Marek's disease virus-1 unique gene LORF1 is involved in viral replication and MDV-1/Md5-induced atrophy of the bursa of Fabricius. by Chenyi Bao, Jun Chu, Qi Gao, Shasha Yang, Xiaoyu Gao, Wenwen Chen, Fuchun Yang, Fei Jiang, Chenxi Tong, Mingyi Lei, Linlin Jiao, Jitong Li, Kexin Wei, Xue Lian, Kai Li, Suresh Kumar Tikoo, Nikolaus Osterrieder, Lorne A Babiuk, Yufeng Li, Yong-Sam Jung, Yingjuan Qian

“…To this end, an infectious bacterial artificial chromosome (BAC) harboring the complete genome of the MDV-1 very virulent strain Md5 was generated, and the rescued rMd5 maintained biological properties similar to the parental virus both in vitro and in vivo. …”
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Construction of an lncRNA-mediated ceRNA network to investigate the inflammatory regulatory mechanisms of ischemic stroke. by Meimei Xu, Shan Yuan, Xing Luo, Mengsi Xu, Guangze Hu, Zhe He, Xinyuan Yang, Rui Gao

“…Long non-coding RNAs (lncRNAs) are among the most abundant types of non-coding RNAs in the genome and exhibit particularly high expression levels in the brain, where they play crucial roles in various neurophysiological and neuropathological processes. …”
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Development of a 3-MicroRNA Signature and Nomogram for Predicting the Survival of Patients with Uveal Melanoma Based on TCGA and GEO Databases by Jun Zuo, Hongquan Ye, Jing Tang, Jianqun Lu, Qi Wan

“…Methods. miRNA and mRNA sequencing data for 80 UM patients were obtained from The Cancer Genome Atlas (TCGA) database. The patients were further randomly assigned to a training set (n = 40, used to identify key miRNAs) and a testing set (n = 40, used to internally verify the signature). …”
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Polymorphism of microsattelite loci within the grape germplasm collection maintained at the Dagestan Experiment Station of VIR by M. M. Agakhanov, V. A. Volkov, P. S. Ulianich, K. M. Abdullaev, E. N. Kislin

“…As for any other large germplasm collections, the problem of genetic identification of the accessions and their originality is critical for the ampelographical collection. Genome of Vitis vinifera L. contains many polymorphic microsatellite loci, their allele diversity could be used to reveal the genetic structure of the ex situ collection as well as for the identification of duplicates. …”
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Diversity of reverse-transcriptase-containing viruses through global metagenomics by Kaiyang Zheng, Yantao Liang, Yan Zhang, David Páez-Espino, Hongbing Shao, Yeong Yik Sung, Wen Jye Mok, Li Lian Wong, Shi Wang, Andrew McMinn, Min Wang

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Polymorphism of monogenic scab resistance loci in apple varieties by A. S. Lyzhin, N. N. Savel’eva

“…Biological material was represented by apple cultivars of different environmental and geographical origin. Total genomic DNA was extracted from fresh leaves using CTAB methods according to the DArT protocols. …”
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Machine learning-random forest model was used to construct gene signature associated with cuproptosis to predict the prognosis of gastric cancer by Xiaolong Liu, Pengxian Tao, He Su, Yulan Li

“…Transcriptome and clinical data of patients with GC were collected from The Cancer Genome Atlas and Gene Expression Omnibus datasets. …”
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The Studies of Chlorogenic Acid Antitumor Mechanism by Gene Chip Detection: The Immune Pathway Gene Expression by Tian Yi Kang, Hua Rong Yang, Jie Zhang, Dan Li, Jie Lin, Li Wang, XiaoPing Xu

“…Here, we have utilized a whole mouse genome oligo microarray (4*44K) to analyze gene expression level of female BALB/c mice (implanted with EMT-6 sarcoma cells) after treatment with low, medium, and high-dose CA (5 mg/kg, 10 mg/kg, and 20 mg/kg), docetaxel, interferon, and normal saline separately at 6 time points (3rd, 6th, 9th, 12th, 15th, and 18th days after administration). …”
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Evolutionary analysis of the DHHCs in Saccharinae by Hao Wen, Xinyu Liu, Xueting Zhao, Tingting Zhao, Cuilian Feng, Hailong Chang, Jungang Wang, Jishan Lin

“…Ka/Ks ratio analysis indicated that gene duplication in these species was primarily driven by whole-genome duplication (WGD) and dispersed duplication (DSD), with DHHC genes evolving under strong purifying selection. …”
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Potential biomarkers for predicting the risk of thyroid cancer in immunosenescence: a population-based and externally validated multi omics study by Qian Li, Yuanyuan Zhao, Jiawei Yan, Chao He

