Development of a latency model for HIV-1 subtype C and the impact of long terminal repeat element genetic variation on latency reversal by Shreyal Maikoo, Robert-Jan Palstra, Krista L. Dong, Tokameh Mahmoudi, Thumbi Ndung'u, Paradise Madlala

“…To address this scientific gap, we constructed a minimal genome retroviral vector expressing HIV-1C consensus transactivator of transcription protein (Tat) and green fluorescent protein (GFP) under the control of either HIV-1C consensus LTR (C731CC) or the transmitted/founder (T/F) LTRs derived from PLWH (CT/F731CC), produced corresponding LTR pseudotyped viruses using a vesicular stomatitis virus (VSV-G) pseudotyped Envelope vector and the pCMVΔR8.91 packaging vector containing HIV-1 accessory and rev genes. …”
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Comparative evaluation of various DNA extraction methods and analysis of DNA degradation levels in commercially marketed Chestnut rose juices and beverages by Yongchao Ren, Yunlong Ma, Yanqi Li, Yun Song, WeiWei Zhao, Xuncai Huang, Danmin Yu, Jian Li, Zuogang Xu, Wenjun Zhao

“…However, obtaining amplifiable genomic DNA in this process is a significant obstacle in gene studies. …”
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CASC8 activates the pentose phosphate pathway to inhibit disulfidptosis in pancreatic ductal adenocarcinoma though the c-Myc-GLUT1 axis by Hong-Fei Yao, Jieqiong Ge, Jiahao Chen, Xiaoyan Tang, Chunjing Li, Xiao Hu, Abousalam Abdoulkader Ahmed, Yunlong Pu, Guihua Zhou, Tongyi Zhang, Zhiwei Cai, Chongyi Jiang

“…CASC8 expression and its clinical correlations were analyzed using data from The Cancer Genome Atlas (TCGA) and further verified by chromogenic in situ hybridization assay in PDAC tissues. …”
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Characterization and fungicides sensitivity of Colletotrichum species causing Hydrangea macrophylla anthracnose in Beijing, China by Juan Zhao, Juan Zhao, Yanli Cheng, Yanli Cheng, Yayong Liu, Yayong Liu, Xiaojing Shi, Taotao Zhang, Taotao Zhang, Wentao Qin, Wentao Qin

“…Based on morphological characteristics and phylogenetic analysis of six genomic loci including rDNA-ITS, ACT, TUB2, CAL, CHS-1, and GAPDH, these isolates were identified as belonging to six Colletotrichum species. …”
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Toward autism spectrum disorders and Williams-Beuren syndrome co-occurrence condition in Tunisian patients: Genetic insights by Rim Khelifi, Afef Jelloul, Houda Ajmi, Wafa Slimani, Sarra Dimassi, Khouloud Rjiba, Manel Dardour, Moez Gribaa, Ali Saad, Soumaya Mougou-Zerelli

“…A comprehensive evaluation using karyotyping, fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (array-CGH) was performed.ResultsAll patients were clinically diagnosed and confirmed to have WBS through karyotyping and FISH analysis. …”
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A simple and efficient method to extract polar metabolites from guar leaves (Cyamopsis tetragonoloba (L.) Taub.) for GC-MS metabolome analysis by S. B. Teplyakova, A. L. Shavarda, T. V. Shelenga, E. A. Dzyubenko, E. K. Potokina

“…Due to the progress of “omics” technologies and the marker-assisted selection, there is a huge interest in the studies that compare the metabolites of various guar varieties, employing metabolomics as a method of functional genomics. For a large-scale screening of guar germplasm from the VIR collection, it is important to choose an efficient method to extract metabolites from samples. …”
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A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential by M. P. Ponomarenko, I. V. Chadaeva, P. M. Ponomarenko, A. G. Bogomolov, D. Yu. Oshchepkov, E. B. Sharypova, V. V. Suslov, A. V. Osadchuk, L. V. Osadchuk, Yu. G. Matushkin

“…To date, Belyaev’s discovery has already been repeatedly confirmed, for example, by independent observations during deer domestication, during the use of rats as laboratory animals, after the reintroduction of endangered species such as Przewalski’s horse, and during the creation of a Siberian reserve population of the Siberian grouse when it had reached an endangered status in natural habitats. A genome-wide comparison among humans, several domestic animals, and some of their wild congeners has given rise to the concept of self-domestication syndrome, which includes autism spectrum disorders. …”
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Identification of SETD4 as an Onco‐Immunological Biomarker Encompassing the Tumor Microenvironment, Prognoses, and Therapeutic Responses in Various Human Cancers by Yuyun Zhong, Ruiqi Wang, Zijie Huang, Zhaoting Hu, Bin Peng, Bin Chen, Liyue Sun

“…Methods Utilizing The Cancer Genome Atlas database, and other publicly accessible platforms, we comprehensively analyzed SETD4 gene expression, methylation patterns, and prognostic significance. …”
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SHP2 promotes the epithelial-mesenchymal transition in triple negative breast cancer cells by regulating β-catenin by Shihan Qian, Jingjing Zhu, Qing Han, Huang Cheng, Huaibin Zhou

“…Methods In this study, we conducted bioinformatics analysis of the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases to examine PTPN11 (encoding SHP2) expression levels and perform survival analysis in TNBC. …”
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The role of the KIBRA and APOE genes in developing spatial abilities in humans by A. V. Kazantseva, R. F. Enikeeva, Yu. D. Davydova, R. N. Mustafin, Z. R. Takhirova, S. B. Malykh, M. M. Lobaskova, T. N. Tikhomirova, E. K. Khusnutdinova

