Comparative analysis of the DNA isolated from thyme leaves using different methods by I. V. Bulavin, O. A. Grebennikova, V. A. Brailko, S. A. Feskov, I. V. Mitrofanova

“…Among the tested kits and methods, CTAB + 2% PVP provided thyme DNA suitable for PCR and, presumably, for genome library preparation. The low cost of reagents for this technique makes it applicable for future mass analysis of plant material.…”
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Drug Efficacy Recommendation System of Glioblastoma (GBM) Using Deep Learning by Sajid Naveed, Mujtaba Husnain, Ali Samad, Amna Ikram, Hina Afreen, Ghulam Gilanie, Najah Alsubaie

“…Therefore, drug efficacy recommendation systems are very useful in the treatment of various types of cancers. The Genomics of Drug Sensitivity in Cancer (GDSC) database was used as the primary data source, containing 135,242 cell line-drug interactions, inhibitory concentration of cancer drug for more than 800 cancer cell lines. …”
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mRNA technology as one of the promising platforms for the SARS-CoV-2 vaccine development by A. A. Ilyichev, L. A. Orlova, S. V. Sharabrin, L. I. Karpenko

“…After the genome sequence of SARS-CoV-2 (Severe acute respiratory syndrome-related coronavirus 2) was published and the number of infected people began to increase rapidly, many global companies began to develop a vaccine. …”
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Newly identified single-nucleotide polymorphism associated with the transition from nonalcoholic fatty liver disease to liver fibrosis: results from a nested case-control study in... by Yitong Ling, Yu Xuan Yang, Yan Chun Chen, Jing Hao Wang, Dong Ge Feng, Shi Jian Xiang, Xiaoyu Zhang, Jun Lyu, Sha Sha Li

“…To quantify gene expression, we used real-time PCR with fluorescence detection.Results The study analyzed data from 5467 participants (1094 cases and 4373 controls). Genome-wide association analysis identified nine significant loci, including the novel rs2073080 variant, strongly associated with NAFLD-associated hepatic fibrosis. …”
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Enzymes enabling the biosynthesis of various C20 polyunsaturated fatty acids in a sea urchin Hemicentrotus pulcherrimus by Yingying Peng, Yutaka Haga, Naoki Kabeya

“…Specifically, 3 fatty acid desaturases (FadsA, FadsC1 and FadsC2) and 13 elongation of very-long-chain fatty acids proteins (Elovl-like, Elovl1/7-like, Elovl2/5-like, Elovl4-like, Elovl8-like and Elovl6-like A–H) were identified in their genome and transcriptomes. Functional analysis showed that FadsA and FadsC2 function as a Δ5 desaturase and a Δ8 desaturase, respectively, enabling the conversion of 18:2n-6 and 18:3n-3 into ARA and EPA, respectively, along with Elovl, particularly Elovl6-like C. …”
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Activin levels correlate with lymphocytic infiltration in epithelial ovarian cancer by Elizabeth T. Evans, Emily F. Page, Alex Seok Choi, Zainab Shonibare, Andrea G. Kahn, Rebecca C. Arend, Karthikeyan Mythreye

“…Immune gene expression profile was further explored within the TCGA‐OV cohort derived from The Cancer Genome Atlas (TCGA). Immunohistochemical analysis was performed to evaluate activin A and T‐cell markers CD8 and FoxP3 at the protein level. …”
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Characterization of the First Marine Pestivirus, Phocoena Pestivirus (PhoPeV) by Lars Söder, Denise Meyer, Olaf Isken, Norbert Tautz, Matthias König, Alexander Postel, Paul Becher

“…No degradation of IRF3 and an increased expression of the type 1 interferon-stimulated antiviral protein Mx1 was observed in porcine cells infected with PhoPeV whose genome lacks the N^pro encoding region. …”
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Clinical Utility of Combined Tissue and Plasma Next-Generation Sequencing in Patients With Advanced, Treatment-Naïve NSCLC by Helena Bote-de Cabo, MD, Marco Siringo, MD, Esther Conde, MD, PhD, Susana Hernández, PhD, Fernando López-Ríos, MD, PhD, Alicia Castelo-Loureiro, MD, Esther García-Lorenzo, MD, Javier Baena, MD-PhD, Mercedes Herrera, MD, Ana Belén Enguita, MD, Yolanda Ruano, PhD, Jon Zugazagoitia, MD, PhD, Luis Paz-Ares, MD, PhD

“…Methods: We retrospectively collected clinical and genomic data from 275 patients with treatment-naïve advanced NSCLC who had undergone plasma-based NGS at diagnosis in our institution. …”
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Whole blood transcriptome profiles of trypanotolerant and trypanosusceptible cattle highlight a differential modulation of metabolism and immune response during infection by Trypan... by Peylhard, Moana, Berthier, David, Dayo, Guiguigbaza-Kossigan, Chantal, Isabelle, Sylla, Souleymane, Nidelet, Sabine, Dubois, Emeric, Martin, Guillaume, Sempéré, Guilhem, Flori, Laurence, Thévenon, Sophie

“…To this end, whole blood genome-wide transcriptome of three trypanotolerant taurine breeds (N’Dama, Lagune and Baoulé), one susceptible zebu (Zebu Fulani) and one African taurine x zebu admixed breed (Borgou) were profiled by RNA sequencing at four time points, one before and three during infection. …”
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Revisiting ABC Transporters and Their Clinical Significance in Glioblastoma by Brandon Wee Siang Phon, Shalini Sundramurthi Chelliah, Dina El-Rabie Osman, Saatheeyavaane Bhuvanendran, Ammu Kutty Radhakrishnan, Muhamad Noor Alfarizal Kamarudin