“…ObjectivesGenome-wide association studies (GWAS) have pinpointed several risk loci linked to thyroid cancer; however, the discovery of new plasma proteins implicated in immunosenescence continues to pose significant challenges. …”
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Uncovering the genetic basis of antiviral polyketide limocrocin biosynthesis through heterologous expression by Sofiia Melnyk, Marc Stierhof, Dmytro Bratiichuk, Franziska Fries, Rolf Müller, Yuriy Rebets, Andriy Luzhetskyy, Bohdan Ostash

“…No other natural products have been isolated from this bacterium so far, despite the presence of a rich repertoire of specialized metabolite biosynthesis gene clusters (smBGCs) within its genome. Heterologous expression of smBGCs in suitable chassis speeds up the discovery of the natural products hidden behind these sets of genes. …”
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Identification of DLEC1 D215N Somatic Mutation in Formalin Fixed Paraffin Embedded Melanoma and Melanocytic Nevi Specimens by Ricardo Vieira, Maria José Simões, Susana Carmona, Conceição Egas, Carlos Faro, Américo Figueiredo

“…DLEC1 D215N somatic mutation (COSM36702) was identified in a melanoma cell line through whole genome sequencing. However, little is known about the implication and prevalence of this mutation in primary melanomas or in melanocytic nevi. …”
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Using spectrometric analysis for indirect estimation of 146S component concentration while measuring FMDV RNA amount by M. I. Doronin, D. V. Mikhalishin, N. Ye. Kamalova, A. V. Borisov

“…As expected, no FMDV genome or 146S particles were detected in the negative control sample.…”
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Revealing systematic changes in the transcriptome during the transition from exponential growth to stationary phase by Hyun Gyu Lim, Ye Gao, Kevin Rychel, Cameron Lamoureux, Xuwen A. Lou, Bernhard O. Palsson

“…This study demonstrates how the combination of genome-scale datasets and new data analytics reveals the fundamental characteristics of a key transition in the life cycle of bacteria.IMPORTANCENutrient limitations are critical environmental perturbations in bacterial physiology. …”
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Associations between sleep traits and colorectal cancer: a mendelian randomization analysis by Xiangyue Meng, Enshuo Fan, Dan Lv, Yongjing Yang, Shixin Liu

“…Publicly accessible GWAS (Genome-Wide Association Study) data were used to identify these variants to investigate the putative causal relationships between sleep traits and CRC. …”
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The Mediation of Circulating Inflammatory Proteins in the Causal Pathway from Immune Cells to COPD by Yan K, Wang Y, Xin P

“…The objective of this study was to ascertain the causal relationship between immune cells and COPD and to quantify the potential role of circulating inflammatory proteins as mediators.Methods: A two-sample Mendelian randomisation analysis was conducted involving 731 immune cells, 91 inflammatory proteins and COPD, utilising summary-level data from genome-wide association studies. The causal relationships between immune cells, inflammatory proteins and COPD were sequentially analysed by multivariate Mendelian randomisation and validated using Bayesian weighted Mendelian randomisation. …”
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Molecular Assessment of Domain I of Apical Membrane Antigen I Gene in Plasmodium falciparum: Implications in Plasmodium Invasion, Taxonomy, Vaccine Development, and Drug Discovery by Che Roland Achungu, Damian Nota Anong, Robert Adamu Shey, Cevie Jesenta Tabe

“…The creation of a universal malaria vaccine based on the AMA1 antigen is challenging due to these knowledge limitations. This study used genome mining techniques to look for these particular short peptides in PfAMA1. …”
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Molecular complexity of quantitative immunity in plants: from QTL mapping to functional and systems biology by Chauveau, Carine, Roby, Dominique

“…First, from genetic analyses by QTL (Quantitative Trait Locus) mapping and GWAs (Genome Wide Association studies), the identification, cloning and functional analysis of this gene have been used as a starting point for the exploration of the multiple and coordinated pathways acting together to mount the QDR response dependent on RKS1. …”
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Isolation, characterization and therapeutic efficacy of lytic bacteriophage ZK22 against Salmonella Typhimurium in mice by Yihong Sun, Qing Qu, Yanhua Huang, Shuo Zhou, Hua Xiang, Wei Wang

“…It exhibited favorable capability against 20 strains of S. Typhimurium. The genome of ZK22 consisted of a double-stranded DNA with a total length of 47,066 base pairs and a GC content of 45.71%. …”
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NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface by Andrea Conte, Nicola Gulmini, Francesco Costa, Matteo Cartura, Felix Bröhl, Francesco Patanè, Francesco Filippini

“…Abstract Background Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. …”
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