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High confidence HIF-1 target genes for quantifying the activation of the HIF-1-mediated hypoxia response. 用于量化HIF-1介导的缺氧反应激活的高置信度HIF-1靶基因。
microPublication biology Pub Date : 2026-09-15 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002304
Camille Ah Desnos, Aura A Tamez Gonzalez, Jeremy M Van Raamsdonk
{"title":"High confidence HIF-1 target genes for quantifying the activation of the HIF-1-mediated hypoxia response.","authors":"Camille Ah Desnos, Aura A Tamez Gonzalez, Jeremy M Van Raamsdonk","doi":"10.17912/micropub.biology.002304","DOIUrl":"https://doi.org/10.17912/micropub.biology.002304","url":null,"abstract":"<p><p>The hypoxia-inducible factor 1 ( HIF-1 )-mediated hypoxia response is an evolutionarily conserved stress response that enables adaptation to conditions of low oxygen and mitochondrial dysfunction. This pathway has been shown to affect both stress resistance and longevity. HIF-1 activity is regulated by EGL-9 , VHL-1 , and RHY-1 and induces the expression of genes involved in metabolism and cellular resilience. To find genes that can be used to monitor HIF-1 activation, we compared HIF-1 modulated genes identified by multiple RNA-seq experiments and HIF-1 target genes identified by ChIP-seq experiments. We identified high-confidence HIF-1 target genes that provide robust markers of pathway activation.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119896","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
Quantification of calreticulin redistribution in LNCaP prostate cancer cells using a fixed-cell imaging workflow. 使用固定细胞成像工作流程定量LNCaP前列腺癌细胞中的钙调钙蛋白再分布。
microPublication biology Pub Date : 2026-09-15 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002112
Janiyah Vogle, Kandace Rankin, Courtney Thomas
{"title":"Quantification of calreticulin redistribution in LNCaP prostate cancer cells using a fixed-cell imaging workflow.","authors":"Janiyah Vogle, Kandace Rankin, Courtney Thomas","doi":"10.17912/micropub.biology.002112","DOIUrl":"https://doi.org/10.17912/micropub.biology.002112","url":null,"abstract":"<p><p>Calreticulin (CRT) is an endoplasmic reticulum chaperone that can localize to the cell surface under stress, where it functions as a damage-associated molecular pattern. Quantifying surface-exposed CRT in prostate cancer models is challenging due to low baseline expression and variability in imaging workflows. We describe a fixed-cell immunofluorescence method to distinguish intracellular and surface CRT in LNCaP cells. Cells treated with thapsigargin exhibited increased surface localization. We introduce a redistribution factor (RF = ectoCRT/(ectoCRT + endoCRT)) to quantify CRT partitioning. This approach provides a reproducible framework for assessing CRT redistribution using standard fluorescence microscopy.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119868","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
Maximum performance, repeatability, and intraindividual variability of sprinting in common wall lizards ( Podarcis muralis ). 普通壁虎（足蜥）冲刺的最大性能、可重复性和个体差异性。
microPublication biology Pub Date : 2026-09-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002072
Madelyn C Browning, Lindsey Mayor, Halle Kozak, Gabrielle Abshire, Isabel Allo, Alida C Askill, Allison Bogan, Hayley Browning, Halle Dacek, Lan Do, Sam Frary, Sydney Gassert, Aida Gesink, Caleb Gunn, Landon Key, Ella M Neuenschwander, Brittney C Parks, Evelyn Waltz, Aidan Weir, Eric J Gangloff, Bryan H Juarez