“…Using the datasets in The Cancer Genome Atlas and Gene Expression Omnibus, we found upregulated ABC transporters that either negatively impacted survival in univariate analyses (ABCA1, ABCA13, ABCB9, ABCD4) or were independent negative prognosis factors for patients with GBM (ABCA13, ABCB9). …”
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Exercise-induced methylation of the Serhl2 promoter and implication for lipid metabolism in rat skeletal muscle by Mutsumi Katayama, Kazuhiro Nomura, Jonathan M. Mudry, Alexander V. Chibalin, Anna Krook, Juleen R. Zierath

“…To determine the skeletal muscle DNA methylation signature of endurance swim training, we used whole-genome methylated DNA immunoprecipitation (MeDIP) sequencing. …”
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Сandidate SNP-markers of rheumatoid arthritis that can significantly alter the affinity of the TATA-binding protein for human gene promoters by I. V. Chadaeva, D. A. Rasskazov, E. B. Sharypova, I. A. Drachkova, E. A. Oshchepkova, L. K. Savinkova, P. M. Ponomarenko, M. P. Ponomarenko, N. A. Kolchanov, V. A. Kozlov

“…That is why, RA fits the main idea of postgenomic predictive-preventive personalized medicine that is to give a chance to those who would like to reduce his/her risk of diseases by bringing his/her conditions and lifestyle in line with the data on his/her genome sequenced. This is very important, since doctors consider RA as one of the most frequent causes of disability. …”
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Innovative applications and future trends of multiparametric PET in the assessment of immunotherapy efficacy by Tingting Qiao, Tingting Qiao, Zhaoping Cheng, Yanhua Duan

“…The integration of multi-omics data (including genomics and proteomics) with PET imaging enhanced the sensitivity and accuracy of efficacy prediction. …”
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A DNA-Methylated Sight on Autoimmune Inflammation Network across RA, pSS, and SLE by Xingqiang Wang, Dongyun Lei, Jie Ding, Shuang Liu, Li Tao, Fan Zhang, Jiangyun Peng, Jian Xu

“…In this study, we integrated 5 Cytokine-Chips from genome-wide DNA methylation datasets of the 3 kind of AIDs, delta-beta value was calculated for intergroup difference, and comprehensive bioinformatics analyses of cytokine genes with aberrant methylations were performed. 125 shared differential methylation variabilities (DMVs) were identified. …”
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Tumour DNA methylation markers associated with breast cancer survival: a replication study by Elaheh Zarean, Shuai Li, Ee Ming Wong, Enes Makalic, Roger L. Milne, Graham G. Giles, Catriona McLean, Melissa C. Southey, Pierre-Antoine Dugué

“…Candidate methylation sites (N = 22) and signatures (N = 3) potentially associated with breast cancer survival were identified from five prior studies that used The Cancer Genome Atlas (TCGA) methylation dataset, which shares key characteristics with the MCCS: comparable sample size, tissue type (formalin-fixed paraffin-embedded; FFPE), technology (Illumina HumanMethylation450 array), and participant characteristics (age, ancestry, and disease subtype and severity). …”
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Cell-free DNA release following psychosocial and physical stress in women and men by A. S. Limberg, F. Berg, E. Köper, C. Lindgraf, C. Gevers, R. Kumsta, E. M. Hummel, D. A. Moser

“…To overcome this, a multiplex quantitative polymerase chain reaction (qPCR) protocol targeting L1PA2 elements, which are prevalent in the human genome, was utilized. The analysis indicated significantly elevated levels of cf-nDNA in both plasma and saliva in all participants, irrespective of gender, following psychosocial and physical stress. …”
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Causal associations of ambient particulate matter 10 and Alzheimer’s disease: result from a two-sample multivariable Mendelian randomization study by Zehan Huang, Guodong He, Shuo Sun, Yingqing Feng, Yuqing Huang

“…Material and methods Genome-wide association studies (GWAS) for PM10 from UK Biobank, AD from EBI GWAS and IEU OpenGWAS were used for discovery and replication, respectively. …”
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Effects of the auxin-dependent degradation of the cohesin and condensin complexes on the repair of distant DNA double-strand breaks in mouse embryonic stem cells by A. V. Smirnov, A. S. Ryzhkova, A. M. Yunusova

“…Cohesin knockdown was recently shown to stimulate frequencies of genomic deletions produced by distant paired DSBs, but does not affect DNA repair of a single or close DSBs. …”
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Phage display as a tool for identifying HIV-1 broadly neutralizing antibodies by A. N. Chikaev, A. P. Rudometov, Yu. A. Merkulyeva, L. I. Karpenko

“…Each phage particle in a library displays peptides or proteins fused to its coat protein and simultaneously carries the DNA sequence encoding the displayed peptide/protein in its genome. The biopanning procedure allows isolation of specific clones for almost any target, and due to the physical link between the genotype and the phenotype of recombinant phage particles it is possible to determine the structure of selected molecules. …”
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Common themes in architecture and interactions of prokaryotic PolB2 and Pol V mutasomes inferred from in silico studies by Kęstutis Timinskas, Albertas Timinskas, Česlovas Venclovas

“…We used highly accurate AlphaFold structural models, coupled with protein sequence and genome context analysis to comprehensively characterize PolB2 and its associated proteins, PPB2, a small helical protein, and iRadA, a catalytically inactive Rad51 homolog. …”
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