“…According to neurobiological hypotheses, individual differences in cognitive abilities may be attributed to the functioning of genes involved in the regulation of neurogenesis and synaptic plasticity. In addition, genome-wide association studies identified rs17070145 located in the KIBRA gene, which was associated with individual differences in episodic memory. …”
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Re-annotation of SARS-CoV-2 proteins using an HHpred-based approach opens new opportunities for a better understanding of this virus by Brézellec, Pierre

“…Since the publication of the genome of SARS-CoV-2 – the causative agent of COVID-19 – in January 2020, many bioinformatic tools have been applied to annotate its proteins. …”
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Minerals, Toxic Heavy Metals, and Antioxidant Properties of Honeys from Bangladesh by Sudip Paul, Md. Sakib Hossen, E. M. Tanvir, Rizwana Afroz, Delwar Hossen, Sagarika Das, Nikhil Chandra Bhoumik, Nurul Karim, Farha Matin Juliana, Siew Hua Gan, Md. Ibrahim Khalil

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UBE2J1 is identified as a novel plasma cell-related gene involved in the prognosis of high-grade serous ovarian cancer by Yunjie Tian, Ruoyu Dong, Yingxia Guan, Ying Wang, Wei Zhao, Jun Zhang, Shan Kang

“…The effects of immune cell markers on prognosis were analyzed via univariate Cox regression, least absolute shrinkage and selection operator (LASSO) and gene set variation analysis (GSVA) of bulk sequencing data from The Cancer Genome Atlas (TCGA)-HGSOC cohort. Finally, the effects of key markers on HGSOC cells were evaluated via Cell Counting Kit-8 (CCK-8), Transwell, colony formation, wound healing, immunofluorescence and in vivo tumor growth assays. …”
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Analysing DNA methylation and transcriptomic signatures to predict prostate cancer recurrence risk by Fahad M. Aldakheel, Hadeel Alnajran, Shatha A. Alduraywish, Ayesha Mateen, Mohammed S. Alqahtani, Rabbani Syed

“…This study employs a machine learning approach to identify DNA methylation and RNA expression biomarkers predictive of PCa recurrence using datasets from The Cancer Genome Atlas (TCGA). We analyzed 49,133 genes, identifying 684 differentially methylated genes (DMGs) and 691 differentially expressed genes (DEGs) between recurrence and non-recurrence groups. …”
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Causal Association Between Obstructive Sleep Apnea and Migraine: A Bidirectional Mendelian Randomization Study by Wang YP, Wei HX, Hu YY, Zhang C, Niu YM

“…Investigating the causation will assist in understanding the etiology of OSA and migraine.Methods: Bidirectional two-sample Mendelian randomization (MR) and multivariable MR (MVMR) approaches were carried out to investigate the causal link between OSA and migraine. The public genome-wide association study (GWAS) data for OSA, migraine, and subtypes were obtained from the IUE open GWAS project and the FinnGen consortium. …”
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Epigallocatechin gallate (EGCG) modulates senescent endothelial cell-monocyte communication in age-related vascular inflammation by Sarvatit Patel, Kai Ellis, Kai Ellis, Corey A. Scipione, Jason E. Fish, Jason E. Fish, Jason E. Fish, Jason E. Fish, Kathryn L. Howe, Kathryn L. Howe, Kathryn L. Howe, Kathryn L. Howe, Kathryn L. Howe

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Effect of trace elements and nutrients on 21 autoimmune diseases: a Mendelian randomization study by Ming-Jie Jia, Hua-Fang Yin, Ying-Chao Liang, Feng Jiang, Hui-Lin Li, Hui-Lin Li

“…However, whether there is a genetic causal effect between serum trace elements, nutrients, and autoimmune diseases remains unclear.ObjectiveThis study aims to investigate the causal effects of serum trace elements and nutrients on 21 autoimmune diseases using Mendelian randomization (MR).MethodsSingle nucleotide polymorphisms for the exposure factors (serum trace elements and vitamins) were obtained from the published UK Biobank database and genome-wide association study (GWAS) public databases. …”
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Nerve Enlargement in Patients with INF2 Variants Causing Peripheral Neuropathy and Focal Segmental Glomerulosclerosis by Quynh Tran Thuy Huong, Linh Tran Nguyen Truc, Hiroko Ueda, Kenji Fukui, Koichiro Higasa, Yoshinori Sato, Shinichi Takeda, Motoshi Hattori, Hiroyasu Tsukaguchi

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GnIH secreted by green light exposure, regulates bone mass through the activation of Gpr147 by Yu You, Konglin Huo, Liang He, Tongyue Wang, Lei Zhao, Rong Li, Xiaoqing Cheng, Xuebin Ma, Zhiying Yue, Stefan Siwko, Ning Wang, Lujian Liao, Mingyao Liu, Jian Luo

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Molecular cytogenetic characteristics of new spring bread wheat introgressive lines resistant to stem rust by O. A. Baranova, I. G. Adonina, S. N. Sibikeev

“…By cytogenetic analysis of these lines using fluorescent (FISH) and genomic (GISH) in situ hybridization, introgressions from Ae. speltoides (line L664), T. timopheevii (lines L758, L971, L995/1, L997 and L1110), Thinopyrum ponticum = Ag. elongatum (2n = 70) (L664, L758, L960, L971, L997 and L1110), as well as introgressions from T. dicoccum (L657 and L664), T. kiharae (L960) and S. cereale (L935 and L968) were detected. …”
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