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Protocol for developing digital 3D zoological collections for research and academic training in a biodiversity global crisis scenario. 在生物多样性全球危机的情况下，开发用于研究和学术培训的数字3D动物收藏的协议。
IF 1.3
STAR Protocols Pub Date : 2026-05-08 DOI: 10.1016/j.xpro.2026.104549
Constanza Delgado, Amadis Lillo, Carolina Cuevas, Laura Tavera, Emmanuel Vega, Felipe Gamonal, Jeremías Norambuena, Cristián E Hernández
{"title":"Protocol for developing digital 3D zoological collections for research and academic training in a biodiversity global crisis scenario.","authors":"Constanza Delgado, Amadis Lillo, Carolina Cuevas, Laura Tavera, Emmanuel Vega, Felipe Gamonal, Jeremías Norambuena, Cristián E Hernández","doi":"10.1016/j.xpro.2026.104549","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104549","url":null,"abstract":"<p><p>Digital biological collections are an important source of information for preserving natural heritage and serve as a scientific-pedagogical tool. Here, we present the first protocol for the 3D digitization of zoological collections in Chile. We describe the steps and challenges in scanning and modeling specimens from the UdeC Museum of Zoology, together with procedures for creating the digital repository of biological collections. This protocol contributes to greater accessibility of biological information, thereby supporting policy decision-making for biodiversity conservation.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104549"},"PeriodicalIF":1.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for identifying genetic modifiers of phenotypes in individuals with disease-associated variants. 鉴定具有疾病相关变异的个体表型的遗传修饰因子的方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-08 DOI: 10.1016/j.xpro.2026.104546
Corrine Smolen, Matthew Jensen, Santhosh Girirajan
{"title":"Protocol for identifying genetic modifiers of phenotypes in individuals with disease-associated variants.","authors":"Corrine Smolen, Matthew Jensen, Santhosh Girirajan","doi":"10.1016/j.xpro.2026.104546","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104546","url":null,"abstract":"<p><p>The variable expressivity of disease-associated variants suggests a role for secondary variants in modifying the clinical presentation of these primary variants. Here, we present a protocol for identifying associations of secondary variants with phenotypes. We describe steps for prioritizing distinct classes of secondary variants throughout the genome. We then detail statistical procedures for finding associations of secondary variants and phenotypes in individuals carrying disease-associated variants. For complete details on the use and execution of this protocol, please refer to Jensen et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104546"},"PeriodicalIF":1.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing using PacBio HiFi or Oxford Nanopore Technologies. 使用PacBio HiFi或Oxford Nanopore Technologies对粪便样本进行长读宏基因组测序的高通量处理方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-08 DOI: 10.1016/j.xpro.2026.104526
Jeremiah J Minich
{"title":"Protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing using PacBio HiFi or Oxford Nanopore Technologies.","authors":"Jeremiah J Minich","doi":"10.1016/j.xpro.2026.104526","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104526","url":null,"abstract":"<p><p>Long-read sequencing, whether using PacBio (PB) or Oxford Nanopore Technologies (ONT), requires high-molecular-weight (HMW) DNA at high purity and free of contaminants. Here, we present a protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing. We describe steps for microbial inactivation, nucleic acid stabilization, and HMW DNA extraction. We then detail procedures for DNA cleanup, shearing, library preparation, and DNA sequencing. For complete details on the use and execution of this protocol, please refer to Minich et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104526"},"PeriodicalIF":1.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for ex vivo culture of neonate mouse ovaries to study early follicle activation. 研究早期卵泡激活的新生小鼠卵巢离体培养方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-08 DOI: 10.1016/j.xpro.2026.104539
Julie Feld Madsen, Stine Bundgaard Birkebæk, Karin Lykke-Hartmann
