microPublication biologyPub Date : 2025-02-15eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001487
Kalli J Simmons, Amandine R Lambert, Marius W Loekken, Lorelei G Schreiner, Corey R Copley, Torrent H Murthy, Amani S Nelson, David B Rosenberg, Adrian L Vanderputten, Alex Broussard, Kathryn Shriver, Marie P Fogarty
{"title":"Genome Sequences of three CT cluster Bacteriophages isolated in Durham, North Carolina on <i>Gordonia rubripertincta</i>.","authors":"Kalli J Simmons, Amandine R Lambert, Marius W Loekken, Lorelei G Schreiner, Corey R Copley, Torrent H Murthy, Amani S Nelson, David B Rosenberg, Adrian L Vanderputten, Alex Broussard, Kathryn Shriver, Marie P Fogarty","doi":"10.17912/micropub.biology.001487","DOIUrl":"https://doi.org/10.17912/micropub.biology.001487","url":null,"abstract":"<p><p>PotPie, HippoPololi and BillDoor are bacteriophages with siphoviral morphologies that were isolated from soil in North Carolina using <i>Gordonia rubripertincta</i> . The three phages are all grouped in the CT cluster, with genomes of 48182 bp, 45423 bp, and 44875 bp, respectively, and are predicted to be lytic.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143545059","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}
microPublication biologyPub Date : 2025-02-14eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001503
Lesley A Turner, Anna Bowman Fletcher, Alaina H Willet, Kathleen L Gould
{"title":"Characterization and comparison of temperature-sensitive <i>Schizosaccharomyces pombe</i> mutants of the septation initiation network scaffolds, Cdc11 and Sid4.","authors":"Lesley A Turner, Anna Bowman Fletcher, Alaina H Willet, Kathleen L Gould","doi":"10.17912/micropub.biology.001503","DOIUrl":"10.17912/micropub.biology.001503","url":null,"abstract":"<p><p>The <i>Schizosaccharomyces pombe</i> septation initiation network (SIN) is required for cytokinesis and septation. The SIN includes a protein kinase cascade that is assembled at spindle pole bodies (SPBs) in a cell cycle specific manner on a scaffold consisting of Cdc11 , related to human centriolin, and the a-helical protein Sid4 . Here, we characterized temperature-sensitive <i>cdc11</i> and <i>sid4</i> mutants isolated in the 1990s. We determined the mutations within each allele, examined their phenotypes, and analyzed their growth compared with previously characterized mutant alleles. The new mutants described here expand the toolkit for studying how the SIN assembles at SPBs.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143545012","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}
microPublication biologyPub Date : 2025-02-14eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001386
Maya Qaddourah, Sajith Jayasinghe
{"title":"Bioinformatics Analysis Suggests That SE_1780 Protein From <i>Staphylococcus Epidermidis</i> May Be a Member of the Fph Family of Lipases.","authors":"Maya Qaddourah, Sajith Jayasinghe","doi":"10.17912/micropub.biology.001386","DOIUrl":"https://doi.org/10.17912/micropub.biology.001386","url":null,"abstract":"<p><p>The Protein Data Bank entry for protein SE_1780 from <i>Staphylococcus epidermidis</i> lists the function as unknown. We leveraged the framework outlined in the Biochemistry Authentic Scientific Inquiry Laboratory and used bioinformatics tools to ascertain the function of the protein. Based on our analysis, we posit that SE_1780 is a lipase of the α/β hydrolase family with a proposed active site catalytic triad composed of Ser 144, Asp 235, and His 269. Further we identified the lipase FphD as having significant sequence identity to protein SE_1780 and suggest that the protein is a member of the Fph family of lipases from <i>S. epidermidis</i> .</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143545003","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}
microPublication biologyPub Date : 2025-02-13eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001038
Megan E Lawson, Ryan J Dufur, Braden Wright, Isabel G Wellik, Lindsey J Long, Jeffrey S Thompson, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>Roc1a</i> in <i>Drosophila mojavensis</i>.","authors":"Megan E Lawson, Ryan J Dufur, Braden Wright, Isabel G Wellik, Lindsey J Long, Jeffrey S Thompson, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.001038","DOIUrl":"10.17912/micropub.biology.001038","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>Regulator of cullins 1a</i> ( <i>Roc1a</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":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11868922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143545056","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}
microPublication biologyPub Date : 2025-02-12eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001467
