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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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 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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CircRNA-miRNA-mRNA regulatory network in high-altitude hypobaric hypoxia-induced hearing impairment and hearing acclimatization by Danzeng Awang, Kanzi Danzeng, Tianheng Wang, Quzong Deji, Mengting Huang, Hailong Ren, Xinzhu Liu, Binghan Zhao, Lanzi Gongga

“…The DEmRNAs in this network were functionally annotated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses based on Metascape. Results: The ABR assay indicated that hearing impairment happened on day 30 and hearing acclimatization occurred on day 60. …”
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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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Identification and verification of autophagy-related gene signatures and their association with immune infiltration and drug responsiveness in epilepsy by Han-han He, Xiao-ge Zhang, Fen-fang Chen

“…Additionally, the functional enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied. The hub ARDEGs were identified through CytoHubba, followed by the LASSO analysis. …”
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