Mammalian Genome最新文献_第8页

Retraction Note: Circ_0069718 promotes the progression of breast cancer by up-regulating NFIB through sequestering miR-590-5p. 注:Circ_0069718通过隔离miR-590-5p上调NFIB，促进乳腺癌的进展。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10001-8

Yongsheng Zhao, Xiaocha Ma, Weihua Shi

引用次数: 1

GWAS using low-pass whole genome sequence reveals a novel locus in canine congenital idiopathic megaesophagus. GWAS利用低通全基因组序列揭示了犬先天性特发性巨食管的一个新基因座。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2023-09-01 Epub Date: 2023-04-11 DOI: 10.1007/s00335-023-09991-2

Sarah M Bell, Jacquelyn M Evans, Elizabeth A Greif, Kate L Tsai, Steven G Friedenberg, Leigh Anne Clark

{"title":"GWAS using low-pass whole genome sequence reveals a novel locus in canine congenital idiopathic megaesophagus.","authors":"Sarah M Bell, Jacquelyn M Evans, Elizabeth A Greif, Kate L Tsai, Steven G Friedenberg, Leigh Anne Clark","doi":"10.1007/s00335-023-09991-2","DOIUrl":"10.1007/s00335-023-09991-2","url":null,"abstract":"Congenital idiopathic megaesophagus (CIM) is a gastrointestinal disorder of dogs wherein the esophagus is dilated and swallowing activity is reduced, causing regurgitation of ingesta. Affected individuals experience weight loss and malnourishment and are at risk for aspiration pneumonia, intussusception, and euthanasia. Great Danes have among the highest incidences of CIM across dog breeds, suggesting a genetic predisposition. We generated low-pass sequencing data for 83 Great Danes and used variant calls to impute missing whole genome single-nucleotide variants (SNVs) for each individual based on haplotypes phased from 624 high-coverage dog genomes, including 21 Great Danes. We validated the utility of our imputed data set for genome-wide association studies (GWASs) by mapping loci known to underlie coat phenotypes with simple and complex inheritance patterns. We conducted a GWAS for CIM with 2,010,300 SNVs, identifying a novel locus on canine chromosome 1 (P-val = 2.76 × 10-10). Associated SNVs are intergenic or intronic and are found in two clusters across a 1.7-Mb region. Inspection of coding regions in high-coverage genomes from affected Great Danes did not reveal candidate causal variants, suggesting that regulatory variants underlie CIM. Further studies are necessary to assess the role of these non-coding variants.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10276674","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}

引用次数: 0

Retraction Note: MiR-519d-3p enhances the sensitivity of non-small-cell lung cancer to tyrosine kinase inhibitors. 注:MiR-519d-3p增强了非小细胞肺癌对酪氨酸激酶抑制剂的敏感性。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10003-6

Qiang Zhen, Yaxiao Zhang, Lina Gao, Renfeng Wang, Weiwei Chu, Xiaojian Zhao, Zhe Li, Huixian Li, Bing Zhang, Baolei Lv, Jiabao Liu

引用次数: 0

The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. 生物属性本体（OBA）--生命科学的计算特征。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 Epub Date: 2023-04-19 DOI: 10.1007/s00335-023-09992-1

Ray Stefancsik, James P Balhoff, Meghan A Balk, Robyn L Ball, Susan M Bello, Anita R Caron, Elissa J Chesler, Vinicius de Souza, Sarah Gehrke, Melissa Haendel, Laura W Harris, Nomi L Harris, Arwa Ibrahim, Sebastian Koehler, Nicolas Matentzoglu, Julie A McMurry, Christopher J Mungall, Monica C Munoz-Torres, Tim Putman, Peter Robinson, Damian Smedley, Elliot Sollis, Anne E Thessen, Nicole Vasilevsky, David O Walton, David Osumi-Sutherland

{"title":"The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.","authors":"Ray Stefancsik, James P Balhoff, Meghan A Balk, Robyn L Ball, Susan M Bello, Anita R Caron, Elissa J Chesler, Vinicius de Souza, Sarah Gehrke, Melissa Haendel, Laura W Harris, Nomi L Harris, Arwa Ibrahim, Sebastian Koehler, Nicolas Matentzoglu, Julie A McMurry, Christopher J Mungall, Monica C Munoz-Torres, Tim Putman, Peter Robinson, Damian Smedley, Elliot Sollis, Anne E Thessen, Nicole Vasilevsky, David O Walton, David Osumi-Sutherland","doi":"10.1007/s00335-023-09992-1","DOIUrl":"10.1007/s00335-023-09992-1","url":null,"abstract":"Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10276689","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}

引用次数: 0

Essential genes: a cross-species perspective. 基本基因：跨物种视角。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 Epub Date: 2023-03-10 DOI: 10.1007/s00335-023-09984-1

