Decoding gene expression dynamics in planktonic and biofilm cells of Streptococcus mutans: regulation and role of mutanofactin genes in biofilm formation by Muhammad Afzal, Miguel Carda-Diéguez, Susanne Bloch, Susanne Bloch, Leon G. S. Thies, Alex Mira, Christina Schäffer

“…MufC, a transcriptional regulator of the TetR/AcrR-family, acts as a positive regulator of the muf operon in strain NMT4863. Bioinformatic analysis pinpointed a 20-bp regulatory sequence in the muf operon promoter region (5′-AAATGAGCTATAATTCATTT-3′). …”
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To Develop Biomarkers for Diabetic Nephropathy Based on Genes Related to Fibrosis and Propionate Metabolism and Their Functional Validation by Sha Li, Jingshan Chen, Wenjing Zhou, Yonglan Liu, Di Zhang, Qian Yang, Yuerong Feng, Chunli Cha, Li Li, Guoyong He, Jun Li

“…The drug–gene network contained UROKINASE–PLG, ATENOLOL–AGT, and other interaction relationship pairs. Via bioinformatic analyses, the risk of fibrosis and propionate metabolism-related biomarkers in DN were explored, thereby providing novel ideas for research related to DN diagnosis and treatment.…”
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Long-term effects of linear versus macrocyclic GBCAs on gene expression in the central nervous system of mice by Chuanbing Wang, Yuxia Tang, Jiajia Tang, Jie Zhang, Siqi Wang, Feiyun Wu, Shouju Wang

“…Ribonucleic acid (RNA) sequencing and bioinformatic analyses identified differentially expressed genes (DEGs), with validation by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blot (WB). …”
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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

“…Consequently, understanding how tumours adapt to CIN is critical for identifying novel therapeutic targets. Methods Bioinformatic analyses were conducted to identify genes overexpressed in PCa tissues using The Cancer Genome Atlas (TCGA) and GEO datasets. …”
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Elucidating the pharmacological foundations and mechanisms of the Sihai Shuyu formula in treating Graves’ disease through integrated serum metabolomics and network pharmacology wit... by Xiaoju Liu, Xingjia Li, Wenbin Huang, Yifan Cui, Fengyun Cheng, Guofang Chen, Guofang Chen, Xiaodong Mao, Chao Liu, Chao Liu, Shuhang Xu

“…A comprehensive analysis of the multi-level bioinformatic analysis, including protein-protein interactions (PPI) and functional pathways of the targets, was conducted, followed by verification through immunohistochemistry (IHC) to clarify SHSY’s pharmacological basis and action mechanisms in treating GD.ResultsAfter 8 weeks of treatment, SHSY significantly reduced serum T4 and TRAb levels in GD mice and enhanced the morphology of thyroid tissues. …”
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Celastrol promotes DNA damage and apoptosis in uterine corpus endometrial carcinoma via promotion of KAT2B-mediated RBPJ acetylation and repression of MCM4 transcription by Lipeng Pei, Yan Zhu, Wenpeng Li, Bin Xu, Jingli Sun

“…We determined tumor growth in xenograft nude mice. Bioinformatic analysis, protein coimmunoprecipitation (Co-IP), luciferase assay, cell experiments were performed to reveal the relationship of Celastrol/KAT2B/RBPJ/MCM4 in UCEC. …”
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Nisin A-producing Lactococcus cremoris formulations for pre- and post-milking teat disinfection modulate the bovine milk microbiota by Alessandra Gazzola, Camilla Ceccarani, Bianca Castiglioni, Filippo Biscarini, Stefano Morandi, Tiziana Silvetti, Renata Piccinini, Milena Brasca, Paola Cremonesi

“…Microbial communities were investigated by cultural and sequence-based methods, and analyzed through bioinformatic and statistical approaches. Results Clear differences in bacterial community composition were observed among groups, with higher species richness in TR, especially of Staphylococcus, Enterococcus, Lactococcus, and Streptococcus genera. …”
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RETRACTED ARTICLE: Bone mesenchymal stem cell-derived exosomal microRNA-7-5p inhibits progression of acute myeloid leukemia by targeting OSBPL11 by Duanfeng Jiang, Xin Wu, Xiaoying Sun, Wei Tan, Xin Dai, Youbang Xie, Ashuai Du, Qiangqiang Zhao

