microPublication biology最新文献

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Eurasian beaver ( Castor fiber ) mating behavior. 欧亚海狸(蓖麻纤维)的交配行为。
microPublication biology Pub Date : 2025-02-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001454
Henrik Bringmann
{"title":"Eurasian beaver ( <i>Castor fiber</i> ) mating behavior.","authors":"Henrik Bringmann","doi":"10.17912/micropub.biology.001454","DOIUrl":"https://doi.org/10.17912/micropub.biology.001454","url":null,"abstract":"<p><p>Eurasian beavers ( <i>Castor fiber</i> ) typically mate in the water at night, and observations of mating beavers are extremely scarce. As a result, little is known about their mating behavior. Here, I provide video documentation of beavers mating in the River Elbe during daylight, offering a unique opportunity to observe their mating behavior. The mating cycle consisted of: 1) a phase of self-grooming on land, 2) followed by the male pushing the female into the water and following her, and 3) copulation taking place in the water. This cycle was repeated several times throughout the same day. These observations contribute to our limited understanding of Eurasian beaver mating behavior.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574976","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
PCR-fingerprinting of culturable yeasts from commercially obtained beers: a simple and engaging applied microbiological laboratory exercise. 从商业啤酒中提取可培养酵母的pcr指纹图谱:一个简单而引人入胜的应用微生物实验室练习。
microPublication biology Pub Date : 2025-02-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001381
Walter P Pfliegler, Alexandra Imre, University Of Debrecen Biotechnology BSc Class Of, István Pócsi
{"title":"PCR-fingerprinting of culturable yeasts from commercially obtained beers: a simple and engaging applied microbiological laboratory exercise.","authors":"Walter P Pfliegler, Alexandra Imre, University Of Debrecen Biotechnology BSc Class Of, István Pócsi","doi":"10.17912/micropub.biology.001381","DOIUrl":"10.17912/micropub.biology.001381","url":null,"abstract":"<p><p>Yeast and fermented products present an opportunity to introduce students to applied microbiology. We designed and implemented a project-oriented laboratory class where yeasts from bottled beverages were isolated and compared using DNA fingerprinting and Sanger-sequencing. We recovered 17 <i>Saccharomyces</i> isolates, and two non- <i>Saccharomyces</i> yeasts. Fingerprinting identified two groups of closely related <i>Saccharomyces</i> isolates in unrelated beer styles, later identified as diastatic and wine yeasts using phylogenomics. Isolates from traditional products thus may not represent the original fermentation. We believe that the interlinked nature of topics and the simple basis can elevate engagement and performance of students during such a class.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574978","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
BALROG-MON: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-Metagenomic Oxford Nanopore. BALROG-MON:高通量的基因组-元基因组牛津纳米孔细菌抗菌性分析管道。
microPublication biology Pub Date : 2025-02-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001427
Edward Bird, Victoria Pickens, David Molik, Kristopher Silver, Dana Nayduch
{"title":"BALROG-MON: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-Metagenomic Oxford Nanopore.","authors":"Edward Bird, Victoria Pickens, David Molik, Kristopher Silver, Dana Nayduch","doi":"10.17912/micropub.biology.001427","DOIUrl":"10.17912/micropub.biology.001427","url":null,"abstract":"<p><p>BALROG-MON is a Nextflow pipeline for automated analysis of metagenomic long-read data to detect pathogens, annotate antimicrobial resistance genes (ARGs), link ARGs to specific pathogens, predict ARG origin (e.g., plasmid, chromosomal) and optionally perform steps like community analysis. With both assembly-based and assembly-free workflows, BALROG-MON is applicable to a wide range of sample types with low or high coverage, varying complexities and origins. Optional genome binning provides a comprehensive overview of ARGs within the dataset. BALROG-MON additionally presents results in summarized reports, overall serving as a flexible analysis tool for exploring diverse metagenomic samples for pathogens and antibiotic resistance.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569031","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
Peach ( Prunus persica ) TAC1 protein interaction with a LIGHT HARVESTING CHLOROPHYLL A/B BINDING (LHCB) homolog and transcriptomic analyses reveal connections to photosynthesis. 桃(Prunus persica) TAC1蛋白与光收获叶绿素a /B BINDING (LHCB)同源和转录组学分析揭示了与光合作用的联系。
microPublication biology Pub Date : 2025-02-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001371
Jessica M Waite, Erik Burchard, Chris Dardick, Courtney A Hollender
