Mammalian Genome最新文献

{"title":"Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals.","authors":"Imke Tammen, Marius Mather, Tosso Leeb, Frank W Nicholas","doi":"10.1007/s00335-024-10059-y","DOIUrl":"10.1007/s00335-024-10059-y","url":null,"abstract":"<p><p>Online Mendelian Inheritance in Animals (OMIA) is a freely available curated knowledgebase that contains information and facilitates research on inherited traits and diseases in animals. For the past 29 years, OMIA has been used by animal geneticists, breeders, and veterinarians worldwide as a definitive source of information. Recent increases in curation capacity and funding for software engineering support have resulted in software upgrades and commencement of several initiatives, which include the enhancement of variant information and links to human data resources, and the introduction of ontology-based breed information and categories. We provide an overview of current information and recent enhancements to OMIA and discuss how we are expanding the integration of OMIA into other resources and databases via the use of ontologies and the adaptation of tools used in human genetics.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"556-564"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141982751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of somatic mutations and structural variations in domestic pig.","authors":"Seong Gyu Kwon, Geon Hue Bae, Joo Hee Hong, Jeong-Woo Choi, June Hyug Choi, Nam Seop Lim, CheolMin Jeon, Nanda Maya Mali, Mee Sook Jun, JaeEun Shin, JinSoo Kim, Eun-Seok Cho, Man-Hoon Han, Ji Won Oh","doi":"10.1007/s00335-024-10058-z","DOIUrl":"10.1007/s00335-024-10058-z","url":null,"abstract":"<p><p>Understanding somatic mutations and structural variations in domestic pigs (Sus scrofa domestica) is critical due to their increasing importance as model organisms in biomedical research. In this study, we conducted a comprehensive analysis through whole-genome sequencing of skin, organs, and blood samples. By examining two pig pedigrees, we investigated the inheritance and sharedness of structural variants among fathers, mothers, and offsprings. Utilizing single-cell clonal expansion techniques, we observed significant variations in the number of somatic mutations across different tissues. An in-house developed pipeline enabled precise filtering and analysis of these mutations, resulting in the construction of individual phylogenetic trees for two pigs. These trees explored the developmental relationships between different tissues, revealing insights into clonal expansions from various anatomical locations. This study enhances the understanding of pig genomes, affirming their increasing value in clinical and genomic research, and provides a foundation for future studies in other animals, paralleling previous studies in mice and humans. This approach not only deepens our understanding of mammalian genomic variations but also strengthens the role of pigs as a crucial model in human health and disease research.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"645-656"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142036270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mutant mouse resource and research center (MMRRC) consortium: the US-based public mouse repository system.","authors":"Yuksel Agca, James Amos-Landgraf, Renee Araiza, Jennifer Brennan, Charisse Carlson, Dominic Ciavatta, Dave Clary, Craig Franklin, Ian Korf, Cathleen Lutz, Terry Magnuson, Fernando Pardo-Manuel de Villena, Oleg Mirochnitchenko, Samit Patel, Dan Port, Laura Reinholdt, K C Kent Lloyd","doi":"10.1007/s00335-024-10070-3","DOIUrl":"10.1007/s00335-024-10070-3","url":null,"abstract":"<p><p>Now in its 25th year, the Mutant Mouse Resource and Research Center (MMRRC) consortium continues to serve the United States and international biomedical scientific community as a public repository and distribution archive of laboratory mouse models of human disease for research. Supported by the National Institutes of Health (NIH), the MMRRC consists of 4 regionally distributed and dedicated vivaria, offices, and specialized laboratory facilities and an Informatics Coordination and Service Center (ICSC). The overarching purpose of the MMRRC is to facilitate groundbreaking biomedical research by offering an extensive repertoire of mutant mice that are essential for advancing the understanding of human physiology and disease. The function of the MMRRC is to identify, acquire, evaluate, characterize, cryopreserve, and distribute mutant mouse strains to qualified biomedical investigators around the nation and the globe. Mouse strains accepted from the research community are held to the highest scientific standards to optimize reproducibility and enhance scientific rigor and transparency. All submitted strains are thoroughly reviewed, documented, and validated using extensive scientific quality control measures. In addition, the MMRRC conducts resource-related research on cryopreservation, mouse genetics, environmental conditions, and other topics that enhance operations of the MMRRC. Today, the MMRRC maintains an archive of mice, cryopreserved embryos and sperm, embryonic stem (ES) cell lines, and murine hybridomas for nearly 65,000 alleles. Since its inception, the MMRRC has fulfilled more than 20,000 orders from 13,651 scientists at 8441 institutions worldwide. The MMRRC also provides numerous services to assist researchers, including scientific consultation, technical assistance, genetic assays, microbiome analysis, analytical phenotyping, pathology, cryorecovery, husbandry, breeding and colony management, infectious disease surveillance, and disease modeling. The ICSC coordinates MMRRC operations, interacts with researchers, and manages the website (mmrrc.org) and online catalogue. Researchers benefit from an expansive list of well-defined mouse models of disease that meet the highest scientific standards while submitting investigators benefit by having their mouse strains cryopreserved, protected, and distributed in compliance with NIH policies.