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_998,413 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 wa...
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
Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding
In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, through metabarcoding, provides insight into the species composition of Berberidis Radix in Chinese patent medicines.PMID:38395205 | DOI:10.1016/j.ygeno.2024.110812 (Source: Genomics)
Source: Genomics - February 23, 2024 Category: Genetics & Stem Cells Authors: Hui Li None Abdullah Hongxia Yang Hua Guo Ye Yuan Ibrar Ahmed Guohui Li Yu Wang Yanxu Chang Peter Poczai Xiaoxuan Tian Source Type: research
Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding
In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, through metabarcoding, provides insight into the species composition of Berberidis Radix in Chinese patent medicines.PMID:38395205 | DOI:10.1016/j.ygeno.2024.110812 (Source: Genomics)
Source: Genomics - February 23, 2024 Category: Genetics & Stem Cells Authors: Hui Li None Abdullah Hongxia Yang Hua Guo Ye Yuan Ibrar Ahmed Guohui Li Yu Wang Yanxu Chang Peter Poczai Xiaoxuan Tian Source Type: research
Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding
In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, through metabarcoding, provides insight into the species composition of Berberidis Radix in Chinese patent medicines.PMID:38395205 | DOI:10.1016/j.ygeno.2024.110812 (Source: Genomics)
Source: Genomics - February 23, 2024 Category: Genetics & Stem Cells Authors: Hui Li None Abdullah Hongxia Yang Hua Guo Ye Yuan Ibrar Ahmed Guohui Li Yu Wang Yanxu Chang Peter Poczai Xiaoxuan Tian Source Type: research
Amino acid metabolism and MAP kinase signaling pathway play opposite roles in the regulation of ethanol production during fermentation of sugarcane molasses in budding yeast
In this study, a batch fermentation model has been used to examine ethanol titers of deletion mutants for all yeast nonessential genes in this yeast genome. A total of 42 genes are identified to be involved in ethanol production during fermentation of sugarcane molasses. Deletion mutants of seventeen genes show increased ethanol titers, while deletion mutants for twenty-five genes exhibit reduced ethanol titers. Two MAP kinases Hog1 and Kss1 controlling the high osmolarity and glycerol (HOG) signaling and the filamentous growth, respectively, are negatively involved in the regulation of ethanol production. In addition, twe...
Source: Genomics - February 22, 2024 Category: Genetics & Stem Cells Authors: Linghuo Jiang Yuzhi Shen Yongqiang Jiang Weiping Mei Liudan Wei Jinrong Feng Chunyu Wei Xiufan Liao Yiping Mo Lingxin Pan Min Wei Yiying Gu Jiashi Zheng Source Type: research
Amino acid metabolism and MAP kinase signaling pathway play opposite roles in the regulation of ethanol production during fermentation of sugarcane molasses in budding yeast
In this study, a batch fermentation model has been used to examine ethanol titers of deletion mutants for all yeast nonessential genes in this yeast genome. A total of 42 genes are identified to be involved in ethanol production during fermentation of sugarcane molasses. Deletion mutants of seventeen genes show increased ethanol titers, while deletion mutants for twenty-five genes exhibit reduced ethanol titers. Two MAP kinases Hog1 and Kss1 controlling the high osmolarity and glycerol (HOG) signaling and the filamentous growth, respectively, are negatively involved in the regulation of ethanol production. In addition, twe...
Source: Genomics - February 22, 2024 Category: Genetics & Stem Cells Authors: Linghuo Jiang Yuzhi Shen Yongqiang Jiang Weiping Mei Liudan Wei Jinrong Feng Chunyu Wei Xiufan Liao Yiping Mo Lingxin Pan Min Wei Yiying Gu Jiashi Zheng Source Type: research
Clinical value of FAT1 mutations to indicate the immune response in colorectal cancer patients
Genomics. 2024 Feb 14:110808. doi: 10.1016/j.ygeno.2024.110808. Online ahead of print.ABSTRACTImmunotherapy is currently approved for CRC whose tumors have high MSI-H. To find additional biomarkers for immunotherapy in CRC, targeted sequencing was performed on tumor tissues from a discovery cohort of 161 CRC patients. Validation cohorts from the cBioPortal were also used for survival and tumor cell infiltration analyses. The FAT1-mutated CRC group often co-occurred with MSI events and displayed a higher TMB compared to the FAT1 wild-type CRC. Overall survival was higher in patients with FAT1 mutations than in patients with...
Source: Genomics - February 16, 2024 Category: Genetics & Stem Cells Authors: Wei Zhu Lan Yang Yu Gao Yi Zhou Yuqian Shi Kaihua Liu Ruoying Yu Yang Shao Wentong Zhang Guosheng Wu Junjun He Source Type: research
Clinical value of FAT1 mutations to indicate the immune response in colorectal cancer patients
Genomics. 2024 Feb 14:110808. doi: 10.1016/j.ygeno.2024.110808. Online ahead of print.ABSTRACTImmunotherapy is currently approved for CRC whose tumors have high MSI-H. To find additional biomarkers for immunotherapy in CRC, targeted sequencing was performed on tumor tissues from a discovery cohort of 161 CRC patients. Validation cohorts from the cBioPortal were also used for survival and tumor cell infiltration analyses. The FAT1-mutated CRC group often co-occurred with MSI events and displayed a higher TMB compared to the FAT1 wild-type CRC. Overall survival was higher in patients with FAT1 mutations than in patients with...
