Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia by Natasha Spottiswoode, Alexandra Tsitsiklis, Victoria T. Chu, Hoang Van Phan, Catherine DeVoe, Christina Love, Rajani Ghale, Joshua Bloomstein, Beth Shoshana Zha, Cole P. Maguire, Abigail Glascock, Aartik Sarma, Peter M. Mourani, Katrina L. Kalantar, Angela Detweiler, Norma Neff, Sidney C. Haller, COMET Consortium, Joseph L. DeRisi, David J. Erle, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Matthew F. Krummel, Michael A. Matthay, Prescott G. Woodruff, Carolyn S. Calfee, Charles R. Langelier

“…Assessment of the pulmonary transcriptome reveals suppressed TNFα signaling in patients with 2°BP, and sensitivity analyses suggest this finding is mediated by corticosteroid treatment. …”
Get full text

Aidi injection inhibits the migration and invasion of gefitinib-resistant lung adenocarcinoma cells by regulating the PLAT/FAK/AKT pathway by Jingyuan Zhang, Siyun Yang, Xiaodong Chen, Fanqin Zhang, Siyu Guo, Chao Wu, Tieshan Wang, Haojia Wang, Shan Lu, Chuanqi Qiao, Xiaoguang Sheng, Shuqi Liu, Xiaomeng Zhang, Hua Luo, Qinglin Li, Jiarui Wu

“…The molecular mechanism of ADI was further studied using whole-transcriptome sequencing technology. Bioinformatics and molecular biology methods were employed to validate the critical targets of ADI. …”
Get full text

Revisiting the female germline cell development by Youmei Huang, Yunlong Zhang, Jiahong Yang, Xinpeng Xi, Yanfen Liu, Hanyang Cai, Yuan Qin

“…Single-cell transcriptome/spatial transcriptomics analysis helps to investigate complex cellular systems at the single-cell level, reflecting the biological complexity of different cell types. …”
Get full text

Intratracheal Aerosolization of <i>Nocardia farcinica</i> in Mice Optimizes Bacterial Distribution and Enhances Pathogenicity Compared to Intranasal Inoculation and Intratracheal I... by Bingqian Du, Ziyu Song, Jirao Shen, Jiang Yao, Shuai Xu, Xiaotong Qiu, Min Yuan, Zhenjun Li

“…ITA provides a more consistent and severe model of <i>N. farcinica</i> pneumonia in mice than IN and ITI, which can make the bacteria more evenly distributed in the lungs, leading to more severe pathological damage and higher mortality rates. …”
Get full text

GPER1 is involved in shaping tumor immune microenvironment and its expression is decreased in NSCLC tumorigenesis by Zhenhua Li, Chao Xie, Jingjing Cui, Hui Xu, Dingbiao Li

“…In addition, we report a ceRNA network that may provide new insight into the roles of GPER1 in NSCLC development.…”
Get full text

Nurr1 deficiency impairs autophagy-lysosomal function through GBA-dependent transcriptional regulation in Parkinson’s disease pathogenesis by Cheng Cheng, Cheng Cheng, Huijia Yang, Lulu Tian, Yang Ni, Congcong Jia, Weidong Le, Qingshan Wang

“…Previous studies on Nurr1 have mainly focused on the development and maintenance of midbrain dopaminergic neurons, while the potential involvement of Nurr1 in ALP regulation remains uncharacterized.MethodsStable Nurr1 knockdown cells and inducible Nurr1 knockout mice were generated. Transcriptome sequencing and analysis was utilized to confirm the altered pathways and differentially expression genes associated with ALP. …”
Get full text

Melatonin Enhances the Low-Calcium Stress Tolerance by Regulating Brassinosteroids and Auxin Signals in Wax Gourd by Jingjing Chang, Xuemei Zhu, Yixuan Lian, Jing Li, Xiao Chen, Zhao Song, Lei Chen, Dasen Xie, Baige Zhang

“…This study aimed to assess the effects of melatonin on Ca absorption, the antioxidant system, and root morphology under low-Ca (LCa) stress conditions, as well as to identify key regulatory factors and signaling pathways involved in these processes using transcriptome analysis. Under LCa conditions, wax gourd seedling exhibited significant decreases in Ca accumulation, showed inhibition of root growth, and demonstrated the occurrence of oxidative damage. …”
Get full text

Pharmacoinformation studies of chondroprotectors by A. M. Lila, I. Yu. Torshin, A. N. Gromov, V. A. Semenov, O. A. Gromova

“…These methods include: 1) analysis of big data (selection of texts of scientific publications, search for new biomarkers); 2) computer analysis of texts (automatic classification of texts by content, identification of pseudoscientific texts); 3) analysis of metric maps (visualization and analysis of complex patterns, including clustering) and 4) chemoinformation analysis, including the assessment of the effect of drugs on the transcriptome, proteome and microbiome of a person. The article provides examples of the application of these methods of pharmacoinformatics to chondroprotectors containing standardized forms of chondroitin sulfate and glucosamine sulfate.…”
Get full text

Progress of researches on the differential diagnosis of Pneumocystis jiroveci infection and colonization by LI Xingchen, TONG Jin

