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Genome Sequences of Streptomyces griseus Phages Destructrice and Rikishi. 灰色链霉菌破坏噬菌体和Rikishi的基因组序列。
microPublication biology Pub Date : 2026-04-07 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001954
Elizabeth A Powell, Allison O Wortman, Kathryn E Tyler, Karina Alfonso-Perez, Giselle A Bez, Caroline R Buechlein, Michael D Day, Tasline T Diab, Isabella G Henderson, Tosin E Ishola, Ross S Rider, Dalton N Seiler, Colin S Stooksberry, Allyson E Wary, Julie A Merkle
{"title":"Genome Sequences of <i>Streptomyces griseus</i> Phages Destructrice and Rikishi.","authors":"Elizabeth A Powell, Allison O Wortman, Kathryn E Tyler, Karina Alfonso-Perez, Giselle A Bez, Caroline R Buechlein, Michael D Day, Tasline T Diab, Isabella G Henderson, Tosin E Ishola, Ross S Rider, Dalton N Seiler, Colin S Stooksberry, Allyson E Wary, Julie A Merkle","doi":"10.17912/micropub.biology.001954","DOIUrl":"https://doi.org/10.17912/micropub.biology.001954","url":null,"abstract":"<p><p>This paper describes the complete genome sequences of two novel bacteriophages isolated using <i>Streptomyces griseus</i> . Destructrice is a podovirus bacteriophage with a 45,548 bp genome assigned to the actinobacteriophage cluster BF. In contrast, Rikishi is a cluster BE2 siphovirus with a 132,567 bp genome.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791275","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 two Gordonia rubripertincta cluster CS4 Bacteriophages, Vitaenoii and Philon9. 两个红带戈登菌群CS4噬菌体Vitaenoii和Philon9的全基因组序列
microPublication biology Pub Date : 2026-04-07 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001957
Joshua T McMenemy, Amanda I Acra, Elisabeth A Alexander, Vanessa K Cordovez, Morgan M Fitzpatrick, Dayanara Mejia, Chaeli H Smith, Marie P Fogarty
{"title":"Complete Genome Sequence of two <i>Gordonia rubripertincta</i> cluster CS4 Bacteriophages, Vitaenoii and Philon9.","authors":"Joshua T McMenemy, Amanda I Acra, Elisabeth A Alexander, Vanessa K Cordovez, Morgan M Fitzpatrick, Dayanara Mejia, Chaeli H Smith, Marie P Fogarty","doi":"10.17912/micropub.biology.001957","DOIUrl":"https://doi.org/10.17912/micropub.biology.001957","url":null,"abstract":"<p><p>We report the discovery and genome sequences of bacteriophages Vitaenoii and Philon9, isolated from soil samples collected in Durham, North Carolina using the host <i>Gordonia rubripertincta</i> NRRL B-16540. The phages have siphoviral morphology and are assigned to bacteriophage subcluster CS4.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791109","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
Cynaropicrin inhibits pancreatic cancer cell viability and disrupts cellular redox homeostasis. Cynaropicrin抑制胰腺癌细胞活力并破坏细胞氧化还原稳态。
microPublication biology Pub Date : 2026-04-06 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002097
Heather R Leek, Abby L Oberhelman, Sam R Rew, Olivia M Janss, Cole D Davidson
{"title":"Cynaropicrin inhibits pancreatic cancer cell viability and disrupts cellular redox homeostasis.","authors":"Heather R Leek, Abby L Oberhelman, Sam R Rew, Olivia M Janss, Cole D Davidson","doi":"10.17912/micropub.biology.002097","DOIUrl":"https://doi.org/10.17912/micropub.biology.002097","url":null,"abstract":"<p><p>Pancreatic cancer accounts for approximately 8% of all cancer-related deaths. The compound cynaropicrin (CNP) has been investigated recently in several cancer models and has been shown to decrease cell viability. We used sulforhodamine B and trypan blue assays to measure cell viability following CNP treatment in PANC-1 cells. CNP reduced cell viability in a concentration-dependent manner (IC <sub>50</sub> = 5.29 µM) and significantly decreased free thiol levels. Finally, <i>in silico</i> docking demonstrated the potential for CNP to bind the DNA-binding domain of NF-κB. These data support further investigation of CNP as a potential therapeutic candidate in pancreatic cancer.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791096","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
