Differential mRNA profiles reveal the potential roles of genes involved in lactate stimulation in mouse macrophages
Genomics. 2024 Mar 1:110814. doi: 10.1016/j.ygeno.2024.110814. Online ahead of print.ABSTRACTLactate is a glycolysis end product, and its levels are markedly associated with disease severity, morbidity, and mortality in sepsis. It modulates key functions of immune cells, including macrophages. In this investigation, transcriptomic analysis was performed using lactic acid, sodium lactate, and hydrochloric acid-stimulated mouse bone marrow-derived macrophages (iBMDM), respectively, to identify lactate-associated signaling pathways. After 24 h of stimulation, 896 differentially expressed genes (DEG) indicated were up-regulati...
Source: Genomics - March 3, 2024 Category: Genetics & Stem Cells Authors: Limian Cao Chencheng Feng Haoming Ye Heng Zhao Zhimin Shi Jun Li Yayun Wu Ruojue Wang Qianru Li Jinquan Liang Qiang Ji Hao Gu Min Shao Source Type: research
Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function
Genomics. 2024 Mar 1:110819. doi: 10.1016/j.ygeno.2024.110819. Online ahead of print.ABSTRACTLong noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chines...
Source: Genomics - March 3, 2024 Category: Genetics & Stem Cells Authors: Pei Wang Zhipeng Liu Xia Zhang Hailong Huo Lina Wang Hongmei Dai Fuhua Yang Guiying Zhao Jinlong Huo Source Type: research
Differential mRNA profiles reveal the potential roles of genes involved in lactate stimulation in mouse macrophages
Genomics. 2024 Mar 1:110814. doi: 10.1016/j.ygeno.2024.110814. Online ahead of print.ABSTRACTLactate is a glycolysis end product, and its levels are markedly associated with disease severity, morbidity, and mortality in sepsis. It modulates key functions of immune cells, including macrophages. In this investigation, transcriptomic analysis was performed using lactic acid, sodium lactate, and hydrochloric acid-stimulated mouse bone marrow-derived macrophages (iBMDM), respectively, to identify lactate-associated signaling pathways. After 24 h of stimulation, 896 differentially expressed genes (DEG) indicated were up-regulati...
Source: Genomics - March 3, 2024 Category: Genetics & Stem Cells Authors: Limian Cao Chencheng Feng Haoming Ye Heng Zhao Zhimin Shi Jun Li Yayun Wu Ruojue Wang Qianru Li Jinquan Liang Qiang Ji Hao Gu Min Shao Source Type: research
The oral microbiome of newly diagnosed tuberculosis patients; a pilot study
CONCLUSION: These observations suggest significant variations in diversity, relative abundance and functional potential of oral microbiota of TB patients compared to healthy controls thereby suggesting potential role of oral bacterial dysbiosis in TB pathogenesis. However, longitudinal studies using powerful metagenomic and transcriptomic approaches are crucial to identify and these findings.PMID:38431030 | DOI:10.1016/j.ygeno.2024.110816 (Source: Genomics)
Source: Genomics - March 2, 2024 Category: Genetics & Stem Cells Authors: Muhammad Shahzad Muhammad Saeed Humaira Amin Nada Binmadi Zafar Ullah Sana Bibi Simon C Andrew Source Type: research
Arginine (315) is required for the PLIN2-CGI-58 interface and plays a functional role in regulating nascent LDs formation in bovine adipocytes
This study is the first to study amino acids on the PLIN2 interface during interaction with CGI-58 in bovine and highlight the role played by PLIN2 in the regulation of bovine adipocyte lipogenesis.PMID:38431031 | DOI:10.1016/j.ygeno.2024.110817 (Source: Genomics)
Source: Genomics - March 2, 2024 Category: Genetics & Stem Cells Authors: Peiwei Li Chugang Mei Sayed Haidar Abbas Raza Gong Cheng Yue Ning Le Zhang Linsen Zan Source Type: research
Screening of hair follicle telogen-associated circRNAs in sheep and construction of their ceRNA network
In this study, five 2-year-old Dorper ewes with extreme hair-shedding phenotype (S) and three Dorper ewes with non-shedding (N) phenotype were selected for subsequent analyses. For RNA extraction, skin tissues were collected on 27th September 2019 (S1, N1), 3rd January 2020 (S2, N2), and 17th March 2020 (S3, N3), which were then subjected to RNA-seq. RNA-seq technology revealed 20,185 novel circRNAs in the hair follicles of Dorper sheep. Among them, 1450 circRNAs were differentially expressed (DE). Clustering heatmap and expression pattern analyses were performed on DE circRNAs, which indicated 78 circRNAs with T pattern (...