{"title":"Maximum performance, repeatability, and intraindividual variability of sprinting in common wall lizards ( <i>Podarcis muralis</i> ).","authors":"Madelyn C Browning, Lindsey Mayor, Halle Kozak, Gabrielle Abshire, Isabel Allo, Alida C Askill, Allison Bogan, Hayley Browning, Halle Dacek, Lan Do, Sam Frary, Sydney Gassert, Aida Gesink, Caleb Gunn, Landon Key, Ella M Neuenschwander, Brittney C Parks, Evelyn Waltz, Aidan Weir, Eric J Gangloff, Bryan H Juarez","doi":"10.17912/micropub.biology.002072","DOIUrl":"https://doi.org/10.17912/micropub.biology.002072","url":null,"abstract":"<p><p>The repeatability of functional traits like physiological maxima (maximum performance) measures the reliability of underlying measurements. However, best practices for analyzing maximal performance while accounting for within-individual variation are lacking. Here, we quantify the coefficient of variation and repeatability of maximum sprinting speed in common wall lizards ( <i>Podarcis muralis</i> ) from Cincinnati, USA. We use insights from experimental data and bootstrap resampling to discuss strategies for analyzing physiological maxima while accounting for within-individual variation. Relative to assuming greater among- than within-individual variation, our proposals offer greater precision in parameter estimates and statistical test results with increased power, thus improving scientific reproducibility.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119855","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 eef1a1l1 expression stability and promoter-driven reporter activity during zebrafish development. 斑马鱼发育过程中eef1a1l1表达稳定性和启动子驱动报告子活性的评估。
microPublication biology Pub Date : 2026-09-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002410
Nicole A Aponte-Santiago, Nicole Suren, Yingxin Su, Coral N Halanych, Maile N Matubrew, Erin Song, Ian A Swinburne, David Q Matus, Daniel E Wagner
{"title":"Evaluation of eef1a1l1 expression stability and promoter-driven reporter activity during zebrafish development.","authors":"Nicole A Aponte-Santiago, Nicole Suren, Yingxin Su, Coral N Halanych, Maile N Matubrew, Erin Song, Ian A Swinburne, David Q Matus, Daniel E Wagner","doi":"10.17912/micropub.biology.002410","DOIUrl":"https://doi.org/10.17912/micropub.biology.002410","url":null,"abstract":"<p><p>Housekeeping genes are widely used as experimental references for gene expression, yet many exhibit substantial variation within and between cell types. Using Zebrafish Meta Atlas Project (ZMAP), we found <i>eef1a1l1</i> to be ubiquitously and highly expressed across zebrafish embryonic cell types, developmental stages, and studies. Transgenic reporters driven by 2.2-kb or 2.6-kb <i>eef1a1l1</i> -derived regulatory sequences showed broad embryonic expression, and single-cell profiling revealed that reporter abundance covaried with that of the endogenous <i>eef1a1l1</i> transcript. These findings further support <i>eef1a1l1</i> as a reference for embryonic gene expression and the use of its regulatory sequence as a practical, multipurpose transgenic driver.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119891","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
Capture and characterization of antibiotic resistance plasmids from Beargrass Creek, an urban watershed in Louisville, KY. 从肯塔基州路易斯维尔市的一个城市流域Beargrass Creek中捕获和表征抗生素抗性质粒。
microPublication biology Pub Date : 2026-09-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002240
Savonna Carrie, Andrew Goeppner, Landon Patel, David S Treves
{"title":"Capture and characterization of antibiotic resistance plasmids from Beargrass Creek, an urban watershed in Louisville, KY.","authors":"Savonna Carrie, Andrew Goeppner, Landon Patel, David S Treves","doi":"10.17912/micropub.biology.002240","DOIUrl":"https://doi.org/10.17912/micropub.biology.002240","url":null,"abstract":"<p><p>The objective of this work was to capture and characterize antibiotic resistant plasmids from Beargrass Creek in Louisville, KY, an extensive urban watershed that receives combined sewer overflow and surface runoff. Twenty-eight plasmids captured from creek water were screened for antibiotic resistance, surveyed for common antibiotic resistance genes, and subjected to restriction digestion to determine common plasmid backbones. Based on this analysis, five plasmids were chosen for sequencing that revealed TEM-type β-lactamases conferring ampicillin resistance and <i>tetA</i> associated with tetracycline resistance. This work provides a better understanding of plasmid borne antibiotic resistance and plasmid diversity in urban watersheds.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119615","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
