The content of yellow pigments in durum wheat (Titicum durum Desf.) grains: biosynthesis, genetic control, marker selection by P. N. Malchikov, M. G. Myasnikova

“…Molecular labeling of quantitative trait loci (QTL) that control the synthesis of the carotenoid pigment and the yellowness index (YI) found that they are distributed across all chromosomes of the durum wheat genome. The main QTLs, which determine 60 % of the variation of the trait, were mapped to 7AL and 7BL chromosome. …”
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Interconnections between BDH1-plasma protein-type 2 diabetes Mellitus: a mediated mendelian randomization analysis using plasma proteomics by Yi-Ying Liu, Yue-Yang Zhang, Qin Wan

“…This study primarily employed the Mendelian Randomization (MR) method, leveraging genetic data from numerous large-scale, publicly accessible genome-wide association studies (GWAS). Within this framework, we adopted a two-step, two-sample MR approach to evaluate the relationships between BDH1, plasma proteins, and type 2 diabetes. …”
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Sex differences in the association between fasting glucose and ischemic stroke incidence in people without diabetes: a 19-year prospective cohort study in Korea by Hyun Yi Kook, U Chul Ju, Yong Soo Cho, Eujene Jung, Hyun Ho Ryu

“…We used data from the Genome and Epidemiology Study (KoGES). The primary exposure was serum FBG obtained at the first interview. …”
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Annotation-free deep learning algorithm trained on hematoxylin & eosin images predicts epithelial-to-mesenchymal transition phenotype and endocrine response in estrogen receptor-po... by Kaimin Hu, Yinan Wu, Yajing Huang, Meiqi Zhou, Yanyan Wang, Xingru Huang

“…To confirm the presence of morphological discrepancies in tumor tissues of ER+ breast cancer classified as epithelial- and mesenchymal-phenotypes according to EMT-related transcriptional features, we trained deep learning algorithms based on EfficientNetV2 architecture to assign the phenotypic status for each patient utilizing hematoxylin & eosin (H&E)-stained slides from The Cancer Genome Atlas database. Our classifier model accurately identified the precise phenotypic status, achieving an area under the curve (AUC) of 0.886 at the tile-level and an AUC of 0.910 at the slide-level. …”
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Genetic association between immune-mediated inflammatory diseases and peripheral artery disease: a Mendelian randomization study by Haichao Wu, Dandan Zheng, Long Zhou, Qiang Wang, Tao Wang, Siyuan Liang

“…To corroborate previous research, we conducted Mendelian randomization (MR) analysis with the aim of clarifying the associations of various IMIDs with PAD. two-sample MR analysis was conducted to investigate the potential causal association between eight common IMIDs (including rheumatoid arthritis (RA), Crohn’s disease (CD), ulcerative colitis (UC), systemic lupus erythematosus (SLE), ankylosing spondylitis(AS), psoriasis(PSO), multiple sclerosis(MS), and hashimoto thyroiditis(HT)) and PAD. Genome-wide association study (GWAS) was used to identify genetic variants associated with IMIDs and PAD. …”
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Two cellular models for analyzing mitochondrial heteroplasmy by Yaning Hu, Lin Jiang, Wen Liu, Xingbo Zhao

“…Heteroplasmy is commonly observed in eukaryotes due to mitochondrial genome (mtDNA) mutation, paternal leakage, mitochondria transplantation/mitotherapy, and somatic cell nuclear transfer (SCNT). …”
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Gene expression signatures between Limia perugiae (Poeciliidae) populations from freshwater and hypersaline habitats, with comparisons to other teleosts. by Elizabeth J Wilson, Nick Barts, John L Coffin, James B Johnson, Carlos M Rodríguez Peña, Joanna L Kelley, Michael Tobler, Ryan Greenway

“…We used RNA-sequencing (RNA-seq) to investigate genome-wide variation in gene expression between a hypersaline population and a freshwater population of the livebearing fish species Limia perugiae (Poeciliidae). …”
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Identification of Signal Pathways and Hub Genes of Pulmonary Arterial Hypertension by Bioinformatic Analysis by Rui-Qi Wei, Wen-Mei Zhang, Zhe Liang, Chunmei Piao, Guangfa Zhu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed and visualized by R and Cytoscape software. …”
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Predictors of intrahepatic cholangiocarcinoma recurrence after surgical treatment by E. V. Kondratyev, A. D. Smirnova, G. G. Karmazanovsky, A. S. Tyan, N. N. Britskaya, M. G. Efanov, B. N. Gurmikov

“…We analyzed databases and diagnostic images of Vishnevsky National Medical Research Center of Surgery and Loginov Moscow Clinical Research Center for the period from April 2016 to January 2022 using the key queries «intrahepatic cholangiocarcinoma», «liver», «hepatocellular carcinoma», «metastases», «radio genomics». 142 patients with liver neoplasms were identified, including 90 cases of ICC, 31 cases of hepatocellular carcinoma and 21 cases of metastatic liver lesions, all morphologically verified (histologic and immunohistochemical analysis of biopsy material).Results. …”
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Validation and the role of PDK4 relevant to ferroptosis in degenerative lumbar disc disease by Wenhao Chen, Wanliang Yang, Bin Meng, Xingkun Wang, Heng Duan, Qian Xu, Hao Li

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on DEGs. …”
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Human blood metabolites and gastric cancer: a Mendelian randomization analysis by Chao Zhang, Dao Lai Huang, Kun Zhou, Jin Tao Cai, Dang Liu, Ming Hao Tan, Guan Yu Zhu, Xiang Hua Wu

