Comprehensive analysis of cuproptosis-related genes in immune infiltration and development of a novel diagnostic model for acute kidney injury by Yajing Li, Yingxue Ding

“…Our study aimed to investigate the involvement of cuproptosis-related genes (CRGs) in AKI.Methods Identification of CRGs was conducted using differential expression analysis, and subsequent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using human sequencing profiles. …”
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The bacterial response regulator ArcA uses a diverse binding site architecture to regulate carbon oxidation globally. by Dan M Park, Md Sohail Akhtar, Aseem Z Ansari, Robert Landick, Patricia J Kiley

“…Here we provide new mechanistic insight into how the balance between reduced and oxidized electron carriers is regulated at the level of gene expression by mapping the regulon of the response regulator ArcA from Escherichia coli, which responds to the quinone/quinol redox couple via its membrane-bound sensor kinase, ArcB. Our genome-wide analysis reveals that ArcA reprograms metabolism under anaerobic conditions such that carbon oxidation pathways that recycle redox carriers via respiration are transcriptionally repressed by ArcA. …”
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The Progression of Mycosis Fungoides During Treatment with Mogamulizumab: A BIO-MUSE Case Study of the Tumor and Immune Response in Peripheral Blood and Tissue by Angelica Johansson, Eirini Kalliara, Emma Belfrage, Teodor Alling, Paul Theodor Pyl, Anna Sandström Gerdtsson, Urban Gullberg, Anna Porwit, Kristina Drott, Sara Ek

“…<b>Methods:</b> We applied 10× genomics-based single-cell RNA sequencing to CD3+ peripheral T-cells, combined with T-cell receptor sequencing, to samples collected at multiple timepoints during the progression of the disease. …”
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Genetic Diversity of Human Enterovirus in Kazakhstan, during 2022 by Dinara Kamalova, Assel Akhmetova, Asylulan Amirgazin, Igor Sytnik, Viktoriya Rudenko, Gulzhan Yessimkhanova, Dinagul Bayesheva, Sergey Yegorov, Alexander Shevtsov

“…We then genotyped enteroviral subtypes associated with AM (n = 50) and HA (n = 9) using next-generation sequencing (NGS) on the viral protein 1 (VP1), followed up by whole-genome sequencing of the isolated viral species. All identified EVs were species B EV, consisting of five echoviruses (E6, E9, E11, E21, and E25) and three coxsackieviruses (CVA9, CVB3, and CVB5) serotypes within the cohort. …”
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Determination of mutagenicity of chemical compounds, physical factors and environmental pollutants by the Drosophila melanogaster wing somatic mutation and recombination test by L. P. Zakharenko, I. K. Zakharov

“…SMART can be used to evaluate the effect of various factors on the genome: physical (temperature, various types of radiation, electromagnetic fields), biogenic (genetic, physiological, infectious factors) and a wide range of chemical compounds. …”
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Bioinformatic Prediction of Novel microRNAs Encoded in Krüppel-like Factor 4 Gene by Mina Zahiri, Maryam Hassanlou, Amir-Reza Javanmard, Nooshin Bijari

“…The analysis of the obtained sequences showed that they are highly conserved, which indicates their importance in the genome. The results obtained in this study show the power and functionality of bioinformatics tools. …”
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High-throughput tracking enables systematic phenotyping and drug repurposing in C. elegans disease models by Thomas J O'Brien, Ida L Barlow, Luigi Feriani, André EX Brown

“…Here, we show that high-throughput imaging and quantitative phenotyping can be conducted systematically on a panel of C. elegans disease model strains. We used CRISPR genome-editing to create 25 worm models of human Mendelian diseases and phenotyped them using a single standardised assay. …”
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Comprehensive Pan-Cancer Analysis and Functional Studies Reveal SLC2A6 as a Ferroptosis Modulator in Hepatocellular carcinoma by Guohong Yan, Hailian Huang, Ziyan Lu, Meifeng Chen, Xiang Wang, Pei Zhong, Chongjiu Qin, Shutian Mo, Chuangye Han, Xiaoling Luo, Xinping Ye

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. …”
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Creation of a novel zebrafish model with low DHA status to study the role of maternal nutrition during neurodevelopment by Katherine M. Ranard, Bruce Appel

“…Here, we create a novel DHA-deficient zebrafish model by 1) disrupting elovl2, a key gene in the DHA biosynthesis pathway, via CRISPR/Cas9 genome editing, and 2) feeding mothers a DHA-deficient diet. …”
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Unveiling the role of SYNGR4 in breast cancer development: a novel target for immunotherapy by Jie Ma, Hongtao Wang, Zhengwei Gui, Yuanrong Yang

