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Evaluation of two new antibodies for recognition of CldU in DNA fiber assay applications.
microPublication biology Pub Date : 2025-01-31 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001485
Anthony Widjaja, Julia M Sidorova
{"title":"Evaluation of two new antibodies for recognition of CldU in DNA fiber assay applications.","authors":"Anthony Widjaja, Julia M Sidorova","doi":"10.17912/micropub.biology.001485","DOIUrl":"10.17912/micropub.biology.001485","url":null,"abstract":"<p><p>DNA fiber assays are indispensable tools for studying DNA damage and replication stress responses <i>in vivo</i> at the single replication fork level. These assays typically rely on antibodies recognizing IdU and CldU. Historically, the availability of CldU-reactive antibodies has been limited to one reagent (clone BU1/75(ICR1)). We validated two alternative antibodies for CldU detection in DNA fiber assays. One of these antibodies can be readily paired with a common IdU-reactive antibody, and we confirmed that it produces quantitatively similar CldU track length results vis-à-vis the BU1/75 antibody. The new reagents should boost versatility of DNA fiber assays, facilitating DNA replication research.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11829213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434553","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
Erratum: Corrigendum: tRNA Arg binds in vitro TDP-43 RNA recognition motifs and ligand of Ate1 protein LIAT1.
microPublication biology Pub Date : 2025-01-31 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001527
{"title":"Erratum: Corrigendum: tRNA <sup>Arg</sup> binds <i>in vitro</i> TDP-43 RNA recognition motifs and ligand of Ate1 protein LIAT1.","authors":"","doi":"10.17912/micropub.biology.001527","DOIUrl":"https://doi.org/10.17912/micropub.biology.001527","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.17912/micropub.biology.001224.].</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11787625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143082473","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
Evaluation of two environmental DNA (eDNA) approaches for monitoring hemlock woolly adelgid (HWA).
microPublication biology Pub Date : 2025-01-31 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001346
Kathryn Geller, Charlyn Partridge
{"title":"Evaluation of two environmental DNA (eDNA) approaches for monitoring hemlock woolly adelgid (HWA).","authors":"Kathryn Geller, Charlyn Partridge","doi":"10.17912/micropub.biology.001346","DOIUrl":"10.17912/micropub.biology.001346","url":null,"abstract":"<p><p>Eastern hemlocks ( <i>Tsuga canadensis)</i> are experiencing significant mortality due to the invasive insect, hemlock wooly adelgid (HWA) ( <i>Adelges tsuga)</i> . Common monitoring methods for HWA detection include visual assessment of hemlock trees for the presence of ovisac material. However, this method requires time and resources to survey large areas. We compared two methods, ball sampling coupled with genetic analysis and passive environmental DNA (eDNA) sampling, and evaluated their ability to detect HWA in infested and high-risk areas using qPCR. We found that the two methods were equally effective at detecting HWA and could serve as supplemental methods for early HWA monitoring.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11829212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434550","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
Antibiotic production by soil bacteria under aerobic and micro-oxic conditions. 有氧和微氧条件下土壤细菌的抗生素生产。
microPublication biology Pub Date : 2025-01-31 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001440
Cierra Paaaina-Daquioag, Disha Byadarahalli Mohan Kumar, Debra R Kerr, Leonardo Romero, Kurt M Regner
{"title":"Antibiotic production by soil bacteria under aerobic and micro-oxic conditions.","authors":"Cierra Paaaina-Daquioag, Disha Byadarahalli Mohan Kumar, Debra R Kerr, Leonardo Romero, Kurt M Regner","doi":"10.17912/micropub.biology.001440","DOIUrl":"10.17912/micropub.biology.001440","url":null,"abstract":"<p><p>Antimicrobial resistance presents a significant global challenge, undermining the effectiveness of antibiotic therapies and complicating disease management. The origin and spread of antibiotic-resistance genes outpaces the antibiotic discovery process, highlighting an urgent need for new approaches. This study investigated the production of antibiotics by soil bacteria under aerobic and micro-oxic conditions as part of a course-based research experience designed to introduce undergraduates to the global antibiotic resistance crisis. Significant differences in the diameters of the zones of inhibition against three tester strains were observed under differing oxygen concentrations. Soil isolates were identified with 16S rRNA sequence analysis.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11829214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434535","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
Secreted autotransporter toxin produced by probiotic Escherichia coli Nissle 1917 enhances neurodegeneration in Caenorhabditis elegans.
microPublication biology Pub Date : 2025-01-30 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001366
Graham Redweik, Ding Xue
{"title":"Secreted autotransporter toxin produced by probiotic <i>Escherichia coli</i> Nissle 1917 enhances neurodegeneration in <i>Caenorhabditis elegans</i>.","authors":"Graham Redweik, Ding Xue","doi":"10.17912/micropub.biology.001366","DOIUrl":"10.17912/micropub.biology.001366","url":null,"abstract":"<p><p>First isolated during World War I, <i>Escherichia coli</i> Nissle 1917 (ECN) is an intensively studied bacterium that produces several factors that can inhibit pathogenic bacteria to promote gut health. These findings have led to its commercialization as a probiotic bacterium widely available for human consumption. Notably, the genome of ECN is highly analogous to many extraintestinal pathogenic <i>E. coli</i> (ExPEC) strains that do cause diseases in humans. Both ECN and ExPEC carry the <i>sat</i> gene which encodes a cytotoxic serine autotransporter toxin (Sat). Given that the role of ECN Sat in human disease has been poorly studied, we sought to implement the nematode <i>C. elegans</i> as a model for analyzing how ECN Sat may impact human neurodegenerative disease. Using multiple <i>C. elegans</i> disease models, we find that ECN Sat induces significantly higher neurodegeneration in several <i>C. elegans</i> models we tested. Although preliminary, our early findings suggest that careful studies are paramount to assess the impact of ECN to humans susceptible of neurodegenerative disease to determine the long-term safety of ECN as a commercial probiotic.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11822469/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416502","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 eIF4E1 in Drosophila yakuba.
