microPublication biology最新文献

{"title":"Structures of <i>Cutibacterium acnes</i> hyaluronate lyases suggest a correlation between active site opened/closed state and conformation of abutting loop.","authors":"Randall McNally, Ramachandran Murali","doi":"10.17912/micropub.biology.001237","DOIUrl":"10.17912/micropub.biology.001237","url":null,"abstract":"<p><p>The structures of hyaluronate lyases from two <i>Cutibacterium acnes</i> strains have been reported recently and show open catalytic clefts. We compared these open structures with more closed structures of homologous lyases and found that the conformation of a loop that abuts the catalytic cleft is seemingly correlated with the opening and closing of the cleft. We illustrate that the loop conformation seen in the open lyase appears incompatible with a closed catalytic cleft, and vice versa; however, mutations designed to disrupt the loop conformation did not significantly affect catalytic activity.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11322831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141984126","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}

{"title":"Endoplasmic reticulum and inner nuclear membrane ubiquitin-conjugating enzymes Ubc6 and Ubc7 confer resistance to hygromycin B in <i>Saccharomyces cerevisiae</i>.","authors":"Sophia L Owutey, Katrina A Procuniar, Emmanuel Akoto, Jacob C Davis, Rachel M Vachon, LiLi F O'Malley, Hayden O Schneider, Philip J Smaldino, Jason D True, Ashley L Kalinski, Eric M Rubenstein","doi":"10.17912/micropub.biology.001276","DOIUrl":"10.17912/micropub.biology.001276","url":null,"abstract":"<p><p>Aberrant endoplasmic reticulum (ER) and inner nuclear membrane (INM) proteins are destroyed through ER-associated degradation (ERAD) and INM-associated degradation (INMAD). We previously showed the Hrd1, Doa10, and Asi ERAD and INMAD ubiquitin ligases (E3s) in <i>Saccharomyces cerevisiae</i> confer resistance to hygromycin B, which distorts the ribosome decoding center. Here, we assessed the requirement of Ubc6 and Ubc7, the primary ERAD and INMAD ubiquitin-conjugating enzymes (E2s) for hygromycin B resistance. Loss of either E2 sensitized cells to hygromycin B, with <i>UBC7</i> deletion having a greater impact, consistent with characterized roles for Ubc6 and Ubc7 in ER and INM protein quality control.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141977371","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}

{"title":"A new eye lens structure associated with capsule/basement membrane growth.","authors":"Wouterus Tm Gruijters","doi":"10.17912/micropub.biology.000828","DOIUrl":"10.17912/micropub.biology.000828","url":null,"abstract":"<p><p>Eye lens capsules contained a previously overlooked structure possibly derived from the Zonule of Zinn or lens epithelium. Sheep lens capsule inner surface revealed periodic stripes spaced at about 8µm over an area of more than 200µm long and wide. Ultra thin sections of a similar area revealed the periodic insertion of cell feet into the lens capsule with numerous vesicles. Cryosections of entire mouse eyes confirmed a similar looking structure. The structure appears in an area of basement membrane growth. A stylized foot-feet model is offered to help visualize the structure in 3D.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141977370","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}

