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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
Temporal induction of the homeodomain transcription factor Nkx2-1 is sufficient to respecify foregut and hindgut endoderm to a pulmonary fate in Xenopus laevis. 在非洲爪蟾中，同源结构域转录因子Nkx2-1的时间诱导足以重新指定前肠和后肠内胚层的肺命运。
microPublication biology Pub Date : 2025-05-07 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001610
Brian A Hyatt, Erin Lundberg, Rachael Eye, Scott A Rankin, Aaron M Zorn
{"title":"Temporal induction of the homeodomain transcription factor Nkx2-1 is sufficient to respecify foregut and hindgut endoderm to a pulmonary fate in <i>Xenopus laevis</i>.","authors":"Brian A Hyatt, Erin Lundberg, Rachael Eye, Scott A Rankin, Aaron M Zorn","doi":"10.17912/micropub.biology.001610","DOIUrl":"10.17912/micropub.biology.001610","url":null,"abstract":"<p><p>The ability of transcription factors (TFs) to regulate cell fate decisions is paramount in developmental, homeostatic, and pathogenic contexts. The homeodomain TF NKX2-1 is an essential and evolutionarily conserved master regulator of pulmonary fate in vertebrates. In this study, we tested the spatial-temporal ability of Xenopus and Human NKX2-1 to respecify foregut and hindgut endoderm in developing <i>Xenopus laevis</i> embryos into a pulmonary fate, as indicated by expression of pulmonary surfactant genes <i>sftpc</i> and <i>sftpb</i> . Interestingly, we find that both Human and Xenopus NKX2-1 can induce the ectopic expression of pulmonary surfactant genes in foregut and hindgut endoderm over a wide range of developmental times, as well as suppress the expression of midgut and hindgut specific genes. These results suggest a single pulmonary TF can reprogram developing endoderm and specify pulmonary fate. In addition, our work provides a comparative platform for future studies investigating how mutations in Human <i>NKX2-1</i> may affect its transcriptional activity.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129622","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
Pep12 is important for proteasome microautophagy under low glucose conditions. 在低糖条件下，Pep12对蛋白酶体微自噬很重要。
microPublication biology Pub Date : 2025-05-07 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001579
Kyle VanderVen, Conner Butcher, Remi' Fokine, Jianhui Li
{"title":"Pep12 is important for proteasome microautophagy under low glucose conditions.","authors":"Kyle VanderVen, Conner Butcher, Remi' Fokine, Jianhui Li","doi":"10.17912/micropub.biology.001579","DOIUrl":"10.17912/micropub.biology.001579","url":null,"abstract":"<p><p>Autophagic degradation of proteasomes is a highly conserved mechanism for regulating proteasome homeostasis in eukaryotes. Here we show that Pep12, a t-SNARE protein, is important for intralumenal vesicle formation in the vacuole and proteasome microautophagy under low glucose conditions. Deleting <i>PEP12</i> in yeast cells, <i>Saccharomyces cerevisiae</i> , blocked proteasome fragmentation, by which the ESCRT-dependent microautophagy selectively degrades aberrant proteasomes. Accumulation of aberrant proteasomes interfered with proteasome condensate formation in <i>pep12∆</i> cells. Autophagic bodies were present, but intralumenal vesicles and proteasome microautophagy were absent in the vacuole of <i>pep12∆</i> cells. Therefore, Pep12 plays an important role in proteasome microautophagy.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12096180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129620","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
Skeletal muscle TFEB overexpression does not increase neurogenesis markers in the young female hippocampus. 骨骼肌TFEB过表达不增加年轻女性海马的神经发生标志物。
microPublication biology Pub Date : 2025-05-06 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001612
Mia Hakian, Ian Matthews, Constanza J Cortes
{"title":"Skeletal muscle TFEB overexpression does not increase neurogenesis markers in the young female hippocampus.","authors":"Mia Hakian, Ian Matthews, Constanza J Cortes","doi":"10.17912/micropub.biology.001612","DOIUrl":"10.17912/micropub.biology.001612","url":null,"abstract":"<p><p>Adult hippocampal neurogenesis (AHN), the process in which new neurons are formed in the dentate gyrus of the hippocampus, declines with age and is highly responsive to voluntary wheel running in mice. This exercise-activated increase in AHN is believed to contribute to the cognitive and neurotrophic benefits of exercise on the aging and neurodegenerative disease-afflicted brain. However, our current understanding of the decline in AHN remains male-centric, with very few studies examining the effects of age and/or running on AHN in the female