“…Methods Dysregulated miR-7-5p in AML patients was identified using qRT-PCR and its clinical significance was explored. Bioinformatic analysis revealed the target gene OSBPL11 that could be regulated by miR-7-5p. …”
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Circ_0001084/miR-181c-5p/PTPN4 Axis Mitigates Cardiomyocyte Injury by Modulating the TLR4/NF-κB Pathway: Insights into Therapeutic Potential for Myocardial Reperfusion Injury by Deng H, Fan Q, Huang L, Ouyang W, Zhu W

“…Non-coding RNAs, including miRNAs, have been increasingly recognized for their roles in regulating cardiomyocyte responses to hypoxia/reoxygenation (H/R) injury. miR-181c-5p, in particular, has been implicated in inflammatory and apoptotic processes, suggesting its potential involvement in exacerbating cellular damage.Methods: This study combined bioinformatic and experimental techniques to investigate myocardial injury. …”
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Genomic characteristics and molecular epidemiology of MRSA from medical centers in Mexico: Results from the Invifar network. by Gabriela Echaniz-Avilés, Luis Ángel Núñez-García, Eduardo Rodríguez-Noriega, Consuelo Velázquez-Acosta, Luis Esaú López-Jácome, Eduardo López-Gutiérrez, Talia Pérez-Vicelis, Cristina Torres-Báez, Ulises Garza-Ramos, Nadia Rodríguez-Medina, Juan Manuel Barajas-Magallón, Rosario Vázquez-Larios, Aldo Rafael Silva-Gamiño, Rafael Franco-Cendejas, Adolfo Gómez-Quiroz, Elvira Garza-González

“…In addition, WGS was performed using a NovaSeq platform, and a bioinformatic analysis was conducted using several tools.…”
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Evolutionary and functional divergence of Sfx, a plasmid-encoded H-NS homolog, underlies the regulation of IncX plasmid conjugation by Avril Wang, Martha Cordova, William Wiley Navarre

“…The negative regulation of F-plasmid conjugation is partially mediated by the chromosomal nucleoid-structuring protein (H-NS). Recent bioinformatic analyses have revealed that plasmid-encoded H-NS homologs are widespread and exhibit high sequence diversity. …”
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Developing a risk score using liquid biopsy biomarkers for selecting Immunotherapy responders and stratifying disease progression risk in metastatic melanoma patients by Amalia Azzariti, Simona De Summa, Tommaso M. Marvulli, Ivana De Risi, Giuseppe De Palma, Roberta Di Fonte, Rossella Fasano, Simona Serratì, Sabino Strippoli, Letizia Porcelli, Michele Guida

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Predicting Treatment Outcomes in Patients with Low Back Pain Using Gene Signature-Based Machine Learning Models by Youzhi Lian, Yinyu Shi, Haibin Shang, Hongsheng Zhan

“…Differentially expressed genes (DEGs) between the two groups were identified through bioinformatic analysis. Key genes were selected using five machine learning models, including Lasso, Elastic Net, Random Forest, SVM, and GBM. …”
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CCR7 and CD48 as Predicted Targets in Acute Rejection Related to M1 Macrophage after Pediatric Kidney Transplantation by Jie Zhang, Jun Pei, Chengjun Yu, Jin Luo, Yifan Hong, Yi Hua, Guanghui Wei

“…Through a comprehensive bioinformatic analysis, our findings may provide predictive and therapeutic targets for AR after KT.…”
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Genomic detection of Panton-Valentine Leucocidins encoding genes, virulence factors and distribution of antiseptic resistance determinants among Methicillin-resistant S. aureus iso... by Masoud A. Juma, Tolbert Sonda, Boaz Wadugu, Davis Kuchaka, Mariana Shayo, Petro Paulo, Patrick Kimu, Livin E. Kanje, Melkiory Beti, Marco Van Zwetselaar, Blandina Mmbaga, Happiness Kumburu

