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Depletion of UNK-1 affects head locomotive behaviors in Caenorhabditis elegans. UNK-1基因的缺失影响秀丽隐杆线虫头部运动行为。
microPublication biology Pub Date : 2025-06-11 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001659
Lexin Gitler, Callista Yee
{"title":"Depletion of UNK-1 affects head locomotive behaviors in <i>Caenorhabditis elegans</i>.","authors":"Lexin Gitler, Callista Yee","doi":"10.17912/micropub.biology.001659","DOIUrl":"10.17912/micropub.biology.001659","url":null,"abstract":"<p><p>During development, transcription factors execute genetic programs to define and shape the nervous system. We previously reported the transcription factor EGL-43 /Mecom regulates expression of numerous genes important for neuronal development in <i>C. elegans</i> . Here we characterized the function of one EGL-43 target, UNK-1 /Unkempt, a conserved RNA-binding protein. Using genome editing, we introduced an auxin-inducible degron tag and mNeonGreen into the <i>unk-1</i> locus. We observed cytoplasmic expression of UNK-1 in many head neurons. Depletion of UNK-1 resulted in increased head oscillations, a phenotype typically associated with defects in neurotransmitter synthesis. Our study links UNK-1 to head motor control in <i>C. elegans</i> .</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12198978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144509858","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
WRNexo is not required to maintain normal sex ratios in Drosophila: A CURE-Based Investigation. WRNexo在果蝇中不需要维持正常的性别比例：一项基于治疗的研究。
microPublication biology Pub Date : 2025-06-09 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001620
Elyse Bolterstein, Shubhangee Mungre, Kara Nuss, Eric P Stoffregen
{"title":"WRNexo is not required to maintain normal sex ratios in Drosophila: A CURE-Based Investigation.","authors":"Elyse Bolterstein, Shubhangee Mungre, Kara Nuss, Eric P Stoffregen","doi":"10.17912/micropub.biology.001620","DOIUrl":"10.17912/micropub.biology.001620","url":null,"abstract":"<p><p><i>WRNexo</i> and <i>Blm</i> , Drosophila orthologs of human WRN and BLM RecQ helicases, play crucial roles in DNA replication and repair. Using a Course-based Undergraduate Research Experience (CURE) in an introductory Biology course, we investigated whether <i>WRNexo <sup>Δ</sup></i> mutants exhibit a progeny sex-bias similar to <i>Blm</i> mutants. Chi-square analyses revealed no deviation from expected Mendelian ratios or sex-bias among <i>WRNexo <sup>Δ</sup></i> offspring. These findings suggest that WRNexo does not affect sex-specific survival and may not be essential for replication of highly repetitive DNA sequences. Our study demonstrates that CUREs effectively engage students in hypothesis-driven research while contributing meaningfully to genomic stability studies.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12186118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487459","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
Rap1 activity and localization is regulated by Rab40/CRL5 facilitated mono-ubiquitylation. Rap1的活性和定位受Rab40/CRL5促进的单泛素化调控。
microPublication biology Pub Date : 2025-06-09 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001629
Andrew Neumann, Revathi Sampath, Ke-Jun Han, Rytis Prekeris
{"title":"Rap1 activity and localization is regulated by Rab40/CRL5 facilitated mono-ubiquitylation.","authors":"Andrew Neumann, Revathi Sampath, Ke-Jun Han, Rytis Prekeris","doi":"10.17912/micropub.biology.001629","DOIUrl":"10.17912/micropub.biology.001629","url":null,"abstract":"<p><p>The Rap family of GTPases are emerging as major regulators of actin dynamics and cell migration. However, how Rap GTPases are activated and targeted to their subcellular localization remains to be fully understood. Recent work has shown that Rab40/CRL5-dependent mono-ubiquitylation is required for Rap2 activation. Here, we show that Rap1 is also mono-ubiquitylated by a Rab40/CRL5 E3 ubiquitin ligase complex and that Rap1 mono-ubiquitylation is necessary for Rap1 localization to both the plasma membrane and nuclear envelope. In summary, this work shows that Rab40/CRL5 is a major regulator of the activity and spatiotemporal dynamics of the Rap family of GTPases.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12186120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487457","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
The genetic mapping and phenotypic analysis of Patronin F.1.1 in Drosophila melanogaster. 黑腹果蝇光顾蛋白F.1.1的遗传定位及表型分析。
microPublication biology Pub Date : 2025-06-09 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001564