Carapics: A Web-based Platform for Semi-quantitative Analysis of Structural Change in Biological Samples. Carapics：一个半定量分析生物样品结构变化的网络平台。
microPublication biology Pub Date : 2026-04-06 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002048
Gary H Dickinson, Sejong Yoon, Nate Sorvino, Sameer Kamal, Corin J Hoppe, Isra Ahmad, W Christopher Long
{"title":"Carapics: A Web-based Platform for Semi-quantitative Analysis of Structural Change in Biological Samples.","authors":"Gary H Dickinson, Sejong Yoon, Nate Sorvino, Sameer Kamal, Corin J Hoppe, Isra Ahmad, W Christopher Long","doi":"10.17912/micropub.biology.002048","DOIUrl":"https://doi.org/10.17912/micropub.biology.002048","url":null,"abstract":"<p><p>Environmental stress can alter and damage biological structures with functional consequences. Inspired by observations of Tanner crabs after 2-year exposure to ocean acidification, we observed that crabs held at low pH appeared to have damaged claws. Patterns, however, were complex and three-dimensional, making quantification difficult. We developed a survey-based approach where evaluators could score the extent of damage in images of claws. We present a software tool for the creation of image surveys. The software allows users to quickly upload batches of images, parse file names, and generate surveys. Collected data is returned to the user, associated with treatment conditions.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147790964","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
Directionality bias in T/A cloning. T/A克隆中的方向性偏差。
microPublication biology Pub Date : 2026-04-06 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002065
Valeria Dountcheva, Athanasios Bubulya, Labib Rouhana
{"title":"Directionality bias in T/A cloning.","authors":"Valeria Dountcheva, Athanasios Bubulya, Labib Rouhana","doi":"10.17912/micropub.biology.002065","DOIUrl":"https://doi.org/10.17912/micropub.biology.002065","url":null,"abstract":"<p><p>T/A cloning is a popular method for generating recombinant DNA plasmids. This method relies on single A:T nucleotide base pairs between PCR product ends and vector. Theoretically, the directionality of insert ligation with relation to the vector is random. However, we have continuously observed directionality bias using the pGEM-T Vector System for T/A cloning in a Course-based Undergraduate Research Experience (CURE). Cloning of over 400 inserts has shown directional bias higher than 74% ( <i>p-</i> value < 0.0005) \"sense\" to the T7 promoter of the vector <i>.</i> Awareness of biased insertion directionality in our applications reduces time and cost in cloning and downstream analyses.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097059/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791217","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-term quantification and brief-pulse optogenetic perturbation of nucleocytoplasmic GtaC dynamics during Dictyostelium development. 盘柱体发育过程中核胞质GtaC动力学的长期定量和短脉冲光遗传扰动。
microPublication biology Pub Date : 2026-04-06 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002037
Kensuke Yamashita, Tetsuya Muramoto
{"title":"Long-term quantification and brief-pulse optogenetic perturbation of nucleocytoplasmic GtaC dynamics during Dictyostelium development.","authors":"Kensuke Yamashita, Tetsuya Muramoto","doi":"10.17912/micropub.biology.002037","DOIUrl":"https://doi.org/10.17912/micropub.biology.002037","url":null,"abstract":"<p><p>Transcription factor nucleocytoplasmic dynamics play a key role in developmental gene regulation. In <i>Dictyostelium</i> , the transcription factor GtaC exhibits nucleocytoplasmic shuttling, but its shuttling trajectory across multicellular aggregation has not been systematically quantified. Using a knock-in strain, we tracked GtaC dynamics from starvation through aggregation and quantified developmental changes in shuttling period, amplitude, and synchrony. Notably, brief-pulse optogenetic activation of cAMP at higher input frequencies reproduced the reported attenuation of GtaC shuttling amplitude with high temporal precision and minimal phototoxicity. Together, long-term quantification and brief-pulse optogenetic cAMP perturbation show that GtaC nucleocytoplasmic shuttling is developmentally tuned in a frequency-dependent manner.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791400","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
