Gut microbial subtypes and clinicopathological value for colorectal cancer by Shuwen Han, Jing Zhuang, Yifei Song, Xinyue Wu, Xiaojian Yu, Ye Tao, Jian Chu, Zhanbo Qu, Yinhang Wu, Shugao Han, Xi Yang

“…Methods Stool samples from 914 volunteers (376 CRCs, 363 advanced adenomas, and 175 normal controls) were included for 16S rRNA sequencing. Unsupervised learning was used to generate gut microbial subtypes. …”
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基于生物信息学途径筛选缺血性脑卒中关键基因及药物预测 by 于瑜, 王钟兴

“…最后用Connectivity Map数据库预测脑卒中的潜在作用药物。结果共筛出521个差异mRNA，其中421个上调、100个下调，其中2个关键基因<italic>Drd4</italic>（<italic>P</italic>=0.000 019）和<italic>Hcar2</italic>（<italic>P</italic>=0.000 094）经qRT-PCR实验证实在脑缺血后表达均升高。…”
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High Glucose Induces Endothelial COX2 and iNOS Expression via Inhibition of Monomethyltransferase SETD8 Expression by Jie Qi, Qichao Wu, Qian Cheng, Xiangyuan Chen, Minmin Zhu, Changhong Miao

“…High glucose inhibited SETD8 expression, and overexpression of SETD8 diminished the effects of high glucose treatment. Consistently, RNA silencing of SETD8 led to the opposite effect. …”
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Chromosome-scale assembly and annotation of the wild wheat relative Aegilops comosa by Hongna Li, Shams ur Rehman, Rui Song, Liang Qiao, Xiaohua Hao, Jing Zhang, Kairong Li, Lifeng Hou, Wanyi Hu, Le Wang, Shisheng Chen

“…A total of 39,057 gene models were annotated through a combination of homoeologous proteins, Iso-seq, and RNA-seq data. Comparative genome analysis revealed a terminal intrachromosomal translocation on chromosome 2 M in Ae. comosa. …”
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Betacoronaviruses Differentially Activate the Integrated Stress Response to Optimize Viral Replication in Lung-Derived Cell Lines by David M. Renner, Nicholas A. Parenti, Nicole Bracci, Susan R. Weiss

“…Interestingly, genetic ablation of growth arrest and DNA damage-inducible protein (GADD34) expression, an inducible protein phosphatase 1 (PP1)-interacting partner targeting eIF2α for dephosphorylation, did not significantly alter HCoV-OC43 or SARS-CoV-2 replication, while siRNA knockdown of the constitutive PP1 partner, constitutive repressor of eIF2α phosphorylation (CReP), dramatically reduced HCoV-OC43 replication. …”
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RETRACTED ARTICLE: CKS2 induces autophagy-mediated glutathione metabolic reprogramming to facilitate ferroptosis resistance in colon cancer by Leilei Yang, Chengfeng Fang, Jiaju Han, Yufeng Ren, Zaiping Yang, Lingyan Shen, Dinghai Luo, Ruili Zhang, Yan Chen, Shenkang Zhou

“…Methods Bioinformatics and RNA-seq analyses were employed to study genes associated with the ferroptosis signaling pathway. …”
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The Characteristic of Biofilm Formation in ESBL-Producing K. pneumoniae Isolates by Xiaofang Gao, Haili Wang, Zhijuan Wu, Pan Sun, Wei Yu, Donghua Chen, Yuhua Mao, Lili Fang, Jia Qian, Li Li, Qian Peng, Yanping Han

“…The ability of above four ESBL-producing K. pneumoniae isolates to agglutinate in a mannose-resistant manner or in a mannose-sensitive manner, as well as RNA sequencing-based transcriptome results, showed that type 3 fimbriae play a significant role in biofilm formation. …”
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胚胎干细胞分化为表皮样细胞的基因表达谱差异研究

“…方法：利用人羊膜建立体外诱导体系，将小鼠ESC诱导定向分化为ELC，做3次生物学重复，分别取未分化的ESC和诱导分化的ELC提取总RNA进行扩增、Cy3标记，与NimbleGen 135k 小鼠全基因表达谱芯片（含44170个基因）杂交，荧光扫描，筛选出差异表达基因，并进行GO分析和pathway分析，用实时定量PCR对结果进行验证。…”
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Comprehensive Analysis of the Mechanism of Anoikis in Hepatocellular Carcinoma by Dongqian Li, Qian Bao, Shiqi Ren, Haoxiang Ding, Chengfeng Guo, Kai Gao, Jian Wan, Yao Wang, MingYan Zhu, Yicheng Xiong

“…The Cell-Type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was used to determine the proportions of immune cell types. …”
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Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T by Christian Suarez, Stefan Ratering, Torsten Hain, Moritz Fritzenwanker, Alexander Goesmann, Jochen Blom, Trinad Chakraborty, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Sylvia Schnell

“…Furthermore, the complete E19T genome sequence helps to define its previously reported unclear 16S rRNA gene-based phylogenetic affiliation. Hartmannibacter forms a distinct subcluster with genera Methylobrevis, Pleomorphomonas, Oharaeibacter, and Mongoliimonas subclustered with genera belonging to Rhizobiales.…”
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Microbial Contamination and Food Safety Aspects of Cassava Roasted Flour (“Rale”) in Mozambique by Andreia Massamby, Su-lin L. Leong, Bettina Müller, Lucas Tivana, Volkmar Passoth, Custódia Macuamule, Mats Sandgren