“…Bacterial analysis was carried out using classical microbiological techniques and whole genome sequencing (WGS) using the Illumina Nextseq 550 sequencer platform. Several bioinformatic tools were used, KmerFinder 3.2 was used for species identification, MLST 2.0 tool was used for Multilocus Sequence Typing and SCCmecFinder 1.2 was used for SCCmec typing. …”
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Differentiation status determines the effects of IFNγ on the expression of PD-L1 and immunomodulatory genes in melanoma by Teitur Sævarsson, Adrián López García de Lomana, Ólafur Sánchez, Veerle van Esch, Gunnar Bjarni Ragnarsson, Siggeir Fannar Brynjólfsson, Eiríkur Steingrímsson, Berglind Ósk Einarsdóttir

“…The effects of inhibitor treatments and siRNA mediated knockdowns were evaluated via qPCR and western blotting. Bioinformatic analysis of publicly available RNA sequencing data, consisting of 45 patient derived melanoma cell lines, with or without IFNγ treatment, was conducted to assess the generalizability of the in vitro results. …”
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Genome analysis of colistin-resistant Salmonella isolates from human sources in Guizhou of southwestern China, 2019–2023 by Jingtong Wu, Yongxian Wen, Lv You, Xiaoyu Wei, Xiaoyu Wei, Junhua Wang, Ge Zhu, Shijun Li

“…To further evaluate the molecular epidemiology, the CL-R Salmonella isolates underwent whole-genome sequencing (WGS) analysis followed by bioinformatic analysis.ResultsA total of 43 CL-R isolates (4.6%) were identified from 933 Salmonella isolates, of which 39 isolates being MDR (resistance to three or more classes of antimicrobials). …”
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LncRNA LUCAT1 offers protection against human coronary artery endothelial cellular oxidative stress injury through modulating hsa-miR-6776-5p/LRRC25 axis and activating autophagy f... by Yanjun Wang, Xin Zhang, Mengmeng Ren, Shu He, Hengjie Bie, Mengyang Duan, Zhiyuan Chen, Qiaowei Jia, Boyu Chi, Xiongkang Gan, Chengcheng Li, Yahong Fu, Hanxiao Zhou, Sheng Zhang, Qian Zhang, Fenghui An, Xiumei Chen, Enzhi Jia

“…Results (1) The expression of LC3, Beclin1, ATG5, and ATG7 demonstrated a consistent decline whereas p62 expression exhibited an opposite increase as atherosclerosis progressed; (2) Autophagy levels was significantly elevated in HCAECs under oxidative stress, while inhibition of the initial stage of autophagy with 3-MA exacerbated cellular damage; (3) The lncRNA LUCAT1/hsa-miR-6776-5p/LRRC25 axis was established through bioinformatic prediction and validated by dual-luciferase reporter assay, which resulted in a significant decrease in autophagy levels in HCAECs; (4) In total, p62, ATG7, lncRNA LUCAT1 and LRRC25 were validated as robust diagnostic biomarkers for CAD. …”
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VACCIMEL, an allogeneic melanoma vaccine, efficiently triggers T cell immune responses against neoantigens and alloantigens, as well as against tumor-associated antigens by Ibel Carri, Ibel Carri, Erika Schwab, Juan Carlos Trivino, Erika M. von Euw, Morten Nielsen, Morten Nielsen, José Mordoh, María Marcela Barrio

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Intervening Non-Small-Cell Lung Cancer Progression by Cell Membrane Coated Platycodin D via Regulating Hsa-miR-1246/FUT9/GSK3β Pathway by Zheng S, Xie Z, Zhou Z, Wang S, Xin Y, Lin J, Cheng K, Lu T, Qi R, Guo Y

“…Predicted miRNA targets were validated via dual-luciferase reporter assays and Western blotting following bioinformatic prediction. PD’s metastatic inhibitory potential in NSCLC was evaluated in an in vivo lung cancer metastasis model. …”
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