Characterization of the Complete Genome of Arthrobacter globiformis Cluster FF Bacteriophage QuinnAvery. 球形节杆菌FF噬菌体QuinnAvery全基因组的研究
microPublication biology Pub Date : 2026-04-06 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001994
Elaine P Akst, Demelash Areda, Eric J Battaglioli, Christopher W Beck, Marina L Bogush, Steven M Caruso, Anne M Cedergren-Healy, Saroj V Chirravuri, Davida L Crossley, Katherine D'Amico-Willman, Veronique A Delesalle, Rebekah F Hare, Deborah L Harris, Jennifer R Ingram, Vedham Karpakakunjaram, Behnam Khatabi, Karen K Klyczek, Jonathan N Lawson, Cori Leonetti, Stephanie L Mathews, Matthew T McDonald, Katelyn M Mika, Ugonna C Morikwe, Zachary L Nikolakis, Xavier S Purroy, Amy B Ryan, Heather S Schiller, Mozhgan Sepehri, David E Starkey, Levi Storks, Kissaou T Tchedre, Ana C Vallor, Nic M Vega, Daniel E Velez-Ramirez, Emily E Whitaker, Daniel C Williams, Nicholas M Young, Christina H Zagorac, Deborah Jacobs-Sera, Denise Monti, Daniel A Russell, Bethany Wise, Marcie H Warner
{"title":"Characterization of the Complete Genome of <i>Arthrobacter globiformis</i> Cluster FF Bacteriophage QuinnAvery.","authors":"Elaine P Akst, Demelash Areda, Eric J Battaglioli, Christopher W Beck, Marina L Bogush, Steven M Caruso, Anne M Cedergren-Healy, Saroj V Chirravuri, Davida L Crossley, Katherine D'Amico-Willman, Veronique A Delesalle, Rebekah F Hare, Deborah L Harris, Jennifer R Ingram, Vedham Karpakakunjaram, Behnam Khatabi, Karen K Klyczek, Jonathan N Lawson, Cori Leonetti, Stephanie L Mathews, Matthew T McDonald, Katelyn M Mika, Ugonna C Morikwe, Zachary L Nikolakis, Xavier S Purroy, Amy B Ryan, Heather S Schiller, Mozhgan Sepehri, David E Starkey, Levi Storks, Kissaou T Tchedre, Ana C Vallor, Nic M Vega, Daniel E Velez-Ramirez, Emily E Whitaker, Daniel C Williams, Nicholas M Young, Christina H Zagorac, Deborah Jacobs-Sera, Denise Monti, Daniel A Russell, Bethany Wise, Marcie H Warner","doi":"10.17912/micropub.biology.001994","DOIUrl":"https://doi.org/10.17912/micropub.biology.001994","url":null,"abstract":"<p><p>Phage QuinnAvery produces turbid plaques in <i>Arthrobacter globiformis</i> B-2979 lawns, displays a siphovirus morphology, and is clustered with FF actinobacteriophages. The 43,177 bp genome of QuinnAvery is predicted to contain a tRNA-Arg(TCT) gene and 69 protein-coding genes. Homologs of a subset of QuinnAvery's predicted genes have putative roles in viral structure, particle assembly, host cell lysis, and lysogeny. QuinnAvery's genome is predicted to contain two tyrosine integrases, similar to many other cluster FF phages. However, the area immediately surrounding the integration cassette in QuinnAvery is distinct from all other annotated members of cluster FF.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13097055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147791078","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
Crithidia fasciculata gene of unknown function CFAC1_070014400 encodes a putative alpha/beta hydrolase with a conserved active site. 功能未知的麻瓜基因CFAC1_070014400编码一种具有保守活性位点的α / β水解酶。
microPublication biology Pub Date : 2026-04-03 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.001967
Justin Davis
