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Genome Sequence of the Mycobacterium smegmatis Bacteriophage Eugenia. 耻垢分枝杆菌噬菌体优生体基因组序列。
microPublication biology Pub Date : 2024-12-14 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001401
Vipaporn Phuntumart, Lucia Boulos, Bella Nunnally, Isabella Lima, John Motter, Olivia Sidoti, Sam Rutherford, Hsin-Ho Wei, Raymond Larsen, Jill H Zeilstra-Ryalls
{"title":"Genome Sequence of the <i>Mycobacterium smegmatis</i> Bacteriophage Eugenia.","authors":"Vipaporn Phuntumart, Lucia Boulos, Bella Nunnally, Isabella Lima, John Motter, Olivia Sidoti, Sam Rutherford, Hsin-Ho Wei, Raymond Larsen, Jill H Zeilstra-Ryalls","doi":"10.17912/micropub.biology.001401","DOIUrl":"10.17912/micropub.biology.001401","url":null,"abstract":"<p><p>We report the discovery and genome sequence of mycobacteriophage Eugenia, isolated from soil samples collected in Akron, OH. Eugenia is a double-stranded DNA virus with a genome size of 69,139 bp, featuring 104 predicted protein-encoding genes, with 32 of these genes assigned putative functions.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11682537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904361","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
Redox-Responsive Polymeric Nanogels as Efficient mRNA Delivery Vehicles in Caenorhabditis elegans. 氧化还原反应聚合物纳米凝胶作为秀丽隐杆线虫mRNA的高效递送载体。
microPublication biology Pub Date : 2024-12-10 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001428
Rupali Dabas, Alan Koh, David Carling, Nazila Kamaly, André E X Brown
{"title":"Redox-Responsive Polymeric Nanogels as Efficient mRNA Delivery Vehicles in <i>Caenorhabditis elegans</i>.","authors":"Rupali Dabas, Alan Koh, David Carling, Nazila Kamaly, André E X Brown","doi":"10.17912/micropub.biology.001428","DOIUrl":"10.17912/micropub.biology.001428","url":null,"abstract":"<p><p>Efficient delivery of sensitive nucleic acid payloads, including mRNA, in <i>Caenorhabditis elegans</i> remains challenging, especially with traditional, labor-intensive transgenesis methods. We addressed these challenges using polymeric nanogels (NGs) as an advanced platform for mRNA delivery in <i>C. elegans</i> . These polymeric delivery vehicles can be engineered to suit desired applications owing to their chemical versatility, resulting from the ability to conjugate multiple functional groups onto the same backbone. Here, we validate the <i>in vivo</i> RNA delivery potential of redox-responsive NGs. The NGs showed up to 72.4 % RNA encapsulation and 6.61 % loading efficiencies and facilitated the controlled release of the mRNA payloads at intracellular concentrations of the reducing agent glutathione, where most of the RNA was released within 24 hours. As a proof of concept, we successfully delivered green fluorescent protein (GFP)-expressing mRNA using NGs in <i>C. elegans</i> for the first time. Physicochemical characterization revealed uniform NG size and charge, and fluorescence microscopy confirmed GFP expression in the gut after 24 hours of treatment. Our findings show NGs' potential as an mRNA delivery system in <i>C. elegans</i> .</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900759","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
Complete annotated genome sequence of Microbacterium paraoxydans phage Evcara, a cluster GI podovirus isolated from compost. 从堆肥中分离的一种簇状胃肠道足病毒——副氧微杆菌噬菌体Evcara的全基因组序列。
microPublication biology Pub Date : 2024-12-08 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001398
Hannah B Bonogafsky, Kelly M Freer, Taylor B Sanderson, Kira A Yost, Ayden J Pyle, Ginavieve Rowley, Maria D Gainey
{"title":"Complete annotated genome sequence of <i>Microbacterium paraoxydans</i> phage Evcara, a cluster GI podovirus isolated from compost.","authors":"Hannah B Bonogafsky, Kelly M Freer, Taylor B Sanderson, Kira A Yost, Ayden J Pyle, Ginavieve Rowley, Maria D Gainey","doi":"10.17912/micropub.biology.001398","DOIUrl":"10.17912/micropub.biology.001398","url":null,"abstract":"<p><p>Bacteriophage Evcara is a podovirus isolated on <i>Microbacterium paraoxydans</i> NRRL B-24275. Its genome is 16,285 bp in length and contains 22 predicted protein-coding genes. Evcara, has been assigned to cluster GI with <i>Microbacterium</i> <i>foliorum</i> phages PineapplePizza and Curie that share 10 homologues with the well-characterized <i>Bacillus subtilis</i> phage phi29.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883814","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 Dsor1 in Drosophila persimilis. persimilis果蝇Dsor1同源基因的基因模型。
