microPublication biologyPub Date : 2024-12-05eCollection Date: 2024-01-01DOI: 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}
{"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}
microPublication biologyPub Date : 2024-12-03eCollection Date: 2024-01-01DOI: 10.17912/micropub.biology.001318
Alycia Ashby, Patrick Murphy, James Jukosky, Chery A Whipple
{"title":"The Effects of Perfluorooctanesulfonic acid (PFOS) on Human Umbilical Vein Endothelial Cells (HUVECs) Proliferation and Gene Expression and its Implications on Fetal Development.","authors":"Alycia Ashby, Patrick Murphy, James Jukosky, Chery A Whipple","doi":"10.17912/micropub.biology.001318","DOIUrl":"10.17912/micropub.biology.001318","url":null,"abstract":"<p><p>Polyfluoro-alkyl substances (PFAS) are widely distributed environmental contaminants linked to human toxicity and developmental delays, especially low birthweight (LBW). In this study, Human Umbilical Vein Endothelial Cells (HUVECs) were exposed to the PFAS perfluorooctanesulfonic acid (PFOS). After 48-hours, their proliferation, and differential gene expression were assessed. A small, yet significant, reduction in proliferation was seen at 50 μg/mL and 75 μg/mL. RNA sequencing showed that estrogen response and notch signaling pathways were significantly altered. This study increases our understanding of how PFAS may interfere with endothelial cell (HUVECs) functions which may have larger effects on fetal growth, development, and birthweight.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659881/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878940","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}
microPublication biologyPub Date : 2024-12-02eCollection Date: 2024-01-01DOI: 10.17912/micropub.biology.001357
Brianna Barruga, Sabrina Benitez, Emily Bouit, Tristan Bouit, Earick Cagang, Joshua Cantos, Dylan Carpio, Jaden Chen, Sungyoung Choi, Rita Dementyev, Ethan Dewri, Christian Dominguez, Alexandria Falvo, Christian Figueroa, Elva Garcia, Yannik Gibson, Dulce Guevara, Katie Jang, Michael Kelly, Caleb Kim, Nicole Kim, Raymond Kim, Julia Ko, Alyssa Lee, Yumin Lee, Rosalia Marenco, Moses Milano, Soojeong Moon, Kristen Ngo, Brian Nguyen, Eddie Nguyen, Ashley Perdomo, Elizabeth Paul, Ester Peiro, Daphne Prakash, Jennifer Ramon, Leslie Rodriguez, Emily Sandoval Plouffe, Joanna Shelim, Elizabeth Ton, Adam Tsao, Tabitha Usery, Madyson Vaca, Ethan Wang, Stuart Wettstein, Noboyuki Yano, Grace Young, Jiacheng Zhang, Arturo Diaz
{"title":"Complete Genome Sequences of Phages EarickHC, Figueroism, FinalFrontier, SBlackberry, Skylord, and Slay isolated using <i>Microbacterium foliorum</i>.","authors":"Brianna Barruga, Sabrina Benitez, Emily Bouit, Tristan Bouit, Earick Cagang, Joshua Cantos, Dylan Carpio, Jaden Chen, Sungyoung Choi, Rita Dementyev, Ethan Dewri, Christian Dominguez, Alexandria Falvo, Christian Figueroa, Elva Garcia, Yannik Gibson, Dulce Guevara, Katie Jang, Michael Kelly, Caleb Kim, Nicole Kim, Raymond Kim, Julia Ko, Alyssa Lee, Yumin Lee, Rosalia Marenco, Moses Milano, Soojeong Moon, Kristen Ngo, Brian Nguyen, Eddie Nguyen, Ashley Perdomo, Elizabeth Paul, Ester Peiro, Daphne Prakash, Jennifer Ramon, Leslie Rodriguez, Emily Sandoval Plouffe, Joanna Shelim, Elizabeth Ton, Adam Tsao, Tabitha Usery, Madyson Vaca, Ethan Wang, Stuart Wettstein, Noboyuki Yano, Grace Young, Jiacheng Zhang, Arturo Diaz","doi":"10.17912/micropub.biology.001357","DOIUrl":"10.17912/micropub.biology.001357","url":null,"abstract":"<p><p>Phages EarickHC, Figueroism, FinalFrontier, SBlackberry, Skylord, and Slay were isolated from soil samples collected around Southern California using the host <i>Microbacterium foliorum .</i> All six phages are lytic and have a siphoviral morphology. Genomes are 39,843 to 52,992 bp in length and contain 58 to 91 protein coding genes.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878916","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}
microPublication biologyPub Date : 2024-11-30eCollection Date: 2024-01-01DOI: 10.17912/micropub.biology.000715
Megan E Lawson, Graham M Jones, Megan Runion, Drew Sims, Austin Young, Olivia Briggs, Lindsey J Long, Solomon Tin Chi Chak, Indrani Bose, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>ImpL2</i> in <i>Drosophila simulans</i>.","authors":"Megan E Lawson, Graham M Jones, Megan Runion, Drew Sims, Austin Young, Olivia Briggs, Lindsey J Long, Solomon Tin Chi Chak, Indrani Bose, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000715","DOIUrl":"10.17912/micropub.biology.000715","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>Ecdysone-inducible gene L2</i> ( <i>ImpL2</i> ) in the May 2017 (Princeton ASM75419v2/DsimGB2) Genome Assembly (GenBank Accession: GCA_000754195.3 ) of <i>Drosophila simulans</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":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830483","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}
microPublication biologyPub Date : 2024-11-30eCollection Date: 2024-01-01DOI: 10.17912/micropub.biology.000856
Abigail Myers, Alexa Hoffman, Mindy Natysin, Andrew M Arsham, Joyce Stamm, Jeffrey S Thompson, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog <i>Myc</i> in <i>Drosophila ananassae</i>.","authors":"Abigail Myers, Alexa Hoffman, Mindy Natysin, Andrew M Arsham, Joyce Stamm, Jeffrey S Thompson, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000856","DOIUrl":"10.17912/micropub.biology.000856","url":null,"abstract":"<p><p>Gene model for the ortholog of Myc ( <i>Myc</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":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830481","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}