{"title":"Peach ( <i>Prunus persica</i> ) TAC1 protein interaction with a LIGHT HARVESTING CHLOROPHYLL A/B BINDING (LHCB) homolog and transcriptomic analyses reveal connections to photosynthesis.","authors":"Jessica M Waite, Erik Burchard, Chris Dardick, Courtney A Hollender","doi":"10.17912/micropub.biology.001371","DOIUrl":"10.17912/micropub.biology.001371","url":null,"abstract":"<p><p>Plants receive and interpret external light, gravity, and temperature cues to both set and change the angles of their lateral organs for optimal growth and development. In recent years, the roles of the IGT/LAZY protein family in integrating light and gravity cues have become increasingly apparent. Here we investigated protein-protein interactions for peach ( <i>Prunus persica</i> ) TAC1 (PpeTAC1). <i>TAC1</i> is a light-regulated IGT/LAZY family member involved in maintaining outward growth of lateral branches in numerous plant species. Using a yeast-two-hybrid screen with a peach library, we identified three candidate protein interactors, including a LIGHT HARVESTING CHLOROPHYLL A/B BINDING (LHCB) family protein. We found that neither <i>TAC1</i> silencing nor <i>PpeTAC1</i> overexpression in plum ( <i>P. domestica</i> ) altered chlorophyll content, despite a recent finding that <i>LAZY1</i> -silenced plum trees have chlorotic leaves due to reduced chlorophyll. However, we identified multiple differentially expressed chloroplast-, photosynthesis-, and light-related genes between <i>tac1</i> mutant and standard peaches. Collectively, we identified connections between <i>PpeTAC1</i> and chloroplasts, photosynthesis-related machinery, and light. This data supports a role for the TAC1 protein as an integrator of light perception into mechanisms controlling lateral organ orientation in concert with or in parallel to the LAZY/DRO gravitropic-response pathway.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574979","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
SMCT1 has a low affinity to PDZ domain containing 1 protein. SMCT1对含有1蛋白的PDZ结构域具有低亲和力。
microPublication biology Pub Date : 2025-02-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001502
Qingyang Zhang, Jacob Clinton, Kristina Westerlund, Carsten Mim
{"title":"SMCT1 has a low affinity to PDZ domain containing 1 protein.","authors":"Qingyang Zhang, Jacob Clinton, Kristina Westerlund, Carsten Mim","doi":"10.17912/micropub.biology.001502","DOIUrl":"10.17912/micropub.biology.001502","url":null,"abstract":"<p><p>Sodium-coupled monocarboxylate transporter 1 (SMCT1) is a membrane transporter abundantly expressed in colon, kidney, thyroid, brain; and silenced in cancer cells. It transports monocarboxylic acids with little specificity into cells. Based on pulldown experiments, it was proposed that the scaffolding protein PDZ Domain Containing 1 (PDZK1) regulates its surface expression and increases SMCT1's transportation efficiency. Here, we performed pull-down assays, Surface Plasmon Resonance (SPR), and Micro Scale Thermophoresis (MST) to evaluate the affinity between SMCT1 and two PDZ domains in PDZK1. Our results show that SMCT1 binds to these PDZ domains. However, the estimated equilibrium dissociation constants are higher than in canonical PDZ domains and likely physiological not relevant.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574980","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
Yeast mutation rates in alternative carbon sources reflect the influence of reactive oxygen species. 酵母在不同碳源中的突变率反映了活性氧的影响。
microPublication biology Pub Date : 2025-02-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001429
Keerthana Thota, Jacob D Fredette-Roman, Nathaniel P Sharp
{"title":"Yeast mutation rates in alternative carbon sources reflect the influence of reactive oxygen species.","authors":"Keerthana Thota, Jacob D Fredette-Roman, Nathaniel P Sharp","doi":"10.17912/micropub.biology.001429","DOIUrl":"10.17912/micropub.biology.001429","url":null,"abstract":"<p><p>Environmental conditions can influence mutation rates, but the reasons are often unclear. Budding yeast can utilize many carbon sources, with variation in the degree of fermentation versus respiration. Since aerobic respiration produces mutagenic reactive oxygen species, we hypothesized that yeast grown in media promoting aerobic respiration would show higher mutation rates. We found significant differences across five media types, with the highest mutation rate in pyruvate and the lowest in glucose. However, mutation rates responded to respiration rate in a nonlinear fashion, suggesting that the degree of respiration in a given environment is only partly predictive of mutation rate.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574982","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
The Complete Genome Sequences of Bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo isolated using Microbacterium foliorum. 利用叶状微杆菌分离噬菌体ASegato、DejaVu、Judebell和RicoCaldo的全基因组序列。
microPublication biology Pub Date : 2025-02-19 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001443
Robert Logan, Mahlet Abebe Biratu, Maria Andreea Busila, Ignacio Fernandez Busto, Nathan Caldwell, Peyton Chestnut, Hycell Colmenares Duno, Ricardo Cuello, Dhazyah Johnson, Jeniush Kark, Curvan Lawrnece, Jhemerial Arnique Lewis, Wod-Dardely Maglorie, Andrea Mendoza, Wesely Mills, Edoardo Miranda Colombo, Isabela Pacifico, Olivia Peters, Helen Pham, Izabel Renee Pozar, Madison Rearick, Jenna Reed, Ana Romero, Beatriz De Oliveira Segato, Hayden Turner, Sami Walaieh, Matthew Waterman
