Emerging Resistance and Virulence Patterns in <i>Salmonella enterica</i>: Insights into Silver Nanoparticles as an Antimicrobial Strategy by Irina Gheorghe-Barbu, Ilda Czobor Barbu, Rareș-Ionuț Dragomir, Ioana Cristina Marinaș, Miruna Silvia Stan, Radu Pericleanu, Andreea Ștefania Dumbravă, Liviu-Iulian Rotaru, Simona Paraschiv, Leontina Mirela Bănică, Ionuț Pecete, Dan Oțelea, Violeta Corina Cristea, Mircea Ioan Popa, Marilena Monica Țânțu, Marius Surleac

“…., <i>invA</i>, <i>spvC</i>, <i>pldA</i>, and <i>held</i>). Whole-genome sequencing (WGS) was performed on 19 selected isolates. …”
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Structural and functional features of phytoene synthase isoforms PSY1 and PSY2 in pepper Capsicum annuum L. cultivars by E. A. Dyachenko, M. A. Filyushin, G. I. Efremov, E. A. Dzhos, A. V. Shchennikova, E. Z. Kochieva

“…A key regulator of carotenoid biosynthesis is the phytoene synthase encoded by the PSY gene. The Capsicum annuum genome contains two isoforms of this enzyme, localized in leaf (PSY2) and fruit (PSY1) plastids. …”
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In silico analysis of hub genes and regulatory networks implicates the putamen in non-motor Parkinson’s disease disorders by Stephen Tunmise Akanbi, Joshua Ayodele Yusuf, Thompson Oluwaferanmi Ayandele, Dayo Samson Oladipupo, Darasimi Racheal Olorunlowu, Blessing Dorcas Olawuyi, Joshua Oluwafisayo Adepoju, Dolapo Emmanuel Opasina, Elizabeth Kehinde Opoola, Uchenna Victor Ugwuanyi, Olufunto Omodele Adeleye

“…Enrichment analysis of target genes was conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Also, we constructed transcription factor (TF)-hub gene expression networks, miRNA-hub gene expression networks, and disease hub gene association networks using the JASPAR database, Tarbase database, and DisGeNET via NetworkAnalyst platform, respectively. …”
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Proteomic analysis of spinal dorsal horn in prior exercise protection against neuropathic pain by Binglin Chen, Jiabao Guo, Chan Gong, Chenchen Zhu, Yang Wu, Shengbo Wang, Yili Zheng, Haixia Lu

“…Gene Ontology (GO) annotations, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein–protein interaction networks were employed to explore the biological importance of DEPs. …”
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Rumen DNA virome and its relationship with feed efficiency in dairy cows by Xiaohan Liu, Yifan Tang, Hongyi Chen, Jian-Xin Liu, Hui-Zeng Sun

“…Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. …”
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Expression of the NUP153 and YWHAB genes from their canonical promoters and alternative promoters of the LINE-1 retrotransposon in the placenta of the first trimester of pregnancy by V. V. Demeneva, E. N. Tolmacheva, T. V. Nikitina, E. A. Sazhenova, S. Yu. Yuriev, A. Sh. Makhmutkhodzhaev, A. S. Zuev, S. A. Filatova, A. E. Dmitriev, Ya. A. Darkova, L. P. Nazarenko, I. N. Lebedev, S. A. Vasilyev

“…The placenta has a unique hypomethylated genome. Due to this feature of the placenta, there is a potential possibility of using regulatory elements derived from retroviruses and retrotransposons, which are suppressed by DNA methylation in the adult body. …”
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Obstructive sleep apnea and structural and functional brain alterations: a brain-wide investigation from clinical association to genetic causality by Kang Wu, Qiming Gan, Yuhong Pi, Yanjuan Wu, Wenjin Zou, Xiaofen Su, Sun Zhang, Xinni Wang, Xinchun Li, Nuofu Zhang

“…Additionally, large-scale Mendelian randomization analyses were performed using genome-wide association study (GWAS) data on OSA and 3935 brain imaging-derived phenotypes (IDPs), assessed in up to 33,224 individuals between December 2023 and March 2024, to explore potential genetic causality between OSA and alterations in whole brain structure and function. …”
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Shaoyao Gancao decoction alleviates paclitaxel-induced cognitive impairment by activating PTEN/PI3K/AKT pathway to inhibit NETs formation by Xu Ying, Su Yue, Hu Yuwen, Li Xiang, Zhou Ziyan, Yuan Ningning, Ji Xiaowei, Jiang Ruoyu, Wang Wenzhu, Zhang Yafeng, Zhai Guojie, Cheng Xiaolan

“…Finally, Mendelian randomization was performed using genome-wide association analysis data of PTEN and cognitive disorders in OpenGWAS database. …”
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Methodological aspects in gastroenteric methane evaluation trial in water buffalo by Maria Chiara La Mantia, Emanuela Rossi, Francesco Cenci, David Meo Zilio, Roberto Steri, Miriam Iacurto, Antonella Chiariotti

“…It has been hypothesized that the host’s genome ultimately controls rumen microbial communities, but numerous samples are needed to achieve robust results. …”
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MTMR6 downregulation contributes to cisplatin resistance in oral squamous cell carcinoma by Kah Young Lee, Su Young Oh, Heon-Jin Lee, Tae-Geon Kwon, Jin-Wook Kim, Chang-Geol Shin, Su-Hyung Hong, So-Young Choi