Lucas Gruber, Idalia Soto, Tristan Correa, Esmeralda Apodaca, Brian Arreola, Jhamiley Cabral, Kristine Chen, Miguel Correo Galicia, Joanna Gomez, Ellaine Hao, Brisa Hernandez, Darien L Holland, Crystal Jara-Pichardo, Gwyniever M Lonzame, Abigail Ortiz Olguin, Rheana Romero, Devon Walker, Spencer G Amacher, Cooper Christie, Lillian G Coats, Aubrey Gerhardt, Claire A Holsted, Stephen R Kraizel, Ashley Krumlaw, Alex Stevens, Haleigh Stover, Chloe M Sullivan, Hailey Wyse, Danielle R Hamill, Jacob D Kagey, Kayla L Bieser
{"title":"The genetic mapping and phenotypic analysis of <i>Patronin <sup>F.1.1</sup></i> in <i>Drosophila melanogaster</i>.","authors":"Lucas Gruber, Idalia Soto, Tristan Correa, Esmeralda Apodaca, Brian Arreola, Jhamiley Cabral, Kristine Chen, Miguel Correo Galicia, Joanna Gomez, Ellaine Hao, Brisa Hernandez, Darien L Holland, Crystal Jara-Pichardo, Gwyniever M Lonzame, Abigail Ortiz Olguin, Rheana Romero, Devon Walker, Spencer G Amacher, Cooper Christie, Lillian G Coats, Aubrey Gerhardt, Claire A Holsted, Stephen R Kraizel, Ashley Krumlaw, Alex Stevens, Haleigh Stover, Chloe M Sullivan, Hailey Wyse, Danielle R Hamill, Jacob D Kagey, Kayla L Bieser","doi":"10.17912/micropub.biology.001564","DOIUrl":"10.17912/micropub.biology.001564","url":null,"abstract":"<p><p>The multi-institutional Fly-CURE project is an undergraduate genetics research initiative centered on <i>Drosophila melanogaster</i> as a model organism. This study aimed to characterize and map mutations discovered through a Flp/FRT EMS screen to investigate complex interactions among genes associated with cell division, growth, and apoptosis leading to abnormal cell proliferation. The <i>F.1.1</i> mosaic phenotype resulted in a rough eye phenotype with an overall decrease in representation of mutant tissue. To genetically map the location of the <i>F.1.1</i> mutation, flies with genotype <i>FRT42D,F.1.1, Dark<sup>82</sup> /CyO</i> were crossed with the Bloomington 2R Deficiency Kit. The resultant F1 progeny were analyzed to pinpoint mapping deficiencies. The genomic region containing the <i>Patronin</i> gene was identified and sequencing confirmed the novel allele of <i>Patronin<sup>F.1.1</sup></i> .</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12186119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144487458","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
Multi-Channel Nuclear Analysis: An ImageJ/FIJI Plugin for Automated Nuclear Segmentation and Multi-Channel Fluorescence Analysis. 多通道核分析：一个ImageJ/斐济插件自动核分割和多通道荧光分析。
microPublication biology Pub Date : 2025-06-06 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001590
Ariel Waisman
{"title":"Multi-Channel Nuclear Analysis: An ImageJ/FIJI Plugin for Automated Nuclear Segmentation and Multi-Channel Fluorescence Analysis.","authors":"Ariel Waisman","doi":"10.17912/micropub.biology.001590","DOIUrl":"10.17912/micropub.biology.001590","url":null,"abstract":"<p><p>Quantitative analysis of fluorescence microscopy images is essential for studying expression levels, subcellular localization and co-occurrence of proteins and other biomolecules. While several automated tools exist for specific applications, there remains a need for user-friendly, customizable tools that can analyze multi-channel fluorescence images with nuclear segmentation capabilities. Here we present Multi-Channel Nuclear Analysis, an open-source ImageJ/FIJI plugin that combines the robust nuclear segmentation capabilities of StarDist with versatile multi-channel analysis features. The tool provides a graphical user interface for configuring analysis parameters, processes multiple images in batch mode, and generates both individual and consolidated measurement tables to facilitate downstream analysis. A companion tool for merging separate channel files into multi-channel images extends compatibility to diverse microscopy systems. Together, these tools enable researchers without extensive programming experience to perform comprehensive quantitative analysis of nuclear-centered multi-channel fluorescence images.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478144","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 elegans Exhibits Selective Chemotaxis to Cancer Cell-Conditioned Media. 秀丽隐杆线虫对癌细胞条件培养基表现出选择性趋化性。
microPublication biology Pub Date : 2025-06-05 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001618
Ridvan Aziz Ayaz, Deniz Yozlu, Elif Damla Arisan
{"title":"<i>Caenorhabditis elegans</i> Exhibits Selective Chemotaxis to Cancer Cell-Conditioned Media.","authors":"Ridvan Aziz Ayaz, Deniz Yozlu, Elif Damla Arisan","doi":"10.17912/micropub.biology.001618","DOIUrl":"10.17912/micropub.biology.001618","url":null,"abstract":"<p><p><i>Caenorhabditis elegans</i> is emerging as a valuable model for investigating chemosensory responses to disease-associated molecular cues recently. In this study, we examined the chemotaxis behavior of <i>C. elegans</i> toward the conditioned media from cancerous MIA PaCa-2 and PANC-1 cells and non-cancerous PNT1A cells. Untrained wild-type worms exhibited orientation to PNT1A media compared to the controls. Most importantly, training with cancer-conditioned media led to altered chemotaxis behavior, indicating olfactory learning. These findings support the use of <i>C. elegans</i> as a sensitive and adaptable system for detecting cancer-associated metabolites and demonstrate its potential role in non-invasive cancer screening applications and training-based models.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12179693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478143","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 Roc1a in Drosophila ananassae. 果蝇Roc1a同源基因的基因模型研究。
