microPublication biology最新文献

{"title":"Transcriptomic Analysis of CAD Cell Differentiation.","authors":"Carlos A Cevallos, Anna Leigh White, Brooke A Fazio, Lillian S Wendt, Jasmine W Feng, Dora Posfai, April L Horton, John M Warrick, Omar Alberto Quintero-Carmona","doi":"10.17912/micropub.biology.001574","DOIUrl":"https://doi.org/10.17912/micropub.biology.001574","url":null,"abstract":"<p><p>CAD cells were derived from Cath.a cells, a mouse central nervous system catecholaminergic cell line. Serum-starved CAD cells undergo morphological changes and resemble isolated neurons when observed by microscopy. We carried out an RNAseq transcriptomic analysis to examine differentiated CAD cells for expression signatures related to neuronal functions, identifying ~1900 transcripts whose expression changed with differentiation. Pathview analysis identified ~80 KEGG pathway gene sets that were differentially expressed, including upregulation of at least 13 neuron-related pathways. This dataset can be explored more deeply, allowing further investigation into expression changes relevant to studying neuronal functions in this easy-to-culture model system.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144025875","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":"Revealing Rotational Characteristics of the Uniflagellate Mutant of <i>Chlamydomonas reinhardtii</i> through DeepLabCut-Based Autotracking.","authors":"Azusa Kage, Ken H Nagai, Takayuki Nishizaka, Kenta Ishimoto","doi":"10.17912/micropub.biology.001535","DOIUrl":"https://doi.org/10.17912/micropub.biology.001535","url":null,"abstract":"<p><p>Tracking eukaryotic flagella and cilia often requires manual clicking, even in the age of digital imaging. We developed an autotracking method using DeepLabCut, a CNN-based, marker-less tracking tool originally designed for animal behavior. Applying this method, we uncovered rotational characteristics of <i>Chlamydomonas reinhardtii</i> <i>uni1</i> , a uniflagellate mutant. Live <i>uni1</i> cells predominantly rotated counterclockwise under a coverslip when viewed from above, whereas demembranated models exhibited slower, more clockwise rotation. These differences likely stem from alterations in the three-dimensional flagellar waveform.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060541","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":"Influence of Substrate Color on Oyster Shell Colonization.","authors":"Pauline Lawrence, Samantha Dishong, Elizabeth Hamman","doi":"10.17912/micropub.biology.001519","DOIUrl":"https://doi.org/10.17912/micropub.biology.001519","url":null,"abstract":"<p><p>This study investigated the influence of substrate color on the recruitment and colonization of <i>Crassostrea virginica</i> reef-associated organisms in an artificial reef system in the St. Mary's River. Substrate color significantly affected community abundance, but the specific pattern depended on locomotion and species. The sessile community preferred blue substrate, which was largely driven by the strong settlement preference of tube-forming polychaetes (serpulid worms). Motile species showed recruitment preference for red shells. Mud coverage and erosion negatively affected the recruitment of sessile species but did not affect motile species recruitment.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045846","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":"The effect of temperature on asexual reproduction in <i>Hydra vulgaris</i>.","authors":"Jameelah Destry, Kelso Cochran, Aide Macias-Muñoz","doi":"10.17912/micropub.biology.001508","DOIUrl":"https://doi.org/10.17912/micropub.biology.001508","url":null,"abstract":"<p><p><i>Hydra vulgaris</i> is a model cnidarian used for interdisciplinary studies in biology, yet its reproductive responses to environmental changes remain underexplored. This study examined how temperature affects asexual reproduction (budding) rates and population growth in <i>H. vulgaris</i> . We placed <i>Hydra</i> in two thermal environments, 15°C and 25°C, to compare differences in population growth, number of budding polyps, number of buds, and budding rates under 'cold' and 'hot' conditions. Our findings indicate that <i>Hydra</i> populations exhibit increased growth through asexual budding at higher temperatures.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12053359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052668","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>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}