Pilar Cacheiro, Damian Smedley

引用次数: 0

A consensus score to combine inferences from multiple centres. 将多个中心的推论结合起来的共识得分。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 Epub Date: 2023-05-08 DOI: 10.1007/s00335-023-09993-0

Hamed Haselimashhadi, Kolawole Babalola, Robert Wilson, Tudor Groza, Violeta Muñoz-Fuentes

引用次数: 0

Bridging mouse and human anatomies; a knowledge-based approach to comparative anatomy for disease model phenotyping. 连接小鼠和人体解剖;以知识为基础的方法来比较解剖学疾病模型表型。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10005-4

Jesús Ruberte, Paul N Schofield, John P Sundberg, Alfonso Rodriguez-Baeza, Ana Carretero, Colin McKerlie

引用次数: 2

Retraction Note: LncRNA TLR8-AS1 suppresses miR-34a maturation in hepatocellular carcinoma to suppress cell proliferation and migration. 注:LncRNA TLR8-AS1在肝细胞癌中抑制miR-34a成熟，抑制细胞增殖和迁移。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10004-5

Xin Shi, Hu Chen, Wei Wang, Bingzheng Yan, Zhikai Yang, Jingpo Zhang

引用次数: 0

INFRAFRONTIER: mouse model resources for modelling human diseases. INFRAFRONTIER:用于人类疾病建模的小鼠模型资源。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-10010-7

Asrar Ali Khan, Gema Valera Vazquez, Montse Gustems, Rafaele Matteoni, Fei Song, Philipp Gormanns, Sabine Fessele, Michael Raess, Martin Hrabĕ de Angelis

{"title":"INFRAFRONTIER: mouse model resources for modelling human diseases.","authors":"Asrar Ali Khan, Gema Valera Vazquez, Montse Gustems, Rafaele Matteoni, Fei Song, Philipp Gormanns, Sabine Fessele, Michael Raess, Martin Hrabĕ de Angelis","doi":"10.1007/s00335-023-10010-7","DOIUrl":"https://doi.org/10.1007/s00335-023-10010-7","url":null,"abstract":"Over the last decade, INFRAFRONTIER has positioned itself as a world-class Research Infrastructure for the generation, phenotyping, archiving, and distribution of mouse models in Europe. The INFRAFRONTIER network consists of 22 partners from 15 countries, and is continuously enhancing and broadening its portfolio of resources and services that are offered to the research community on a non-profit basis. By bringing together European rodent model expertise and providing valuable disease model services to the biomedical research community, INFRAFRONTIER strives to push the accessibility of cutting-edge human disease modelling technologies across the European research landscape. This article highlights the latest INFRAFRONTIER developments and informs the research community about its extensively utilised services, resources, and technical developments, specifically the intricacies of the INFRAFRONTIER database, use of Curated Disease Models, overview of the INFRAFRONTIER Cancer and Rare Disease resources, and information about its main state-of-the-art services.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10382402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9902960","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}

引用次数: 0

Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus). 诺都士山羊(Capra hircus)全基因组测序及基因组分析。

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2023-09-01 DOI: 10.1007/s00335-023-09990-3

Mevlüt Arslan

{"title":"Whole-genome sequencing and genomic analysis of Norduz goat (Capra hircus).","authors":"Mevlüt Arslan","doi":"10.1007/s00335-023-09990-3","DOIUrl":"https://doi.org/10.1007/s00335-023-09990-3","url":null,"abstract":"Artificial and natural selective breeding of goats has resulted in many different goat breeds all around the world. Norduz goat is one of these breeds, and it is a local goat breed of Turkey. The goats are favorable due to pre-weaning viability and reproduction values compared to the regional breeds. Development in sequencing technologies has let to understand huge genomic structures and complex phenotypes. Until now, such a comprehensive study has not been carried out to understand the genomic structure of the Norduz goats, yet. In the study, the next-generation sequencing was carried out to understand the genomic structure of Norduz goat. Real-time PCR was used to evaluate prominent CNVs in the Norduz goat individuals. Whole genome of the goat was constructed with an average of 33.1X coverage level. In the stringent filtering condition, 9,757,980 SNPs, 1,536,715 InDels, and 290 CNVs were detected in the Norduz goat genome. Functional analysis of high-impact SNP variations showed that the classical complement activation biological process was affected significantly in the goat. CNVs in the goat genome were found in genes related to defense against viruses, immune response, and cell membrane transporters. It was shown that GBP2, GBP5, and mammalian ortholog GBP1, which are INF-stimulated GTPases, were found to be high copy numbers in the goats. To conclude, genetic variations mainly in immunological response processes suggest that Norduz goat is an immunologically improved goat breed and natural selection could take an important role in the genetical improvements of the goats.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9954959","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}

引用次数: 0