Dual role of Cathepsin S in cutaneous melanoma: insights from mendelian randomization and bioinformatics analysis by Linsa Zhou, Qiang Zhou, Qian Guo, Peng Lai, Chen Rui, Wanqing Li, Xuemei Chen, Yue Zhuo, Xiaoping Zhong, Sen Lin

“…Methods The Gene Expression Omnibus (GEO) database was used to obtain differential genes for CM and normal skin, and the Genome-Wide Association Studies (GWAS) analysis offered summary-level melanoma data for CM. …”
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Germline variants of the genes involved in NF-kB activation are associated with the risk of COPD and lung cancer development by Baranasic Jurica, Niazi Yasmeen, Chattopadhyay Subhayan, Rumora Lada, Ćorak Lorna, Dugac Andrea Vukić, Jakopović Marko, Samaržija Miroslav, Försti Asta, Knežević Jelena

“…We extracted summary data of variants in 1511 immune-related genes from COPD and LC genome-wide association studies (GWAS) from the UK Biobank. …”
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Regulatory signatures involved in the cell cycle pathway contribute to egg production heterosis in chicken by Jingwei Yuan, Yuanmei Wang, Yanyan Sun, Yunlei Li, Aixin Ni, Qin Li, Hanhan Yang, Xinying Xu, Yunhe Zong, Hui Ma, Jilan Chen

“…Conclusion Our study characterized the dynamic profile of genome-wide gene expression in ovary and highlighted the role of dominant expression of cell cycle pathway genes in heterosis. …”
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Global insights into MRSA bacteremia: a bibliometric analysis and future outlook by Jia-Yi Lin, Jia-Yi Lin, Jia-Kai Lai, Jia-Kai Lai, Jian-Yi Chen, Jian-Yi Chen, Jia-Yu Cai, Jia-Yu Cai, Zhan-Dong Yang, Zhan-Dong Yang, Liu-Qingqing Yang, Liu-Qingqing Yang, Liu-Qingqing Yang, Ze-Tao Zheng, Ze-Tao Zheng, Xu-Guang Guo, Xu-Guang Guo, Xu-Guang Guo

“…Future research will rely on integrating genomics, AI, and machine learning to drive personalized treatment. …”
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Comparative analysis of the primary structure and production of recombinant poly(ADP-ribose)polymerase 1 of long-lived Heterocephalus glaber by K. N. Naumenko, A. R. Nurislamov, K. D. Nazarov, V. S. Fishman, A. A. Popov, I. O. Petruseva, A. N. Evdokimov, O. I. Lavrik

“…DNA repair is a most important cellular process that helps maintain the integrity of the genome and is currently considered by researchers as one of the factors determining the maximum lifespan. …”
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Glycated Serum Protein Genetics and Pleiotropy with Cardiometabolic Risk Factors by Matthew P. Johnson, Ryan Keyho, Nicholas B. Blackburn, Sandra Laston, Satish Kumar, Juan Peralta, Suman S. Thapa, Bradford Towne, Janardan Subedi, John Blangero, Sarah Williams-Blangero

“…The aim of this study was to estimate the heritability of GSP and GSP expressed as a percentage of total serum albumin (%GA) using a variance component approach and localize genomic regions (QTLs) that harbor genes likely to influence GSP and %GA trait variation in a large extended multigenerational pedigree from Jiri, Nepal (n=1,800). …”
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Study on the multidrug resistance and transmission factors of Staphylococcus aureus at the ‘animal–environment–human’ interface in the broiler feeding cycle by Fangyuan Hu, Fangyuan Hu, Yaopeng Liu, Yaopeng Liu, Lin Wang, Juan Wang, Na Liu, Yan Li, Xiaoxiao Duan, Junwei Wang, Mingzhe Lu, Junhui Liu, Zhina Qu, Keguang Han

