microPublication biology最新文献

{"title":"<i>In vivo</i> detection of ALFA-tagged proteins in <i>C. elegans</i> with a transgenic fluorescent nanobody.","authors":"Sophie Quintin, Maria Izabella Saad, Grégory Amann, Anne-Cécile Reymann","doi":"10.17912/micropub.biology.001542","DOIUrl":"https://doi.org/10.17912/micropub.biology.001542","url":null,"abstract":"<p><p>To track tagged endogenous proteins <i>in vivo</i> , we created a <i>C. elegans</i> strain expressing a fluorescently-labelled nanobody directed against the ALFA-tag epitope. The strain, which expresses an anti-ALFA nanobody fused to mKate2, is healthy and allows clear detection of the ALFA-tagged junction protein DLG-1 at all stages. This method is adapted for live imaging, circumvents the need of immuno-histochemistry, and opens perspective to study protein function <i>in vivo</i> . The future detection of sensitive proteins can therefore be envisaged in nematodes by using transgenic nanobodies, or chromobodies, in combination with ALFA-tagging by CRISPR.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12048842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058132","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":"Complete annotated genome sequence of <i>Microbacterium foliorum</i> phage Delphidian, isolated from soil in Philadelphia, Pennsylvania.","authors":"Dondra S Bailey, Alison Moyer, Muyang Chunga, Prajanya Prabakaran, Bhumika Parnerkar, Dominique Dotson, Mariam Allison, Shardaye Beasley, Annalyse Belton, Candace Braxton, Delonn Dixon, Taylor Fullwood, Monique Hines, Tremaine Holmes, Tochi Iwuji, Mysia Johnson, Braxton Kess, Atiatunur Kukoyi, Erin Laster, Tanae Moore-Buchannon, Khalil Oliver, Kyara Parham, Seetra Parris, Alysha Pulliam-Robinson, Lashawna Robinson, Marcus Smith, Christiana Whitfield, Kayla Whitfield, Viviana Wamiru","doi":"10.17912/micropub.biology.001490","DOIUrl":"https://doi.org/10.17912/micropub.biology.001490","url":null,"abstract":"<p><p>The bacteriophage Delphidian contains a 41,595 bp DNA genome with 62 predicted protein-coding genes and no tRNA genes. Delphidian infects <i>Microbacterium foliorum</i> NRRL B-24224 and is predicted to be lytic. Based on gene content similarity to sequenced actinobacteriophages, it has been assigned to cluster EA1.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051780","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":"Gene model for the ortholog of <i>rictor</i> in <i>Drosophila ananassae</i>.","authors":"Anne E Backlund, Brooklin Bain, Kayton Kite, Carter Babbitt, Lindsey J Long, Judith Leatherman, Brian Schwartz, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000982","DOIUrl":"https://doi.org/10.17912/micropub.biology.000982","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>rapamycin-insensitive companion of Tor</i> ( <i>rictor</i> ) in the May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ) of <i>Drosophila ananassae</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":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12046423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144055091","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>Cassiopea xamachana</i> polyp feeding under husbandry conditions.","authors":"Victoria Sharp, Kendra Pfeil, Kaitlin Kitch, Mónica Medina","doi":"10.17912/micropub.biology.001561","DOIUrl":"https://doi.org/10.17912/micropub.biology.001561","url":null,"abstract":"<p><p>Research on the upside-down jellyfish <i>Cassiopea xamachana</i> has increased in the past few decades, hence the need for more efficient husbandry protocols. We tested the effect of weekly feeding frequencies, light cycles, and nutrient supplements on symbiotic and aposymbiotic polyp asexual reproduction and mortality. <i>C. xamachana</i> polyps have better survivorship and reproduction when kept in a day/night cycle and given additional food beyond <i>Artemia</i> nauplii.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022712","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":"Hatchlings and Neonate Turtle Gonads Have Spatially Restricted Neural Processes.","authors":"Jeanette Wyneken, Boris M Tezak, Debra Lee Miller","doi":"10.17912/micropub.biology.001327","DOIUrl":"https://doi.org/10.17912/micropub.biology.001327","url":null,"abstract":"<p><p>Morphological and molecular evidence explains the lack of nociception (\"pain\") associated with very small, laparoscopic gonadal biopsy in neonate turtles. This safe procedure serves to verify neonate sex of late-maturing species, such as sea turtles. Ethical concerns about the potential for biopsy pain, inferred from mammals, limited access to sex verification biopsy for decades. Yet, standard behavioral evidence of pain during biopsy (e.g., escape attempts, biting, guarding behavior after biopsy, inappetence) were negative. Morphological and molecular evidence early in ontogeny, shows that, unlike mice, young turtles have limited neural processes to the gonadal medulla and none reach the cortical layer.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144054992","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":"Investigating the Effects of <i>Arabidopsis thaliana</i> Cruciferin Double Knockouts on Amino Acid Profiles, Dry Seed Proteome, and Oxidative Stress Levels.","authors":"Clement Bagaza, Huda Ansaf, Abou Yobi, Ruthie Angelovici","doi":"10.17912/micropub.biology.001441","DOIUrl":"https://doi.org/10.17912/micropub.biology.001441","url":null,"abstract":"<p><p>As plant seeds mature, they accumulate large quantities of seed storage proteins, which are a vital source of carbon, nitrogen, and sulfur necessary for establishing the seedling, especially during the transition from the heterotrophic to the photoautotrophic stage. However, seed storage proteins in many crop seeds are deficient in essential amino acids, which cannot be synthesized by humans and monogastric animals and must be obtained from the diet. Lysine and tryptophan are the most deficient amino acids in cereal seeds, while methionine is the most deficient amino acid in legumes. In the last few decades, extensive research has been done to improve the nutritional quality of seed crops. However, much of this effort was hindered due to the conserved