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Increased dietary iron alters taxonomic composition and function of zebrafish gut microbiome. 饲料铁的增加改变了斑马鱼肠道微生物群的分类组成和功能。
microPublication biology Pub Date : 2026-04-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001220
Stuart Gordon, Sam Evans, Kobie Kirven, Megan Whisonant
{"title":"Increased dietary iron alters taxonomic composition and function of zebrafish gut microbiome.","authors":"Stuart Gordon, Sam Evans, Kobie Kirven, Megan Whisonant","doi":"10.17912/micropub.biology.001220","DOIUrl":"https://doi.org/10.17912/micropub.biology.001220","url":null,"abstract":"<p><p>Gut microbiota are crucial to both gastrointestinal tract health and host well-being. Oral iron supplementation is commonly used, but knowledge of iron's impact on the gut microbiome is limited. Using Zebrafish ( <i>Danio rerio</i> ) as a model organism, we tested effects of increased dietary iron on gut taxonomic composition and function. Increased dietary iron significantly altered the zebrafish microbiome taxonomic composition and enriched physiological conditions of aerobic respiration. Mass spectrometry (GCMS and LCMS), utilized to measure primary metabolite and lipid levels, pointed to significant increases in amino acids under increased iron supplementation, but no significant change in lipid metabolite levels.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126321/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824479","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
Culture method for promoting efficient ciliary growth in the Chlamydomonas pf23 mutant defective in dynein preassembly. 促进动力蛋白预组装缺陷衣藻pf23突变体纤毛生长的培养方法。
microPublication biology Pub Date : 2026-04-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002069
Ryosuke Yamamoto, Takahide Kon
{"title":"Culture method for promoting efficient ciliary growth in the <i>Chlamydomonas</i> <i>pf23</i> mutant defective in dynein preassembly.","authors":"Ryosuke Yamamoto, Takahide Kon","doi":"10.17912/micropub.biology.002069","DOIUrl":"https://doi.org/10.17912/micropub.biology.002069","url":null,"abstract":"<p><p><i>Chlamydomonas reinhardtii</i> is an ideal model organism for studying the cytoplasmic preassembly of ciliary dyneins. However, under normal liquid-culture conditions, <i>Chlamydomonas</i> preassembly-deficient mutants often show no cilia or a small number of ciliated cells (i.e., low ciliation ratio), which hinders further analysis of both ciliary dyneins and the phenotypes of these mutants. In this brief report, we present a modified culture method for one of the <i>Chlamydomonas</i> preassembly-deficient mutants, <i>pf23</i> . This method enables researchers to obtain enough <i>pf23</i> cilia for small-scale biochemical, biophysical, structural and phenotypic analyses.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824506","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
An analysis of the bacterial and fungal diversity of the fecal material of gopher tortoises. 地鼠龟粪便中细菌和真菌多样性分析。
microPublication biology Pub Date : 2026-04-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002029
Lauren M K Vankoningsveld, Richard W McLaughlin, Durward L Bevis
{"title":"An analysis of the bacterial and fungal diversity of the fecal material of gopher tortoises.","authors":"Lauren M K Vankoningsveld, Richard W McLaughlin, Durward L Bevis","doi":"10.17912/micropub.biology.002029","DOIUrl":"https://doi.org/10.17912/micropub.biology.002029","url":null,"abstract":"<p><p>The gopher tortoise ( <i>Gopherus polyphemus</i> ) is listed in the State of Florida as a threatened species. It is well known that the microbiota of the host is imperative to health promotion and disease mitigation. The diversity of the gut microbiota of the tortoise has not been extensively surveyed. &nbsp;In this study, we examined both the bacterial and fungal diversity in the fecal material of this animal using bacterial tag-encoded flexible-Titanium (FLX) amplicon pyrosequencing (bTEFAP) and fungal tag-encoded FLX amplicon pyrosequencing.&nbsp; In the six samples, there were 16 total bacterial phyla identified with Bacillota (54.55 to 86.13%) as the most dominant and two fungal phyla identified with Ascomycota (79.64 to 97.32%) as the most predominant.&nbsp; Interestingly, the pathogenic fungus <i>Candida tropicalis</i> was detected in all samples suggesting the tortoise could be a reservoir of zoonotic fungi.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147824442","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
Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1. 蛋白质组学揭示了外着丝点蛋白KNL1的广泛磷酸化调控。
microPublication biology Pub Date : 2026-04-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002102
Abby C Jurasin, Anderson R Frank, Sue Biggins