Source: Genomics - March 2, 2024 Category: Genetics & Stem Cells Authors: Haoran Sun Xiaochun Yuan Ningyue Zhang Zhongze Luo Liang Zhang Xinhai Li Source Type: research
From sequences to therapeutics: Using machine learning to predict chemically modified siRNA activity
This study presents the first application of ML to efficiently classify chemically modified siRNAs on the basis of sequence and chemical modification patterns alone. Three algorithms were evaluated at three classification thresholds and compared according to sensitivity, specificity, consistency of feature weights with empirical knowledge, and performance using an external validation dataset. Finally, possible directions for future research were proposed.PMID:38431033 | DOI:10.1016/j.ygeno.2024.110815 (Source: Genomics)
Source: Genomics - March 2, 2024 Category: Genetics & Stem Cells Authors: Dominic D Martinelli Source Type: research
Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. 'Cabernet Franc') skin coloration
This study generated whole genome DNA methylation maps to characterize DNA methylomes of grape (cv. 'Cabernet Franc') skins and examine their functional significance during grape skin coloration. We sampled grape skin tissues at three key stages (the early stage of grape berry swelling, the late stage of grape berry swelling and the veraison) during which the color of grape berries changed from green to red. DNA methylation levels of grape skins at the three stages were higher in transposable element regions than in the genic regions, and the CG and CHG DNA methylation levels of the genic region were higher than the CHH DN...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Ao Li Fengxia Wang Tingting Ding Ke Li Huiping Liu Qingtian Zhang Qian Mu Hongjun Zhao Shouming Shan Pengfei Wang Source Type: research
Discovery of a novel miRNA involved in the regulation of male infertility in zebrafish
In this study, by analyzing miRNA transcriptome of the mature triploid zebrafish testis afflicted with spermatogenic dysfunctions, leading to the identification of 36 miRNAs that are differentially expressed in comparison with diploid, which are predicted to target 2737 genes. Subsequent functional annotation of these genes pinpointed two miRNAs might association with spermatogenesis. Inhibitory experiments showed that NC_007115.7.7_998413 inhibited conducts a substantial decline in sperm density, and conducted lower embryo fertilization rate than control. And putative target genes qRT-PCR evaluation showed that spata2 was...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Wen Fu Feng Liu Yingying Wang Ze Li Wenpei Deng Wenbin Liu Jinhui Liu Liangyue Peng Yamei Xiao Source Type: research
Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. 'Cabernet Franc') skin coloration
This study generated whole genome DNA methylation maps to characterize DNA methylomes of grape (cv. 'Cabernet Franc') skins and examine their functional significance during grape skin coloration. We sampled grape skin tissues at three key stages (the early stage of grape berry swelling, the late stage of grape berry swelling and the veraison) during which the color of grape berries changed from green to red. DNA methylation levels of grape skins at the three stages were higher in transposable element regions than in the genic regions, and the CG and CHG DNA methylation levels of the genic region were higher than the CHH DN...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Ao Li Fengxia Wang Tingting Ding Ke Li Huiping Liu Qingtian Zhang Qian Mu Hongjun Zhao Shouming Shan Pengfei Wang Source Type: research
Discovery of a novel miRNA involved in the regulation of male infertility in zebrafish