“…The results obtained from the Illumina 16S rRNA gene sequencing can be considered a complementary technique to the plating methods relied on in this study. …”
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The Maternal Microbiome Programs the m6A Epitranscriptome of the Mouse Fetal Brain and Intestine by Zhuoyu Xiao, Sun Liu, Zengguang Li, Jinru Cui, Hailan Wang, Zihan Wang, Qihuan Ren, Laixin Xia, Zhijian Wang, Yuan Li

“…Although it has been shown that the microbiome affects the mRNA m6A modification of the host, it remains unclear whether the maternal microbiome affects m6A epitranscriptome of the fetus so as to impact fetal development. …”
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Pulmonary Bacterial Communities in Surgically Resected Noncystic Fibrosis Bronchiectasis Lungs Are Similar to Those in Cystic Fibrosis by Heather Maughan, Kristopher S. Cunningham, Pauline W. Wang, Yu Zhang, Marcelo Cypel, Cecilia Chaparro, D. Elizabeth Tullis, Thomas K. Waddell, Shaf Keshavjee, Mingyao Liu, David S. Guttman, David M. Hwang

“…Methods. Bacterial 16S rRNA gene libraries were constructed from lung tissue of 10 non-CF bronchiectasis and 21 CF patients, followed by DNA sequencing of isolates from each library. …”
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Qufeng epimedium decoction alleviates rheumatoid arthritis through CYLD-antagonized NF-kB activation by deubiquitinating Sirt1 by Zhiming Wu, Peng Zhang, Wenyan Huang, Yifen Zhou, Zhengliu Cao, Chunhong Wu

“…The interactions between Sirt1 and CYLD were validated through Co-immunoprecipitation (Co-IP) and RNA-FISH assay. Results: Administration with Qufeng epimedium decoction attenuated inflammatory damage, excessive proliferation, and FLSs pyroptosis in an RA rat model. …”
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A metabologenomics approach reveals the unexplored biosynthetic potential of bacteria isolated from an Amazon Conservation Unit by Ana Carolina Favacho Miranda de Oliveira, Bruna Domingues Vieira, Rafael de Felício, Lucas da Silva e Silva, Adonney Allan de Oliveira Veras, Diego Assis das Graças, Artur Silva, Rafael Azevedo Baraúna, Daniela Barretto Barbosa Trivella, Maria Paula Cruz Schneider

“…The sequencing of the 16S rRNA gene classified the strains ACT015, ACT016, and FIR094 within the genera Streptomyces, Rhodococcus, and Brevibacillus, respectively. …”
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A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields by Fangming Zhu, Takehiro Kamiya, Toru Fujiwara, Masayoshi Hashimoto, Siyu Gong, Jindong Wu, Hiromi Nakanishi, Masaru Fujimoto

“…In this study, we performed amplicon sequencing targeting fungal ITS and the bacterial 16S rRNA gene to characterize and compare bacterial and fungal community dynamics of the rice root endosphere and soil in organic and conventional paddy fields. …”
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Grazing Intensity Modifies Soil Microbial Diversity and Their Co-Occurrence Networks in an Alpine Steppe, Central Tibet by Mingxue Xiang, Zepeng Liang, Yanjie Zhang, Junxi Wu, Tao Ma, Lha Duo, Xianzhou Zhang, Gang Fu

“…We used high-throughput sequencing to find the sequences of bacterial 16S rRNA and fungal ITS gene amplicons. Then, we analyzed their alpha and beta diversities and set up co-occurrence networks that show how often they occur together. …”
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Neuroprotective and Antiapoptotic Activity of Lineage-Negative Bone Marrow Cells after Intravitreal Injection in a Mouse Model of Acute Retinal Injury by Anna Machalińska, Dorota Rogińska, Ewa Pius-Sadowska, Miłosz P. Kawa, Edyta Paczkowska, Michał Rudnicki, Renata Lejkowska, Bartłomiej Baumert, Barbara Wiszniewska, Bogusław Machaliński

“…Moreover, global gene expression at day 7 was analyzed by RNA arrays. We observed that Lin−BMCs integrated into outer retinal layers improving morphological retinal structure and induced molecular changes such as downregulation of proapoptotic caspase-3 gene, a decrease in BAX/BCL-2 gene ratio, and significant elevation of BDNF expression. …”
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Phenolic compounds from Chaenomeles speciosa alleviate inflammation in lipopolysaccharide-treated RAW264.7 macrophages via the NF-κB and MAPK pathways by Fuxia Hu, Chao Liu, Fengqin Wang, Changxin Zhou, Maotong Zhu, Dongxiao Sun-Waterhouse, Zhaosheng Wang

“…The extract suppressed the levels of nitric oxide (NO), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and interleukin-1β (IL-1β), and the mRNA and protein expressions of nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). …”
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QTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration by Jayshree Advani, Puja A. Mehta, Andrew R. Hamel, Sudeep Mehrotra, Christina Kiel, Tobias Strunz, Ximena Corso-Díaz, Madeline Kwicklis, Freekje van Asten, Rinki Ratnapriya, Emily Y. Chew, Dena G. Hernandez, Sandra R. Montezuma, Deborah A. Ferrington, Bernhard H. F. Weber, Ayellet V. Segrè, Anand Swaroop

“…We have analyzed array-based DNA methylation profiles of 160 human retinas with co-measured RNA-seq and >8 million genetic variants, uncovering sites of genetic regulation in cis (37,453 methylation quantitative trait loci and 12,505 expression quantitative trait loci) and 13,747 DNA methylation loci affecting gene expression, with over one-third specific to the retina. …”
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