“…Based on the concept of “One Health,” this study analyzed the multidrug resistance and transmission factors of S. aureus isolated from the “animal–environment–human” interface during one feeding cycle of commercial broilers in China by using antimicrobial susceptibility testing and whole genome sequencing (WGS) technologies. The results showed that in stage 1, the isolation rate of S. aureus was 1.32% (6/453), that of workers was 25.0% (4/16), and that of environmental samples was 0.69% (2/287), and the multidrug resistance rate was 83.33%. …”
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Gastric Cancer Cell Lines Have Different MYC-Regulated Expression Patterns but Share a Common Core of Altered Genes by Jersey Heitor da S. Maués, Helem Ferreira Ribeiro, Giovanny R. Pinto, Luana de Oliveira Lopes, Letícia M. Lamarão, Carla Mariana F. Pessoa, Caroline de Fátima Aquino Moreira-Nunes, Raimundo Miranda de Carvalho, Paulo P. Assumpção, Juan A. Rey, Rommel M. Rodríguez Burbano

“…The DEGs were picked using Sailfish software, followed by Gene Set Enrichment Analysis (GSEA) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis using KEGG. We found 11 significantly enriched gene sets by using enrichment score (ES), False Discovery Rate (FDR), and nominal P-values. …”
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Comprehensive Analysis of Competing Endogenous RNA Network Focusing on Long Noncoding RNA Involved in Cirrhotic Hepatocellular Carcinoma by Yuli Zhang, Dinggui Chen, Miaomiao Yang, Xianfeng Qian, Chunmei Long, Zhongwei Zheng

“…The lncRNA, miRNA, and mRNA expression datasets were obtained from Gene Expression Omnibus and The Cancer Genome Atlas. Based on miRanda and TargetScan, the HCC-specific ceRNA network was constructed to illustrate the coexpression regulatory relationship of lncRNAs, miRNAs, and mRNAs. …”
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The trend of phylogenetic and epitope variations of SARS-CoV-2 Omicron sub-lineages in Iran by Mehdi Shabani, Ahmad Nejati, Jila Yavarian, Jila Yavarian, Kaveh Sadeghi, Sevrin Zadheidar, Akram Sadat Ahmadi, Monire Ghadirali, Arghavan Zebardast, Adel Abedi, Mohammad Hossein Najmi, Nazanin-Zahra Shafiei-Jandaghi, Talat Mokhtari-Azad

“…The present study evaluated and compared these important variations among different Omicron sub-lineages in Iran.MethodologyFrom October 2023 to August 2024, high coverage whole genome sequences of 49 SARS-CoV-2 strains were subjected to phylogenetic analysis and evaluation of B cell, CD4+, and CD8+ T cell epitopes in Iran National Influenza Centre.ResultsThe phylogenetic tree exhibited eight Nextstrain clades (21L, 22F, 23B, 23H, 23D, 24A, 24B, and 24C) in 48 studied strains, and one recombinant strain (XDK.1). …”
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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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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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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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Deficiency of ATF3 facilitates both angiotensin II‐induced and spontaneously formed aortic aneurysm and dissection development by activating cGAS–STING pathway by Yifan Du, Poyi Hu, Xiangchao Ding, Dashuai Wang, Jingjing Luo, Sheng Le, Lingyun Ren, Manhua Chen, Ping Ye, Jiahong Xia

“…Conclusions Our study indicates that ATF3 is essential for genomic DNA stability in VSMCs through the P21–cGAS–STING pathway, suggesting that enhancing ATF3 expression in VSMCs could help prevent sporadic AAD. …”
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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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Specific shoot formation in Miscanthus sacchariflorus (Poaceae) under different environmental factors and DNA passportization using ISSR markers by O. V. Dorogina, N. S. Nuzhdina, G. A. Zueva, Yu. A. Gismatulina, O. Yu. Vasilyeva

“…As a result of ISSR-analysis of genomic DNA in the M. sacchariflorus population, unique molecular polymorphic fragments were identified, which can be used for identification and DNA passportization at the inter-population level. …”
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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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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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