microPublication biology Pub Date : 2025-06-04 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001036
Megan E Lawson, Kelsey Gammage, Calvin Dexel, Lindsey J Long, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>Roc1a</i> in <i>Drosophila ananassae</i>.","authors":"Megan E Lawson, Kelsey Gammage, Calvin Dexel, Lindsey J Long, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.001036","DOIUrl":"10.17912/micropub.biology.001036","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>Regulator of cullins 1a</i> ( <i>Roc1a</i> ) in the <i>Drosophila ananassae</i> May 2011 (Agencourt dana_caf1/DanaCAF1) Genome Assembly (GenBank Accession: GCA_000005115.1 ). 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":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328008","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 Ilp3 in Drosophila ananassae. 果蝇Ilp3同源基因的基因模型研究。
microPublication biology Pub Date : 2025-06-04 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.000958
Madeline L Gruys, James O'Brien, Alyssa C Koehler, Alejandro Almazan, Katheryn Opperman, Rachel Sterne-Marr, Zeynep Ozsoy, Maire Kate Sustacek, Jacqueline Wittke-Thompson, Andrew M Arsham, Stephanie Toering Peters, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>Ilp3</i> in <i>Drosophila ananassae</i>.","authors":"Madeline L Gruys, James O'Brien, Alyssa C Koehler, Alejandro Almazan, Katheryn Opperman, Rachel Sterne-Marr, Zeynep Ozsoy, Maire Kate Sustacek, Jacqueline Wittke-Thompson, Andrew M Arsham, Stephanie Toering Peters, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000958","DOIUrl":"10.17912/micropub.biology.000958","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>Insulin-like peptide 3</i> ( <i>Ilp3</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":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328006","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 lin-28 in Drosophila simulans. 拟果蝇同源基因lin-28的基因模型。
microPublication biology Pub Date : 2025-06-04 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.000963
Megan E Lawson, Hannan Saeed, Cassie Tran, Simran Chhina, Jack A Vincent, Brian Schwartz, Kellie S Agrimson, Christopher E Ellison, Chinmay P Rele, Laura K Reed
{"title":"Gene model for the ortholog of <i>lin-28</i> in <i>Drosophila simulans</i>.","authors":"Megan E Lawson, Hannan Saeed, Cassie Tran, Simran Chhina, Jack A Vincent, Brian Schwartz, Kellie S Agrimson, Christopher E Ellison, Chinmay P Rele, Laura K Reed","doi":"10.17912/micropub.biology.000963","DOIUrl":"10.17912/micropub.biology.000963","url":null,"abstract":"<p><p>Gene model for the ortholog of <i>lin-28</i> ( <i>lin-28</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":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328007","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
CompMap: an allele-specific expression read counter based on competitive mapping. CompMap：基于竞争映射的等位基因特异性表达式读取计数器。
microPublication biology Pub Date : 2025-06-02 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001599
Santiago Sanchez-Ramirez, Asher Cutter
{"title":"CompMap: an allele-specific expression read counter based on competitive mapping.","authors":"Santiago Sanchez-Ramirez, Asher Cutter","doi":"10.17912/micropub.biology.001599","DOIUrl":"10.17912/micropub.biology.001599","url":null,"abstract":"<p><p>Gene regulatory changes acting <i>cis</i> and <i>trans</i> to a gene can be inferred with allele-specific expression (ASE) transcriptomes from interspecies and inter-population hybrids and their parents. Problems of mapping bias and excessive information loss, however, can arise unintentionally from cumbersome analysis pipelines. We introduce CompMap, a self-contained method in Python that generates allele-specific expression counts from genotype-specific alignments. CompMap sorts and counts reads, not just SNPs, by comparing read-mapping statistics to parental alignments within homologous regions. Ambiguous alignments resolve proportionally to allele-specific counts or statistically using a binomial distribution. Simulations with CompMap show low error rates in assessing regulatory divergence.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328005","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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