microPublication biology Pub Date : 2025-01-29 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001020
Bailey Lose, Jeremy Girard, Josephine Hayes, Lane Weast, Natalie Minkovsky, Sarah Justice, Jack A Vincent, James J Youngblom, Lindsey J Long, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>eIF4E1</i> in <i>Drosophila yakuba</i>.","authors":"Bailey Lose, Jeremy Girard, Josephine Hayes, Lane Weast, Natalie Minkovsky, Sarah Justice, Jack A Vincent, James J Youngblom, Lindsey J Long, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.001020","DOIUrl":"10.17912/micropub.biology.001020","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>eukaryotic translation initiation factor 4E1</i> ( <i>eIF4E1</i> ) in the Dyak_CAF1 Genome Assembly (GenBank Accession: GCA_000005975.1 ) of <i>Drosophila yakuba</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":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11822466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416501","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
Better utilization of inorganic nitrogen compared to organic nitrogen by a plant symbiotic fungal isolate of Alternaria alternata.
microPublication biology Pub Date : 2025-01-29 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001403
Beatrice Bock, Lexie Curry, Catherine Gehring
{"title":"Better utilization of inorganic nitrogen compared to organic nitrogen by a plant symbiotic fungal isolate of <i>Alternaria alternata</i>.","authors":"Beatrice Bock, Lexie Curry, Catherine Gehring","doi":"10.17912/micropub.biology.001403","DOIUrl":"10.17912/micropub.biology.001403","url":null,"abstract":"<p><p><i>Alternaria alternata</i> , a fungus that causes plant diseases, is also a Dark Septate Endophyte (DSE) that can enhance host plant growth by improving access to soil nutrients like nitrogen. To test the environmental factors influencing this relationship, we explored whether <i>A. alternata</i> can utilize both organic and inorganic nitrogen. Our results showed that an <i>A. alternata</i> isolate grew 133% larger in an inorganic nitrogen medium than in an organic nitrogen medium. These findings suggest the need for further research on other DSE taxa and nitrogen forms to better understand fungal nitrogen use.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11822465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416499","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 eIF4E1 in Drosophila ananassae.
microPublication biology Pub Date : 2025-01-29 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001026
McKenzie Chamberlain, Ali Christie, Jeremy Girard, Hannah M Shaver, Lindsey J Long, James J Youngblom, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>eIF4E1</i> in <i>Drosophila ananassae</i>.","authors":"McKenzie Chamberlain, Ali Christie, Jeremy Girard, Hannah M Shaver, Lindsey J Long, James J Youngblom, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.001026","DOIUrl":"10.17912/micropub.biology.001026","url":null,"abstract":"<p><p>Gene model for the ortholog of eukaryotic translation initiation factor 4E1 ( <i>eIF4E1</i> ) in the 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":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11822467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416500","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
Expression profiles of phytosulfokine signalling components in sorghum drought stress-adaptive response. 高粱干旱胁迫适应反应中植物硫辛信号成分的表达谱。
microPublication biology Pub Date : 2025-01-28 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001284
Tatenda Goche, Rudo Ngara, Stephen Chivasa
{"title":"Expression profiles of phytosulfokine signalling components in sorghum drought stress-adaptive response.","authors":"Tatenda Goche, Rudo Ngara, Stephen Chivasa","doi":"10.17912/micropub.biology.001284","DOIUrl":"10.17912/micropub.biology.001284","url":null,"abstract":"<p><p>Phytosulfokine (PSK) signalling promotes drought adaptation in drought-sensitive plants. However, whether naturally drought-tolerant plants deploy PSK signalling in drought is unknown. We are using two sorghum varieties with different drought response phenotypes to investigate tolerance mechanisms. We show that PSK signalling components have high constitutive expression before stress in the drought-tolerant variety. In contrast, gene expression is low in the drought-sensitive variety and is induced after drought exposure. Ability of the drought-tolerant sorghum variety to maintain elevated PSK signalling under optimal water availability suggests that genetic and physiological factors driving drought tolerance may be linked to elevated constitutive PSK signalling.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11815484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143411862","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
Two K2P Channels, TWK-46 and TWK-26 do not affect C. elegans Egg-Laying Behavior.
microPublication biology Pub Date : 2025-01-27 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001477
Li Chen, Isabel Beets, William Schafer
{"title":"Two K2P Channels, TWK-46 and TWK-26 do not affect <i>C. elegans</i> Egg-Laying Behavior.","authors":"Li Chen, Isabel Beets, William Schafer","doi":"10.17912/micropub.biology.001477","DOIUrl":"10.17912/micropub.biology.001477","url":null,"abstract":"<p><p>Two-pore domain potassium channels, also known as K2P channels, play vital roles in maintaining the resting membrane potential in excitable cells, affecting a variety of physiological processes across species. The <i>Caenorhabditis elegans</i> ( <i>C. elegans</i> ) genome contains 46 different K2P-encoding genes, yet most of their functions remain unknown. Here, we have investigated the possible roles of two <i>C. elegans</i> K2P channel genes - <i>twk-26</i> and <i>twk-46</i> - that are expressed in the egg-laying neural circuit by characterizing the egg-laying behavior of null mutants generated by CRISPR/Cas9 gene editing. However, using a variety of assays, we did not observe significant differences in egg-laying behavior between <i>twk-26</i> and <i>twk-46</i> mutants and wild-type worms <i>.</i></p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400939","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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