microPublication biology Pub Date : 2024-12-08 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.000853
Alyssa C Koehler, Emma Seay, Hannah Ewing, Zachary Mearse, Ana Maria Rocha de Almeida, Sara Cline, Jamie Siders, Lindsey J Long, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>Dsor1</i> in <i>Drosophila persimilis</i>.","authors":"Alyssa C Koehler, Emma Seay, Hannah Ewing, Zachary Mearse, Ana Maria Rocha de Almeida, Sara Cline, Jamie Siders, Lindsey J Long, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000853","DOIUrl":"10.17912/micropub.biology.000853","url":null,"abstract":"<p><p>Gene model for the ortholog of Downstream of raf1 ( <i>Dsor1</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":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883819","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 Ilp5 in Drosophila ananassae. 果蝇Ilp5同源基因的基因模型研究。
microPublication biology Pub Date : 2024-12-08 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.000782
Megan E Lawson, Madeline McAbee, Rae A Lucas, Scott Tanner, Jacqueline Wittke-Thompson, Tara A Pelletier, Zeynep Ozsoy, Rachel Sterne-Marr, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>Ilp5</i> in <i>Drosophila ananassae</i>.","authors":"Megan E Lawson, Madeline McAbee, Rae A Lucas, Scott Tanner, Jacqueline Wittke-Thompson, Tara A Pelletier, Zeynep Ozsoy, Rachel Sterne-Marr, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000782","DOIUrl":"10.17912/micropub.biology.000782","url":null,"abstract":"<p><p>Gene model for the ortholog of Insulin-like peptide 5 ( <i>Ilp5</i> ) in the <i>D. ananassae</i> 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":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883825","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
Developing robust quantitative PCR primers for comparative biomass analysis of Tall Fescue (Festuca arundinacea) and its Epichloë endophyte. 建立高羊茅及其Epichloë内生菌生物量比较分析的定量PCR引物。
microPublication biology Pub Date : 2024-12-06 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001275
Darrian Talamantes, Caitlin Kirkpatrick, Jason Wallace
{"title":"Developing robust quantitative PCR primers for comparative biomass analysis of Tall Fescue (Festuca arundinacea) and its Epichloë endophyte.","authors":"Darrian Talamantes, Caitlin Kirkpatrick, Jason Wallace","doi":"10.17912/micropub.biology.001275","DOIUrl":"10.17912/micropub.biology.001275","url":null,"abstract":"<p><p>Tall fescue ( <i>Festuca arundinacea</i> ) is a widely adopted forage and turf grass. This is partly due to a fungal endophyte, <i>Epichloë coenophiala,</i> which confers both abiotic and biotic stress tolerance. Although PCR primers exist to test for endophyte presence, these were not designed to quantitatively analyze the amount of fungus in the plant. In this study, we test different primer sets for quantitative biomass analysis of tall fescue and <i>E. coenophiala.</i> We report standard curves, r-squared, and efficiency values for every primer set and identify those most suited for qPCR in this system.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11663250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878928","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
Complete genome sequence of Microbacterium foliorum singleton phage Magritte. 叶状微杆菌单噬菌体Magritte全基因组序列。
microPublication biology Pub Date : 2024-12-06 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001377
Elvira Eivazova, Jenna St Pierre, Miriam Galindo, James Bautista, Annaleisa Matzirakis, Madalyn Falletti, Elynor Fix, Levi Fritsch
{"title":"Complete genome sequence of <i>Microbacterium foliorum</i> singleton phage Magritte.","authors":"Elvira Eivazova, Jenna St Pierre, Miriam Galindo, James Bautista, Annaleisa Matzirakis, Madalyn Falletti, Elynor Fix, Levi Fritsch","doi":"10.17912/micropub.biology.001377","DOIUrl":"10.17912/micropub.biology.001377","url":null,"abstract":"<p><p>Actinobacteriophage Magritte was isolated from soil in Columbia, TN using <i>Microbacterium foliorum</i> as a host. Magritte is a singleton with a siphovirus morphology and a large genome of 133,228 bp encoding 250 predicted genes, including 26 tRNA genes.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11663251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878878","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
Dietary B vitamins influence the Drosophila melanogaster preference for dietary yeast. 膳食B族维生素影响黑腹果蝇对膳食酵母的偏好。
microPublication biology Pub Date : 2024-12-05 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001354
Dean B Peterson, John Chaston, Andrew T Call
