Mammalian Genome最新文献_第7页

MicroRNA expression profiling of ovine epithelial cells stimulated with the Staphylococcus aureus in vitro. 用金黄色葡萄球菌刺激体外绵羊上皮细胞的 MicroRNA 表达谱分析。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-12-01 Epub Date: 2024-08-31 DOI: 10.1007/s00335-024-10062-3

Ghulam Asghar Sajid, Muhammad Jasim Uddin, Saif Adil Abbood Al-Janabi, Abdiaziz Nur Ibrahim, Mehmet Ulas Cinar

{"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":"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.","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}

引用次数: 0

A map of canine sequence variation relative to a Greenland wolf outgroup. 相对于格陵兰狼外群的犬科序列变异图。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-12-01 Epub Date: 2024-08-01 DOI: 10.1007/s00335-024-10056-1

Anthony K Nguyen, Peter Z Schall, Jeffrey M Kidd

{"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":"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.","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}

引用次数: 0

Causal relationship between imaging-derived phenotypes and neurodegenerative diseases: a Mendelian randomization study. 成像表型与神经退行性疾病之间的因果关系：孟德尔随机研究。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-12-01 Epub Date: 2024-08-24 DOI: 10.1007/s00335-024-10065-0

Jiaxin Yang, Chao Tang

{"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":"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.","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}

引用次数: 0

Investigating the effects of a cryptic splice site in the En2 splice acceptor sequence used in the IKMC knockout-first alleles. 研究IKMC基因敲除等位基因中使用的En2剪接受体序列中一个隐性剪接位点的影响。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-12-01 Epub Date: 2024-10-01 DOI: 10.1007/s00335-024-10071-2

Prerna Nair, Karen P Steel, Morag A Lewis

{"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":"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.","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}

引用次数: 0

Review on camel genetic diversity: ecological and economic perspectives. 骆驼遗传多样性综述：生态和经济视角。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-12-01 Epub Date: 2024-07-29 DOI: 10.1007/s00335-024-10054-3

Meena Bagiyal, Ram Parsad, Sonika Ahlawat, Ritika Gera, Pooja Chhabra, Upasna Sharma, Reena Arora, Rekha Sharma

{"title":"Review on camel genetic diversity: ecological and economic perspectives.","authors":"Meena Bagiyal, Ram Parsad, Sonika Ahlawat, Ritika Gera, Pooja Chhabra, Upasna Sharma, Reena Arora, Rekha Sharma","doi":"10.1007/s00335-024-10054-3","DOIUrl":"10.1007/s00335-024-10054-3","url":null,"abstract":"Camels, known as the \"Ship of the Desert,\" play a vital role in the ecosystems and economies of arid and semi-arid regions. They provide meat, milk, transportation, and other essential services, and their resilience to harsh environments makes them invaluable. Despite their similarities, camel breeds exhibit notable differences in size, color, and structure, with over 40 million camels worldwide. This number is projected to increase, underscoring their growing significance. Economically, camels are crucial for food production, tourism, and trade, with camel racing being particularly significant in Arab countries. Their unique physiological traits, such as low disease susceptibility and efficient water conservation, further enhance their value. Camel products, especially meat and milk, offer substantial nutritional and therapeutic benefits, contributing to their high demand. Genetic diversity studies have advanced our understanding of camels' adaptation to extreme environments. Functional genomics and whole-genome sequencing have identified genes responsible for these adaptations, aiding breeding programs and conservation efforts. High-throughput sequencing has revealed genetic markers linked to traits like milk production and disease resistance. The development of SNP chips has revolutionized genetic studies by providing a cost-effective alternative to whole-genome sequencing. These tools facilitate large-scale genotyping, essential for conserving genetic diversity and improving breeding strategies. To prevent the depletion of camel genetic diversity, it is crucial to streamline in situ and ex situ conservation efforts to maintain their ecological and economic value. A comprehensive approach to camel conservation and genetic preservation, involving advanced genomic technologies, reproductive biotechniques, and sustainable management practices, will ensure their continued contribution to human societies.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":" ","pages":"621-632"},"PeriodicalIF":2.7,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792805","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

Fluorescent reporter mouse models for genome editing: choices and challenges. 用于基因组编辑的荧光报告小鼠模型：选择与挑战。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-10-28 DOI: 10.1007/s00335-024-10079-8

Christopher J Walkey

引用次数: 0

Preclinical research (on rare diseases): we need to talk about health equity. 临床前研究（罕见病）：我们需要讨论健康公平问题。