{"title":"Protocol for ex vivo culture of neonate mouse ovaries to study early follicle activation.","authors":"Julie Feld Madsen, Stine Bundgaard Birkebæk, Karin Lykke-Hartmann","doi":"10.1016/j.xpro.2026.104539","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104539","url":null,"abstract":"<p><p>Establishing an ex vivo culture of neonatal ovaries enables controlled investigation of early follicle dynamics. Here, we present a protocol for isolating ovaries from neonatal female mice for maintaining intact ovarian architecture by ex vivo culture on a membrane allowing access to defined medium. We describe procedures for media preparation, ovary dissection, culture setup, and follicle development by stereomicroscopy and histological assessment. This protocol provides a platform for examining the regulation of the primordial-to-primary transition and growth. For complete details on the use and execution of this protocol, please refer to Amoushahi et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104539"},"PeriodicalIF":1.3,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Preparation of cleared whole-mount urethra and urinary bladder from transcardially perfused mice for immunolabeling and analysis by CLSM. 经心包灌注小鼠清除后的全尿道和膀胱的制备及其免疫标记和CLSM分析。
IF 1.3
STAR Protocols Pub Date : 2026-05-07 DOI: 10.1016/j.xpro.2026.104542
Uwe Pfeil, Felix Dettler, Alexander Perniss, Praju Vikas Anekal, Lora Bankova, Paula Montero LIopis, Klaus Deckmann
{"title":"Preparation of cleared whole-mount urethra and urinary bladder from transcardially perfused mice for immunolabeling and analysis by CLSM.","authors":"Uwe Pfeil, Felix Dettler, Alexander Perniss, Praju Vikas Anekal, Lora Bankova, Paula Montero LIopis, Klaus Deckmann","doi":"10.1016/j.xpro.2026.104542","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104542","url":null,"abstract":"<p><p>The distribution of cells within organs, their involvement in tissue structure, and their organization in three-dimensional networks are important aspects in the analysis and understanding of biological processes. Here, we present a protocol for preparing whole-mount urethra and urinary bladder from transcardially perfused mice for immunolabeling and analysis by confocal laser scanning microscopy. We describe steps for perfusion, preparation, tissue clearing, and analysis using confocal laser scanning microscopy. We then detail procedures for three-dimensional processing of the murine urethra and urinary bladder. For complete details on the use and execution of this protocol, please refer to Schmidt et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104542"},"PeriodicalIF":1.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for a saline-free surgical preparation of adult Drosophila for chronic in vivo brain imaging. 成人果蝇慢性体内脑成像的无盐手术准备方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-07 DOI: 10.1016/j.xpro.2026.104550
Ruibao Zhu, Salah Khorbtli, Jingmin Zhang, Zhuchen Fu, Cheng Huang
{"title":"Protocol for a saline-free surgical preparation of adult Drosophila for chronic in vivo brain imaging.","authors":"Ruibao Zhu, Salah Khorbtli, Jingmin Zhang, Zhuchen Fu, Cheng Huang","doi":"10.1016/j.xpro.2026.104550","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104550","url":null,"abstract":"<p><p>Longitudinal brain imaging is essential for understanding neural mechanisms. Here, we present a saline-free, chronic preparation for repeated neural recording in adult Drosophila over multiple days. We describe steps for mounting flies, performing manual surgery on the head cuticle without external saline, and resealing the opening to create a transparent optical window. We demonstrate the utility of this approach by tracking single-neuron spiking and neuronal calcium dynamics over 7-10 days. This protocol is potentially applicable to other insect species.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104550"},"PeriodicalIF":1.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for gaze estimation using facial orientation in marmosets during a social preference test. 在社会偏好测试中使用狨猴面部方向的凝视估计协议。
IF 1.3
STAR Protocols Pub Date : 2026-05-07 DOI: 10.1016/j.xpro.2026.104556
Zefeng Wei, Maria Harbers, Atsu Aiba
{"title":"Protocol for gaze estimation using facial orientation in marmosets during a social preference test.","authors":"Zefeng Wei, Maria Harbers, Atsu Aiba","doi":"10.1016/j.xpro.2026.104556","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104556","url":null,"abstract":"<p><p>Here, we present an open-source platform for evaluating social preference in common marmosets using image-based visual stimuli and gaze estimation. We describe the procedures for setting up the behavioral test, training marmosets to perform the test, and analyzing the resulting data with the provided code. This platform enables simple and noninvasive assessment of social attention toward social visual stimuli. For complete details on the use and execution of this protocol, please refer to Harbers et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104556"},"PeriodicalIF":1.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol to generate endothelial cell-specific knockout mouse models using Cas9/Cdh5-Cre mice coupled with sgRNA. 使用Cas9/Cdh5-Cre小鼠偶联sgRNA生成内皮细胞特异性敲除小鼠模型的方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-07 DOI: 10.1016/j.xpro.2026.104551