{"title":"Dietary B vitamins influence the <i>Drosophila melanogaster</i> preference for dietary yeast.","authors":"Dean B Peterson, John Chaston, Andrew T Call","doi":"10.17912/micropub.biology.001354","DOIUrl":"10.17912/micropub.biology.001354","url":null,"abstract":"<p><p>The microbiota influences the <i>Drosophila melanogaster</i> dietary preference for yeast (DPY). We previously identified four transposon insertion mutants in <i>Acetobacter fabarum</i> that significantly influence fly DPY, and three of these insertions were in genes that are associated with thiamine metabolism. Here, we tested if thiamine influences fly DPY in monoassociated flies. We show that thiamine and other B vitamins influence fly DPY and that the different mutants have distinct DPY responses to thiamine supplementation. Together, these experiments identify specific nutritional effectors of <i>D. melanogaster</i> DPY.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878932","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 ubiquinone precursor analogue does not clearly increase the growth rate of Caenorhabditis inopinata. 泛醌前体类似物不能明显提高隐杆线虫的生长速度。
microPublication biology Pub Date : 2024-12-05 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001235
Gavin C Woodruff, Kimberly A Moser
{"title":"A ubiquinone precursor analogue does not clearly increase the growth rate of <i>Caenorhabditis inopinata</i>.","authors":"Gavin C Woodruff, Kimberly A Moser","doi":"10.17912/micropub.biology.001235","DOIUrl":"10.17912/micropub.biology.001235","url":null,"abstract":"<p><p>The evolution of developmental rates may drive morphological change. <i>Caenorhabditis inopinata</i> develops nearly twice as slowly as <i>Caenorhabditis elegans</i> . <i>clk-1</i> encodes a hydroxylase required for synthesizing ubiquinone, and mutant <i>clk-1</i> slow growth phenotypes can be rescued by supplying animals with a ubiquinone precursor analogue, 2,4-dihydroxybenzoate. RNA-seq data showing low <i>clk-1</i> expression raised the possibility that <i>C. inopinata</i> grows slowly because of reduced ubiquinone biosynthesis. <i>C. inopinata</i> did not reveal a clear reduction in the age of maturation when reared on 2,4-dihydroxybenzoate. Further scrutiny of RNA-seq results revealed multiple ubiquinone metabolism genes have low expression in <i>C. inopinata</i> . Divergent <i>clk-1</i> expression alone may not be a major driver of the evolution of slow development in this species.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878851","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
Loss of function in rpms-1 does not enhance phenotypes of rpm-1 mutants. rpm-1的功能丧失不会增强rpm-1突变体的表型。
microPublication biology Pub Date : 2024-12-05 eCollection Date: 2024-01-01 DOI: 10.17912/micropub.biology.001396
Yue Sun, Daniela Gaio, Bokun Xie, Kentaro Noma, Zilu Wu, Yishi Jin
{"title":"Loss of function in <i>rpms-1</i> does not enhance phenotypes of <i>rpm-1</i> mutants.","authors":"Yue Sun, Daniela Gaio, Bokun Xie, Kentaro Noma, Zilu Wu, Yishi Jin","doi":"10.17912/micropub.biology.001396","DOIUrl":"10.17912/micropub.biology.001396","url":null,"abstract":"<p><p>The <i>C. elegans</i> E3 ubiquitin ligase RPM-1 consists of 3,766 amino acids, with a RING finger domain at the C-terminus that functions to target the DLK-1 kinase for degradation for synapse development and axon termination. <i>rpms-1 (</i> for <i>rpm-1 short,</i> aka F07B7.12 <i>)</i> resides 35 kb away from <i>rpm-1</i> on chromosome V, and is a near-perfect 12 kb duplication of <i>rpm-1 ,</i> including the entire promoter region and coding sequences. RPMS-1 consists of 1,964 amino acids and is identical to the N-terminal half of RPM-1 , except the last 40 amino acids. Previous studies showed that transgenic overexpression of the duplicated region of <i>rpm-1 (+)</i> did not rescue synapse defects of <i>rpm-1</i> loss of function mutants. Here, using CRISPR editing, we generated a double knockout of <i>rpm-1</i> and <i>rpms-1</i> . We find that axon and synapse defects in <i>rpm-1rpms-1</i> double mutants resemble those in <i>rpm-1</i> single mutants. Expression levels of endogenously tagged DLK-1 protein are increased to a comparable degree in <i>rpm-1</i> and <i>rpm-1rpms-1</i> mutants, compared to the control. These data, along with previous transgene expression analysis, support the idea that <i>rpms-1</i> does not have a major role in RPM-1-mediated cellular processes.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878937","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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