journal
https://read.qxmd.com/read/38510276/hybrid-de-novo-and-haplotype-resolved-genome-assembly-of-vechur-cattle-elucidating-genetic-variation
#21
JOURNAL ARTICLE
Poorvishaa V Muthusamy, Rajesh Vakayil Mani, Shivani Kumari, Manpreet Kaur, Balu Bhaskar, Rajeev Raghavan Pillai, Thankappan Sajeev Kumar, Thapasimuthu Vijayamma Anilkumar, Nongmaithem Sadananda Singh
Cattle contribute to the nutritional needs and economy of a place. The performance and fitness of cattle depend on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding, and availability of relevant reference genomes is essential. In the present study, the genome of a Vechur calf was sequenced on both short-read Illumina and long-read Nanopore sequencing platforms. The hybrid de novo assembly approach was deployed to obtain an average contig length of 1...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38510275/comparative-stigmatic-transcriptomics-reveals-self-and-cross-pollination-responses-to-heteromorphic-incompatibility-in-plumbago-auriculata-lam
#22
JOURNAL ARTICLE
Di Hu, Di Lin, Shouli Yi, Suping Gao, Ting Lei, Wenji Li, Tingdan Xu
"Heteromorphic self-incompatibility" (HetSI) in plants is a mechanism of defense to avoid self-pollination and promote outcrossing. However, the molecular mechanism underlying HetSI remains largely unknown. In this study, RNA-seq was conducted to explore the molecular mechanisms underlying self-compatible (SC, "T × P" and "P × T") and self-incompatible (SI, "T × T" and "P × P") pollination in the two types of flowers of Plumbago auriculata Lam. which is a representative HetSI plant. By comparing "T × P" vs...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38510274/identification-of-a-novel-kcnt2-variant-in-a-family-with-developmental-and-epileptic-encephalopathies-a-case-report-and-literature-review
#23
Fengji Cui, Tuoya Wulan, Qian Zhang, Victor Wei Zhang, Yuhua Jiang
Background: Developmental and epileptic encephalopathies (DEEs) are a group of heterogeneous neurodevelopmental diseases characterized mainly by developmental delay/intellectual disability and early-onset epilepsy. Researchers have identified variations in the KCNT2 gene (OMIM* 610044) as the cause of DEE type 57 (MIM# 617771). Case presentation: We report in this study a 46-year-old woman who presented with early-onset epilepsy, intellectual disability, hypertrichosis, coarse facial features, and short stature...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38510273/editorial-non-coding-rna-elements-as-regulators-of-host-pathogen-interactions
#24
EDITORIAL
Margarida Gama-Carvalho, Nham Tran
No abstract text is available yet for this article.
2024: Frontiers in Genetics
https://read.qxmd.com/read/38510272/elucidating-the-role-of-twist1-in-ulcerative-colitis-a-comprehensive-bioinformatics-and-machine-learning-approach
#25
JOURNAL ARTICLE
Wenjie Ou, Zhaoxue Qi, Ning Liu, Junzi Zhang, Xuguang Mi, Yuan Song, Yanqiu Fang, Baiying Cui, Junjie Hou, Zhixin Yuan
Background: Ulcerative colitis (UC) is a common and progressive inflammatory bowel disease primarily affecting the colon and rectum. Prolonged inflammation can lead to colitis-associated colorectal cancer (CAC). While the exact cause of UC remains unknown, this study aims to investigate the role of the TWIST1 gene in UC. Methods: Second-generation sequencing data from adult UC patients were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, and characteristic genes were selected using machine learning and Lasso regression...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38505829/editorial-molecular-and-breeding-mechanisms-for-enhanced-performance-in-underutilized-leguminous-crops-in-africa
#26
EDITORIAL
Lydia N Horn, M T Labuschagne
No abstract text is available yet for this article.
