T-cell receptor beta variable gene polymorphism predicts immune-related adverse events during checkpoint blockade immunotherapy by Linghua Wang, Siqing Fu, Aung Naing, Funda Meric-Bernstam, Carl Morrison, Joud Hajjar, Mingxuan Xu, Anas Alshawa, Bettzy Stephen, Ying Yuan, Jordi Rodon Ahnert, Abdulrazzak Zarifa, Shrutii Sarda, Timothy Looney, Sapna P Patel, Geoffrey M Lowman, Dzifa Yawa Duose, Jeffrey M Conroy, Evan Kwiatkowski

“…However, the repetitive nature of the TCRB locus and incomplete genome assembly has hampered the evaluation of TRBV polymorphisms in the past.Patients and methods We used a novel method for long-amplicon next generation sequencing of rearranged TCRB chains from peripheral blood total RNA to evaluate the link between TRBV polymorphisms and irAEs in patients treated with immunotherapy for cancer. …”
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A study of the influence of the T2DL.2DS-2SS translocation and the 5S(5D) substitution from <i>Aegilops speltoides</i> on breeding-valuable traits of common wheat by R. O. Davoyan, I. V. Bebykina, E. R. Davoyan, A. N. Zinchenko, Y. S. Zubanova, D. M. Boldakov, V. I. Basov, E. D. Badaeva, I. G. Adonina, E. A. Salina

“…This research is aimed at studying 14 introgression lines with the T2DL.2DS-2SS translocation and the 5S(5D) substitution from Aegilops speltoides obtained from crossing common wheat varieties (Aurora, Krasnodarskaya 99, Nika Kubani) with the genome-substituted form Avrodes (BBAASS). Hybrid lines with different combinations of T2DL.2DS-2SS and T1BL.1RS translocations and 5S(5D) substitution were characterized by resistance to leaf and yellow rusts, productivity components and technological qualities of grain. …”
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Characterization of three novel Helicobacter species infecting stomachs of dogs and cats: Helicobacter gastrocanis sp. nov., Helicobacter gastrofelis sp. nov., and Helicobacter fel... by Emiko Rimbara, Sae Aoki, Masato Suzuki, Hirotaka Kobayashi, Taisuke Nakagawa, Yuko Goto-Koshino, Sachiyo Nomura, Sachiyo Nomura, Wan-Ying Du, Hidenori Matsui, Shigetarou Mori, Keigo Shibayama, Tsuyoshi Kenri, Koichi Ohno

“…However, none of their whole genomes showed more than average nucleotide identity (ANI) threshold value (95–96%) to any Helicobacter species (85.1, 86.7, and 86.6% ANI, respectively, with H. heilmannii ASB1T), including when compared to each other. …”
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Combining single-cell analysis and molecular docking techniques to construct a prognostic model for colon adenocarcinoma and uncovering inhibin subunit βb as a novel therapeutic ta... by Qinqing Wu, Qinqing Wu, Lu Ye, Yuwei Wu, Mengyu Zhao, Mengyu Zhao, Jiaxin Lu, Yanping Yu, Yanping Yu, Yixiao Niu, Yixiao Niu, Luxiao Zhang, Peijun Zuo, Peijun Zuo

“…However, the specific biological link between anoikis and COAD, as well as its mechanisms in tumor progression, remains unclear, making it a potential new direction for therapeutic strategy research.MethodsWe employed transcriptomic data and clinical information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to pinpoint differentially expressed anoikis-related genes (ARGs) in COAD. …”
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LIPUS promotes osteogenic differentiation of rat BMSCs and osseointegration of dental implants by regulating ITGA11 and focal adhesion pathway by Chao Liang, Yuqing Zhang, Yuwei Yan, Wei Geng, Jun Li, Xiu Liu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to identify enriched functional terms and signalling pathways for differentially expressed genes from LIPUS-treated rat BMSC RNAseq data obtained from the GEO database. …”
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Relationship Between RNF213 p.R4810K and Echocardiographic Findings in Patients with Cerebrovascular Diseases: A Multicenter Prospective Cohort Study by Kotaro Noda, Yorito Hattori, Tatsuya Nishii, Hiroki Horinouchi, Yuriko Nakaoku, Soshiro Ogata, Yasunobu Inagaki, Ryotaro Asano, Takeshi Yoshimoto, Kunihiro Nishimura, Takeshi Ogo, Yoshikazu Nakaoka, Masafumi Ihara

“…Methods and Results We investigated patients registered in the National Cerebral and Cardiovascular Center Genome Registry between May 2017 and August 2021 who underwent echocardiography. …”
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Evaluation of recombinant proteins <i>T. pallidum</i> Тр0163 and Тр0971 as antigens for the diagnosis of syphilis using enzyme immunoassay by Natalia V. Arbuzova, Marina V. Shpilevaya, Georgii L. Katunin, Oleg E. Kuznetsov, Nikita Yu. Nosov, Viсtoria S. Solomka

“…With the deciphering of the T. pallidum genome and the application of bioinformatics and immunoproteomics, many recombinant T. pallidum proteins have emerged that have been evaluated for their diagnostic value, some of which are used as diagnostic antigens in commercial tests. …”
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Identification of the Transcriptional Networks and the Involvement in Angiotensin II-Induced Injury after CRISPR/Cas9-Mediated Knockdown of Cyr61 in HEK293T Cells by Junjie Wang, Dongdong Fu, Soulixay Senouthai, Yan Jiang, Rentong Hu, Yanwu You

“…Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to determine biofunctions and signaling pathways. …”
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Vulnerability for alcohol use disorder after adverse childhood experiences (AUDACE): protocol for a longitudinal fMRI study assessing neuropsychobiological risk factors for relapse by Falk Kiefer, Cagdas Türkmen, Noah Machunze, Haoye Tan, Sarah Gerhardt, Sabine Vollstädt-Klein

