Borrelia burgdorferi tolerates alteration to P66 porin function in a murine infectivity model by Christa H. Fierros, Marie-Line Faucillion, Beth L. Hahn, Phillip Anderson, Mari Bonde, Julie R. Kessler, Matthew C. Surdel, Kyler S. Crawford, Yan Gao, Jieqing Zhu, Jieqing Zhu, Sven Bergström, Jenifer Coburn, Jenifer Coburn

“…Interestingly, four isolates that were recovered for p66 sequencing from mouse tissues revealed novel secondary point mutations in genomic p66. However, these secondary mutations did not rescue P66 porin function. …”
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Matrix Metalloproteinase-9 is associated with tumor microenvironment remodeling of bladder cancer by Fang Fang, Tiange Wu, Mengxue Wang, Wenchao Li, Zonghao You, Ming Chen, Han Guan

“…We utilized these two algorithms to analyze the immune components of 433 bladder cancer cases from The Cancer Genome Atlas database, aiming to compensate for the current lack of large-sample single-cell information. …”
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Antioxidant and cytotoxic potentials of Streptomyces gilvigriseus MUSC 26T isolated from mangrove soil in Malaysia by Hooi-Leng Ser, Wai-Fong Yin, Kok-Gan Chan, Tahir Mehmood Khan, Bey-Hing Goh, Learn-Han Lee

“…By the same token, the availability of its genome sequence allows further investigation into the biosynthetic gene clusters responsible for the production of these compounds which could essentially accelerate its development as chemopreventive drug(s).…”
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Applying the Concept of Peptide Uniqueness to Anti-Polio Vaccination by Darja Kanduc, Candida Fasano, Giovanni Capone, Antonella Pesce Delfino, Michele Calabrò, Lorenzo Polimeno

“…To design peptide-based anti-polio vaccines exempt from potential cross-reactivity risks and possibly able to reduce rare potential adverse events such as the postvaccine paralytic poliomyelitis due to the tendency of the poliovirus genome to mutate. Methods. Proteins from poliovirus type 1, strain Mahoney, were analyzed for amino acid sequence identity to the human proteome at the pentapeptide level, searching for sequences that (1) have zero percent of identity to human proteins, (2) are potentially endowed with an immunologic potential, and (3) are highly conserved among poliovirus strains. …”
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A Comprehensive Methodological Review of Major Developments in Bioinformatics Pipelines for Transcriptomic Data Analysis by Awais ALi, Syed Luqman Ali, Abdelkarem Omneya

“…Materials and Methods: This review highlights recent software and database improvements for processing RNA-Seq data, including steps like matching sequences to the genome, reconstructing RNA molecules, and measuring RNA abundance. …”
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GAMG alleviates liver fibrosis through inducing ferroptosis in inflammatory macrophages via the IRF1/SLC7A11 signaling pathway by Qing Pang, Shuai Zhou, Yong Wang, Hongtao Pan, Zhixin Wang, Xilaing Qin, Chao Zhu, Shilei Chen, Huichun Liu, Xiaosi Hu, Hao Jin

“…Single-cell RNA sequencing revealed that GAMG significantly affected the changes of macrophage subsets in LF, and Funrich analysis identified IRF1 as a key transcription factor regulating the macrophage genome. IRF1 was significantly increased while ferroptosis related SLC7A11 was significantly down-regulated in GAMG treated inflammatory macrophages. …”
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A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain by Pere Gelabert, Victoria Oberreiter, Lawrence Guy Straus, Manuel Ramón González Morales, Susanna Sawyer, Ana B. Marín-Arroyo, Jeanne Marie Geiling, Florian Exler, Florian Brueck, Stefan Franz, Fernanda Tenorio Cano, Sophie Szedlacsek, Evelyn Zelger, Michelle Hämmerle, Brina Zagorc, Alejandro Llanos-Lizcano, Olivia Cheronet, José-Miguel Tejero, Thomas Rattei, Stephan M. Kraemer, Ron Pinhasi

“…Additionally, we provide phylogenetic analyses on 70 sedaDNA mtDNA genomes of fauna including the densest Iberian Pleistocene sampling of C. lupus. …”
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Peripheral Blood DNA Methylation Changes in Response to <i>Centella asiatica</i> Treatment in Aged Mice by Olivia Monestime, Brett A. Davis, Cora Layman, Kandace J. Wheeler, Wyatt Hack, Jonathan A. Zweig, Amala Soumyanath, Lucia Carbone, Nora E. Gray

“…Reduced representation bisulfite sequencing (RRBS) was used to identify genome-wide differential methylation in the blood of CAW-treated aged mice compared to vehicle-treated aged mice. …”
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Comprehensive analysis reveals the tumor suppressor role of macrophage signature gene FCER1G in hepatocellular carcinoma by Deyu Kong, Yiping Zhang, Linxin Jiang, Nana Long, Chengcheng Wang, Min Qiu

“…This study utilized single-cell RNA sequencing and genomic analysis to explore the characteristic genes of macrophages in HCC and their impact on patient prognosis. …”
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Post-mortem and histological lesions in the European minks (Mustela lutreola) induced by spontaneous infection with coronavirus SARS-CoV-2 by I. A. Subbotina, I. N. Gromov