Isa Özdemir, Florian A Steiner
{"title":"<i>sqt-3(sc63)</i> is an alternative CRISPR/Cas9 co-conversion marker in <i>Caenorhabditis elegans</i>.","authors":"Isa Özdemir, Florian A Steiner","doi":"10.17912/micropub.biology.001467","DOIUrl":"10.17912/micropub.biology.001467","url":null,"abstract":"<p><p>The identification of genome-edited individuals by CRISPR/Cas9 in <i>Caenorhabditis elegans</i> often relies on the introduction of a second mutation with a visible phenotype. Popular targets for such co-conversion are <i>dpy-10</i> and <i>sqt-1</i> , both located on chromosome II. In this study, we introduce <i>sqt-3 ( sc63 )</i> <i>V</i> as an alternative CRISPR/Cas9 co-conversion marker to facilitate the generation and detection of genome edits in <i>C. elegans</i> . Its location on chromosome V makes <i>sqt-3</i> a desirable alternative to <i>dpy-10</i> and <i>sqt-1</i> when editing targets on chromosome II. Additionally, the conserved nature of <i>sqt-3</i> provides a potential applicability in other nematode species.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11868924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544943","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}
microPublication biologyPub Date : 2025-02-12eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001517
Stephen A Banse, Anna L Coleman-Hulbert, Christine A Sedore, Erik Johnson, Gordon J Lithgow, Monica Driscoll, Patrick C Phillips
{"title":"<i>Caenorhabditis</i> Intervention Testing Program: all-trans retinoic acid-related compounds tamibarotene and bakuchiol do not extend lifespan in <i>Caenorhabditis</i> nematodes.","authors":"Stephen A Banse, Anna L Coleman-Hulbert, Christine A Sedore, Erik Johnson, Gordon J Lithgow, Monica Driscoll, Patrick C Phillips","doi":"10.17912/micropub.biology.001517","DOIUrl":"10.17912/micropub.biology.001517","url":null,"abstract":"<p><p>The <i>Caenorhabditis</i> Intervention Testing Program recently characterized the longevity-promoting effects of the vitamin A derivative all-trans retinoic acid (atRA). Here, we test two atRA-related compounds, tamibarotene and bakuchiol, for longevity effects in three strains of <i>Caenorhabditis</i> species. Both tamibarotene, a potent RAR agonist, and bakuchiol, a meroterpene derived from <i>Psoralea corylifolia</i> , showed no significant increase in lifespan across a dosage range of six concentrations. Additionally, bakuchiol was broadly toxic at higher doses. These findings highlight the specificity of atRA's longevity effects and suggest that compounds related to atRA may not universally promote lifespan extension.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11868923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143544993","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}
microPublication biologyPub Date : 2025-02-11eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001489
MacKenzie Patterson, Adriana R Andrus, Conner Bell, Justin J Bromell, Daniel Buchanan, Diana H Chammout, Wisler X Charles, Joseph E Cummings, Anabelle Dabesh, Nixon Deleon Garcia, Kevin W Dickerson, Toritsemose R Emiko, Sara Fathi, Tavis J Floyd, Hailee Gragg, Senai B Griffin, Lauren Heininger, Amber Ibrahim, Cameron Ivey, Ahmad Jackson, Lamar Jackson, Deepthy Jeeva, Leland E Jones, Kinaan Kana, Anthony S Kemp, Ayyoob Khan, Megan Rose Kowal, Shane J Kowaleski, Tristan C Lago, Eli Lynch, Shirin Maalhagh Fard, Khalil Makki, Tanya Moaikel, Jordan M Mosby, Dallas A Ricketts, Reese J Saho, Florine Sanchez, Caden H Sauerbrey, Paul C Sprowl, Kaitlyn M Sullivan, Michael Thomas, Jaden J Tripette, Chimezie Ugbaja, Gregory A Volcy, Jamarr Watson, De'Andre Williams, Kayla L Bieser, Alexandra Peister, Jamie Siders, Jacob D Kagey
{"title":"The <i>M.3.2</i> mutation in <i>Drosophila melanogaster</i> mapped as a novel allele of <i>tout-velu</i>.","authors":"MacKenzie Patterson, Adriana R Andrus, Conner Bell, Justin J Bromell, Daniel Buchanan, Diana H Chammout, Wisler X Charles, Joseph E Cummings, Anabelle Dabesh, Nixon Deleon Garcia, Kevin W Dickerson, Toritsemose R Emiko, Sara Fathi, Tavis J Floyd, Hailee Gragg, Senai B Griffin, Lauren Heininger, Amber Ibrahim, Cameron Ivey, Ahmad Jackson, Lamar Jackson, Deepthy Jeeva, Leland E Jones, Kinaan Kana, Anthony S Kemp, Ayyoob Khan, Megan Rose Kowal, Shane J Kowaleski, Tristan C Lago, Eli Lynch, Shirin Maalhagh Fard, Khalil Makki, Tanya Moaikel, Jordan M Mosby, Dallas A Ricketts, Reese J Saho, Florine Sanchez, Caden H Sauerbrey, Paul C Sprowl, Kaitlyn M Sullivan, Michael Thomas, Jaden J Tripette, Chimezie Ugbaja, Gregory A Volcy, Jamarr Watson, De'Andre Williams, Kayla L Bieser, Alexandra Peister, Jamie Siders, Jacob D Kagey","doi":"10.17912/micropub.biology.001489","DOIUrl":"10.17912/micropub.biology.001489","url":null,"abstract":"<p><p>In <i>Drosophila melanogaster</i> genetic screens are often used to identify genes associated with different biological processes. Here, we have utilized the Flp/FRT system to generate mitotic clones within the developing eye. These clones were screened for mutations that disrupt cell division, organ patterning, and cell growth. One such mutation from this screen, mutant M.3.2, resulted in an expansion of the cuticle within the area normally covered by ommatidium as well as an overall smaller eye size. Genetic and molecular mapping revealed this mutation to be in the gene, t <i>out-velu</i> ( <i>ttv</i> ).