“…A survival analysis based on The Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma (HNSCC) dataset was performed to evaluate the correlation between MTMR6 expression and patient outcomes following cisplatin treatment. …”
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Integrating single-cell RNA-Seq and bulk RNA-Seq data to explore the key role of fatty acid metabolism in hepatocellular carcinoma by Hua Dai, Xin Tao, Yuansen Shu, Fanrong Liu, Xiaoping Cheng, Xiushen Li, Bairui Shu, Hongcheng Luo, XuXiang Chen, Zhaorui Cheng

“…Data procurement encompassed transcriptomic and clinical datasets from HCC patients, sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) repositories. …”
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Detection of CRISPR‒Cas and type I R–M systems in Klebsiella pneumoniae of human and animal origins and their relationship to antibiotic resistance and virulence by Xue Li, Ling Wang, Jinghuan Lin, Yingjuan Gu, Zhihua Liu, Jing Hu

“…In this study, the whole genomes of 520 strains of K. pneumoniae from GenBank, including 325 from humans and 195 from animals, were collected for CRISPR‒Cas systems and type I R-M systems, virulence genes, antibiotic resistance genes, and multilocus sequence typing detection. …”
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NALCN expression is down-regulated and associated with immune infiltration in gastric cancer by Xuewei Li, Xuewei Li, Na Wu, Chen Wang, Beibei Pei, Xiaoyan Ma, Jun Xie, Jun Xie, Wenhui Yang

“…Data obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were utilized to investigate the correlation between NALCN expression and immune cell infiltration in GC. …”
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Identification of biomarkers for the diagnosis of type 2 diabetes mellitus with metabolic associated fatty liver disease by bioinformatics analysis and experimental validation by Guiling Wu, Guiling Wu, Sihui Wu, Sihui Wu, Tian Xiong, Tian Xiong, Tian Xiong, You Yao, You Yao, Yu Qiu, Yu Qiu, Yu Qiu, Liheng Meng, Cuihong Chen, Xi Yang, Xi Yang, Xi Yang, Xinghuan Liang, Yingfen Qin

“…We utilised protein–protein interactions (PPIs), Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes to identify T2DM-associated MAFLD genes and potential mechanisms. …”
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High-throughput methylation sequencing reveals novel biomarkers for the early detection of renal cell carcinoma by Wenhao Guo, Weiwu Chen, Jie Zhang, Mingzhe Li, Hongyuan Huang, Qian Wang, Xiaoyi Fei, Jian Huang, Tongning Zheng, Haobo Fan, Yunfei Wang, Hongcang Gu, Guoqing Ding, Yicheng Chen

“…Using a training set from The Cancer Genome Atlas (TCGA) dataset of 443 early-stage RCC tumors and matched normal tissues, we applied LASSO regression and identified 23 methylation signatures. …”
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Association between chronic obstructive pulmonary disease and osteoporosis: Mendelian randomization combined with bibliometric analysis by Fangjun Yang, Huaming Wang, Miaomiao Liu, Shengtai Pei, Xiaoming Qiu

“…These BMD measurements were derived primarily from a genome-wide association study (GWAS) and summary statistics from the International Genetic Factors Consortium for Osteoporosis (GEFOS). …”
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Identification of potential druggable targets for endometriosis through Mendelian randomization analysis by Peng Chen, Xin Wei, Xiao-Ke Li, Yi-Hang Zhou, Yi-Hang Zhou, Qi-Fang Liu, Ling Ou-Yang

“…This study aimed to identify both cerebrospinal fluid (CSF) and plasma protein markers as promising therapeutic targets for EM.MethodsWe utilized Mendelian randomization (MR) analysis to explore potential disease-causing proteins, utilizing genetic datasets from genome-wide association studies (GWAS) and protein quantitative trait loci (pQTL) analyses. …”
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EHMT2‐mediated R‐loop formation promotes the malignant progression of prostate cancer via activating Aurora B by Yuyang Zhang, Mingqin Su, Yiming Chen, Li Cui, Wei Xia, Renfang Xu, Dong Xue, Xiansheng Zhang, Xingliang Feng

“…Methods Bioinformatic analyses were conducted to identify genes overexpressed in PCa tissues using The Cancer Genome Atlas (TCGA) and GEO datasets. Western blotting and immunohistochemistry assays were applied to determine the expression levels of euchromatic histone lysine methyltransferase 2 (EHMT2), pT232‐Aurora B and Cullin 3 (CUL3). …”
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Exome sequencing reveals a rare damaging variant in GRIN2C in familial late-onset Alzheimer's disease by Elisa Rubino, Maria Italia, Elisa Giorgio, Silvia Boschi, Paola Dimartino, Tommaso Pippucci, Fausto Roveta, Clara Maria Cambria, Gabriella Elia, Andrea Marcinnò, Salvatore Gallone, Ekaterina Rogaeva, Flavia Antonucci, Alfredo Brusco, Fabrizio Gardoni, Innocenzo Rainero

“…Methods Affected and unaffected members from a Northern Italian family were included. Genomic DNA from family members was extracted and initially screened for pathogenic mutations in APP, PSEN1, and PSEN2, and screened for 77 genes associated with neurodegenerative conditions using NeuroX array assay. …”
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Radiogenomics and machine learning predict oncogenic signaling pathways in glioblastoma by Abdul Basit Ahanger, Syed Wajid Aalam, Tariq Ahmad Masoodi, Asma Shah, Meraj Alam Khan, Ajaz A. Bhat, Assif Assad, Muzafar Ahmad Macha, Muzafar Rasool Bhat

“…This research contributes to advancing precision medicine in GBM management, highlighting the importance of integrating radiomics with genomic data to understand tumor behavior and treatment response better.…”
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