“…Profound and detailed studies of the virus circulation in the European mink population and the clinical manifestations of the disease, comprehensive approaches to the disease diagnosis, including epidemiological studies, clinical and post-mortem examinations, molecular genetic laboratory diagnostics (polymerase chain reaction and full-genome sequencing) contributed to better understanding of the disease features. …”
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Brain gliomas new transcriptomic discoveries from differentially expressed genes to therapeutic targets by Shiwen Pei, Zhiquan Jiang, Hongwei Cheng

“…Gene set enrichment analysis and immunocytometric analysis further explored the biological functions and pathways of identified genes, which were validated using The Cancer Genome Atlas and Genotype-Tissue Expression datasets. …”
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A Novel 8-Gene Prognostic Signature for Survival Prediction of Uveal Melanoma by Zhongjun Tang, Kebo Cai

“…In the validation phase, the signature was validated in The Cancer Genome Atlas database. Results. Forty-one genes were identified as hub genes of metastasis by WGCNA. …”
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Liquid Chromatography-Mass Spectrometry-Based Untargeted Metabolomics Analysis of Differential Metabolites in Three Types of Boza Made from Different Raw Materials by WANG Qi, GAO Yan, XUE Juanjuan, ZENG Jun, HUO Xiangdong, ZHAO Zhongkai

“…According to Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway enrichment analysis, these differential metabolites mainly participated in the biosynthesis of various secondary metabolites in plants, the biosynthesis of phenylpropanoids, the biosynthesis and degradation of flavonoids, and other metabolic pathways. …”
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Characterization of tumor evolution by functional clonality and phylogenetics in hepatocellular carcinoma by Zeynep Kacar, Eric Slud, Doron Levy, Julián Candia, Anuradha Budhu, Marshonna Forgues, Xiaolin Wu, Arati Raziuddin, Bao Tran, Jyoti Shetty, Yotsawat Pomyen, Jittiporn Chaisaingmongkol, Siritida Rabibhadana, Benjarath Pupacdi, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Chirayu Auewarakul, Suleeporn Sangrajrang, Chulabhorn Mahidol, Mathuros Ruchirawat, Xin Wei Wang

“…Furthermore, we observe significant B cell enrichment in linear trees compared to non-linear trees suggesting the need for further research to uncover potential variations in immune cell types within genomically determined phylogeny types. These results hint at the possibility that tumor cells and their microenvironment may collectively influence the tumor evolution process.…”
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The association between type 2 diabetes and asthma incidence: a longitudinal analysis considering genetic susceptibility by Fei Chen, Ying Yang, Liping Yu, Lulu Song, Cong Zhang, Yifan He, Lili Wu, Wanlu Ma, Bo Zhang

“…A polygenic risk score (PRS) for asthma was derived from genome-wide association studies summary. Cox regression models were used to assess the association between T2D and asthma, incorporating the asthma PRS. …”
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<i>Thermithiobacillus plumbiphilus</i> AAFK—Arsenic-Resistant Bacteria Isolated from Arsenopyrite Material by Artem Shaikin, Anton Zvonarev, Mikhail Vainshtein, Tatiana Abashina

“…The first description of complete genome for the species <i>T. plumbiphilus</i> was also carried out and discovered genes providing the As resistance. …”
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A cross-tissue transcriptome-wide association study identified susceptibility genes for age-related macular degeneration by Hongfan Yang, Haofei Huang, Kunlin Pu

“…Multi-marker Analysis of Genomic Annotation (MAGMA) was employed to validate results and identify reliable susceptibility genes, followed by summary data-based Mendelian randomization (SMR) and colocalization analyses to explore causal associations. …”
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Nuclear Position and Shape Deformation of Chromosome 8 Territories in Pancreatic Ductal Adenocarcinoma by Sylvia Timme, Eberhard Schmitt, Stefan Stein, Jutta Schwarz-Finsterle, Jenny Wagner, Axel Walch, Martin Werner, Michael Hausmann, Thorsten Wiech

“…This decreased roundness of CTs may reflect the genomic and transcriptional alterations in carcinoma.…”
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Association between Genetic Instability and Helicobacter pylori Infection in Gastric Epithelial Dysplasia by Jin Su Kim, Woo Chul Chung, Kang-Moon Lee, Chang Nyol Paik, Kyeong Soo Lee, Hye Ji Kim, Young Wook Kim, Ji Han Jung, Seung June Noh, Yun Kyung Lee

“…In gastric carcinogenesis, changes of DNA methylation appear to be an early molecular event, and the genome-wide methylation state is closely correlated with the level of long interspersed nucleotide element-1 (LINE-1) methylation. …”
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Nonylphenol promotes epithelial-mesenchymal transition in colorectal cancer cells by upregulating miR-151a-3p by Biao Wang, Nianjie Zhang, Lin Dai, Yuanwei Zhang, Shuo Yin, Xuefeng Yang

“…Analysis of The Cancer Genome Atlas (TCGA) data revealed increased expression levels of miR-151a-3p in CRC tissues. …”
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