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har-1/CHCHD10 mutations induce neurodegeneration and mitochondrial fragmentation in Caenorhabditis elegans. har1 /CHCHD10突变可诱导秀丽隐杆线虫的神经变性和线粒体断裂。
microPublication biology Pub Date : 2025-05-15 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001597
Audrey Labarre, Ericka Guitard, Gilles Tossing, J Alex Parker
{"title":"<i>har-1/CHCHD10</i> mutations induce neurodegeneration and mitochondrial fragmentation in <i>Caenorhabditis elegans</i>.","authors":"Audrey Labarre, Ericka Guitard, Gilles Tossing, J Alex Parker","doi":"10.17912/micropub.biology.001597","DOIUrl":"10.17912/micropub.biology.001597","url":null,"abstract":"<p><p><i>CHCHD10</i> encodes a mitochondrial protein that plays a role in cristae morphology and oxidative phosphorylation, with mutations associated with neurodegenerative diseases, including the spectrum of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). The <i>Caenorhabditis elegans</i> ortholog of <i>CHCHD10</i> is <i>har-1</i> , which can be used to model CHCHD10-related neurodegenerative diseases. We focused on two <i>har-1</i> mutant strains: one featuring a 260 bp deletion ( <i>gk3124</i> ) and the other with a G73E point mutation ( <i>ad2155</i> ). Both <i>har-1</i> mutants displayed progressive paralysis, degeneration of GABAergic motor neurons, and mitochondrial fragmentation. These strains may be valuable tools for investigating pathogenic mechanisms and therapeutic strategies for neurodegenerative diseases.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201016","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
Collaborative research efforts benefit both Primarily Undergraduate Institution faculty and students and a biotechnology company in reproducibility project. 在可重复性项目中，合作研究工作使主要本科院校的教师和学生以及生物技术公司受益。
microPublication biology Pub Date : 2025-05-14 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001604
Kristen C Johnson, Lori Hensley, Christin Pruett, Lyndsay Avery, Roslyn Crowder, Laura Diaz-Martinez, Rebecca Giorno, Audrey Kim, Paul Kim, Adriana LaGier, Jamie Newman, Elizabeth Padilla-Crespo, Nik Tsotakos, Nathan Reyna
{"title":"Collaborative research efforts benefit both Primarily Undergraduate Institution faculty and students and a biotechnology company in reproducibility project.","authors":"Kristen C Johnson, Lori Hensley, Christin Pruett, Lyndsay Avery, Roslyn Crowder, Laura Diaz-Martinez, Rebecca Giorno, Audrey Kim, Paul Kim, Adriana LaGier, Jamie Newman, Elizabeth Padilla-Crespo, Nik Tsotakos, Nathan Reyna","doi":"10.17912/micropub.biology.001604","DOIUrl":"10.17912/micropub.biology.001604","url":null,"abstract":"<p><p>Undergraduate students often have limited access to industry-focused research opportunities. To address this, faculty and students from 10 primarily undergraduate institutions collaborated with Sampling Human, a biotechnology company, to test a biocytometry workflow for single-cell analysis. The project engaged 15 students with varying levels of research experience and demonstrated that prior research expertise was not essential for successfully using the workflow. Participants followed standardized protocols and generated reproducible data comparable to that of PhD-level scientists. Despite some technical challenges, 91.7% of participants completed the study, showcasing the approachability and reliability of the workflow. This collaboration highlights the potential of industry partnerships to expand research opportunities, enhance academic visibility, and foster academic-corporate co-publications.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181938","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
Associative learning by C. elegans is variable when butanone is paired with starvation. 当丁酮与饥饿配对时，秀丽隐杆线虫的联想学习是可变的。
microPublication biology Pub Date : 2025-05-13 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001568
Samiha Tasnim, Amber Liu, Antony Jose
{"title":"Associative learning by <i>C. elegans</i> is variable when butanone is paired with starvation.","authors":"Samiha Tasnim, Amber Liu, Antony Jose","doi":"10.17912/micropub.biology.001568","DOIUrl":"10.17912/micropub.biology.001568","url":null,"abstract":"<p><p>The nematode <i>C. elegans</i> has been reported to show a reduction in its preference for the odorant butanone after prior exposure to butanone coupled with starvation. Here we report unexplained variability in such associative learning. Pre-exposure of unfed worms to butanone resulted in different responses during different trials of subsequent chemotaxis assays - from strong avoidance to enhanced attraction. Given this variation in associative learning despite the artificially controlled lab setting, we speculate that in dynamic natural environments such learning might be rare and highlight the challenge in discovering evolutionarily selected mechanisms that could underlie learning in the wild.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175840","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
Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq. 利用生长试验和RNA-seq研究液体处理机器人移液速度对酵母生长和基因表达的影响。
microPublication biology Pub Date : 2025-05-13 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001566
