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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
Velvety tree ant extract is a chemotaxis repellent for C. elegans. 丝绒树蚁提取物对秀丽隐杆线虫具有趋化性驱避作用。
microPublication biology Pub Date : 2025-05-31 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001531
Malaya Gaerlan, Marco Carrillo, Sofia Ceva, Sowmya Chundi, Binta Diallo, Juliana N Fong, Kelly Huang, Jennifer Jackson, Jasmine Padilla, Leslie Quintana, Katelyn Santa Maria, Sadie M Sarkisian, Paloma R Sequeira, Eva U Tatlock, Penelope R Baker, Luise Bachmann, Soyeon Park, Malia J Perez, Mina E Phipps, Shay Nair Sharma, Yvette Soto-Hernandez, Bryan H Juarez, Cesar Mena, Griselda Morales, Mabel Gonzalez, Katherine Fiocca, Nicole Bradon, Max Madrzyk, Lauren A O'Connell
{"title":"Velvety tree ant extract is a chemotaxis repellent for <i>C. elegans</i>.","authors":"Malaya Gaerlan, Marco Carrillo, Sofia Ceva, Sowmya Chundi, Binta Diallo, Juliana N Fong, Kelly Huang, Jennifer Jackson, Jasmine Padilla, Leslie Quintana, Katelyn Santa Maria, Sadie M Sarkisian, Paloma R Sequeira, Eva U Tatlock, Penelope R Baker, Luise Bachmann, Soyeon Park, Malia J Perez, Mina E Phipps, Shay Nair Sharma, Yvette Soto-Hernandez, Bryan H Juarez, Cesar Mena, Griselda Morales, Mabel Gonzalez, Katherine Fiocca, Nicole Bradon, Max Madrzyk, Lauren A O'Connell","doi":"10.17912/micropub.biology.001531","DOIUrl":"10.17912/micropub.biology.001531","url":null,"abstract":"<p><p>Ants use a range of compounds for interspecies interactions, but the neurogenetic mechanisms mediating these interactions are unclear. Here, we used chemotaxis assays with the nematode <i>Caenorhabditis elegans</i> to test if ant compounds can be detected by the worm nervous system and which chemosensory neurons are required for detection. We found that <i>C. elegans</i> avoid the extracts of velvety tree ants ( <i>Liometopum occidentale</i> ), and this response requires <i>osm-9</i> and <i>tax-4</i> positive neurons. These experiments were conducted by undergraduate students in an upper-division laboratory course, demonstrating how simple behavior assays conducted in a classroom setting can provide practical research experiences and new insights into interspecies interactions.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12175000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328010","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
A Chromosome End Without Terminal Telomere Repeats is Stable for Multiple Cell Divisions. 没有末端端粒重复的染色体末端对多次细胞分裂是稳定的。
microPublication biology Pub Date : 2025-05-30 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001622
Haitao Zhang, Julien Audry, Kurt W Runge
{"title":"A Chromosome End Without Terminal Telomere Repeats is Stable for Multiple Cell Divisions.","authors":"Haitao Zhang, Julien Audry, Kurt W Runge","doi":"10.17912/micropub.biology.001622","DOIUrl":"10.17912/micropub.biology.001622","url":null,"abstract":"<p><p>We have formed new short telomeres in <i>Schizosaccharomyces pombe</i> using an inducible nuclease that cuts near telomere repeats in cells that lack, cannot recruit or cannot fully activate telomerase. Sequencing these new telomeres showed that cells can divide at least 4 times with ~30 bp of non-telomeric sequence at the chromosome end in cells lacking telomerase, which contrasts with current models for the roles of terminal single-stranded telomere repeats and the telomere proteins in telomere protection and replication. Cells that cannot recruit or activate telomerase had similar results, with additional terminal truncations or telomere repeat addition.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303889","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
Quantifying phage-bacteria dynamics in vitro: rapid emergence of phage-resistant mutants for Klebsiella pneumoniae. 体外噬菌体-细菌动力学定量：肺炎克雷伯菌噬菌体耐药突变体的快速出现。
microPublication biology Pub Date : 2025-05-30 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001666
Marcos Rodríguez, Irene Cantallops, Pilar Domingo-Calap, Josep Sardanyés
{"title":"Quantifying phage-bacteria dynamics <i>in vitro:</i> rapid emergence of phage-resistant mutants for <i>Klebsiella pneumoniae</i>.","authors":"Marcos Rodríguez, Irene Cantallops, Pilar Domingo-Calap, Josep Sardanyés","doi":"10.17912/micropub.biology.001666","DOIUrl":"10.17912/micropub.biology.001666","url":null,"abstract":"<p><p>In the quantitative description of evolving phage-bacterial systems, a central challenge lies in accurately identifying the key parameters governing the dynamics of both bacterial and phage populations. This is especially relevant in the case of multidrug-resistant pathogenic bacteria such as <i>Klebsiella sp</i> . This pathogen poses serious health problems due to antibiotic overuse, which causes the emergence of antibiotic-resistant strains and great difficulty in eradicating bacterial infections with antibiotics. Research on phage-bacteria thus becomes a very important topic to provide alternative strategies to eradicate multidrug-resistant bacteria, and thus quantitative descriptions of these processes are of paramount importance. Despite increasing research on this topic, key structural parameters of the populations, such as bacterial growth rates, the impact of phages on bacterial dynamics or the probability of emergence of phage-resistant strains, are often scarce. In this study, we investigated a battery of growth experiments for <i>Klebsiella pneumoniae</i> alone and with the presence of bacteriophage vB_Kpn_2-P4. Using mathematical models we estimate key parameters for these experiments, showing the rapid growth and emergence of phage-resistant mutants which outcompete the susceptible bacteria strains. Our results provide quantitative estimates of these processes and may be useful for understanding phage-bacterial dynamical systems and parameterizing future theoretical and computational models.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328009","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