Source: Genomics - February 16, 2024 Category: Genetics & Stem Cells Authors: Wei Zhu Lan Yang Yu Gao Yi Zhou Yuqian Shi Kaihua Liu Ruoying Yu Yang Shao Wentong Zhang Guosheng Wu Junjun He Source Type: research
Clinical value of FAT1 mutations to indicate the immune response in colorectal cancer patients
Genomics. 2024 Feb 14:110808. doi: 10.1016/j.ygeno.2024.110808. Online ahead of print.ABSTRACTImmunotherapy is currently approved for CRC whose tumors have high MSI-H. To find additional biomarkers for immunotherapy in CRC, targeted sequencing was performed on tumor tissues from a discovery cohort of 161 CRC patients. Validation cohorts from the cBioPortal were also used for survival and tumor cell infiltration analyses. The FAT1-mutated CRC group often co-occurred with MSI events and displayed a higher TMB compared to the FAT1 wild-type CRC. Overall survival was higher in patients with FAT1 mutations than in patients with...
Source: Genomics - February 16, 2024 Category: Genetics & Stem Cells Authors: Wei Zhu Lan Yang Yu Gao Yi Zhou Yuqian Shi Kaihua Liu Ruoying Yu Yang Shao Wentong Zhang Guosheng Wu Junjun He Source Type: research
Clinical value of FAT1 mutations to indicate the immune response in colorectal cancer patients
Genomics. 2024 Feb 14:110808. doi: 10.1016/j.ygeno.2024.110808. Online ahead of print.ABSTRACTImmunotherapy is currently approved for CRC whose tumors have high MSI-H. To find additional biomarkers for immunotherapy in CRC, targeted sequencing was performed on tumor tissues from a discovery cohort of 161 CRC patients. Validation cohorts from the cBioPortal were also used for survival and tumor cell infiltration analyses. The FAT1-mutated CRC group often co-occurred with MSI events and displayed a higher TMB compared to the FAT1 wild-type CRC. Overall survival was higher in patients with FAT1 mutations than in patients with...
Source: Genomics - February 16, 2024 Category: Genetics & Stem Cells Authors: Wei Zhu Lan Yang Yu Gao Yi Zhou Yuqian Shi Kaihua Liu Ruoying Yu Yang Shao Wentong Zhang Guosheng Wu Junjun He Source Type: research
Integrated gene co-expression network analysis and experimental validation revealed potential targets of human urine extract CDA-II in treating chronic myeloid leukemia
CONCLUSION: This study highlights the hub gene and lncRNA/mRNA co-expression network as crucial elements in the context of CDA-II treatment of CML. This insight not only enriches our understanding of CDA-II's mechanism of action but also might provide valuable clues for subsequent experimental studies of CDA-II, and potentially contribute to the discovery of new therapeutic targets for CML.PMID:38325533 | DOI:10.1016/j.ygeno.2024.110806 (Source: Genomics)
Source: Genomics - February 7, 2024 Category: Genetics & Stem Cells Authors: Lei Jiang Haoyuan Hong Shulin Xiang Han Li Jianyu Ji Mei Lan Bin Luo Source Type: research
Integrated gene co-expression network analysis and experimental validation revealed potential targets of human urine extract CDA-II in treating chronic myeloid leukemia
CONCLUSION: This study highlights the hub gene and lncRNA/mRNA co-expression network as crucial elements in the context of CDA-II treatment of CML. This insight not only enriches our understanding of CDA-II's mechanism of action but also might provide valuable clues for subsequent experimental studies of CDA-II, and potentially contribute to the discovery of new therapeutic targets for CML.PMID:38325533 | DOI:10.1016/j.ygeno.2024.110806 (Source: Genomics)
Source: Genomics - February 7, 2024 Category: Genetics & Stem Cells Authors: Lei Jiang Haoyuan Hong Shulin Xiang Han Li Jianyu Ji Mei Lan Bin Luo Source Type: research
Integrated gene co-expression network analysis and experimental validation revealed potential targets of human urine extract CDA-II in treating chronic myeloid leukemia
CONCLUSION: This study highlights the hub gene and lncRNA/mRNA co-expression network as crucial elements in the context of CDA-II treatment of CML. This insight not only enriches our understanding of CDA-II's mechanism of action but also might provide valuable clues for subsequent experimental studies of CDA-II, and potentially contribute to the discovery of new therapeutic targets for CML.PMID:38325533 | DOI:10.1016/j.ygeno.2024.110806 (Source: Genomics)
Source: Genomics - February 7, 2024 Category: Genetics & Stem Cells Authors: Lei Jiang Haoyuan Hong Shulin Xiang Han Li Jianyu Ji Mei Lan Bin Luo Source Type: research
Intestinal epithelial adaptations to vertical sleeve gastrectomy defined at single-cell resolution
Genomics. 2024 Feb 1;116(2):110805. doi: 10.1016/j.ygeno.2024.110805. Online ahead of print.ABSTRACTThe gut plays a key role in regulating metabolic health. Dietary factors disrupt intestinal physiology and contribute to obesity and diabetes, whereas bariatric procedures such as vertical sleeve gastrectomy (VSG) cause gut adaptations that induce robust metabolic improvements. However, our understanding of these adaptations at the cellular and molecular levels remains limited. In a validated murine model, we leverage single-cell transcriptomics to determine how VSG impacts different cell lineages of the small intestinal epi...
Source: Genomics - February 3, 2024 Category: Genetics & Stem Cells Authors: Kieran Koch-Laskowski Ki-Suk Kim Maigen Bethea Kelly N Z Fuller Darleen A Sandoval Praveen Sethupathy Source Type: research
