Screening for transcriptomic associations with Swine Inflammation and Necrosis Syndrome by Katharina Gerhards, Sabrina Becker, Josef Kuehling, Mirjam Lechner, Hermann Willems, Robert Ringseis, Gerald Reiner

“…For this purpose, the three to five least affected (SINS-low) and most SINS affected (SINS-high) 3d-old piglets, each of three boars, a relatively SINS stable Duroc boar (DU), a relatively stable Pietrain boar (PI+) and a highly susceptible Pietrain boar (PI-) were selected from 27 litters of mixed semen to minimize environmental effects. Results A genome-wide expression experiment revealed a huge set of differentially expressed genes that are involved in vasculitis, inflammation and necrosis, keratinization and erythrocyte epitopes. …”
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Automation-aided construction and characterization of Bacillus subtilis PrsA strains for the secretion of amylases by Felix Hamburger, Niels Schlichting, Michael Eichenlaub, Paul Igor Costea, Christopher Sauer, Stefan Jenewein, Johannes Kabisch, Johannes Kabisch

“…To achieve this, six genome-reduced strains and nine PrsA proteins were systematically selected based on their cultivation performance and the production of two reference amylases. …”
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Gene Expression Profiling of IL-17A-Treated Synovial Fibroblasts from the Human Temporomandibular Joint by Toshio Hattori, Naomi Ogura, Miwa Akutsu, Mutsumi Kawashima, Suguru Watanabe, Ko Ito, Toshirou Kondoh

“…Here, we investigated the roles of IL-17A in temporomandibular joint disorders (TMD) using genome-wide analysis of synovial fibroblasts isolated from patients with TMD. …”
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Serine/threonine protein kinase mediates rifampicin resistance in Brucella melitensis through interacting with ribosomal protein RpsD and affecting antioxidant capacity by Yaqin Yuan, Wenqing Ning, Junjie Chen, Jiquan Li, Tianqi Xue, Cuihong An, Lingling Mao, Guangzhi Zhang, Shizhong Zhou, Jiabo Ding, Xiaowen Yang, Jianqiang Ye

“…., and the identified STPK or its pathway can serve as a potential target for new drug development against rifampicin-resistant Brucella spp.IMPORTANCENew rifampicin resistance gene in Brucella melitensis is identified via bioinformatics predictions and a whole-genome transposon mutant library, new mechanisms of rifampicin resistance in B. melitensis, and new function of serine/threonine protein kinase gene and its interaction proteins.…”
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The plant germplasm and herbarium (WIR) collections maintained at VIR as contributors to grape genetic diversity conservation, expansion and utilization by M. M. Agakhanov, L. V. Bagmet, N. G. Tikhonova, M. V. Erastenkova, E. N. Kislin, Yu. V. Ukhatova, E. K. Khlestkina

“…It is noted that a common practice at this stage is to knock out the genes responsible for grapevine susceptibility to diseases, whereas a more advantageous approach in the future will be to make targeted changes in the grape genome based on the knowledge of resistance genes in its wild relatives. …”
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Decoding the Methylation Patterns of ABC Transporters in Colorectal Cancer by Nurul Nabilah Norhisan, Rashidah Baharudin, Nurul Qistina Rus Bakarurraini, Nur Alyaa Afifah Md Shahri, Francis Yew Fu Tieng, Imilia Ismail, Muhammad-Redha Abdullah-Zawawi, Learn-Han Lee, Nurul Syakima Ab Mutalib

“…Survival analysis demonstrated the correlation between DNA methylation of individual CpG sites and patient survival probability in colon and rectal adenocarcinoma datasets from The Cancer Genome Atlas. The study provides insights into the epigenetic landscape of ABC genes in CRC, highlighting their potential roles in drug resistance, disease initiation, and progression. …”
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Sources and Transmission Routes of Carbapenem-Resistant <i>Pseudomonas aeruginosa</i>: Study Design and Methodology of the SAMPAN Study by Anneloes van Veen, Selvi N. Shahab, Amber Rijfkogel, Anne F. Voor in ’t holt, Corné H. W. Klaassen, Margreet C. Vos, Yulia Rosa Saharman, Anis Karuniawati, Silvia Zelli, Desy De Lorenzis, Giulia Menchinelli, Giulia De Angelis, Maurizio Sanguinetti, Merel Kemper, Anniek E. E. de Jong, Sima Mohammadi, Valentine Renaud, Irena Kukavica-Ibrulj, Marianne Potvin, Guillaume Q. Nguyen, Jeff Gauthier, Roger C. Levesque, Heike Schmitt, Juliëtte A. Severin

“…Additionally, samples will be taken twice from wet hospital environments and monthly from the hospitals’ (drinking) water system, hospital and municipal wastewater treatment plants, and receiving rivers. Whole-genome sequencing will be performed to characterize CRPA isolates and determine the genetic relatedness among the isolates from different reservoirs. …”
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Nuclear Protein 1 Expression Is Associated with PPARG in Bladder Transitional Cell Carcinoma by Chao Lu, Shenglin Gao, Li Zhang, Xiaokai Shi, Yin Chen, Shuzhang Wei, Li Zuo, Lifeng Zhang

“…However, the role of Nuclear protein 1 in bladder transitional cell carcinoma (BTCC) is still unclear. Methods. The Cancer Genome Atlas database and immunohistochemical analysis were adopted to evaluate Nuclear protein 1 expression in BTCC. …”
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Recent advances in genetics of aggressive behavior by J. D. Davydova, S. S. Litvinov, R. F. Enikeeva, S. B.  Malykh, E. K. Khusnutdinova

“…In addition, there is evidence that the hypothalamic-pituitary system genes (OXT, OXTR, AVPR1A, AVPR1B), the sex hormone receptors genes (ER1, AR), neurotrophin (BDNF) and neuronal apoptosis genes (CASP3, BAX) may also be involved in development of aggressive behavior. The results of Genome-Wide Association Studies (GWAS) have demonstrated that FYN, LRRTM4, NTM, CDH13, DYRK1A and other genes are involved in regulation of aggressive behavior. …”
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CLONING OF GENES ENCODING TRANSMEMBRANE PROTEINS AND PROTEINS RESPONSIBLE FOR AFRICAN SWINE FEVER VIRUS VIRULENCE by Ali Mazloum, N. G. Zinyakov, A. S. Igolkin, N. N. Vlasova

“…Proportion of cloned virus genes was 3.01% of Krasnodar 07/17 isolate genome, hence, total amount of the clone library has reached 7.82%.…”
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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 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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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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