Comprehensive analysis pinpoints CCNA2 as a prognostic and immunological biomarker in non-small cell lung cancer by Liming Zhang, Shaoqiang Wang, Lina Wang

“…Immune infiltration and single-cell sequencing revealed that CCNA2 expression was significantly associated with immune cell infiltration, particularly in Tprolif cells. …”
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Tppp3 is a novel molecule for retinal ganglion cell identification and optic nerve regeneration by Mishal Rao, Ziming Luo, Chia-Chun Liu, Chi-Yu Chen, Shining Wang, Michael Nahmou, Bogdan Tanasa, Aman Virmani, Leah Byrne, Jeffrey L. Goldberg, José-Alain Sahel, Kun-Che Chang

“…Here we investigated Tppp3 in retinal ganglion cells (RGCs) neuroprotection and axonal regeneration using an optic nerve crush (ONC) model in the rodent. Single-cell RNA sequencing identified the expression of Tppp3 in RGCs of mice, macaques, and humans. …”
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The technology landscape for detection of DNA methylation in cancer liquid biopsies by Isabelle Neefs, Joe Ibrahim, Marc Peeters, Guy Van Camp, Ken Op de Beeck

“…Furthermore, we provide some insights into how the field might evolve in the future, where we believe enzymatic conversion might become a new gold standard and direct sequencing methods, such as ONT-sequencing, will get an important place in the epigenetic research field. …”
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Hypermethylation of the PRKCZ Gene in Type 2 Diabetes Mellitus by Li Zou, Shirong Yan, Xueping Guan, Yunjun Pan, Xin Qu

“…Next, methylated DNA immunoprecipitation chip (MeDIP-chip) was used for detection. Bisulfite sequencing PCR (BSP) and gene sequencing were then performed to detect and analyze the correlation between PRKCZ gene promoter methylation and T2DM. …”
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Porcine granulosa cell transcriptomic analyses reveal the differential regulation of lncRNAs and mRNAs in response to all-trans retinoic acid by Jinzhu Meng, Xiuwen Chen, Huabiao Wang, Yixuan Mi, Runsheng Zhou, Hongliang Zhang

“…Methods The lncRNA and mRNA profiles of porcine granulosa cells from ATRA treatment and control group in vitro were constructed through RNA sequencing. Meanwhile, the sequencing data were verified using quantitative polymerase chain reaction (qPCR). …”
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Single-cell transcriptomic profiling of heart reveals ANGPTL4 linking fibroblasts and angiogenesis in heart failure with preserved ejection fraction by Guoxing Li, Huilin Zhao, Zhe Cheng, Junjin Liu, Gang Li, Yongzheng Guo

“…Cells from the hearts were subjected to single-cell sequencing. The key protein expression was measured with Immunohistochemistry and immunofluorescence staining. …”
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A Fosmid Cloning Strategy for Detecting the Widest Possible Spectrum of Microbes from the International Space Station Drinking Water System by Sangdun Choi, Mi Sook Chang, Tara Stuecker, Christine Chung, David A. Newcombe, Kasthuri Venkateswaran

“…Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. …”
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Retinitis Pigmentosa with EYS Mutations Is the Most Prevalent Inherited Retinal Dystrophy in Japanese Populations by Yuuki Arai, Akiko Maeda, Yasuhiko Hirami, Chie Ishigami, Shinji Kosugi, Michiko Mandai, Yasuo Kurimoto, Masayo Takahashi

“…This study found 43 novel sequence variants. In silico analysis suggests that 20 of 25 novel missense variants are pathogenic. …”
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Analysis of whole transcriptome reveals the immune response to porcine reproductive and respiratory syndrome virus infection and tylvalosin tartrate treatment in the porcine alveol... by Kun Du, Yu Xia, Qian Wu, Miao Yin, Hong Zhao, Xi-wen Chen

“…Then, strand-specific RNA-sequencing (ssRNA-seq) and miRNA-sequencing (miRNA-seq) were carried out to profile the whole transcriptome of PAMs in the negative control, PRRSV-infected, and tylvalosin tartrates-treatment group.ResultsThe ssRNA-seq identified 11740 long non-coding RNAs in PAMs. …”
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Microbial bioindicators associated with cadmium uptake in sixteen genotypes of Theobroma cacao by Jennifer E. Schmidt, Caleb A. Lewis, Alana J. Firl, Pathmanathan Umaharan

“…Sequencing highlighted over 200 amplicon sequence variants (ASVs) whose relative abundance was related to cacao leaf and stem Cd content or concentration. …”
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Occurrence, Antimicrobial Resistance, and Virulence Profiles of Salmonella Serovars Isolated from Wild Reptiles in South Africa by Lungile N. Mlangeni, Tsepo Ramatla, Kgaugelo E. Lekota, Cormac Price, Oriel Thekisoe, Che Weldon