Caenorhabditis Intervention Testing Program: the putative mTOR inhibitors Cinnarizine and Meclizine do not extend lifespan in C. elegans. 隐杆线虫炎干预试验计划：假定的mTOR抑制剂Cinnarizine和Meclizine不能延长秀丽隐杆线虫的寿命。
microPublication biology Pub Date : 2026-09-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002198
Erik Johnson, Christine A Sedore, Anna L Coleman-Hulbert, Brian D Onken, Vijaya Madhuri Achanta, Yuhua Song, Gino Cortopassi, Gordon J Lithgow, Monica Driscoll, Patrick C Phillips
{"title":"<i>Caenorhabditis</i> Intervention Testing Program: the putative mTOR inhibitors Cinnarizine and Meclizine do not extend lifespan in <i>C. elegans</i>.","authors":"Erik Johnson, Christine A Sedore, Anna L Coleman-Hulbert, Brian D Onken, Vijaya Madhuri Achanta, Yuhua Song, Gino Cortopassi, Gordon J Lithgow, Monica Driscoll, Patrick C Phillips","doi":"10.17912/micropub.biology.002198","DOIUrl":"10.17912/micropub.biology.002198","url":null,"abstract":"<p><p>The mechanistic target of rapamycin (mTOR), a protein kinase and master cell regulator, is one of the most validated longevity drug targets: mTOR inhibition by compounds like rapamycin has been shown to significantly extend lifespan in numerous model organisms. Here, we tested whether the novel putative mTOR-inhibiting compounds cinnarizine and meclizine could likewise increase lifespan in the nematode <i>C. elegans</i> , following standardized protocols from the <i>Caenorhabditis</i> Intervention Testing Program (CITP). Our results indicate that cinnarizine and meclizine have no effect on <i>C. elegans</i> lifespan at lower doses, and that both compounds exert a toxic effect at higher doses, significantly shortening lifespan.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149076764","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
Renalase Peptide (RP220) Activates MAPK Signaling Pathways in Primary Mouse Skeletal Muscle Cells. Renalase Peptide （RP220）激活小鼠原代骨骼肌细胞MAPK信号通路
microPublication biology Pub Date : 2026-09-14 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002195
Katsuyuki Tokinoya, Yuri Kato, Kai Aoki, Kazuhiro Takekoshi
{"title":"Renalase Peptide (RP220) Activates MAPK Signaling Pathways in Primary Mouse Skeletal Muscle Cells.","authors":"Katsuyuki Tokinoya, Yuri Kato, Kai Aoki, Kazuhiro Takekoshi","doi":"10.17912/micropub.biology.002195","DOIUrl":"https://doi.org/10.17912/micropub.biology.002195","url":null,"abstract":"<p><p>Renalase is a secreted protein that was initially discovered in the kidney and that is also expressed in skeletal muscle. Moreover, renalase peptide RP220 activates MAPK signaling in the kidneys. This study investigated the effects of the RP220 on skeletal muscle using primary cultured cells. Notably, RP220 treatment did not alter the myogenic differentiation phenotype; however, intracellular signaling analyses revealed significant phosphorylation of p38 and ERK, which are MAPK family members. These results indicate that renalase affects MAPK signaling, but its physiological or developmental effects on skeletal muscle are not yet known.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13624854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119846","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
Draft genome assemblies of three Ligilactobacillus salivarius strains isolated from commercial layer hen litter. 绘制从商品蛋鸡窝中分离的三株唾液脂乳杆菌的基因组序列。
microPublication biology Pub Date : 2026-09-11 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002411
Benjamin Brehm-Stecher, Ryan Donaldson, Charlie Fisher, William Jensen, Alex Kottmeyer, Paul Lueth, Matthew Lutz, Elizabeth Makovec, Simon Alexander Radl, Ainsley Wood, Madison Stoltz, Nick Peters, Lucille C Jonas