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"524-536"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142290471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The mouse metabolic phenotyping center (MMPC) live consortium: an NIH resource for in vivo characterization of mouse models of diabetes and obesity.","authors":"Maren Laughlin, Richard McIndoe, Sean H Adams, Renee Araiza, Julio E Ayala, Lucy Kennedy, Louise Lanoue, Louise Lantier, James Macy, Eann Malabanan, Owen P McGuinness, Rachel Perry, Daniel Port, Nathan Qi, Carol F Elias, Gerald I Shulman, David H Wasserman, K C Kent Lloyd","doi":"10.1007/s00335-024-10067-y","DOIUrl":"10.1007/s00335-024-10067-y","url":null,"abstract":"<p><p>The Mouse Metabolic Phenotyping Center (MMPC)Live Program was established in 2023 by the National Institute for Diabetes, Digestive and Kidney Diseases (NIDDK) at the National Institutes of Health (NIH) to advance biomedical research by providing the scientific community with standardized, high quality phenotyping services for mouse models of diabetes and obesity. Emerging as the next iteration of the MMPC Program which served the biomedical research community for 20 years (2001-2021), MMPCLive is designed as an outwardly-facing consortium of service cores that collaborate to provide reduced-cost consultation and metabolic, physiologic, and behavioral phenotyping tests on live mice for U.S. biomedical researchers. Four MMPCLive Centers located at universities around the country perform complex and often unique procedures in vivo on a fee for service basis, typically on mice shipped from the client or directly from a repository or vendor. Current areas of expertise include energy balance and body composition, insulin action and secretion, whole body carbohydrate and lipid metabolism, cardiovascular and renal function, food intake and behavior, microbiome and xenometabolism, and metabolic pathway kinetics. Additionally, an opportunity arose to reduce barriers to access and expand the diversity of the biomedical research workforce by establishing the VIBRANT Program. Directed at researchers historically underrepresented in the biomedical sciences, VIBRANT-eligible investigators have access to testing services, travel and career development awards, expert advice and experimental design consultation, and short internships to learn test technologies. Data derived from experiments run by the Centers belongs to the researchers submitting mice for testing which can be made publicly available and accessible from the MMPCLive database following publication. In addition to services, MMPCLive staff provide expertise and advice to researchers, develop and refine test protocols, engage in outreach activities, publish scientific and technical papers, and conduct educational workshops and training sessions to aid researchers in unraveling the heterogeneity of diabetes and obesity.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"485-496"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142080810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Digital tools of analysis and data integration facilitate synergy between mouse and human brain research and enable translation.","authors":"Sabine M Hölter, Lillian Garrett, Sebastian Bludau, Katrin Amunts","doi":"10.1007/s00335-024-10072-1","DOIUrl":"10.1007/s00335-024-10072-1","url":null,"abstract":"","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"544-550"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142349543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart.","authors":"Ewelina Semik-Gurgul, Klaudia Pawlina-Tyszko, Artur Gurgul, Tomasz Szmatoła, Justyna Rybińska, Tomasz Ząbek","doi":"10.1007/s00335-024-10057-0","DOIUrl":"10.1007/s00335-024-10057-0","url":null,"abstract":"<p><p>DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healthy cold-blooded horses to identify differentially expressed genes (DEGs), differentially expressed miRNA (DE miRNA) and differentially methylated sites (DMSs) between three types of horse tissues. Additionally, based on integrative omics analysis, we described the observed interactions of epigenetic mechanisms with tissue-specific gene expression alterations. The obtained data allowed identification from 4067 to 6143 DMSs, 9733 to 11,263 mRNAs, and 155 to 185 microRNAs, differentially expressed between various tissues. We pointed out specific genes whose expression level displayed a negative correlation with the level of CpG methylation and miRNA expression and revealed biological processes that they enrich. Furthermore, we confirmed and validated the accuracy of the Next-Generation Sequencing (NGS) results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR). This comprehensive analysis forms a strong foundation for exploring the epigenetic mechanisms involved in tissue differentiation, especially the growth and development of the equine heart, lungs, and liver.