An 8X15k oligonucleotide microarray was developed consisting of 2334 Eubalaena glacialis probes and 2166 Tursiops truncatus probes and used to measure the effects, at transcriptomic level, of cadmium exposure in right whale kidney fibroblast cells. Cells were exposed to three concentrations (1 μM, 0.1 μM, and 0.01 μM) of cadmium chloride (CdCl) for three exposure times (1, 4, and 24 h). Cells exposed to 1 μM CdCl for 4 h and 24 h showed upregulated genes involved in protection from metal toxicity and oxidative stress, protein renaturation, apoptosis inhibition, as well as several regulators of cellular processes. Downregulated genes represented a suite of functions including cell proliferation, transcription regulation, actin polymerization, and stress fiber synthesis. The collection of differentially expressed genes in this study support proposed mechanisms of cadmium-induced apoptosis such as ubiquitin proteasome system disruption, Ca homeostasis interference, mitochondrial membrane potential collapse, reactive oxygen species (ROS) production, and cell cycle arrest. The results also have confirmed the right whale microarray as a reproducible tool in measuring differentiated gene expression that could be a valuable asset for transcriptome analysis of other baleen whales and potential health assessment protocols.
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http://dx.doi.org/10.1016/j.cbpc.2020.108946 | DOI Listing |
PLoS One
March 2025
Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi Medical College, Changzhi, Shanxi, China.
Objective: This study aims to investigate and analyze the differentially expressed genes (DEGs) in CD34 + hematopoietic stem cells (HSCs) from patients with myelodysplastic syndromes (MDS) through bioinformatics analysis, with the ultimate goal of uncovering the potential molecular mechanisms underlying pathogenesis of MDS. The findings of this study are expected to provide novel insights into clinical treatment strategies for MDS.
Methods: Initially, we downloaded three datasets, GSE81173, GSE4619, and GSE58831, from the public Gene Expression Omnibus (GEO) database as our training sets, and selected the GSE19429 dataset as the validation set.
STAR Protoc
March 2025
Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China; Shenyang Key Laboratory of Surveillance and Management for Vegetable Diseases and Insect Pests, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China. Electronic address:
Bacteriocytes are specialized insect cells adapted to harbor symbionts. However, their low number in individual whiteflies makes obtaining enough for transcriptome sequencing challenging. Here, we present a protocol for the isolation of whitefly bacteriocytes.
View Article and Find Full Text PDFClin Exp Rheumatol
March 2025
Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
Objectives: The genetic underpinnings of RA remain partially elucidated, motivating our exploration of copy number variations (CNV) and rare variations in the pathogenesis of RA.
Methods: We conducted an integrated analysis of the genome-wide landscape of CNV and exome-wide rare variation associations with RA in the UK Biobank. To strengthen our findings, we corroborated the results by the differentially expressed genes identified from gene expression profiles of synovial tissue of RA patients and health controls.
Brief Bioinform
March 2025
Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 633 Third Avenue, New York, NY 10017, United States.
Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate classification accuracy without undue resource allocation. Current sample size calculation methods rely on assumptions and algorithms that may not align with supervised machine learning techniques for sample classification.
View Article and Find Full Text PDFDiscov Oncol
March 2025
Department of Anorectal Surgery, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, 58 Lushan Rd., Yuelu District, Changsha, 410006, Hunan, People's Republic of China.
Background: Asian cancer patients have become the highest morbidity and mortality group, and gastrointestinal tumors account for the majority of them, so it is urgent to find effective targets. Therefore, ferroptosis-related lncRNAs models were established to predict the prognosis and clinical immune characteristics of GI cancer.
Methods: RNA sequencing and clinical data were collected from the TCGA database (LIHC, STAD, ESCA, PAAD, COAD, CHOL, and READ) of patients with gastrointestinal cancer in Asia.
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