Genomics最新文献_第2页

Transcriptome and metabolome revealed the effects of hypoxic environment on ovarian development of Tibetan sheep.

IF 3.4 2区生物学

Genomics Pub Date : 2024-12-03 DOI: 10.1016/j.ygeno.2024.110973

Dan Zhang, Chao Yuan, Xuejiao An, Tingting Guo, Zengkui Lu, Jianbin Liu

{"title":"Transcriptome and metabolome revealed the effects of hypoxic environment on ovarian development of Tibetan sheep.","authors":"Dan Zhang, Chao Yuan, Xuejiao An, Tingting Guo, Zengkui Lu, Jianbin Liu","doi":"10.1016/j.ygeno.2024.110973","DOIUrl":"10.1016/j.ygeno.2024.110973","url":null,"abstract":"Many studies on the adaptability of Tibetan sheep to hypoxia have been reported, but little attention has been paid to the reproduction of Tibetan sheep living at an altitude of more than 4000 m. In this study, the ovaries of Alpine Merino sheep (AM) living in middle-high altitude areas (2500 m) and the ovaries of Gangba Tibetan sheep (GB) and Huoba Tibetan sheep (HB) living in ultra-high altitude areas (4400 m or more) were collected. Through morphological, transcriptomics and metabolomics, the effects of ultra-high altitude areas on Tibetan sheep ovarian development and the molecular mechanism of sheep's adaptability to ultra-high altitude environment were explored. The results showed that the number of granulosa cells in AM was significantly higher than that in GB and HB. The transcriptome revealed several genes related to follicular development, such as DAPL1, IGFBP1, C5, GPR12, STRA6, BMPER, etc., which were mainly enriched in related pathways such as cell growth and development. Through metabolomics analysis, it was found that the differential metabolites between the three groups of sheep were mainly lipids and lipid-like small molecules, such as Glycerol 3-Phosphate, PC (16: 0 / 18: 3 (9Z, 12Z, 15Z)), mainly enriched in lipid metabolism and other related pathways. The results of combined analysis showed that Tryptophan metabolism and Steroid hormone biosynthesis may have a significant effect on Tibetan sheep follicular development. Some genes (including HSD17B7, CYP11A1, CYP19, HSD3B1, CYP17, etc.) and some metabolites (including Cortisone, 2-Methoxyestrone, etc.) are enriched in these pathways, regulating ovarian and follicular development by affecting estrogen, progesterone, etc.. The results further revealed the molecular mechanism of Tibetan sheep to adapt to the ultra-high altitude environment and maintain normal ovarian and follicular development through the regulation of genes and metabolites.","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110973"},"PeriodicalIF":3.4,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Genomic regions associated with Holstein heifer times bred to artificial insemination and embryo transfer services.

IF 3.4 2区生物学

Genomics Pub Date : 2024-12-02 DOI: 10.1016/j.ygeno.2024.110972

Victoria Kelson, Jennifer Kiser, Kimberly Davenport, Emaly Suarez, Brenda Murdoch, Holly Neibergs

引用次数: 0

The cross-talk between the metabolome and microbiome in a double-hit neonatal rat model of bronchopulmonary dysplasia.

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-29 DOI: 10.1016/j.ygeno.2024.110969

Jing Ding, Jun Xu, Hongkun Wu, Mei Li, Yihan Xiao, Jie Fu, Xiangyu Zhu, Na Wu, Qiang Sun, Yaran Liu