{"title":"Genetic Mapping of <i>prod ^E.3.3</i> , a New Lethal Allele of <i>prod</i>.","authors":"Emma Johnson, Talbot Kinney, Hannah Luellen, Rhiannan Amerud, Daysha R Anderson, Marie Anderson, Arnelyn Mae Andres, Rameel Arshad, Kylie Babin-Howard, Dede G Barrigah, Addison Beauregard, Leah Beise, Nolan Christofferson, Elijah L David, Luke DeWaard, Maya Diaz, Lily Donner, Natalie Ehlinger, Diellza Elmazi, Riley Engelhardt, Tamkanat Farheen, Mark M Figueroa, Soren Flaten, Madison Frush, Elizabeth Gonzalez, Jaylen Goolsby, Estefania Guzman, Logan Hanson, John Hejl, Jackson Heuschel, Brianna Higgins, Brylee Hoeppner, Daijah Hollins, Josette Knutson, Rachel Lemont, Mia Lopez, Samantha Martin, Trinity May, Abby McDade, Nearyroth Men, Ellie Meyer, Caroline R Mickle, Sebastian Mireles, Avery Mize, Jaiden Neuhaus, April Ost, Sarah Piane, Makenzie Pianovski, Aliya Rangel, Jessica Reyes, Alexandra Ruttenberg, Jacob D Sachs, Brandon Schluns, Nicholas Schroeder, Peighton R Skrobot, Cylie Smith, Sydney Stout, Andrew Valenzuela, Kaiden P Vinavich, Amber K Weaver, Michael Yager, Jose Zaragoza, Gabriela Zawadzki, Weam El Rahmany, Nicole L Scheuermann, Hemin P Shah, Kayla L Bieser, Paula Croonquist, Olivier Devergne, Elizabeth E Taylor, Jacqueline K Wittke-Thompson, Jacob D Kagey, Stephanie Toering Peters","doi":"10.17912/micropub.biology.001236","DOIUrl":"10.17912/micropub.biology.001236","url":null,"abstract":"<p><p>The <i>E.3.3</i> mutation was generated in a Flp/FRT EMS screen for conditional mutations that cause growth and developmental defects in a genetic background that blocks apoptosis. The mutations were conditional, based on the <i>Dark ⁸²</i> allele being present on the starting chromosome, and blocking canonical apoptosis in a homozygous state. The <i>E.3.3</i> mosaic eyes exhibit defects in eye development including patches of rough eye and irregular surface structure. Whole Genome Sequencing and complementation mapping revealed <i>E.3.3</i> as an allele of <i>prod</i> . Prod is a DNA-binding protein that binds satellite repeats and is involved in chromocenter formation during mitosis. Here we present a novel allele of <i>prod</i> , <i>prod ^E.3.3</i> , that disrupts the functional region of the Prod protein resulting in disruption of typical eye structure, likely due to disruption of chromatid separation during development.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141977644","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}

{"title":"Transcriptomic Meta-Analysis Identifies Upregulated Clotting and Fibrinolysis Pathways in Colorectal Cancer Tumors Containing Hereditary PMS2 Mismatch Repair Deficiency.","authors":"Trenton M Gibson, Mauri D Spendlove, Naomi Rapier-Sharman, Brett E Pickett","doi":"10.17912/micropub.biology.001159","DOIUrl":"10.17912/micropub.biology.001159","url":null,"abstract":"<p><p>Lynch Syndrome is characterized by deficient mismatch repair (dMMR) components. We performed a meta-analysis of multiple RNA-sequencing datasets from patients with different dMMR variants (PMS2, MLH1, and MSH2) to better characterize the unique transcriptional profiles. Our results reveal enriched signaling pathways from tumor samples with germline mutations in the PMS2 gene including upregulation in pathways related to intrinsic and extrinsic prothrombin activation, fibrinolysis, and uPA/uPAR-mediated signaling. These pathways have been associated with tumor growth, invasiveness, and metastasis. This work provides support for further exploration into the role of PMS2 in tumor development, and as a potential therapeutic mechanism.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11320117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141977372","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}

{"title":"<i>Takakia</i> possesses a key marker of embryophyte sporopollenin.","authors":"Dae-Yeon Suh, Damanpreet K Sraan, Neil W Ashton","doi":"10.17912/micropub.biology.001165","DOIUrl":"10.17912/micropub.biology.001165","url":null,"abstract":"<p><p>The enigmatic moss, <i>Takakia lepidozioides</i> , possesses a particular type III polyketide synthase, ASCL (Anther-Specific Chalcone synthase-Like), that is an identifying marker for genuine sporopollenin in the walls of embryophyte spores and pollen grains. By contrast, a survey of all algae with sequenced genomes confirms that they do not possess ASCL and, therefore, their spore walls are not composed of sporopollenin.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918271","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}