IF 2.7 4区生物学

Mammalian Genome Pub Date : 2024-10-26 DOI: 10.1007/s00335-024-10080-1

Andy Greenfield

引用次数: 0

Mammalian genome research resources available from the National BioResource Project in Japan 日本国家生物资源项目提供的哺乳动物基因组研究资源

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2024-09-11 DOI: 10.1007/s00335-024-10063-2

Saori Mizuno-Iijima, Shoko Kawamoto, Masahide Asano, Tomoji Mashimo, Shigeharu Wakana, Katsuki Nakamura, Ken-ichi Nishijima, Hitoshi Okamoto, Kuniaki Saito, Sawako Yoshina, Yoshihiro Miwa, Yukio Nakamura, Moriya Ohkuma, Atsushi Yoshiki

{"title":"Mammalian genome research resources available from the National BioResource Project in Japan","authors":"Saori Mizuno-Iijima, Shoko Kawamoto, Masahide Asano, Tomoji Mashimo, Shigeharu Wakana, Katsuki Nakamura, Ken-ichi Nishijima, Hitoshi Okamoto, Kuniaki Saito, Sawako Yoshina, Yoshihiro Miwa, Yukio Nakamura, Moriya Ohkuma, Atsushi Yoshiki","doi":"10.1007/s00335-024-10063-2","DOIUrl":"https://doi.org/10.1007/s00335-024-10063-2","url":null,"abstract":"Mammalian genome research has conventionally involved mice and rats as model organisms for humans. Given the recent advances in life science research, to understand complex and higher-order biological phenomena and to elucidate pathologies and develop therapies to promote human health and overcome diseases, it is necessary to utilize not only mice and rats but also other bioresources such as standardized genetic materials and appropriate cell lines in order to gain deeper molecular and cellular insights. The Japanese bioresource infrastructure program called the National BioResource Project (NBRP) systematically collects, preserves, controls the quality, and provides bioresources for use in life science research worldwide. In this review, based on information from a database of papers related to NBRP bioresources, we present the bioresources that have proved useful for mammalian genome research, including mice, rats, other animal resources; DNA-related materials; and human/animal cells and microbes.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"90 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142200549","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

Identifying new molecular signatures and potential therapeutics for idiopathic pulmonary fibrosis: a network medicine approach 识别特发性肺纤维化的新分子特征和潜在疗法：一种网络医学方法

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2024-09-10 DOI: 10.1007/s00335-024-10069-w

Mecbure Nur Akca, Ceyda Kasavi

{"title":"Identifying new molecular signatures and potential therapeutics for idiopathic pulmonary fibrosis: a network medicine approach","authors":"Mecbure Nur Akca, Ceyda Kasavi","doi":"10.1007/s00335-024-10069-w","DOIUrl":"https://doi.org/10.1007/s00335-024-10069-w","url":null,"abstract":"Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease characterized by excessive collagen deposition and fibrosis of the lung parenchyma, leading to respiratory failure. The molecular mechanisms underlying IPF pathogenesis remain incompletely understood, hindering the development of effective therapeutic strategies. We have used a network medicine approach to comprehensively analyze molecular interactions and identify novel molecular signatures and potential therapeutics associated with IPF progression. Our integrative analysis revealed dysregulated molecular networks that are central to IPF pathophysiology. We have highlighted key molecular players and signaling pathways that are implicated in aberrant fibrotic processes. This systems-level understanding enables the identification of new biomarkers and therapeutic targets for IPF, providing potential avenues for precision medicine. Drug repurposing analysis revealed several drug candidates with anti-fibrotic, anti-inflammatory, and anti-cancer activities that could potentially slow fibrotic progression and improve patient outcomes. This study offers new insights into the molecular underpinnings of IPF and highlights network medicine approaches in uncovering complex disease mechanisms. The molecular signatures and therapeutic targets identified hold promise for developing precision therapies tailored to individual patients, ultimately advancing the management of this debilitating lung disease.","PeriodicalId":18259,"journal":{"name":"Mammalian Genome","volume":"59 1","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142200547","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

Commentary: The International Mouse Phenotyping Consortium: high-throughput in vivo functional annotation of the mammalian genome 评论：国际小鼠表型协会：哺乳动物基因组的高通量活体功能注释

IF 2.5 4区生物学

Mammalian Genome Pub Date : 2024-09-10 DOI: 10.1007/s00335-024-10068-x

K. C. Kent Lloyd

引用次数: 0