natural phenomenon of proteomic rebalancing that 'resets' the seed's protein-bound amino acid composition despite major alterations to the proteomic sink. Neither the underlying regulatory mechanism nor the natural function of proteomic rebalancing is well understood. To address this gap, we used the model organism <i>Arabidopsis thaliana</i> to investigate the impact of cruciferin (CRU) seed storage protein double knockouts on key biological processes. Amino acid analysis showed that the protein-bound amino acid composition and levels did not change in the mutants despite major alterations in the proteome, especially in the double mutant lacking both CRUA and CRUC ( <i>cruac</i> ). This mutant also has the highest free amino acid changes and experienced the most oxidative stress damage compared to other mutants based on analysis of protein carbonylation and glutathione levels. The mutant that lacks CRUA and CRUB ( <i>cruab</i> ), on the other hand, was the least affected in all the traits examined. These results suggest that CRUs are not functionally redundant, and that each CRU is not replaceable by another in <i>Arabidopsis</i> . The results also show that <i>Arabidopsis</i> seed protein-bound amino acid composition is fully rebalanced in the double CRU mutants despite major proteome alteration.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060205","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":"Human Structural Homologues of SARS-CoV-2 PL ^pro as Anti-Targets: A Strategic Panel Analysis.","authors":"Abdullah I Al-Homoudi, Joseph Engel, Michael D Muczynski, Joseph S Brunzelle, Navnath S Gavande, Ladislau C Kovari","doi":"10.17912/micropub.biology.001418","DOIUrl":"https://doi.org/10.17912/micropub.biology.001418","url":null,"abstract":"<p><p>COVID-19 is caused by SARS-CoV-2, a highly transmissible and pathogenic RNA betacoronavirus. Developing small-molecule antiviral inhibitors of the SARS-CoV-2 papain-like protease (PL ^pro ) is advantageous due to the enzyme's role in processing viral polyproteins and disrupting host immune sensing. Given the structural and functional similarities between PL ^pro and human deubiquitinases (DUBs), small-molecule inhibitors are frequently counter-screened for off-target activity using a panel of human DUBs. Through X-ray crystallography, DALI structural comparisons, and <i>in silico</i> analysis, a high-quality crystal structure of SARS-CoV-2 PL ^pro enabled the identification of the closest structural human homologues of PL ^pro . Among the 27 human DUBs identified, USP46 and USP12 displayed the greatest structural similarity to PL ^pro , with alignment scores below 0.45 and RMSD values of 3.0 Å or less. Additionally, binding sites on ubiquitin-specific protease (USP46) and USP12, ancillary to the active site residues, share high sequence identity to the PL ^pro substrate binding sites that are often engaged by the most potent PL ^pro inhibitors. These findings offer a strong basis for choosing anti-targets and serve as a foundation for designing selective small-molecule PL ^pro inhibitors.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12035650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060176","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":"Gene model for the ortholog of <i>Glys</i> in <i>Drosophila busckii</i>.","authors":"Anne E Backlund, Logan Cohen, Jeremy White, Lain Grillo, Tony Ianniello, Amanda Swedrowski, Melinda A Yang, Jennifer Jemc, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.001095","DOIUrl":"https://doi.org/10.17912/micropub.biology.001095","url":null,"abstract":"<p><p>Gene model for the ortholog of glycogen synthase ( <i>Glys</i> ) in the <i>Drosophia busckii</i> Sep. 2015 (UC Berkeley ASM127793v1/DbusGB1) Genome Assembly (GenBank Accession: GCA_001277935.1 ). 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":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038437/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144014661","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":"Coordinated terrestrial locomotion in California grunion ( <i>Leuresthes tenuis</i> ).","authors":"Clinton Moran, Alice Gibb, Kathryn Dickson","doi":"10.17912/micropub.biology.001431","DOIUrl":"https://doi.org/10.17912/micropub.biology.001431","url":null,"abstract":"<p><p>Terrestrial locomotor behaviors in fishes allow fishes to escape biotic and abiotic pressures in aquatic habitats. Emerging to spawn once a year, California grunion beach themselves during Spring high tides. We described two coordinated behaviors that adult grunion consistently perform during short, but regular, bouts of movement on land: the tail-flip jump and \"sidestepping\" behavior. While tail-flip jumping covered more ground per event, repeated sidestepping allowed grunion to cover comparable ground per unit time. This is the first published kinematic description of grunion locomotor behaviors in terrestrial habitats based on video recordings.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12022797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013864","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":"Standardized Gene Nomenclature for Chicken Scavenger Receptors.","authors":"Coltton Kirkpatrick, Fiona McCarthy","doi":"10.17912/micropub.biology.001559","DOIUrl":"https://doi.org/10.17912/micropub.biology.001559","url":null,"abstract":"<p><p>Scavenger Receptors (SCARs) are a heterogeneous group involved in innate immunity and immunomodulation. We provided standardized nomenclature for chicken SCAR genes in line with other vertebrate nomenclatures. Chicken SCAR genes orthologous to human genes are assigned the same gene names and symbols. Novel SCAR genes were assessed to determine their appropriate class and assigned nomenclature in line with this classification. Notably, chicken has expansions of the MRC and DMBT genes, and the number of these paralogs varies across Sauropsida species. In addition, we identified and classified a further 15 novel SCAR genes, predominantly SCAR class I genes.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12032555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999798","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}