{"title":"Draft genome assemblies of three <i>Ligilactobacillus salivarius</i> strains isolated from commercial layer hen litter.","authors":"Benjamin Brehm-Stecher, Ryan Donaldson, Charlie Fisher, William Jensen, Alex Kottmeyer, Paul Lueth, Matthew Lutz, Elizabeth Makovec, Simon Alexander Radl, Ainsley Wood, Madison Stoltz, Nick Peters, Lucille C Jonas","doi":"10.17912/micropub.biology.002411","DOIUrl":"10.17912/micropub.biology.002411","url":null,"abstract":"<p><p>Direct-fed probiotics in poultry can improve animal nutrition and health while also competing with human foodborne pathogens for colonization of the gastrointestinal tract. The objective of this study was to perform whole-genome sequencing on lactic acid bacteria isolated from commercial chicken litter to characterize genetic markers associated with probiotic potential. Three <i>Ligilactobacillus salivarius</i> strains were selected for whole-genome sequencing using Oxford Nanopore Technology. The genomes contained genes associated with sialic acid utilization, bacteriocin production, and antimicrobial resistance. While these markers may indicate suitability as probiotics in poultry, further experimentation is needed to verify the functionality of the identified genes.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13613153/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066577","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
Chromosome-Scale Assembly of Novel Caenorhabditis sp. 61 (strain JU4110). 新秀丽隐杆线虫sp. 61（菌株JU4110）的染色体尺度组装。
microPublication biology Pub Date : 2026-09-11 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002358
Pooja Lad, Michelle A McCauley, Victoria K Eggers, Janna L Fierst, Karolina Willicott
{"title":"Chromosome-Scale Assembly of Novel <i>Caenorhabditis sp. 61</i> (strain JU4110).","authors":"Pooja Lad, Michelle A McCauley, Victoria K Eggers, Janna L Fierst, Karolina Willicott","doi":"10.17912/micropub.biology.002358","DOIUrl":"10.17912/micropub.biology.002358","url":null,"abstract":"<p><p><i>Caenorhabditis</i> nematodes are similar morphologically but highly distinct on the genetic level, with recent characterizations being based on DNA sequences. Comparisons between the model <i>C. elegans</i> and other <i>Caenorhabditis</i> species have revealed conserved chromosome organization and species-species changes that have improved our understanding of genome evolution. Here, we report a chromosome-scale assembly of a novel <i>Caenorhabditis</i> <i>sp.</i> <i>61</i> (strain JU4110). This reference genome expands the genomic resources available for genus <i>Caenorhabditis</i> and allows for more detailed comparative analyses and greater phylogenomic coverage.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13613155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066566","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
Genipin Alleviates Sleep Deficiencies Caused by α-Synuclein Toxicity in a Drosophila melanogaster Model of Parkinson's Disease. Genipin减轻帕金森病果蝇α-突触核蛋白毒性引起的睡眠不足
microPublication biology Pub Date : 2026-09-10 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002289
Olivia M Davis, Alice H Sappenfield, Robert Fairman
{"title":"Genipin Alleviates Sleep Deficiencies Caused by α-Synuclein Toxicity in a <i>Drosophila melanogaster</i> Model of Parkinson's Disease.","authors":"Olivia M Davis, Alice H Sappenfield, Robert Fairman","doi":"10.17912/micropub.biology.002289","DOIUrl":"10.17912/micropub.biology.002289","url":null,"abstract":"<p><p>Parkinson's disease is predominantly characterized by dopaminergic neurodegeneration linked to toxic aggregation of α‑synuclein. Genipin, a bioactive iridoid, was previously shown to improve the motility and survival deficits caused by pan-neuronal expression of native α-synuclein in a transgenic <i>Drosophila melanogaster</i> model system. We show that expression of α-synuclein causes sleep deficits and that genipin treatment rescued these sleep deficits, increasing total sleep and consolidating nighttime sleep relative to untreated α‑synuclein-expressing fruit flies. Our findings extend genipin's protective profile in <i>Drosophila melanogaster</i> and highlight sleep regulation as an additional phenotype responsive to α‑synuclein-targeted interventions.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13613154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066631","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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