{"title":"Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1.","authors":"Abby C Jurasin, Anderson R Frank, Sue Biggins","doi":"10.17912/micropub.biology.002102","DOIUrl":"10.17912/micropub.biology.002102","url":null,"abstract":"<p><p>Microtubules attach to kinetochores to facilitate chromosome movement to opposite spindle poles. Defective kinetochore-microtubule attachments lead to phosphoryation of the outer kinetochore protein KNL1 at conserved MELT motifs, which triggers spindle assembly checkpoint activation and recruitment of the fibrous corona. To identify additional phosphorylation sites that regulate kinetochores, we treated HEK 293T/17 cells with nocodazole, paclitaxel, or STLC to create defective kinetochore-microtubule attachment states. We then purified KNL1 and performed proteomics and identified 111 phosphorylation sites on KNL1, including several that may be attachment-state specific. These data demonstrate that KNL1 is extensively phosphoregulated in response to treatment with microtubule-disrupting compounds.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13122507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791417","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
Deconvolution of Single-Organism Omics Resolves Cellular and Tissue Dynamics during Aging. 单生物组学的反卷积解决了衰老过程中的细胞和组织动力学。
microPublication biology Pub Date : 2026-04-13 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001989
Youngjun Park, Adam Antebi
{"title":"Deconvolution of Single-Organism Omics Resolves Cellular and Tissue Dynamics during Aging.","authors":"Youngjun Park, Adam Antebi","doi":"10.17912/micropub.biology.001989","DOIUrl":"https://doi.org/10.17912/micropub.biology.001989","url":null,"abstract":"<p><p>The deconvolution of bulk omics data provides enhanced resolution of cell populations within samples and has been widely adopted, particularly in cancer biology. In this study, we applied deconvolution approaches to both transcriptomic and proteomic datasets at single-organism resolution in <i>C. elegans</i> , enabling us to infer cellular and tissue contributions to the whole transcriptome or proteome. Our results demonstrate that deconvolution-derived cellular and tissue proportions can serve as robust proxy readouts for dynamic changes in cells and tissues during aging.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13122506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791180","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
LITE-1 Photoreceptor Mediates Light-Induced Reversal of Ivermectin Paralysis in Caenorhabditis elegans. LITE-1光感受器介导秀丽隐杆线虫伊维菌素麻痹的光诱导逆转。
microPublication biology Pub Date : 2026-04-11 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001983
Magera Shaw, Mylissa Stover, Crystal Shults, Jacob R Manjarrez
{"title":"LITE-1 Photoreceptor Mediates Light-Induced Reversal of Ivermectin Paralysis in <i>Caenorhabditis elegans</i>.","authors":"Magera Shaw, Mylissa Stover, Crystal Shults, Jacob R Manjarrez","doi":"10.17912/micropub.biology.001983","DOIUrl":"https://doi.org/10.17912/micropub.biology.001983","url":null,"abstract":"<p><p>Ivermectin (IVM), a widely used anthelmintic and chemotherapeutic agent in both human and veterinary medicine, targets glutamate-gated chloride channels to induce paralysis in nematodes such as&nbsp; <i>Caenorhabditis elegans</i> . Traditionally, IVM-induced paralysis is assessed under brightfield microscopy. Here, we report that exposure to UV or blue wavelengths can induce spontaneous arousal from the IVM-paralyzed state, initiating with twitching and progressing to full swimming motion during light stimulation. This light-induced arousal response is absent in&nbsp; <i>lite-1</i> &nbsp;null mutants, implicating LITE-1 photoreceptors in mediating this effect. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13110406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791451","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
gPPIpred: A User-Friendly PPI Predictor Based on Protein Molecular Graphs. gPPIpred：基于蛋白质分子图的用户友好的PPI预测器。
microPublication biology Pub Date : 2026-04-10 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001796
Cleverson C Matiolli, Joana Marques, Isabel A Abreu