“…Additionally, saliva cortisol and blood samples will be taken to measure hormonal stress response and to perform genome wide association analyses, respectively. The general linear model will be applied on the first level fMRI analyses, whereas for the second level analyses and analyses of behavioural data, t-tests, regression analyses, repeated-measures and one-way analysis of variances will be used.Ethics and dissemination This study has been approved by the ethics committee of the Medical Faculty Mannheim of Heidelberg University (ethics approval number: 2018-560N-MA with amendment from 29 June 2021). …”
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STING agonism overcomes STAT3-mediated immunosuppression and adaptive resistance to PARP inhibition in ovarian cancer by Changli Qian, Gordon J Freeman, Tao Jiang, Ursula Matulonis, Ziying Lin, Hye-Jung Kim, Anniina Färkkilä, Hua Yu, Xin Cheng, Panagiotis A Konstantinopoulos, Antons Martincuks, Joyce F Liu, Qiwei Wang, Liya Ding, Michael J Kearns, Shaozhen Xie, Inga-Maria Launonen, Thomas M Roberts, Jean J Zhao

“…Signal transducer and activator of transcription 3 (STAT3)-mediated immunosuppression was investigated in vitro by co-culture experiments and in vivo by analysis of immune cells in the tumor microenvironment (TME) of human and mouse PARPi-resistant tumors. Whole genome transcriptome analysis was performed to assess the antitumor immunomodulatory effect of STING (stimulator of interferon genes) agonists on myeloid cells in the TME of PARPi-resistant ovarian tumors. …”
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The expression of BHLHE22 in endometrial carcinoma: Associations with mismatch repair protein expression status, tumor-infiltrating immune cells, programmed death-ligand 1 and clin... by Lin-Yu Chen, Hsing-Yu Chen, Hung-Cheng Lai, Shiou-Fu Lin, Kuo-Chang Wen, Darmawi, Phui-Ly Liew

“…The associations between the clinicopathological characteristics, mismatch repair status, and Kaplan–Meier analyses (including The Cancer Genome Atlas (TCGA) dataset) were analyzed. Results: Twenty-nine of 109 cases (26.6 %) had high BHLHE22 expression, which was associated with higher tumoral CD8, higher stromal CD68 and lower progesterone receptor (PR). …”
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Topologically constrained DNA-mediated one-pot CRISPR assay for rapid detection of viral RNA with single nucleotide resolutionResearch in context by Yanan Li, Ru Xu, Fenglei Quan, Yonghua Wu, Yige Wu, Yongyuan Zhang, Yan Liang, Zhenzhong Zhang, Hua Gao, Ruijie Deng, Kaixiang Zhang, Jinghong Li

“…The capacity of CRISPR/Cas13a for discriminating single nucleotide variant (SNV) in viral genome is leveraged by designing synthetic mismatches and hairpin structure in CRISPR RNA (crRNA), enabling robust discrimination of different SARS-CoV-2 variants. …”
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Identification of ALEKSIN as a novel multi-IRF inhibitor of IRF- and STAT-mediated transcription in vascular inflammation and atherosclerosis by Aleksandra Antonczyk, Katarzyna Kluzek, Natalia Herbich, Mahdi Eskandarian Boroujeni, Bart Krist, Dorota Wronka, Anna Karlik, Lukasz Przybyl, Adam Plewinski, Joanna Wesoly, Hans A. R. Bluyssen

“…This was in line with the common inhibition of ALEKSIN and STATTIC observed on the genome-wide expression of pro-inflammatory IRF/STAT/NF-κB target genes, as well as on the migration of HMECs. …”
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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? by Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter R. Johnston, Paul M. Kirk, Elaine Malosso, Tom W. May, Wieland Meyer, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey M. Yurkov, Ning Zhang, Conrad L. Schoch

“…In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. …”
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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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Integrative analysis of cuproptosis-related lncRNAs: Unveiling prognostic significance, immune microenvironment, and copper-induced mechanisms in prostate cancer by Haitao Zhong, Yiming Lai, Wenhao Ouyang, Yunfang Yu, Yongxin Wu, Xinxin He, Lexiang Zeng, Xueen Qiu, Peixian Chen, Lingfeng Li, Jie Zhou, Tianlong Luo, Hai Huang

“…Methods: Sequencing data and copy number variant data were obtained from 492 patients with PCa from The Cancer Genome Atlas (TCGA) Program. Prognostic models of PCa based on cuproptosis-related lncRNAs were constructed using a multi-level attention graph neural network (MLA-GNN) deep learning algorithm. …”
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Protective effect and mechanism of Sufentanil on acute lung injury in septic mice by Hongqiao Hou, Bowen Jiang, Aiqing Zhu, Junjun Hou, Zhe Qu, Ruping Liu, Aiqun Li

“…To this end, a protein-protein interaction (PPI) network for common targets was first constructed with Swiss Target Prediction Database, GeneCards Database, Draw Venn Diagram Software, STRING 11.5 Database, Cytoscape 3.10.0 Software and Metascape Database, and then key targets were subject to enrichment analysis by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to obtain the key targets of Sufentanil for the treatment of pulmonary sepsis, and then verified by animal experiments. …”
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Bulk and single-cell transcriptome revealed the metabolic heterogeneity in human glioma by Yong Xiao, Mengjie Zhao, Ran Wang, Liang Liu, Chong Xiang, Taiping Li, Chunfa Qian, Hong Xiao, Hongyi Liu, Yuanjie Zou, Xianglong Tang, Kun Yang

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to elucidate the biological functions of genes of interest. …”
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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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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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