{"title":"<i>Crithidia fasciculata</i> gene of unknown function CFAC1_070014400 encodes a putative alpha/beta hydrolase with a conserved active site.","authors":"Justin Davis","doi":"10.17912/micropub.biology.001967","DOIUrl":"10.17912/micropub.biology.001967","url":null,"abstract":"<p><p>A gene of unknown function, CFAC1_070014400 (Transcript ID: CFAC1_070014400.1), identified in <i>Crithidia fasciculata</i> was analyzed using bioinformatic methods to study the sequence and structure of its encoded protein. Results from domain predictions, conservation analysis, and structural comparisons indicate the encoded protein is a member of the alpha/beta hydrolase superfamily and contains a conserved active site. Based on phylogenetic analysis, the encoded protein groups with other putative alpha/beta hydrolase homologs from related kinetoplastid parasites.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13092109/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730861","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
JuNkIE-CLImax: exploring multidimensional images in notebooks and the terminal. JuNkIE-CLImax：探索笔记本和终端中的多维图像。
microPublication biology Pub Date : 2026-04-02 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002120
Rodrigo Fernandez-Gonzalez, Raymond Hawkins
{"title":"JuNkIE-CLImax: exploring multidimensional images in notebooks and the terminal.","authors":"Rodrigo Fernandez-Gonzalez, Raymond Hawkins","doi":"10.17912/micropub.biology.002120","DOIUrl":"10.17912/micropub.biology.002120","url":null,"abstract":"<p><p>Modern microscopy generates multidimensional images. Graphical user interfaces allow visualization of multidimensional images, but image exploration is significantly harder in text-based environments. These include Jupyter notebooks, popular for the distribution of data analysis pipelines; and the terminal, often the only user interface available when accessing images in remote servers. We developed JuNkIE-CLImax, a pair of multidimensional image explorers designed to work in Jupyter notebooks and the terminal, respectively. JuNkIE-CLImax are written in Python, using Rust extensions to optimize performance; they are platform agnostic; and they provide application programming interfaces that enable integration into complex image visualization and analysis pipelines.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13087738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147724980","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
Defining the breakpoints of the v ermilion white ( v w ) mutation, a deletion that removes vermilion, gustatory receptor candidate 58, and norpA . 定义了v百万白（v w）突变的断点，删除了朱红，味觉受体候选58和norpA。
microPublication biology Pub Date : 2026-04-01 eCollection Date: 2026-01-01 DOI: 10.17912/micropub.biology.002073
Josy Joseph, Douglas Rusch, Andrew Zelhof
{"title":"Defining the breakpoints of the v <i>ermilion white</i> ( <i>v <sup>w</sup></i> ) mutation, a deletion that removes <i>vermilion, gustatory receptor candidate 58,</i> and <i>norpA</i> .","authors":"Josy Joseph, Douglas Rusch, Andrew Zelhof","doi":"10.17912/micropub.biology.002073","DOIUrl":"10.17912/micropub.biology.002073","url":null,"abstract":"<p><p>A key mutation for generating transgenics in <i>Tribolium castaneum</i> is <i>vermilion <sup>white</sup></i> ( <i>v <sup>w</sup></i> ). <i>&nbsp;v <sup>w</sup></i> is a deletion that removes most of the <i>vermilion</i> locus, but the upstream breakpoint has not been mapped. Here we report that the second breakpoint is located upstream in the <i>Tribolium</i> homolog of <i>norpA.</i> The <i>v <sup>w</sup></i> deletion is 4434 bps. The deletion eliminates not only <i>vermilion</i> but also <i>gustatory receptor candidate 58</i> and <i>norpA</i> function. Therefore, the <i>v <sup>w</sup></i> mutation is a deficiency that affects three genetic loci. To acknowledge the disruption of multiple loci this genetic mutant will be known as Deficiency <i>vermilion <sup>white</sup></i> , Df ( <i>v <sup>w</sup></i> ).</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2026 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13084372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147724988","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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