Genes, Vol. 15, Pages 407: New Empirical Bayes Models to Jointly Analyze Multiple RNA-Sequencing Data in a Hypophosphatasia Disease Study
In this study, we apply an empirical Bayes model to RNA-sequencing data acquired from the spinal cord and neocortex tissues of a mouse model, individually, to more accurately estimate the genetic effects without bias. More importantly, we further develop two integration methods, weighted gene approach and weighted Z method, to incorporate two RNA-sequencing data into a model for enhancing the effects of genetic markers in the diagnostics of hypophosphatasia disease. The simulation and real data analysis have demonstrated the effectiveness of our proposed integration methods, which can maximize genetic signals identified fr...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Dawson Kinsman Jian Hu Zhi Zhang Gengxin Li Tags: Article Source Type: research
Genes, Vol. 15, Pages 408: Genome-Wide Analysis of Exertional Rhabdomyolysis in Sickle Cell Trait Positive African Americans
The objective of this study was to elucidate the genetic basis of ERM in an SCT-positive African American cohort. SCT-positive African Americans with a personal history of ERM (cases, n = 30) and without history of ERM (controls, n = 53) were enrolled in this study. Whole-genome sequencing was performed on DNA samples isolated from peripheral white blood cells. Participants’ demographic, behavioral, and medical history information was obtained. An additional 131 controls were extracted from SCT-positive subjects of African descent from the 1000 Genomes Project. SCT carriers with ERM were characterized by myot...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Mingqiang Ren Nyamkhishig Sambuughin Ognoon Mungunshukh Daniel Baxter Edgeworth Daniel Hupalo Xijun Zhang Matthew D. Wilkerson Clifton L. Dalgard Francis G. O ’Connor Patricia A. Deuster Tags: Article Source Type: research
Genes, Vol. 15, Pages 409: Regulation of Hair Follicle Growth and Development by Different Alternative Spliceosomes of FGF5 in Rabbits
In conclusion, the expression profile of HF growth and development-related genes can be regulated by FGF5 alternative spliceosomes, inhibiting the proliferation of DPCs and has an influence on the regulation of HF growth in rabbits. This study provides insights to further investigate the mechanism of HF development in rabbits via FGF5 regulation. (Source: Genes)
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Shaoning Sun Bohao Zhao Jiali Li Xiyu Zhang Shuyu Yao Zhiyuan Bao Jiawei Cai Jie Yang Yang Chen Xinsheng Wu Tags: Article Source Type: research
Genes, Vol. 15, Pages 410: Reconstruction of Metabolic & ndash;Protein Interaction Integrated Network of Eriocheir sinensis and Analysis of Ecdysone Synthesis
Genes, Vol. 15, Pages 410: Reconstruction of Metabolic–Protein Interaction Integrated Network of Eriocheir sinensis and Analysis of Ecdysone Synthesis
Genes doi: 10.3390/genes15040410
Authors:
Tong Hao
Zhentao Song
Mingzhi Zhang
Lingrui Zhang
Jiarui Yang
Jingjing Li
Jinsheng Sun
Integrated networks have become a new interest in genome-scale network research due to their ability to comprehensively reflect and analyze the molecular processes in cells. Currently, none of the integrated networks have been reported for higher organisms. Eriocheir sinensis is a typical aquatic animal that grows thro...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Tong Hao Zhentao Song Mingzhi Zhang Lingrui Zhang Jiarui Yang Jingjing Li Jinsheng Sun Tags: Article Source Type: research
Genes, Vol. 15, Pages 412: Genetic Background of Blood & beta;-Hydroxybutyrate Acid Concentrations in Early-Lactating Holstein Dairy Cows Based on Genome-Wide Association Analyses
This study aimed to estimate the genetic parameters of blood BHB and conducted a genome-wide association study (GWAS) based on the estimated breeding value. Phenotypic data were collected from December 2019 to August 2023, comprising blood BHB concentrations in 45,617 Holstein cows during the three weeks post-calving across seven dairy farms. Genotypic data were obtained using the Neogen Geneseek Genomic Profiler (GGP) Bovine 100 K SNP Chip and GGP Bovine SNP50 v3 (Illumina Inc., San Diego, CA, USA) for genotyping. The estimated heritability and repeatability values for blood BHB levels were 0.167 and 0.175, respectively. ...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Yueqiang Wang Zhenyu Wang Wenhui Liu Shuoqi Xie Xiaoli Ren Lei Yan Dong Liang Tengyun Gao Tong Fu Zhen Zhang Hetian Huang Tags: Article Source Type: research
Genes, Vol. 15, Pages 414: Extrachromosomal Circular DNA: An Emerging Potential Biomarker for Inflammatory Bowel Diseases?