Dong-Mei Wang, Chinnaswamy Tiruppathi
{"title":"Protocol to generate endothelial cell-specific knockout mouse models using Cas9/Cdh5-Cre mice coupled with sgRNA.","authors":"Dong-Mei Wang, Chinnaswamy Tiruppathi","doi":"10.1016/j.xpro.2026.104551","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104551","url":null,"abstract":"<p><p>The vascular endothelium is a critical regulator of vascular homeostasis and tissue fluid balance, and mouse models are essential for studying these processes in vivo. Here, we present a protocol to generate adult endothelial cell (EC)-specific gene knockout (KO) mouse models. We describe steps for Cas9-active and Cdh5-Cre-positive (Cas9/Cdh5-Cre) mouse line generation, single guide RNA (sgRNA) design for vector construction, plasmid DNA generation, and liposome preparation. We then detail procedures for liposome/plasmid complex injection, lung harvest, homogenization, protein quantification, and verification with western blotting. For complete details on the use and execution of this protocol, please refer to Wang et al.<sup>1</sup>.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104551"},"PeriodicalIF":1.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rearing, dissection, and temporal transcriptomic profiling protocols to study density-dependent phenotypic plasticity in the genus Schistocerca. 饲养，解剖和时间转录组分析方案研究密度依赖性表型可塑性在血吸虫属。
IF 1.3
STAR Protocols Pub Date : 2026-05-07 DOI: 10.1016/j.xpro.2026.104554
Maéva A Techer, Vivian A Peralta Santana, Brandon Woo, Richelle Marquess, Christopher Brennan, Audélia M C Mechti, Jackson B Linde, Spencer T Behmer, Gregory A Sword, Hojun Song
{"title":"Rearing, dissection, and temporal transcriptomic profiling protocols to study density-dependent phenotypic plasticity in the genus Schistocerca.","authors":"Maéva A Techer, Vivian A Peralta Santana, Brandon Woo, Richelle Marquess, Christopher Brennan, Audélia M C Mechti, Jackson B Linde, Spencer T Behmer, Gregory A Sword, Hojun Song","doi":"10.1016/j.xpro.2026.104554","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104554","url":null,"abstract":"<p><p>Here, we present a protocol for generating gregarious and solitarious density-dependent phenotypes in multiple Schistocerca locust and grasshopper species under controlled environmental conditions. We describe cage setup, feeding, animal handling, and sterile dissection workflows to isolate nervous, chemosensory, gut, fat body, and female reproductive tissues from nymphs and adults. This protocol emphasizes rapid tissue stabilization and RNase-control practices for downstream single-tissue DNA and RNA analyses.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104554"},"PeriodicalIF":1.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protocol for lentiviral generation and transduction of human-derived endometrial epithelial organoids to study uterine function and pathologies. 慢病毒生成和人源性子宫内膜上皮类器官转导研究子宫功能和病理的方案。
IF 1.3
STAR Protocols Pub Date : 2026-05-07 DOI: 10.1016/j.xpro.2026.104558
Sydney E Parks, Diana Monsivais
{"title":"Protocol for lentiviral generation and transduction of human-derived endometrial epithelial organoids to study uterine function and pathologies.","authors":"Sydney E Parks, Diana Monsivais","doi":"10.1016/j.xpro.2026.104558","DOIUrl":"https://doi.org/10.1016/j.xpro.2026.104558","url":null,"abstract":"<p><p>The use of patient-derived endometrial epithelial organoids has revolutionized the field of uterine biology. Here, we present a protocol for generating lentivirus and transducing human-derived endometrial epithelial organoids for the study of endometrial function and pathologies. We describe steps for lentiviral production, lentiviral transduction of endometrial epithelial organoids, and endometrial epithelial organoid passaging. We then detail procedures for validating lentiviral transduction. This protocol allows for knocking down or overexpressing genes of interest, enabling investigation of specific targets in a patient-centric model.</p>","PeriodicalId":34214,"journal":{"name":"STAR Protocols","volume":"7 2","pages":"104558"},"PeriodicalIF":1.3,"publicationDate":"2026-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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