2024: Frontiers in Genetics
https://read.qxmd.com/read/38505828/flexible-gold-standards-for-transcription-factor-regulatory-interactions-in-escherichia-coli-k-12-architecture-of-evidence-types
#27
JOURNAL ARTICLE
Paloma Lara, Socorro Gama-Castro, Heladia Salgado, Claire Rioualen, Víctor H Tierrafría, Luis J Muñiz-Rascado, César Bonavides-Martínez, Julio Collado-Vides
Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. Here, we present for the first time a detailed analysis of the sources of knowledge supporting the collection of transcriptional regulatory interactions (RIs) of Escherichia coli K-12. An RI groups the transcription factor, its effect (positive or negative) and the regulated target, a promoter, a gene or transcription unit. We improved the evidence codes so that specific methods are incorporated and classified into independent groups...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38501058/role-of-circular-rnas-in-lung-cancer
#28
REVIEW
Maksat Babayev, Patricia Silveyra
Lung cancer remains a global public health concern with significant research focus on developing better diagnosis/prognosis biomarkers and therapeutical targets. Circular RNAs (circRNAs) are a type of single-stranded RNA molecules that covalently closed and have ubiquitous expression. These molecules have been implicated in a variety of disease mechanisms, including lung cancer, as they exhibit oncogenic or tumor suppressor characteristics. Recent research has shown an important role that circRNAs play at different stages of lung cancer, particularly in lung adenocarcinoma...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38501057/genetic-interrogation-for-sequence-and-copy-number-variants-in-systemic-lupus-erythematosus
#29
REVIEW
Nicholas Kim-Wah Yeo, Che Kang Lim, Katherine Nay Yaung, Nicholas Kim Huat Khoo, Thaschawee Arkachaisri, Salvatore Albani, Joo Guan Yeo
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38495672/finding-potential-lncrna-disease-associations-using-a-boosting-based-ensemble-learning-model
#30
JOURNAL ARTICLE
Liqian Zhou, Xinhuai Peng, Lijun Zeng, Lihong Peng
Introduction: Long non-coding RNAs (lncRNAs) have been in the clinical use as potential prognostic biomarkers of various types of cancer. Identifying associations between lncRNAs and diseases helps capture the potential biomarkers and design efficient therapeutic options for diseases. Wet experiments for identifying these associations are costly and laborious. Methods: We developed LDA-SABC, a novel boosting-based framework for lncRNA-disease association (LDA) prediction. LDA-SABC extracts LDA features based on singular value decomposition (SVD) and classifies lncRNA-disease pairs (LDPs) by incorporating LightGBM and AdaBoost into the convolutional neural network...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38495671/genome-wide-identification-of-dysregulated-alternative-splicing-and-rna-binding-proteins-involved-in-atopic-dermatitis
#31
JOURNAL ARTICLE
Yaqi Yang, Hao Chen, Qing Jiang, Lin Yang, Rongfei Zhu, Nan Huang
Objectives: We explored the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of atopic dermatitis (AD). Methods: We downloaded RNA-seq data (GSE121212) from 10 healthy control skin samples (healthy, Ctrl), 10 non-lesional skin samples with AD damage (non-lesional, NL), and 10 lesional skin samples with AD damage (lesional, LS). We performed the analysis of differentially expressed genes (DEGs), differentially expressed RBPs (DE-RBPs), alternative splicing (AS), functional enrichment, the co-expression of RBPs and RASEs, and quantitative polymerase chain reaction (qPCR)...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38495670/metabolic-syndrome-traits-exhibit-genotype-by-environment-interaction-in-relation-to-socioeconomic-status-in-the-mexican-american-family-heart-study
#32
JOURNAL ARTICLE
Vincent P Diego, Eron G Manusov, Xi Mao, Marcio Almeida, Juan M Peralta, Joanne E Curran, Michael C Mahaney, Harald Göring, John Blangero, Sarah Williams-Blangero
Background: Socioeconomic Status (SES) is a potent environmental determinant of health. To our knowledge, no assessment of genotype-environment interaction has been conducted to consider the joint effects of socioeconomic status and genetics on risk for metabolic disease. We analyzed data from the Mexican American Family Studies (MAFS) to evaluate the hypothesis that genotype-by-environment interaction (GxE) is an essential determinant of variation in risk factors for metabolic syndrome (MS). Methods: We employed a maximum likelihood estimation of the decomposition of variance components to detect GxE interaction...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38495669/establishment-and-analysis-of-artificial-neural-network-diagnosis-model-for-coagulation-related-molecular-subgroups-in-coronary-artery-disease
#33
JOURNAL ARTICLE
Biwei Zheng, Yujing Li, Guoliang Xiong
Background: Coronary artery disease (CAD) is the most common type of cardiovascular disease and cause significant morbidity and mortality. Abnormal coagulation cascade is one of the high-risk factors in CAD patients, but the molecular mechanism of coagulation in CAD is still limited. Methods: We clustered and categorized 352 CAD paitents based on the expression patterns of coagulation-related genes (CRGs), and then we explored the molecular and immunological variations across the subgroups to reveal the underlying biological characteristics of CAD patients...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38495668/compositional-features-analysis-by-machine-learning-in-genome-represents-linear-adaptation-of-monkeypox-virus