“…The isolates were identified using polymerase chain reaction (PCR) by amplifying the invA gene and were further confirmed by 16S rRNA gene sequencing. Salmonella serovars were detected in chameleons (36.8%), lizards (31.6%), snakes (15.8%), and tortoises (15.8%). …”
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Conducting genetic epidemiology research on hyperuricaemia and gout in an indigenous community in Guam - a feasibility study by Yvette C. Paulino, Frank Camacho, Tristan VC Paulino, Delores J. Lee, Lisa Linda Natividad, Elizabeth Matisoo-Smith, Tony R. Merriman, Anna L. Gosling

“…The results of ongoing genetic sequencing will be used to understand molecular causes of gout in Guam.…”
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Neuroligin-3 R451C induces gain-of-function gene expression in astroglia in an astroglia-enriched brain organoid model by Rui Dang, Mridul Dalmia, Ziyuan Ma, Mengmeng Jin, Kushal Aluru, Vincent R. Mirabella, Ava V. Papetti, Li Cai, Peng Jiang

“…Interestingly, our RNA sequencing data suggest that these mutant astroglia significantly upregulate pathways that support neural functions when compared to isogenic wild-type astroglia. …”
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Exogenous Janus Kinase 617 Codon Influences Small Noncoding RNAs and Gene Expression in Ba/F3 Cells by Yi-Yang Chen, Ying-Hsuan Wang, Chih-Cheng Chen, Cih-En Huang, Chia-Chen Hsu, Shu-Huei Hsiao, Yu-Wei Leu

“…The results of the pathway analysis show that the transformation that self-validated the chosen sequencing target genes is impacted by the JAK-STAT pathway. …”
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Prevalence and methodologies for detection, characterization and subtyping of Listeria monocytogenes and L. ivanovii in foods and environmental sources by Jin-Qiang Chen, Patrick Regan, Pongpan Laksanalamai, Stephanie Healey, Zonglin Hu

“…In this review, we (A) described L. monocytogenes and L. ivanovii, world-wide incidence of listeriosis, and prevalence of various L. monocytogenes strains in food and environmental sources; (B) comprehensively reviewed different types of traditional and newly developed methodologies, including culture-based, antigen/antibody-based, LOOP-mediated isothermal amplification, matrix-assisted laser desorption ionization-time of flight-mass spectrometry, DNA microarray, and genomic sequencing for detection and characterization of L. monocytogenes in foods and environmental sources; (C) comprehensively summarized different subtyping methodologies, including pulsed-field gel electrophoresis, multi-locus sequence typing, ribotyping, and phage-typing, and whole genomic sequencing etc. for subtyping of L. monocytogenes strains from food and environmental sources; and (D) described the applications of these methodologies in detection and subtyping of L. monocytogenes in foods and food processing facilities.…”
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Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes by P. K. Rout, K. Thangraj, A. Mandal, R. Roy

“…We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. …”
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CircUCK2(2,3) promotes cancer progression and enhances synergistic cytotoxicity of lenvatinib with EGFR inhibitors via activating CNIH4–TGFα–EGFR signaling by Xindong Wei, Anfeng Si, Shuai Zhao, Yi Fu, Jilei Li, Kedeerya Aishanjiang, Yujie Ma, Chang Yu, Bo Yu, Chunhong Cui, Hui Wang, Xianming Kong, Shibo Li, Xiaoni Kong, Ying Tong, Hailong Wu

“…Methods We identified circUCK2(2,3) through circRNA sequencing, RT–PCR, and Sanger sequencing. CircUCK2(2,3) levels were measured in two independent HCC cohorts using quantitative real-time PCR (qRT–PCR). …”
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The SERPINB4 gene mutation identified in twin patients with Crohn’s disease impaires the intestinal epithelial cell functions by Xiao-Mei Ouyang, Jun-Hui Lin, Ying Lin, Xian-Ling Zhao, Ya‐Ni Huo, Lai-Ying Liang, Yong-Dong Huang, Gui-Jing Xie, Peng Mi, Zhen-Yu Ye, Bayasi Guleng

“…To identify new targets related to the initiation of CD, we screened a pair of twins with CD, which is a rare phenomenon in the Chinese population, for genetic susceptibility factors. Whole-exome sequencing (WES) of these patients revealed a mutation in their SERPINB4 gene. …”
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EGFR inhibition augments the therapeutic efficacy of the NAT10 inhibitor Remodelin in Colorectal cancer by Yongbin Zheng, Dan Song, Ming Guo, Chenhong Wang, Mingzhen Ma, Gongcai Tao, Licui Liu, Xiaobo He, Fengyu Cao, Dan Luo, Qingchuan Zhao, Zhongyuan Xia, Yanxin An

“…The potential mechanisms of NAT10 in CRC were investigated using RNA sequencing, RNA immunoprecipitation sequencing, and acetylated RNA immunoprecipitation sequencing. …”
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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

“…Resultant amplicons were sequenced via the Ion Torrent and TRBV allele profiles constructed for each individual was correlated with irAE annotations to identify haplotypes associated with severe irAEs (≥ grade 3).Results Our study included 81 patients who had irAEs when treated with immunotherapy for cancer. …”
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