brain. Our lab has recently shown that skeletal muscle-specific overexpression of Transcription Factor E-B (TFEB), a master regulator of lysosomal and mitochondrial function, mimics many of the neuroprotective benefits of exercise during aging and in the context of Alzheimer's disease (AD) pathologies, but the effect of muscle-TFEB overexpression on AHN was unknown. Here we report that female AHN declines in a similar timeline as to what has been reported for the male hippocampus, following a precipitous decline at around 3 months of age that culminates at around 8 months of age. Furthermore, we report that muscle-TFEB overexpression does not prevent this age-associated decrease in AHN, suggesting that the neuroprotective benefits observed in our muscle-TFEB model are independent of AHN.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12093156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144121514","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 Roc1a in Drosophila persimilis. 果蝇Roc1a同源基因的基因模型研究。
microPublication biology Pub Date : 2025-05-01 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001043
Megan E Lawson, Kelsey Gammage, Calvin Dexel, Betty Duan, Elena M Zerkin, Lindsey J Long, Melinda A Yang, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>Roc1a</i> in <i>Drosophila persimilis</i>.","authors":"Megan E Lawson, Kelsey Gammage, Calvin Dexel, Betty Duan, Elena M Zerkin, Lindsey J Long, Melinda A Yang, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.001043","DOIUrl":"10.17912/micropub.biology.001043","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>Regulator of cullins 1a</i> ( <i>Roc1a</i> ) in the May 2011 (Broad dper_caf1/DperCAF1) Genome Assembly (GenBank Accession: GCA_000005195.1 ) of <i>Drosophila persimilis</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":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096068","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 underappreciated, underrecognized problem of fourth chromosome trisomy in Drosophila melanogaster stocks and a simple, general method for building diplo-4 stocks from triplo-4 stocks. 黑腹果蝇种群中第四染色体三体未被重视和认识的问题及从三倍四染色体构建二倍四染色体的简单、通用方法。
microPublication biology Pub Date : 2025-04-29 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001606
Kevin R Cook
{"title":"The underappreciated, underrecognized problem of fourth chromosome trisomy in <i>Drosophila melanogaster</i> stocks and a simple, general method for building diplo-4 stocks from triplo-4 stocks.","authors":"Kevin R Cook","doi":"10.17912/micropub.biology.001606","DOIUrl":"10.17912/micropub.biology.001606","url":null,"abstract":"<p><p>Trisomy of the small, fourth chromosome is common in <i>Drosophila melanogaster</i> stocks. Even though the presence of an extra chromosome can confound the interpretation of experimental crosses, many Drosophila geneticists are unaware of this potential problem. Here I describe a simple method employing a mutation in a haploinsufficient gene to recognize fourth chromosome trisomy and establish disomic stocks from trisomic stocks.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096074","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
A small-scale bacterial-based liquid Culture Method for Steinernema hermaphroditum. 雌雄斯坦纳氏菌的小型细菌液体培养方法。
microPublication biology Pub Date : 2025-04-28 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001549
Nathan Y Rodak, Chieh-Hsiang Tan, Paul W Sternberg
{"title":"A small-scale bacterial-based liquid Culture Method for <i>Steinernema hermaphroditum</i>.","authors":"Nathan Y Rodak, Chieh-Hsiang Tan, Paul W Sternberg","doi":"10.17912/micropub.biology.001549","DOIUrl":"10.17912/micropub.biology.001549","url":null,"abstract":"<p><p>Entomopathogenic nematodes (EPN) infect and kill their insect host with the help of symbiotic bacteria. The only known hermaphroditic (androdiecious) EPN, the clade IV <i>Steinernema hermaphroditum</i> , offers opportunities for exploring both parasitic and mutualistic symbiosis, as well as for evolutionary and developmental studies. Experimental and genetic analysis of this animal is now facilitated through the development of forward and reverse genetic tools and improved culturing techniques. Here, we describe a liquid-culture technique adapted for this worm. The method can be a starting point for the development of large-scale cultivation of the worm and provides a method to generate infective juveniles without an insect host and either with or without its native symbiotic bacteria.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095854","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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