#34
JOURNAL ARTICLE
Sen Zhang, Ya-Dan Li, Yu-Rong Cai, Xiao-Ping Kang, Ye Feng, Yu-Chang Li, Yue-Hong Chen, Jing Li, Li-Li Bao, Tao Jiang
Introduction: The global headlines have been dominated by the sudden and widespread outbreak of monkeypox, a rare and endemic zoonotic disease caused by the monkeypox virus (MPXV). Genomic composition based machine learning (ML) methods have recently shown promise in identifying host adaptability and evolutionary patterns of virus. Our study aimed to analyze the genomic characteristics and evolutionary patterns of MPXV using ML methods. Methods: The open reading frame (ORF) regions of full-length MPXV genomes were filtered and 165 ORFs were selected as clusters with the highest homology...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38487253/megalencephalic-leukoencephalopathy-with-subcortical-cysts-a-variant-update-and-review-of-the-literature
#35
JOURNAL ARTICLE
Emma M J Passchier, Quinty Bisseling, Guy Helman, Rosalina M L van Spaendonk, Cas Simons, René C L Olsthoorn, Hieke van der Veen, Truus E M Abbink, Marjo S van der Knaap, Rogier Min
The leukodystrophy megalencephalic leukoencephalopathy with subcortical cysts (MLC) is characterized by infantile-onset macrocephaly and chronic edema of the brain white matter. With delayed onset, patients typically experience motor problems, epilepsy and slow cognitive decline. No treatment is available. Classic MLC is caused by bi-allelic recessive pathogenic variants in MLC1 or GLIALCAM (also called HEPACAM ). Heterozygous dominant pathogenic variants in GLIALCAM lead to remitting MLC, where patients show a similar phenotype in early life, followed by normalization of white matter edema and no clinical regression...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38487252/acppfel-explainable-deep-ensemble-learning-for-anticancer-peptides-prediction-based-on-feature-optimization
#36
JOURNAL ARTICLE
Mingyou Liu, Tao Wu, Xue Li, Yingxue Zhu, Sen Chen, Jian Huang, Fengfeng Zhou, Hongmei Liu
Background : Cancer is a significant global health problem that continues to cause a high number of deaths worldwide. Traditional cancer treatments often come with risks that can compromise the functionality of vital organs. As a potential alternative to these conventional therapies, Anticancer peptides (ACPs) have garnered attention for their small size, high specificity, and reduced toxicity, making them as a promising option for cancer treatments. Methods : However, the process of identifying effective ACPs through wet-lab screening experiments is time-consuming and requires a lot of labor...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38482385/mechanistic-causes-of-sign-epistasis-and-its-applications
#37
REVIEW
Jinqiu Zhang, Feiyu Chen, Xianghua Li
Mapping genetic variations to phenotypic variations poses a significant challenge, as mutations often combine unexpectedly, diverging from assumed additive effects even in the same environment. These interactions are known as epistasis or genetic interactions. Sign epistasis, as a specific type of epistasis, involves a complete reversal of mutation effects within altered genetic backgrounds, presenting a substantial hurdle to phenotype prediction. Despite its importance, there is a limited systematic overview of the mechanistic causes of sign epistasis...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38482384/sometimes-karyotype-resolves-the-case
#38
JOURNAL ARTICLE
Laura Rodríguez, Elena Barros, Jesica Skaarup Murray
No abstract text is available yet for this article.
2024: Frontiers in Genetics
https://read.qxmd.com/read/38482383/population-genomic-analysis-reveals-genetic-divergence-and-adaptation-in-brachymystax-lenok
#39
JOURNAL ARTICLE
Ping Li, Le Niu, Jianbo Chang, Xiaomei Kou, Wentian Wang, Wenjing Hu, Qigen Liu
Studying how populations in various environments differ genetically is crucial for gaining insights into the evolution of biodiversity. In order to pinpoint potential indicators of divergence and adaptation to diverse environments, we conducted a comprehensive analysis of 3,491,868 single nucleotide polymorphisms (SNPs) derived from five populations of Brachymystax lenok . We discovered significant geographic divergence among these 5 populations, which lack evidence of gene flow among them. Our results further demonstrated that the current distribution pattern of Brachymystax lenok are driven by geographical isolation and changes in oceans and rivers...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38482382/transcriptome-wide-1-methyladenosine-functional-profiling-of-messenger-rna-and-long-non-coding-rna-in-bladder-cancer
#40
JOURNAL ARTICLE
Jian-Jian Yin, Yan-Liang Song, Yu-Feng Guo, Yuan-Heng Dai, Qi Chang, Tao Wang, Guo-Qiang Sun, Ping Lu, Dong-Kui Song, Li-Rong Zhang
Introduction: Post-transcriptional RNA modifications are crucial regulators of tumor development and progression. In many biological processes, N1 -methyladenosine (m1 A) plays a key role. However, little is known about the links between chemical modifications of messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) and their function in bladder cancer (BLCA). Methods: Methylated RNA immunoprecipitation sequencing and RNA sequencing were performed to profile mRNA and lncRNA m1 A methylation and expression in BLCA cells, with or without stable knockdown of the m1 A methyltransferase tRNA methyltransferase 61A (TRMT61A)...
2024: Frontiers in Genetics
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