{"title":"Visualization of gene expression in <i>Pristionchus pacificus</i> with smFISH and in situ HCR.","authors":"Yasmin H Ramadan, Oliver Hobert","doi":"10.17912/micropub.biology.001274","DOIUrl":"10.17912/micropub.biology.001274","url":null,"abstract":"<p><p>Single molecule fluorescence in situ hybridization (smFISH) and in situ hybridization chain reaction (HCR) have become powerful tools to visualize gene expression in many different animal species. We show here that smFISH and in situ HCR can be put to effective use in the satellite nematode model organism <i>Pristionchus pacificus .</i> Examining the expression of a homeobox gene ( <i>Ppa-unc-30)</i> , we found that HCR is more sensitive than smFISH. We confirmed the robustness of HCR by visualization of the expression of several genes involved in neurotransmitter synthesis or transport ( <i>Ppa-unc-25 /GAD, Ppa-unc-17/VAChT, Ppa-eat-4 /VGLUT).</i> Combined with its relative cost-effectiveness compared to smFISH analysis, in situ HCR constitutes a useful addition to the toolbox for <i>P. pacificus</i> research <i>.</i></p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11316217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918273","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}

{"title":"<i>osm-5p-</i> driven fluorophores are differentially expressed in <i>ccpp-1Δ</i> and <i>nekl-4Δ</i> mutant ciliated neurons.","authors":"Kaiden M Power, Maureen M Barr","doi":"10.17912/micropub.biology.001245","DOIUrl":"10.17912/micropub.biology.001245","url":null,"abstract":"<p><p>Intraflagellar transport (IFT) involves the coordinated transport of molecular motors and other proteins and is required for ciliogenesis and ciliary maintenance. The <i>C. elegans</i> IFT protein OSM-5 /IFT88 is expressed in a majority of the ciliated neurons in the animal, and <i>osm-5</i> mutants exhibit structurally defective cilia. The <i>osm-5</i> promoter is commonly used to express genetic constructs in the ciliated neurons. In this study, we show that brightness of <i>osm-5p-</i> driven constructs is altered in mutants of the tubulin deglutamylase <i>ccpp-1</i> and the NIMA-related kinase <i>nekl-4</i> . This raises the possibility that <i>osm-5</i> expression levels may be regulated by <i>ccpp-1</i> and <i>nekl-4</i> .</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11318990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141972419","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}

{"title":"<i>Caenorhabditis elegans brc-1</i> mutation increases the number of COSA-1 foci in <i>him-8</i> and <i>zim-2</i> mutants.","authors":"Takamune T Saito, Koki Yamamoto, Hirohito Minami, Taiki Tsujiue","doi":"10.17912/micropub.biology.001077","DOIUrl":"10.17912/micropub.biology.001077","url":null,"abstract":"<p><p>Crossover designation factors such as COSA-1 are concentrated at the specific DNA double-strand break (DSB) sites to promote crossover formation. <i>zim-1</i> mutants, which show defects in the homologous chromosome pairing of chromosomes II and III, increase the COSA-1 foci/normal bivalent state compared to the expected value. The excess designation was suppressed by an additional mutation in <i>brc-1</i> in <i>zim-1</i> mutants. We demonstrated that the number of COSA-1 foci in <i>him-8</i> and <i>zim-2</i> mutants, showing defects in the pairing of the X and V chromosomes, respectively, increased compared to the expected value, and <i>brc-1</i> mutation accelerated the number of COSA-1 foci in oogenesis.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918270","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}

{"title":"Distance-dependent effects on CRISPR/Cas9-mediated genome editing in <i>Schizosaccharomyces pombe</i> compromise efficiency and create unsought alleles.","authors":"Reine U Protacio, Emory G Malone, Wayne P Wahls","doi":"10.17912/micropub.biology.001248","DOIUrl":"10.17912/micropub.biology.001248","url":null,"abstract":"<p><p>Discrete DNA sites position meiotic recombination at hotspots. We sought to create four different, 15 bp long, candidate regulatory DNA sites within the <i>ura4</i> reporter gene. Each effort employed a fission yeast-optimized CRISPR system (SpEDIT), optimal guide RNA, and one of four homologous recombination templates with 10 to 15 bp substitutions. Remarkably, every Ura ^- transformant analyzed had template-directed, PAM-disabling bp substitutions near (5-6 bp away from) the DSB but no DNA site-generating substitutions at distance (42-56 bp). An unsought novel allele, <i>ura4-P127*</i> , has two substitutions (C379T, C380A) that create a stop codon, rendering strains unable to grow without uracil.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918272","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}