{"title":"The cross-talk between the metabolome and microbiome in a double-hit neonatal rat model of bronchopulmonary dysplasia.","authors":"Jing Ding, Jun Xu, Hongkun Wu, Mei Li, Yihan Xiao, Jie Fu, Xiangyu Zhu, Na Wu, Qiang Sun, Yaran Liu","doi":"10.1016/j.ygeno.2024.110969","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110969","url":null,"abstract":"Bronchopulmonary dysplasia (BPD), a chronic lung disease in preterm infants, is associated with inflammation and high oxygen exposure. However, the effects of antenatal inflammation and postnatal extended hyperoxia on the metabolome and microbiome remain unclear. In this study, pregnant rats received lipopolysaccharide or saline injections on gestational day 20 and were exposed to either 21 % or 80 % oxygen for 4 weeks post-birth. Analysis revealed an increase in Firmicutes, Proteobacteria, and Actinobacteria, with a decrease in Bacteroidetes in BPD rats. Metabolomic analysis identified 78 altered metabolites, primarily lipids, enriched in pathways including arginine biosynthesis, sphingolipid metabolism, and primary bile acid biosynthesis in BPD rats. Integration analysis revealed strong correlations between intestinal microbiota and metabolites in BPD rats. These findings underscored the impact of antenatal inflammation and prolonged postnatal hyperoxia on gut microbiota and serum metabolome, suggesting their role in BPD pathogenesis.","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"110969"},"PeriodicalIF":3.4,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142767960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Rapid sequencing and identification for 18-STRs long amplicon panel using portable devices and nanopore sequencer.

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-27 DOI: 10.1016/j.ygeno.2024.110970

Jiarong Zhang, Tingting Yang, Zihan Xie, Zilin Ren, Linyu Shi, Jiang-Wei Yan, Ming Ni

{"title":"Rapid sequencing and identification for 18-STRs long amplicon panel using portable devices and nanopore sequencer.","authors":"Jiarong Zhang, Tingting Yang, Zihan Xie, Zilin Ren, Linyu Shi, Jiang-Wei Yan, Ming Ni","doi":"10.1016/j.ygeno.2024.110970","DOIUrl":"10.1016/j.ygeno.2024.110970","url":null,"abstract":"STRs are the most commonly used forensic genetic markers for human identification. Nanopore sequencing has shown the advantages of high portability and large data throughput. Previous studies indicate it has great potential for profiling STRs based on the ligation library preparation method. However, this method, which requires more library preparation time and operations, is unsuitable for rapid STR profiling, particularly for field forensic applications. The transposase-based rapid library preparation method offers the possibility to perform human identification using portable instruments. However, the amplicons of conventional STR panels are too small and would be cut into scraps with rapid methods, making them impractical for genotyping. In this study, we developed an 18-STRs multiplex amplification panel with amplicons of ∼1.4 Kbp. The PCR conditions were optimized to be finished within 2 h and 12 min, and the PCR products could undergo rapid methods that involved random fragmentation. We found that, on average, 29.16 % of reads from the long-amplicon panel and rapid library kit covered the whole STR region, sufficient for downstream STR profiling analysis. We conducted a small validation experiment on 24 samples using portable instruments powered by a 1.5 kW‧h portable power source. The entire process took 10.5 h and we obtained enough data from 24 samples to perform trustworthy pairwise identification analysis using the STR profiles. The overall accuracy of the analysis was 95.36 %. In sum, the study evaluated and demonstrated the viability and potential of nanopore sequencing for forensic application in the field.","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110970"},"PeriodicalIF":3.4,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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

Identification of CCR7 as a potential biomarker in polycystic ovary syndrome through transcriptome sequencing and integrated bioinformatics.

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-27 DOI: 10.1016/j.ygeno.2024.110968

Zuwei Yang, Chengliang Zhou, Li Jin, Jiexue Pan

引用次数: 0

Retraction notice to "LncRNA HOTAIR regulates the expression of E-cadherin to affect nasopharyngeal carcinoma progression by recruiting histone methylase EZH2 to mediate H3K27 trimethylation" [Genomics Volume 113, Issue 4, July 2021, Pages 2276-2289]. LncRNA HOTAIR通过招募组蛋白甲基化酶EZH2介导H3K27三甲基化，调节E-cadherin的表达以影响鼻咽癌的进展》的撤稿通知[《基因组学》第113卷第4期，2021年7月，第2276-2289页]。

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-21 DOI: 10.1016/j.ygeno.2024.110939

Feng-Lian Yang, Yu-Xia Wei, Bi-Yun Liao, Gui-Jiang Wei, Hai-Mei Qin, Xiao-Xia Pang, Jun-Li Wang