{"title":"Proteomics analysis reveals the differential impact of the p97 inhibitor CB-5083 on protein levels in various cellular compartments of the HL-60 cell line.","authors":"Wenxuan Huang, Yanping Qiu, Diana Huynh, Ting-Yu Wang, Tsui-Fen Chou","doi":"10.17912/micropub.biology.001372","DOIUrl":"10.17912/micropub.biology.001372","url":null,"abstract":"<p><p>Human p97/VCP is a vital AAA ATPase (ATPase associated with diverse cellular activity) that plays critical roles in protein homeostasis by regulating autophagy, endosomal trafficking, and the ubiquitin-proteasome system. Global proteomics analysis of p97/VCP inhibition with CB-5083 has been performed in HCT116 colon cells. Here, we examined the impact of CB-5083 treatment in another cancer model, the HL-60 acute myeloid leukemia cell line, employing subcellular fractionation combined with label-free proteomics to analyze changes in protein levels across cytoplasmic, nuclear, and insoluble membrane protein compartments. The results reveal distinct compartment-specific protein regulation, providing insight into p97/VCP's cellular mechanisms and its potential for targeted therapeutic applications.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11638764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830971","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}
microPublication biologyPub Date : 2024-11-26eCollection Date: 2024-01-01DOI: 10.17912/micropub.biology.001363
Emma C Mills, Katherine M Wollman, Elizabeth F Waring
{"title":"A Three Month Assessment of Anthropogenic Litter Levels on the Illinois River, Tahlequah, Oklahoma.","authors":"Emma C Mills, Katherine M Wollman, Elizabeth F Waring","doi":"10.17912/micropub.biology.001363","DOIUrl":"10.17912/micropub.biology.001363","url":null,"abstract":"<p><p>Anthropogenic litter is one of the most important factors that influence recreation users and their activities because of its correlation to the river and environmental health. We monitored pollution levels on the Illinois river, near Tahlequah, OK for three months and surveyed the publics opinion on the issue. Our goal was to get this data to local and state management agencies to management practices to keep the scenic Illinois River clean. We found aluminum cans in the most abundant, while survey participants said cigarette butts were of highest observable abundance. A total of 170 people took the survey, and many of them want to see change on the river. Change may have to come from cooperation with commercial float operators.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632524/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815192","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}
microPublication biologyPub Date : 2024-11-25eCollection Date: 2024-01-01DOI: 10.17912/micropub.biology.001362
Caymen Hoffman, Kristina Blanke
{"title":"<i>Calidifontibacillus erzuremensis</i> , <i>Pantoea agglomerans</i> , and <i>Pseudomonas glycinae</i> identified as antibiotic-producers from freshwater.","authors":"Caymen Hoffman, Kristina Blanke","doi":"10.17912/micropub.biology.001362","DOIUrl":"10.17912/micropub.biology.001362","url":null,"abstract":"<p><p>Three water isolates were previously identified as promising antibiotic producers from freshwater sources in Wisconsin, United States. Each isolate produced effective antibiotics against three or more bacterial relatives of antibiotic resistant pathogens. The isolates were identified as <i>Calidifontibacillus erzuremensis</i> , <i>Pantoea agglomerans</i> , and <i>Pseudomonas glycinae</i> through 16S rRNA sequencing and further characterized with biochemical tests to verify the genus and species of each isolate.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11626404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142803922","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}
microPublication biologyPub Date : 2024-11-23eCollection Date: 2024-01-01DOI: 10.17912/micropub.biology.001404
Michelle E Brown, Diego A Hernandez-Urbina, Caroline Kumsta
{"title":"Low humidity enhances thermotolerance in <i>Caenorhabditis elegans</i>.","authors":"Michelle E Brown, Diego A Hernandez-Urbina, Caroline Kumsta","doi":"10.17912/micropub.biology.001404","DOIUrl":"10.17912/micropub.biology.001404","url":null,"abstract":"<p><p>Humidity is an important environmental factor that causes physiological changes in organisms. In humans, high humidity disrupts thermoregulation by limiting heat dissipation, leading to heat stress. While <i>Caenorhabditis elegans</i> lacks comparable thermoregulatory systems, humidity may still impact its heat tolerance by affecting cellular stress responses. We tested this by subjecting <i>C. elegans</i> to heat shock under different humidity conditions and found that lower humidity during heat shock improved survival compared to higher humidity. These findings demonstrate that humidity is an important variable affecting thermotolerance in <i>C. elegans</i> and should be standardized in heat-stress experiments.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2024 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11625312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142803935","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}