o Scaldaferri
Inflammatory bowel disease (IBD) comprising ulcerative colitis and Crohn’s disease is a chronic immune-mediated disease which affects the gastrointestinal tract with a relapsing and remitting course, causing lifelong morbidity. IBD pathogenesis is determined by multiple factors including genetics, immune and microbial factors, and environmental factors. Although therapy options are expanding, remission rates are unsatisfiable, and together with the disease course, response to therapy remains unpredictable. Therefore, the identification of biomarkers that are predictive for the disease course...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Valentina Petito Federica Di Vincenzo Lorenza Putignani Maria T. Abreu Birgitte Regenberg Antonio Gasbarrini Franco Scaldaferri Tags: Review Source Type: research
Genes, Vol. 15, Pages 411: Genome-Wide Association Study Uncovers Genomic Regions Associated with Coleoptile Length in a Worldwide Collection of Oat
This study provides new insights into the genetic architecture of coleoptile length in oats. (Source: Genes)
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Pingping Zhou Yuankun Liu Mengxian Yang Honghai Yan Tags: Article Source Type: research
Genes, Vol. 15, Pages 413: Causal Associations of Glaucoma and Age-Related Macular Degeneration with Cataract: A Bidirectional Two-Sample Mendelian Randomisation Study
This study investigated the potential causal relationship between glaucoma and AMD with cataract using genetic data from multi-ethnic populations. Single-nucleotide polymorphisms (SNPs) associated with exposure to cataract were selected as instrumental variables (IVs) from genome-wide association studies using meta-analysis data from BioBank Japan and UK Biobank. A bidirectional two-sample Mendelian randomisation (MR) study was conducted to assess the causal estimates using inverse variance weighted, MR-Egger, and MR pleiotropy residual sum and outlier tests. SNPs with (p < 5.0 × 10−8...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Je Hyun Seo Young Lee Tags: Article Source Type: research
Genes, Vol. 15, Pages 415: Identification of Quantitative Trait Loci and Candidate Genes Controlling Seed Dormancy in Eggplant (Solanum melongena L.)
This study provides a foundation for the further exploration of genes related to the regulation of seed dormancy and the elucidation of the molecular mechanism of eggplant seed dormancy and germination. (Source: Genes)
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Jiaqi Ai Wuhong Wang Tianhua Hu Haijiao Hu Jinglei Wang Yaqin Yan Hongtao Pang Yong Wang Chonglai Bao Qingzhen Wei Tags: Article Source Type: research
Genes, Vol. 15, Pages 416: Association of TMEM106B with Cortical APOE Gene Expression in Neurodegenerative Conditions
irier
The e4 allele of the apolipoprotein E gene is the strongest genetic risk factor for sporadic Alzheimer’s disease. Nevertheless, how APOE is regulated is still elusive. In a trans-eQTL analysis, we found a genome-wide significant association between transmembrane protein 106B (TMEM106B) genetic variants and cortical APOE mRNA levels in human brains. The goal of this study is to determine whether TMEM106B is mis-regulated in Alzheimer’s disease or in other neurodegenerative conditions. Available genomic, transcriptomic and proteomic data from human brains were downloaded from the Mayo Cl...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Cynthia Picard Justin Miron Judes Poirier Tags: Article Source Type: research
Genes, Vol. 15, Pages 404: DRANetSplicer: A Splice Site Prediction Model Based on Deep Residual Attention Networks
In this study, we developed a novel deep learning model, DRANetSplicer, that integrates residual learning and attention mechanisms for enhanced accuracy in capturing the intricate features of splice sites. We constructed multiple datasets using the most recent versions of genomic data from three different organisms, Oryza sativa japonica, Arabidopsis thaliana and Homo sapiens. This approach allows us to train models with a richer set of high-quality data. DRANetSplicer outperformed benchmark methods on donor and acceptor splice site datasets, achieving an average accuracy of (96.57%, 95.82%) across the three organisms. Com...