{"title":"The Complete Genome Sequences of Bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo isolated using <i>Microbacterium foliorum</i>.","authors":"Robert Logan, Mahlet Abebe Biratu, Maria Andreea Busila, Ignacio Fernandez Busto, Nathan Caldwell, Peyton Chestnut, Hycell Colmenares Duno, Ricardo Cuello, Dhazyah Johnson, Jeniush Kark, Curvan Lawrnece, Jhemerial Arnique Lewis, Wod-Dardely Maglorie, Andrea Mendoza, Wesely Mills, Edoardo Miranda Colombo, Isabela Pacifico, Olivia Peters, Helen Pham, Izabel Renee Pozar, Madison Rearick, Jenna Reed, Ana Romero, Beatriz De Oliveira Segato, Hayden Turner, Sami Walaieh, Matthew Waterman","doi":"10.17912/micropub.biology.001443","DOIUrl":"10.17912/micropub.biology.001443","url":null,"abstract":"<p><p>We report the discovery and characterization of bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo, isolated from grass samples collected in Quincy, Massachusetts, using <i>Microbacterium foliorum</i> B-24224 as the isolation host. Based on gene content similarity, these phages are assigned to actinobacteriophage clusters ED2, ED1, EG, and EK2 respectively.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11883469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574981","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
Epitope tags are not created equal: Disruption of cellular function of a translation factor by a short viral tag. 表位标签并不等同:短病毒标签对翻译因子细胞功能的干扰。
microPublication biology Pub Date : 2025-02-18 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001452
Brooke Barker, Chloe Cannon, Hannah Umphlett, Eun Suk Kim, Brett D Keiper
{"title":"Epitope tags are not created equal: Disruption of cellular function of a translation factor by a short viral tag.","authors":"Brooke Barker, Chloe Cannon, Hannah Umphlett, Eun Suk Kim, Brett D Keiper","doi":"10.17912/micropub.biology.001452","DOIUrl":"10.17912/micropub.biology.001452","url":null,"abstract":"<p><p>Cellular identity and fate are determined by the proteins synthesized. Initiation of mRNA translation requires an important translation factor, eIF4G ( <i>ifg-1</i> in <i>C. elegans</i> ). Embryos use mRNA translational control for spatial and temporal regulation of protein synthesis. Using CRISPR engineering, we added in-frame epitope and fluorescent tags (V5, Myc, Flag, GFP, and mCherry) to IFG-1 . Tagged forms containing the V5 epitope caused embryonic arrest. Internal disruption of the V5 tag restored viability at 25°C. This study demonstrates that the molecular nature of a small epitope tag is sufficient to disrupt <i>C. elegans</i> embryogenesis.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569036","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 Sequence of Mycobacterium Phage Guppsters. 分枝杆菌噬菌体 Guppsters 的基因组序列。
microPublication biology Pub Date : 2025-02-17 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001450
Emma K Alley, Lexi C Hill, Mya E Houglum, Maggie R Lamppa, Khailee K Pack, Hailey D Pageau, Cale J Prosen, Kylie R Richards, Kendra S Royer, Emily A Slettedahl, Ian L Strusz, Lydia A Wiita, Jillian C Zeidler, Daniel E Westholm
{"title":"Genome Sequence of Mycobacterium Phage Guppsters.","authors":"Emma K Alley, Lexi C Hill, Mya E Houglum, Maggie R Lamppa, Khailee K Pack, Hailey D Pageau, Cale J Prosen, Kylie R Richards, Kendra S Royer, Emily A Slettedahl, Ian L Strusz, Lydia A Wiita, Jillian C Zeidler, Daniel E Westholm","doi":"10.17912/micropub.biology.001450","DOIUrl":"10.17912/micropub.biology.001450","url":null,"abstract":"<p><p>Mycobacterium Phage Guppsters was isolated on <i>Mycobacterium smegmatis</i> mc <sup>2</sup> 155, displays a siphovirus morphology, and possesses a 54,835 base pair genome. Based on gene content similarity, Guppsters is assigned to cluster F1. Unlike a majority of F1 phages, Guppsters does not encode mycobacteriophage mobile elements.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877149/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560130","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
Gene model for the ortholog of mts in Drosophila mojavensis. 莫扎文果蝇 mts 同源物的基因模型。
microPublication biology Pub Date : 2025-02-17 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.000888
Megan E Lawson, Clairine I S Larsen, Madeline McAbee, Scott Tanner, Jeffrey S Thompson, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>mts</i> in <i>Drosophila mojavensis</i>.","authors":"Megan E Lawson, Clairine I S Larsen, Madeline McAbee, Scott Tanner, Jeffrey S Thompson, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000888","DOIUrl":"10.17912/micropub.biology.000888","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>microtubule star</i> ( <i>mts</i> ) in the D. mojavensis May 2011 (Agencourt dmoj_caf1/DmojCAF1) Genome Assembly (GenBank Accession: GCA_000005175.1 ) of <i>Drosophila mojavensis</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":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560147","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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