Shodai Taguchi, Ryosuke Matsuzawa, Yasuyuki Suda, Kenji Irie, Haruka Ozaki
{"title":"Investigating the effects of liquid handling robot pipetting speed on yeast growth and gene expression using growth assays and RNA-seq.","authors":"Shodai Taguchi, Ryosuke Matsuzawa, Yasuyuki Suda, Kenji Irie, Haruka Ozaki","doi":"10.17912/micropub.biology.001566","DOIUrl":"10.17912/micropub.biology.001566","url":null,"abstract":"<p><p>Assessing the impact of experimental parameters like pipetting speed is essential in life science research but challenging in manual experiments. Recent advancements in laboratory automation enable precise control and systematic evaluation of these parameters. Here, we employed the Opentrons OT-2, an affordable, open-source liquid handling robot, to systematically investigate the effect of pipetting speed on growth and gene expression in the budding yeast <i>Saccharomyces cerevisiae</i> . Growth assays revealed no significant differences across the tested pipetting speeds (ANOVA, p > 0.05). RNA-seq analysis corroborated these findings, demonstrating highly similar gene expression profiles across all 24 samples (minimum Pearson correlation coefficient = 0.9528), with no differentially expressed genes identified by generalized linear model analysis (false discovery rate > 0.01). Our results highlight the utility of robotic platforms in optimizing experimental parameters, improving reproducibility, and enhancing accuracy in biological research, thus providing valuable insights for future applications.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175966","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
Genomic Complexity of ccdc40 in Xenopus : Implications for CRISPR Targeting and Disease Modeling. 爪蟾ccdc40的基因组复杂性：对CRISPR靶向和疾病建模的影响
microPublication biology Pub Date : 2025-05-09 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001596
Takuya Nakayama, Saurabh Kulkarni
{"title":"Genomic Complexity of <i>ccdc40</i> in <i>Xenopus</i> : Implications for CRISPR Targeting and Disease Modeling.","authors":"Takuya Nakayama, Saurabh Kulkarni","doi":"10.17912/micropub.biology.001596","DOIUrl":"10.17912/micropub.biology.001596","url":null,"abstract":"<p><p>Mutations in <i>CCDC40</i> cause primary ciliary dyskinesia in humans. To evaluate the pathogenicity of variants in <i>CCDC40</i> , we examined the genomic structure of this gene in <i>Xenopus tropicalis</i> , a diploid frog suitable as a model for genetic studies. We identified inconsistencies in the current <i>ccdc40</i> gene model and discovered two distinct <i>ccdc40</i> genes near the previously annotated locus. Surprisingly, <i>Xenopus</i> <i>laevis</i> , an allotetraploid species that typically has two homoeologs, contains only one homoeolog ( <i>ccdc40.S</i> ), making it a more suitable genetic model for studying <i>ccdc40</i> function and potentially expediting the functional characterization of CCDC40 variants linked to primary ciliary dyskinesia.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144719","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
UCK2-dependent conversion of cytidine to CTP is required for CTP uptake by Chlamydia trachomatis. 沙眼衣原体摄取CTP需要依赖uck2的胞苷转化为CTP。
microPublication biology Pub Date : 2025-05-09 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001607
Laure Blanchet, Agathe Subtil
{"title":"UCK2-dependent conversion of cytidine to CTP is required for CTP uptake by <i>Chlamydia trachomatis</i>.","authors":"Laure Blanchet, Agathe Subtil","doi":"10.17912/micropub.biology.001607","DOIUrl":"10.17912/micropub.biology.001607","url":null,"abstract":"<p><p><i>Chlamydia trachomatis</i> , an obligate intracellular bacterium, develops into a vacuolar compartment called the inclusion. The bacteria import nucleoside triphosphates (NTPs) present in the inclusion lumen. It remains unclear whether nucleosides enter the inclusion lumen in their native form or as phosphorylated nucleotides. Using click chemistry coupled with fluorescence microscopy we provide evidence that cytidine requires phosphorylation by host uridine-cytidine kinase 2 (UCK2) prior to its incorporation into bacterial nucleic acids. These findings support the hypothesis that nucleosides are converted into nucleotides in the host cytoplasm prior to translocation into the inclusion lumen. Future work should therefore focus on the identification of nucleotide transporter(s) at the inclusion membrane.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102696/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144773","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 Schizosaccharomyces pombe nucleolar protein Nsk1 modulates rDNA silencing during interphase. 裂糖菌核仁蛋白Nsk1调控间期rDNA沉默。
microPublication biology Pub Date : 2025-05-08 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001616
Jun-Song Chen, Sarah M Hanna, Alaina H Willet, Kathleen L Gould