In this study, by analyzing miRNA transcriptome of the mature triploid zebrafish testis afflicted with spermatogenic dysfunctions, leading to the identification of 36 miRNAs that are differentially expressed in comparison with diploid, which are predicted to target 2737 genes. Subsequent functional annotation of these genes pinpointed two miRNAs might association with spermatogenesis. Inhibitory experiments showed that NC_007115.7.7_998413 inhibited conducts a substantial decline in sperm density, and conducted lower embryo fertilization rate than control. And putative target genes qRT-PCR evaluation showed that spata2 was...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Wen Fu Feng Liu Yingying Wang Ze Li Wenpei Deng Wenbin Liu Jinhui Liu Liangyue Peng Yamei Xiao Source Type: research
Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. 'Cabernet Franc') skin coloration
This study generated whole genome DNA methylation maps to characterize DNA methylomes of grape (cv. 'Cabernet Franc') skins and examine their functional significance during grape skin coloration. We sampled grape skin tissues at three key stages (the early stage of grape berry swelling, the late stage of grape berry swelling and the veraison) during which the color of grape berries changed from green to red. DNA methylation levels of grape skins at the three stages were higher in transposable element regions than in the genic regions, and the CG and CHG DNA methylation levels of the genic region were higher than the CHH DN...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Ao Li Fengxia Wang Tingting Ding Ke Li Huiping Liu Qingtian Zhang Qian Mu Hongjun Zhao Shouming Shan Pengfei Wang Source Type: research
Discovery of a novel miRNA involved in the regulation of male infertility in zebrafish
In this study, by analyzing miRNA transcriptome of the mature triploid zebrafish testis afflicted with spermatogenic dysfunctions, leading to the identification of 36 miRNAs that are differentially expressed in comparison with diploid, which are predicted to target 2737 genes. Subsequent functional annotation of these genes pinpointed two miRNAs might association with spermatogenesis. Inhibitory experiments showed that NC_007115.7.7_998413 inhibited conducts a substantial decline in sperm density, and conducted lower embryo fertilization rate than control. And putative target genes qRT-PCR evaluation showed that spata2 was...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Wen Fu Feng Liu Yingying Wang Ze Li Wenpei Deng Wenbin Liu Jinhui Liu Liangyue Peng Yamei Xiao Source Type: research
Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. 'Cabernet Franc') skin coloration
This study generated whole genome DNA methylation maps to characterize DNA methylomes of grape (cv. 'Cabernet Franc') skins and examine their functional significance during grape skin coloration. We sampled grape skin tissues at three key stages (the early stage of grape berry swelling, the late stage of grape berry swelling and the veraison) during which the color of grape berries changed from green to red. DNA methylation levels of grape skins at the three stages were higher in transposable element regions than in the genic regions, and the CG and CHG DNA methylation levels of the genic region were higher than the CHH DN...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Ao Li Fengxia Wang Tingting Ding Ke Li Huiping Liu Qingtian Zhang Qian Mu Hongjun Zhao Shouming Shan Pengfei Wang Source Type: research
Discovery of a novel miRNA involved in the regulation of male infertility in zebrafish
In this study, by analyzing miRNA transcriptome of the mature triploid zebrafish testis afflicted with spermatogenic dysfunctions, leading to the identification of 36 miRNAs that are differentially expressed in comparison with diploid, which are predicted to target 2737 genes. Subsequent functional annotation of these genes pinpointed two miRNAs might association with spermatogenesis. Inhibitory experiments showed that NC_007115.7.7_998413 inhibited conducts a substantial decline in sperm density, and conducted lower embryo fertilization rate than control. And putative target genes qRT-PCR evaluation showed that spata2 was...
Source: Genomics - February 25, 2024 Category: Genetics & Stem Cells Authors: Wen Fu Feng Liu Yingying Wang Ze Li Wenpei Deng Wenbin Liu Jinhui Liu Liangyue Peng Yamei Xiao Source Type: research
