酶/翻译酶在酿酒酵母断裂诱导复制中的多重作用。
microPublication biology Pub Date : 2024-11-07 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001369
Matteo Di Terlizzi, Giordano Liberi, Achille Pellicioli
{"title":"Separation of function mutants underline multiple roles of the Srs2 helicase/translocase in break-induced replication in <i>Saccharomyces cerevisiae</i>.","authors":"Matteo Di Terlizzi, Giordano Liberi, Achille Pellicioli","doi":"10.17912/micropub.biology.001369","DOIUrl":"10.17912/micropub.biology.001369","url":null,"abstract":"<p><p>All cells are commonly exposed to DNA double-strand breaks (DSBs), which must be properly repaired to avoid genomic instability. Break-Induced Replication (BIR) is a Homologous Recombination subpathway, which repairs DSBs resulting in mutagenesis, chromosome translocations and loss of heterozygosity. In budding yeast, the Srs2 DNA helicase/translocase plays both anti- and pro-recombination roles. Interestingly, Srs2 activities are required to support BIR completion. Here, we employ a interchromosomal BIR assay in <i>S. cerevisiae</i> to characterize Cdk1-dependent phosphorylation, ATPase and helicase activities of Srs2. Our results further expand our understanding of the multifaced role played by Srs2 in DSB recombination repair.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11582884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142711722","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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