{"title":"gPPIpred: A User-Friendly PPI Predictor Based on Protein Molecular Graphs.","authors":"Cleverson C Matiolli, Joana Marques, Isabel A Abreu","doi":"10.17912/micropub.biology.001796","DOIUrl":"https://doi.org/10.17912/micropub.biology.001796","url":null,"abstract":"<p><p>Protein-protein interactions (PPIs) govern essential cellular processes but remain challenging to characterize experimentally due to high cost and labor intensity. We present gPPIpred, a scalable computational framework leveraging graph neural networks (GNNs) and attention mechanisms to predict PPIs at residue-level resolution. Proteins are encoded as spatially informed molecular graphs integrating physicochemical features. Using curated structural datasets for training and validation, gPPIpred was fine-tuned to reliably predict positive interactions and actual interacting sites. Attention scores highlight key residues mediating interactions, offering interpretable insights to guide experimental design. gPPIpred combines high predictive performance with explainability, providing a user-friendly pipeline for large-scale PPI discovery.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13109786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791357","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
Evaluating the environmental preferences and spread of the invasive Asian Jumping Worm ( Amynthas spp.) in southwestern Virginia. 维吉尼亚西南部入侵亚洲跳虫（Amynthas spp.）的环境偏好和传播评估。
microPublication biology Pub Date : 2026-04-08 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002000
Adeline Gaudet, Ashley Jernigan
{"title":"Evaluating the environmental preferences and spread of the invasive Asian Jumping Worm ( <i>Amynthas spp.)</i> in southwestern Virginia.","authors":"Adeline Gaudet, Ashley Jernigan","doi":"10.17912/micropub.biology.002000","DOIUrl":"https://doi.org/10.17912/micropub.biology.002000","url":null,"abstract":"<p><p>Asian Jumping Worms (AJW) are an invasive species in North America that can negatively impact soil habitats. This study investigated AJW environmental preferences, movement over time, and overwintering ability in Virginia, USA. Worms were sampled on four dates, two in fall 2024 and two in spring 2025, in four areas with different environmental conditions: (1) well-drained, shady (2) well-drained, mid-day sun (3) moist, shady (4) well-drained, early sun. Results indicate AJW may have delayed invasions in mulched landscapes and a preference for well-drained soil. These findings increase our understanding of AJW environmental patterns, which may help stop their spread.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791191","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
Antimicrobial activity of Janthinobacterium, Pseudomonas , and Pseudoclavibacter bacterial soil isolates. 土壤分离细菌Janthinobacterium， Pseudomonas和pseudoclavibacteria的抑菌活性。
microPublication biology Pub Date : 2026-04-08 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001644
Kelena Snipes, Logan Angelillo, Julia Fugate, Hannah-May Winton, Elias Taylor-Cornejo
{"title":"Antimicrobial activity of <i>Janthinobacterium, Pseudomonas</i> , and <i>Pseudoclavibacter</i> bacterial soil isolates.","authors":"Kelena Snipes, Logan Angelillo, Julia Fugate, Hannah-May Winton, Elias Taylor-Cornejo","doi":"10.17912/micropub.biology.001644","DOIUrl":"https://doi.org/10.17912/micropub.biology.001644","url":null,"abstract":"<p><p>Healthcare, and the world at large, are currently facing an antibiotic crisis caused by the increase in antibiotic resistant bacterial pathogens, combined with divestment in the drug discovery pipeline for new antibiotics. The Tiny Earth Project is a global, student-driven, effort aimed at discovering and isolating new sources of antibiotics from soil microbes that can be used to combat multi-drug resistant bacterial pathogens. This study characterizes the antimicrobial and biochemical properties of three unique bacterial soil isolates from the genera <i>Janthinobacterium</i> , <i>Pseudomonas</i> , and <i>Pseudoclavibacter</i> and their extracted secondary metabolites.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790989","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 of Myoviridae Phage Lethe Isolated In Northern Georgia. 北乔治亚州分离的肌病毒科噬菌体残体基因组。
microPublication biology Pub Date : 2026-04-07 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001984
Paige Alexander, Maggie Blair, Emma Boyen, Lavender Bumgarner, Gabrielle Grogan, Ella Lesperance, Alison Kanak
{"title":"Genome of Myoviridae Phage Lethe Isolated In Northern Georgia.","authors":"Paige Alexander, Maggie Blair, Emma Boyen, Lavender Bumgarner, Gabrielle Grogan, Ella Lesperance, Alison Kanak","doi":"10.17912/micropub.biology.001984","DOIUrl":"https://doi.org/10.17912/micropub.biology.001984","url":null,"abstract":"<p><p>Lethe, a predicted lytic bacteriophage with myovirus morphology, was isolated using <i>Mycobacterium smegmatis mc²155</i> in North Georgia. Lethe has a genome of 155,828 base pairs with 230 predicted ORFs, 34 tRNAs, 1 tmRNA, and 64.70% GC content. Based on gene content, Lethe is assigned to actinobacteriophage cluster C1, sharing up to 99.5% nucleotide identity with members of this cluster.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791303","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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