Transgenic expression of endoplasmic reticulum proteins in C. elegans neurons is prone to causing ER stress. 秀丽隐杆线虫神经元内质网蛋白的转基因表达容易引起内质网应激。
microPublication biology Pub Date : 2025-05-29 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001547
Junhyun Park, Shaul Yogev
{"title":"Transgenic expression of endoplasmic reticulum proteins in <i>C. elegans</i> neurons is prone to causing ER stress.","authors":"Junhyun Park, Shaul Yogev","doi":"10.17912/micropub.biology.001547","DOIUrl":"10.17912/micropub.biology.001547","url":null,"abstract":"<p><p>In studying the endomembrane system, organelle-specific markers tagged with fluorescent proteins are used to visualize individual organelles. However, whether the expression of organelle marker perturbs the organelle's biology is not always apparent. We report that expression of a GFP-tagged Endoplasmic Reticulum (ER) protein causes low levels of ER stress that are challenging to detect in control animals. This stress is revealed only once the ER-associated degradation (ERAD) pathway is compromised. Our results highlight the vulnerability of the ER and suggest that the possible contribution of ER stress to phenotypes obtained with transgenic markers should be considered when interpreting the phenotypes.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303891","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
Genome Sequence of the Cluster EF Bacteriophage TinyMiny, Isolated using Microbacterium foliorum. 叶状微杆菌分离的簇EF噬菌体TinyMiny的基因组序列。
microPublication biology Pub Date : 2025-05-29 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001488
Iain Duffy, Juan Jimenez, Luis Gomez, Alexa Keeler, Aisha Ambrose, Moises Guadarrama, Hailey Kerns, Rachael Martin, Jade Moorehead, Arrianne Orgill, Brianna Reiber, Aisha Severe, Leslie Sivley, Genesis Valentin, John Duncan
{"title":"Genome Sequence of the Cluster EF Bacteriophage TinyMiny, Isolated using <i>Microbacterium foliorum</i>.","authors":"Iain Duffy, Juan Jimenez, Luis Gomez, Alexa Keeler, Aisha Ambrose, Moises Guadarrama, Hailey Kerns, Rachael Martin, Jade Moorehead, Arrianne Orgill, Brianna Reiber, Aisha Severe, Leslie Sivley, Genesis Valentin, John Duncan","doi":"10.17912/micropub.biology.001488","DOIUrl":"10.17912/micropub.biology.001488","url":null,"abstract":"<p><p>The bacteriophage TinyMiny was isolated from a soil sample collected on the campus of the University of Maryland Baltimore County, in Baltimore, Maryland, using the bacterium <i>Microbacterium foliorum</i> NRRL B-24224. TinyMiny is presumed to be a lytic bacteriophage, consisting of a double-stranded DNA genome 57,042 base pairs in length and encoding 86 genes. Based on gene content similarity to actinobacteriophages, TinyMiny is assigned to the EF cluster.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303890","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
Extracellular stimulation in neocortex lacks specificity. 新皮层的细胞外刺激缺乏特异性。
microPublication biology Pub Date : 2025-05-28 eCollection Date: 2025-01-01 DOI: 10.17912/micropub.biology.001539
Linn K Dragsted, Shawniya Alageswaran, Aparna Suvrathan, P Jesper Sjöström
{"title":"Extracellular stimulation in neocortex lacks specificity.","authors":"Linn K Dragsted, Shawniya Alageswaran, Aparna Suvrathan, P Jesper Sjöström","doi":"10.17912/micropub.biology.001539","DOIUrl":"10.17912/micropub.biology.001539","url":null,"abstract":"<p><p>By activating axons, extracellular stimulation elicits synaptic responses in patch-clamped cells. However, because axonal signaling is both orthodromic and antidromic, extracellular stimulation may lack specificity. For example, stimulating neocortical layer (L) 4 to recruit ascending inputs to L2/3 pyramidal cells (PCs) may also antidromically activate presynaptic L2/3 PCs, as their descending axons traverse L4. This contaminates L4→L2/3 activation with L2/3→L2/3 responses, which is problematic since these pathways have different properties. Using 2-photon calcium imaging, we found L2/3 PCs that responded to L4 stimulation even after synaptic blockade, demonstrating antidromic activation. Our findings highlight limitations of extracellular stimulation specificity in neocortex.</p>","PeriodicalId":74192,"journal":{"name":"microPublication biology","volume":"2025 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12159760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287498","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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