引用次数: 0

"Genome-based in silico assessment of biosynthetic gene clusters in Planctomycetota: Evidences of its wide divergent nature". "基于基因组的 Planctomycetota 生物合成基因簇硅学评估：其广泛分歧性质的证据"。

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-20 DOI: 10.1016/j.ygeno.2024.110965

Rita Calisto, Ofélia Godinho, Damien P Devos, Olga M Lage

引用次数: 0

Unveiling the intricate structural variability induced by repeat-mediated recombination in the complete mitochondrial genome of Cuscuta gronovii Willd. 揭示Cuscuta gronovii Willd.完整线粒体基因组中由重复介导的重组诱导的复杂结构变异性

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-19 DOI: 10.1016/j.ygeno.2024.110966

Zhijian Yang, Xue Liu, Xiaohui Qin, Zhen Xiao, Qian Luo, Danni Pan, Hong Yang, Sufeng Liao, Xuanyang Chen

{"title":"Unveiling the intricate structural variability induced by repeat-mediated recombination in the complete mitochondrial genome of Cuscuta gronovii Willd.","authors":"Zhijian Yang, Xue Liu, Xiaohui Qin, Zhen Xiao, Qian Luo, Danni Pan, Hong Yang, Sufeng Liao, Xuanyang Chen","doi":"10.1016/j.ygeno.2024.110966","DOIUrl":"10.1016/j.ygeno.2024.110966","url":null,"abstract":"Cuscuta gronovii Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of C. gronovii. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the nad4 and ccmB genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of C. gronovii but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus Cuscuta.","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110966"},"PeriodicalIF":3.4,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 fundamental and theoretical framework for mutation interactions and epistasis 突变相互作用和表观性的基本理论框架。

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-01 DOI: 10.1016/j.ygeno.2024.110963

Christopher J. Giacoletto , Ronald Benjamin , Jerome I. Rotter , Martin R. Schiller

引用次数: 0

Integrating transcriptomics and proteomics to understand the molecular mechanisms underlying the pathogenesis of type 2 diabetes mellitus 整合转录组学和蛋白质组学，了解 2 型糖尿病发病机制的分子机制。

IF 3.4 2区生物学

Genomics Pub Date : 2024-11-01 DOI: 10.1016/j.ygeno.2024.110964

Shuyao Wei , Feifei Ma , Shanshan Feng , Xiaoqin Ha

{"title":"Integrating transcriptomics and proteomics to understand the molecular mechanisms underlying the pathogenesis of type 2 diabetes mellitus","authors":"Shuyao Wei , Feifei Ma , Shanshan Feng , Xiaoqin Ha","doi":"10.1016/j.ygeno.2024.110964","DOIUrl":"10.1016/j.ygeno.2024.110964","url":null,"abstract":"<div><div>The liver plays an important role in glucose regulation, and their dysfunction is closely associated with the development of type 2 diabetes mellitus (T2DM), and insulin resistance (IR) in hepatocyte mediate the pathogenesis of diabetes mellitus. In T2DM rats and their correlated control, we investigated various genes expression at transcriptional and translational level by utilizing transcriptomic using RNA sequencing (RNA-seq) and proteomics using isobaric tags for relative and absolute quantification (iTRAQ) to disclose potential candidates for Type 2 diabetes diagnosis and therapy. We found the lecithin retinol acyltransferase (Lrat) gene regulate hepatocyte IR in T2DM. Furthermore, BRL-3A cells, rat liver cells, worked as the IR model in vitro study. Hence, Lrat gene was overexpressed in BRL-3A cells to explore the role of Lrat gene in IR by measuring the cellular glucose consumption, TCHO, and LDL-C levels. Finally, we found that Lrat gene can improve the level of glycolipid metabolism in BRL-3A cells and reduce the degree of IR in BRL-3A cells. Therefore, further exploration of Lrat gene related molecular mechanism is meaningful.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"116 6","pages":"Article 110964"},"PeriodicalIF":3.4,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142686676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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