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"600-620"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141982750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MicroRNA expression profiling of ovine epithelial cells stimulated with the Staphylococcus aureus in vitro.","authors":"Ghulam Asghar Sajid, Muhammad Jasim Uddin, Saif Adil Abbood Al-Janabi, Abdiaziz Nur Ibrahim, Mehmet Ulas Cinar","doi":"10.1007/s00335-024-10062-3","DOIUrl":"10.1007/s00335-024-10062-3","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) act as key gene expression regulators, influencing intracellular biological and pathological processes. They are of significant interest in animal genetics as potential biomarkers for animal selection and health. This study aimed to unravel the complex miRNA signature involved in mastitis in in vitro cell culture. For this purpose, we constructed a control and treatment model in ovarian mammary epithelial cells to analyze miRNA responses upon Staphylococcus aureus (S. aureus) stimulation. The high-throughput Illumina Small RNA protocol was employed, generating an average of 7.75 million single-end reads per sample, totaling 46.54 million reads. Standard bioinformatics analysis, including cleaning, filtering, miRNA quantification, and differential expression was performed using the miRbase database as a reference for ovine miRNAs. The results indicated differential expression of 63 miRNAs, including 33 up-regulated and 30 down-regulated compared to the control group. Notably, miR-10a, miR-10b, miR-21, and miR-99a displayed a significant differential expression (p ≤ 0.05) associated to signal transduction, transcriptional pathways, diseases of signal transduction by growth factor receptors and second messengers, MAPK signaling pathway, NF-κB pathway, TNFα, Toll Like Receptor 4 (TLR4) cascade, and breast cancer. This study contributes expanding miRNA databases, especially for sheep miRNAs, and identifies potential miRNA candidates for further study in biomarker identification for mastitis resistance and diagnosis.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"673-682"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A map of canine sequence variation relative to a Greenland wolf outgroup.","authors":"Anthony K Nguyen, Peter Z Schall, Jeffrey M Kidd","doi":"10.1007/s00335-024-10056-1","DOIUrl":"10.1007/s00335-024-10056-1","url":null,"abstract":"<p><p>For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"565-576"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141860169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Causal relationship between imaging-derived phenotypes and neurodegenerative diseases: a Mendelian randomization study.","authors":"Jiaxin Yang, Chao Tang","doi":"10.1007/s00335-024-10065-0","DOIUrl":"10.1007/s00335-024-10065-0","url":null,"abstract":"<p><p>Neurodegenerative diseases are incurable conditions that lead to gradual and progressive deterioration of brain function in patients. With the aging population, the prevalence of these diseases is expected to increase, posing a significant economic burden on society. Imaging techniques play a crucial role in the diagnosis and monitoring of neurodegenerative diseases. This study utilized a two-sample Mendelian randomization (MR) analysis to assess the causal relationship between different imaging-derived phenotypes (IDP) in the brain and neurodegenerative diseases. Multiple MR methods were employed to minimize bias and obtain reliable estimates of the potential causal relationship between the variable exposures of interest and the outcomes. The study found potential causal relationships between different IDPs and Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), and frontotemporal dementia (FTD). Specifically, the study identified potential causal relationships between 2 different types of IDPs and AD, 8 different types of IDPs and PD, 11 different types of imaging-derived phenotypes and ALS, 1 type of IDP and MS, and 1 type of IDP and FTD. This study provides new insights for the prevention, diagnosis, and treatment of neurodegenerative diseases, offering important clues for understanding the pathogenesis of these diseases and developing relevant intervention strategies.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"711-723"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046862","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the effects of a cryptic splice site in the En2 splice acceptor sequence used in the IKMC knockout-first alleles.","authors":"Prerna Nair, Karen P Steel, Morag A Lewis","doi":"10.1007/s00335-024-10071-2","DOIUrl":"10.1007/s00335-024-10071-2","url":null,"abstract":"<p><p>Targeted mouse mutants are a common tool used to investigate gene function. The International Knockout Mouse Consortium undertook a large-scale screen of mouse mutants, making use of the knockout-first allele design that contains the En2 splice acceptor sequence coupled to the lacZ reporter gene. Although the knockout-first allele was designed to interfere with splicing and thus disrupt gene function, the En2 sequence has been reported to be transcribed within the host gene mRNA due to a cryptic splice site within the En2 sequence which allows splicing to the next exon of the host gene. In some circumstances, this has the potential to permit translation of a mutant protein. Here, we describe our computational analysis of all the mouse protein-coding genes with established knockout-first embryonic stem cell lines, and our predictions of their transcription outcome should the En2 sequence be included. As part of the large-scale mutagenesis program, mutant mice underwent a broad phenotyping screen, and their phenotypes are available. No wide-scale effects on mouse phenotypes reported were found as a result of the predicted En2 insertion. However, the En2 insertion was found experimentally in the transcripts of 24 of 35 mutant alleles examined, including the five already described, two with evidence of readthrough. Splicing from the cryptic splice site also has the potential to disrupt expression of the lacZ reporter gene. It is recommended that mutant transcripts be checked for this insertion as well as for leaky transcription in studies involving knockout-first alleles.</p>","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"633-644"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142361751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}