Source: Genes - March 26, 2024 Category: Genetics & Stem Cells Authors: Xueyan Liu Hongyan Zhang Ying Zeng Xinghui Zhu Lei Zhu Jiahui Fu Tags: Article Source Type: research
Genes, Vol. 15, Pages 403: Identification and Potential Roles of Human MicroRNAs in Ebola Virus Infection and Disease Pathogenesis
This study thus confirms and expands on the previous study using the same datasets and demonstrates further the importance of human miRNAs in the host response and EVD pathogenesis during infection. (Source: Genes)
Source: Genes - March 25, 2024 Category: Genetics & Stem Cells Authors: Melvin Mensah-Bonsu Christopher Doss Clay Gloster Perpetua Muganda Tags: Article Source Type: research
Genes, Vol. 15, Pages 402: Myelin-Specific microRNA-23a/b Cluster Deletion Inhibits Myelination in the Central Nervous System during Postnatal Growth and Aging
This study aims to clarify the role of miR-23a/b clusters in myelination using mice with a miR-23a/b cluster deletion (KO mice), specifically in myelin expressing proteolipid protein (PLP). Inducible conditional KO mice were generated by crossing miR-23a/b clusterflox/flox mice with PlpCre-ERT2 mice; the offspring were injected with tamoxifen at 10 days or 10 weeks of age to induce a myelin-specific miR-23a/b cluster deletion. Evaluation was performed at 10 weeks or 12 months of age and compared with control mice that were not treated with tamoxifen. KO mice exhibit impaired motor function and hypoplastic myelin sheaths in...
Source: Genes - March 25, 2024 Category: Genetics & Stem Cells Authors: Shigeki Ishibashi Naosuke Kamei Yuji Tsuchikawa Toshio Nakamae Takayuki Akimoto Shigeru Miyaki Nobuo Adachi Tags: Article Source Type: research
Genes, Vol. 15, Pages 400: Genome-Wide Identification and Expression Analysis of the Starch Synthase Gene Family in Sweet Potato and Two of Its Closely Related Species
This study offers fresh perspectives for enhancing knowledge about the roles of SSs and potential genes to enhance productivity, starch levels, and resistance to environmental stresses in sweet potatoes. (Source: Genes)
Source: Genes - March 25, 2024 Category: Genetics & Stem Cells Authors: Zongjian Sun Zhenqin Li Xiongjian Lin Zhifang Hu Mengzhen Jiang Binquan Tang Zhipeng Zhao Meng Xing Xiaohui Yang Hongbo Zhu Tags: Article Source Type: research
Genes, Vol. 15, Pages 401: Duplicated Copy Number Variant of the Maize 9-Lipoxygenase ZmLOX5 Improves 9,10-KODA-Mediated Resistance to Fall Armyworms
Kolomiets
Extensive genome structure variations, such as copy number variations (CNVs) and presence/absence variations, are the basis for the remarkable genetic diversity of maize; however, the effect of CNVs on maize herbivory defense remains largely underexplored. Here, we report that the naturally occurring duplication of the maize 9-lipoxygenase gene ZmLOX5 leads to increased resistance of maize to herbivory by fall armyworms (FAWs). Previously, we showed that ZmLOX5-derived oxylipins are required for defense against chewing insect herbivores and identified several inbred lines, including Yu796, that contained dupl...
Source: Genes - March 25, 2024 Category: Genetics & Stem Cells Authors: Peiguo Yuan Pei-Cheng Huang Timothy K. Martin Thomas M. Chappell Michael V. Kolomiets Tags: Article Source Type: research