</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11868921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143545061","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}
microPublication biologyPub Date : 2025-02-07eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001394
John Heido, Simon Keng, Hulya Poyrazoglu, Ekta Priyam, Sajith Jayasinghe
{"title":"Not All Bacterial Outer-Membrane Proteins Are β-Barrels.","authors":"John Heido, Simon Keng, Hulya Poyrazoglu, Ekta Priyam, Sajith Jayasinghe","doi":"10.17912/micropub.biology.001394","DOIUrl":"10.17912/micropub.biology.001394","url":null,"abstract":"<p><p>The discovery of Wza, an octomeric helical barrel integral bacterial outer-transmembrane protein, has challenged the widely held understanding that all integral outer-membrane proteins of Gram-negative bacteria are closed β-barrels composed of transmembrane β- strands. Wza is a member of the Outer-Membrane Polysaccharide Exporter family and our bioinformatics analysis suggests that other members of the family may also contain outer-membrane transmembrane segments that are helical. A review of the literature indicates that in addition to Wza, outer-membrane core complex proteins of the type IV secretion systems also contain transmembrane segments that are helical.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11845990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484994","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}
microPublication biologyPub Date : 2025-02-07eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001509
Tyler J Butsch, Alyssa E Johnson, K Adam Bohnert
{"title":"Meiotic activation of Mitf/TFEB declines with age in the <i>Drosophila</i> testis.","authors":"Tyler J Butsch, Alyssa E Johnson, K Adam Bohnert","doi":"10.17912/micropub.biology.001509","DOIUrl":"10.17912/micropub.biology.001509","url":null,"abstract":"<p><p>Lysosome activity regulates germline development in multiple species. In the <i>Drosophila</i> testis, lysosomes activate as germ cells exit mitosis and enter meiosis. Notably, reduced activity of germ-cell lysosomes, which is seen during aging, leads to fewer viable sperm. Here, we investigated the activity of Mitf/TFEB, a master regulator of lysosome biogenesis, during <i>Drosophila</i> spermatogenesis. We discovered that Mitf activity was upregulated in meiotic-stage spermatocytes, consistent with the lysosome-activation pattern. However, Mitf activity in spermatocytes declined in older males, concurrent with reduced expression of a Mitf-targeted V-ATPase component. These findings provide insight into the regulation of upstream lysosome controls during spermatogenesis.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11845987/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484981","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}
microPublication biologyPub Date : 2025-02-07eCollection Date: 2025-01-01DOI: 10.17912/micropub.biology.001444
Jonathan G Lawton, Alyssa D Reddy, Victoria M Herrera, Riley J Strain, Elroie E Mekonnen, Frank W Stearns, Samuel G Obae, Rivka L Glaser
{"title":"Genome sequences of three temperate actinobacteriophages from clusters FA and AS.","authors":"Jonathan G Lawton, Alyssa D Reddy, Victoria M Herrera, Riley J Strain, Elroie E Mekonnen, Frank W Stearns, Samuel G Obae, Rivka L Glaser","doi":"10.17912/micropub.biology.001444","DOIUrl":"10.17912/micropub.biology.001444","url":null,"abstract":"<p><p>Three novel temperate siphoviruses, Juno112, KHumphrey, and ChuckDuck, were isolated from soil at Stevenson University using the bacterium <i>Arthrobacter globiformis</i> B-2979. Based on gene content similarity, Juno112 and KHumphrey are assigned to actinobacteriophage cluster AS3 and ChuckDuck to cluster FA. All three phages encode tyrosine recombinases, with ChuckDuck encoding two.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11845989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143484978","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}
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