“…Although serum G test combined with molecular detection technology, peripheral blood CD4+ T level and independent characterization of trophozoites and cysts by transcriptome sequencing technology may support identifying PJ colonization and diagnosis of infection, unified standards have not yet been established. …”
Get full text

N2-methylguanosine and N2, N2-dimethylguanosine in cytosolic and mitochondrial tRNAs by Jonny Petrosyan, Katherine E. Bohnsack

“…Decoration of cellular RNAs with modified RNA nucleosides is an important layer of gene expression regulation. Throughout the transcriptome, RNA modifications influence the folding, stability and function of RNAs as well as their interactions with RNA-binding proteins. …”
Get full text

Distinct virulence of the microsporidian parasite in honey bees competing habitat by Xiuxiu Wei, Qiang Huang

“…Additionally, time-series transcriptome analysis of both bees and parasites provide insights into host-pathogen interactions. …”
Get full text

Genomics and Precision Medicine: Molecular Diagnostics Innovations Shaping the Future of Healthcare in Qatar by Nader I. AL-Dewik, M. Walid Qoronfleh

“…This minireview describes the impact of clinical genomics disruptive innovations on the healthcare system in order to provide better diagnosis and treatment. The observed evolution is not limited to the point-of-care services. …”
Get full text

Ecological interactions between marine RNA viruses and planktonic copepods by Junya Hirai, Seiji Katakura, Hiromi Kasai, Satoshi Nagai

“…These results show that investigating zooplankton–virus interactions can provide a better understanding of marine ecosystems.…”
Get full text

Mutations in the WUSCHEL-related homeobox1 gene cause an increased leaflet number in soybean by Yawei Li, Li Chu, Peiyun Lyu, Wenhuan Lyu, Ping Xie, Chunting Zhang, Haoxian Feng, Bin Liu, Tuanjie Zhao

“…Consequently, our study not only provides valuable insights into the role of GmWOX1A in soybean leaf development but also offers a potential strategy for high-yield breeding.…”
Get full text

Construction and validation of a prognostic model based on cuproptosis-related genes in patients with multiple myeloma by KANG Zhongmin, KANG Zhongmin, LI Licheng

“…The risk scores of the genes are significantly correlated with immune infiltration in the tumor microenvironment, which providing new molecular markers for individualized therapy. …”
Get full text

Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese by Dan Zhou, Ming Wu, Qilong Tan, Liyang Sun, Yuanxing Tu, Weifang Zheng, Yun Zhu, Min Yang, Kejia Hu, Fang Hu, Xiaohang Xu, Hanyi Zhou, Tian Luo, Fangming Yang, Fuqiang Li, Xin Jin, Huakang Tu, Wenyuan Li, Kui Wu, Xifeng Wu

“…Integrating a genome-transcriptome reference panel of lung tissue in 297 Chinese, we bridged the variant-lung cancer associations, highlighting genes including TP63 and DCBLD1. …”
Get full text

Construction of a stromal cell-related prognostic signature based on a 101-combination machine learning framework for predicting prognosis and immunotherapy response in triple-nega... by Fanrong Li, Congnan Jin, Yacheng Pan, Zheng Zhang, Liying Wang, Jieqiong Deng, Yifeng Zhou, Yifeng Zhou, Binbin Guo, Shenghua Zhang, Shenghua Zhang

“…Advances in single-cell transcriptomics have highlighted the impact of stromal cells on tumor progression, immune suppression, and immunotherapy. …”
Get full text

Comprehensive Integrated Analysis Reveals the Spatiotemporal Microevolution of Cancer Cells in Patients with Bone-Metastatic Prostate Cancer by Yinghua Feng, Xiuli Zhang, Guangpeng Wang, Feiya Yang, Ruifang Li, Lu Yin, Dong Chen, Wenkuan Wang, Mingshuai Wang, Zhiyuan Hu, Yuan Sh, Nianzeng Xing

“…This study aimed to systematically characterize the heterogeneity and microenvironmental adaptation of prostate cancer bone metastases using single-cell transcriptomics. <b>Methods:</b> We integrated the largest single-cell transcriptome dataset to date, encompassing 124 samples from primary prostate tumors, various bone metastatic sites, and non-malignant tissues (e.g., benign prostatic hyperplasia, normal bone marrow). …”
Get full text

An adeno-associated virus gene therapy strategy for anti-obesity treatment by nanocarrier-based delivery systems by Li Li, Wang Wang, Rong Li, Jiayue Guo, Xulin Hu, Yu Pan, Taoyuan Zhang, Sensen Chi, Zili Gu, Gaohui Zhu, Qi Liu, Shuai Tan

“…This innovative design enhances its stability and retention in vivo, providing a robust platform for continuous and efficient gene delivery. …”
Get full text

The extracellular matrix protein type I collagen and fibronectin are regulated by β-arrestin-1/endothelin axis in human ovarian fibroblasts by Ilenia Masi, Flavia Ottavi, Valentina Caprara, Danila Del Rio, Martina Kunkl, Francesca Spadaro, Valerio Licursi, Loretta Tuosto, Anna Bagnato, Laura Rosano’

“…Soluble factors secreted by cancer and stromal cells contribute to stroma remodeling through the secretion of ECM proteins, providing a favorable environment for cancer cell dissemination. …”
Get full text