{"title":"The <i>Schizosaccharomyces pombe</i> nucleolar protein Nsk1 modulates rDNA silencing during interphase.","authors":"Jun-Song Chen, Sarah M Hanna, Alaina H Willet, Kathleen L Gould","doi":"10.17912/micropub.biology.001616","DOIUrl":"10.17912/micropub.biology.001616","url":null,"abstract":"<p><p><i>Schizosaccharomyces pombe</i> Nsk1 acts at kinetochores during mitosis to prevent error-prone chromosome segregation and it is phosphoregulated by Cdk1 . The Clp1 / Cdc14 protein phosphatase, to which Nsk1 binds, reverses Cdk1-mediated phosphorylation of Nsk1 during anaphase. During interphase, Nsk1 localizes exclusively to the nucleolus and its function there is unknown. In this study, we examined whether Nsk1 shares functions in the nucleolus with other known Clp1 / Cdc14 phosphatase substrates that localize there. We found that Nsk1 participates in rRNA silencing but not rDNA segregation, rDNA transcription, or nucleolar organization.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129624","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
Microparticle Bombardment as a Method for Transgenesis in Auanema and Tokorhabditis. 微粒子轰击法在猪肺炎和牛肺炎中的转基因研究。
microPublication biology Pub Date : 2025-05-08 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001585
Tatsuya Yamashita, Andre Pires-daSilva, Shun Oomura, Taichi Kusano, Nami Haruta, Mayu Hasumi, Taisei Kikuchi, Sally Adams, Asako Sugimoto, Ryoji Shinya
{"title":"Microparticle Bombardment as a Method for Transgenesis in <i>Auanema</i> and <i>Tokorhabditis</i>.","authors":"Tatsuya Yamashita, Andre Pires-daSilva, Shun Oomura, Taichi Kusano, Nami Haruta, Mayu Hasumi, Taisei Kikuchi, Sally Adams, Asako Sugimoto, Ryoji Shinya","doi":"10.17912/micropub.biology.001585","DOIUrl":"10.17912/micropub.biology.001585","url":null,"abstract":"<p><p>Functional gene analysis tools in <i>Caenorhabditis elegans</i> are often ineffective in other nematodes due to differences in gonadal morphology and transgene silencing. Here, we established a method to generate stable transgenic lines in the nematodes <i>Auanema freiburgense</i> and <i>Tokorhabditis tufae</i> using microparticle bombardment coupled with hygromycin B selection. Despite using non-codon-optimized GFP, transgenic strains expressing fluorescent markers were obtained in both species. Additionally, an <i>Auanema</i> codon-optimized RFP construct showed robust expression in all tissues. This method will be valuable for future studies into the unusual sex determination, viviparity, and stress resistance in <i>Auanema</i> and <i>Tokorhabditis</i> .</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144770","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
Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays. 评价串联基因阵列内在不稳定性的长读质粒测序策略。
microPublication biology Pub Date : 2025-05-08 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001582
Hiroaki Takesue, Satoshi Okada, Takashi Ito
{"title":"Long-read plasmid sequencing strategy for evaluating intrinsic instability of tandem gene arrays.","authors":"Hiroaki Takesue, Satoshi Okada, Takashi Ito","doi":"10.17912/micropub.biology.001582","DOIUrl":"10.17912/micropub.biology.001582","url":null,"abstract":"<p><p>Tandem gene arrays are inherently unstable, particularly in recombination-prone organisms such as the budding yeast <i>Saccharomyces cerevisiae</i> . However, understanding the nature of this instability-how frequently and to what extent the target array contracts or expands within the genome-remains challenging. As a surrogate approach to this goal, we propose using nanopore long-read sequencing to directly determine the length distribution of a target gene array cloned onto a centromeric plasmid functioning as an artificial chromosome. This strategy will not only allow us to assess the intrinsic instability of the array but also help identify factors that may influence its stability.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144766","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
Insertion of mNeonGreen into the variable domain of DRP-1 permits visualization of functional endogenous protein. 将mNeonGreen插入DRP-1的可变结构域，可以可视化功能内源蛋白。
microPublication biology Pub Date : 2025-05-08 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001588
Eric J Lambie, Barbara Conradt
{"title":"Insertion of mNeonGreen into the variable domain of DRP-1 permits visualization of functional endogenous protein.","authors":"Eric J Lambie, Barbara Conradt","doi":"10.17912/micropub.biology.001588","DOIUrl":"10.17912/micropub.biology.001588","url":null,"abstract":"<p><p>We used CRISPR-Cas9 editing of the genomic <i>drp-1</i> locus in <i>C. elegans</i> to test whether the mitochondrial fission function of DRP-1 was retained following insertion of mNeonGreen into the variable domain. We found that DRP-1 activity remains largely intact despite this large internal insertion. Furthermore, in living cells, the internally tagged protein is readily detectable as discrete puncta associated with mitochondria, which presumably represent prospective mitochondrial scission sites. The internally tagged DRP-1 protein represents a powerful new tool for real time <i>in vivo</i> analyses of mitochondrial fission and DRP-1 function.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12100159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144721","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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