“…IntroductionSYNGR4 is considered to be one of the causative genes for amyotrophic lateral sclerosis, but its role in breast cancer development has not been revealed.MethodsThe expression of SYNGR4 in a variety of malignancies including breast cancer was analyzed using Genotype Tissue Expression (GTEx) and the Cancer Genome Atlas (TCGA) databases and verified by specimens collected from our center. …”
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Identification of KRT16 and ANXA10 as cell cycle regulation genes for lung adenocarcinoma based on self-transcriptome sequencing of surgical samples and TCGA public data mining by Wen-jian Liu, Jia-pan Shen, Ren-quan Zhang, Xiao-yun Fan

“…Methods Differentially expressed genes (DEGs) were identified by self-transcriptome sequencing of tumor tissues and paracancerous tissues resected during surgery and combined with The Cancer Genome Atlas (TCGA) data to screen for the genes associated with LUAD prognosis. …”
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Applications and Challenges of High-Throughput Phenotyping of Crops at Ground and Aviation Scales by Longyue CHEN, Dandan DUAN, Weibing XU, Zuolin LI, Chong ZHAO, Yi JIANG, Yonggang GAO, Wenqing ZUO

“…However, with the increasing development of cutting-edge technologies such as cloud big data processing platforms and artificial intelligence, which have great advantages in processing large-volume and high-complexity data, combined with biotechnology and genomics research methods, HTP of crops will play a pivotal role in combating food shortages caused by global environmental changes and population increase.…”
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PhpCNF-Y transcription factor infiltrates heterochromatin to generate cryptic intron-containing transcripts crucial for small RNA production by Manjit Kumar Srivastav, H. Diego Folco, Patroula Nathanailidou, Anupa T Anil, Drisya Vijayakumari, Shweta Jain, Jothy Dhakshnamoorthy, Maura O’Neill, Thorkell Andresson, David Wheeler, Shiv I. S. Grewal

“…Abstract The assembly of repressive heterochromatin in eukaryotic genomes is crucial for silencing lineage-inappropriate genes and repetitive DNA elements. …”
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Smoking as a causative factor in chronic kidney disease: a two-sample Mendelian randomization study by Yue Yang, Zheng Zhang, Hai-tao Lu, Qian-qian Xu, Li Zhuo, Wen-ge Li

“…This study applied bivariate causal analysis and two-sample Mendelian randomization (MR) methods to examine the association between various smoking behaviors – initiation, cessation, age at initiation, cigarettes smoked per day, and lifetime smoking – and CKD, using genome-wide data. The inverse variance weighted (IVW) method was the primary analytical tool, supported by sensitivity analyses, pleiotropy assessments, and mediation analyses. …”
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Identification and Characterization of the <i>ROP GTPase</i> Gene Family in Strawberry and the Positive Role of <i>FveROP4</i> in Fruit Resistance to Gray Mold by Shuai Zhao, Baode Zhu, Zhijun Zou, Yushan Zhai, Sufeng Liao, Ming Xu, Kunyang Li, Nasir Mehmood, Xiong Liao

“…In this study, we identified 53 <i>ROP</i> genes across the genomes of six Rosaceae species. Based on sequence homology, they were classified into three distinct phylogenetic clades. …”
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Identifiability of mathematical models in medical biology by S. I. Kabanikhin, D. A. Voronov, A. A. Grodz, O. I. Krivorotko

“…Analysis of biological data is a key topic in bioinformatics, computational genomics, molecular modeling and systems biology. The methods covered in this article could reduce the cost of experiments for biological data. …”
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Lysosome and Cytoskeleton Pathways Are Robustly Enriched in the Blood of Septic Patients: A Meta-Analysis of Transcriptomic Data by Jie Ma, Chuanxi Chen, Andreas S. Barth, Chris Cheadle, Xiangdong Guan, Li Gao

“…We identified 6 cohorts consisting of 450 individuals (sepsis = 323, control = 127) providing genome-wide messenger RNA (mRNA) expression data. …”
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Multidisciplinary approach to functional somatic syndromes: study protocol for a population-based prospective cohort study by Hamidreza Roohafza, Harold Snieder, Fatemeh Hadizadeh, Peyman Adibi, Alireza Ani, Ahmad Vaez

“…Human DNA genotyping, microbial amplicon sequencing and urine analysis is under progress for genomics, microbiota and metabolomics profiling, respectively. …”
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Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis... by Spyros I. Papamichos, Dimitrios Margaritis, Ioannis Kotsianidis

“…Till date whether human genome includes species-specific cancer-related genes that could potentially contribute to a higher cancer susceptibility remains obscure. …”
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Decoding TDP-43: the molecular chameleon of neurodegenerative diseases by Jixiang Zeng, Chunmei Luo, Yang Jiang, Tao Hu, Bixia Lin, Yuanfang Xie, Jiao Lan, Jifei Miao

“…Particular emphasis is placed on recent discoveries regarding TDP-43’s involvement in DNA interactions and chromatin dynamics, highlighting its broader impact on gene expression and genome stability. The review also examines the complex pathogenesis of TDP-43-related disorders, discussing the protein’s propensity for aggregation, its effects on mitochondrial function, and its non-cell autonomous impacts on glial cells. …”
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