“…Elevated levels of 3-methyl-2-oxovalerate and piperine may increase the risk of GC, while Phe-Phe dipeptide may have a protective effect. By integrating genomics and metabolomics, we offer a novel perspective on the biological mechanisms underlying GC. …”
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Lipid-lowering drug targets and lung related diseases: a Mendelian randomization study by Haifeng Yu, Xiaofei Zhang, Bian Wen, Shuo Hu, Bin Ni

“…METHODS We extracted genetic variations of six drug target genes from a major genome-wide association study of low-density lipoprotein cholesterol (LDL-C) in individuals predominantly of European ancestry to represent the effects of LDL-C-lowering treatment. …”
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Hypoxia-induced CTCF mediates alternative splicing via coupling chromatin looping and RNA Pol II pause to promote EMT in breast cancer by Parik Kakani, Shruti Ganesh Dhamdhere, Deepak Pant, Rushikesh Joshi, Sachin Mishra, Anchala Pandey, Dimple Notani, Sanjeev Shukla

“…This further regulates the CTCF-mediated RNA polymerase II pause at COL5A1exon64A, leading to its inclusion in promoting the EMT under hypoxia. Genome-wide study indicates the association of gained CTCF occupancy with the alternative splicing of many cancer-related genes, similar to the proposed model. …”
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Glutathione reductase plays a role in the metabolism of methylmercury degradation in Rhodotorula mucilaginosa by Yi Guo, Wenlong Deng, Qigui Mo, You Yu, Zhenwang Zhang, Mingjie Wei, Ruiling Tang, Surui Lu, Yanting Su

“…Unlike the traditional microbial methylmercury degradation pathways, R. mucilaginosa’s genome does not encode the organomercury lyase gene MerB. …”
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Effect of Multiple Gene Copy Number of Bacterial Lipase to Increase Lipase Production in Pichia pastoris by Esti Puspitasari, Yepy Hardi Rustam, Andreas Adhi Satya, Antonius Suwanto, Aris Tri Wahyudi, Rika Indri Astuti

“…Three copies of the lipase gene in pPIC9K_T1.2RQ(3x) recombinant plasmid were integrated into the genome of Pichia pastoris GS115, and quantitative analysis using qPCR technique confirmed that the GS115 transformant strain contained six copies of T1.2RQ gene, indicating two integration events. …”
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ENO1 promotes PDAC progression by inhibiting CD8+ T cell infiltration through upregulating PD-L1 expression via HIF-1α signaling by Aziguli Tulamaiti, Shu-Yu Xiao, Yan Yang, Musitaba Mutailifu, Xia-Qing Li, Shi-Qi Yin, Hong-Tai Ma, Hong-Fei Yao, Lin-Li Yao, Li-Peng Hu, Jun Li, Shu-Heng Jiang, Zhi-Gang Zhang, Yan-Miao Huo, Dong-Xue Li, Xue-Li Zhang

“…Under hypoxic conditions, the “Warburg effect” occurs to meet the nutrient and energy demands of rapid genome replication, remodeling the tumor microenvironment (TME) and influencing tumor immunity. α-Enolase (ENO1) is a multifunctional protein, acting as a glycolytic enzyme that catalyzes the conversion of 2-phosphoglyceric acid to phosphoenolpyruvic acid. …”
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Novel functional eQTL-SNPs associated with susceptibility to occupational pulmonary fibrosis: A multi-stage study by Rui Zhao, Xiaobo Tao, Wendi Zhang, Siqi Li, Shenxuan Zhou, Anhui Ning, Zhenyu Li, Minjie Chu, Wei Wang, Junhong Jiang

“…Methods: We first integrated the genome-wide association studies (GWASs) of IPF and silicosis to obtain the shared SNPs. …”
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Understanding the Impact of Salt Stress on Plant Pathogens Through Phenotypic and Transcriptomic Analysis by Hyejung Jung, Gil Han, Duyoung Lee, Hyun-Kyoung Jung, Young-Sam Kim, Hee Jeong Kong, Young-Ok Kim, Young-Su Seo, Jungwook Park

“…Phenotypic assays revealed that <i>B. gladioli</i> and <i>R. solanacearum</i> are highly sensitive to salt stress, exhibiting significant reductions in growth, motility, and enzyme production, whereas <i>Pcc</i> showed notable tolerance. Pan-genome-based comparative transcriptomics identified co-downregulated patterns in <i>B. gladioli</i> and <i>R. solanacearum</i> under stress conditions, indicating the suppression of bacterial chemotaxis and type III secretion systems. …”
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Multigene Panel Testing in Turkish Hereditary Cancer Syndrome Patients by Esra ARSLAN ATES, Ayberk TURKYILMAZ, Ceren ALAVANDA, Ozlem YILDIRIM, Ahmet Ilter GUNEY

“…In addition, 25 HCS-related genes were sequenced using a multigene panel, and variations were classified according to the American College of Medical Genetics and Genomics (ACMG) criteria. In total, 218 HCS patients predominantly with breast, colorectal, ovarian, gastric, and endometrium cancers were included. …”
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Essential and recurrent roles for hairpin RNAs in silencing de novo sex chromosome conflict in Drosophila simulans. by Jeffrey Vedanayagam, Marion Herbette, Holly Mudgett, Ching-Jung Lin, Chun-Ming Lai, Caitlin McDonough-Goldstein, Stephen Dorus, Benjamin Loppin, Colin Meiklejohn, Raphaëlle Dubruille, Eric C Lai

“…Altogether, these studies support a model in which protamine-derived drivers and hpRNA suppressors drive repeated cycles of sex chromosome conflict and resolution that shape genome evolution and the genetic control of male gametogenesis.…”
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