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Internal transcribed spacer metagenomics data unravelling the core fungal community structure residing the wheat and maize rhizosphere.
Data Brief
February 2025
Department of Biology, Allama Iqbal Open University, Islamabad, Pakistan.
Plants are colonized by a vast array of microorganisms that outstrip plant cell densities and genes, thus referred to as plant's second genome or extended genome. The microbial communities exert a significant influence on the vigor, growth, development and productivity of plants by supporting nutrient acquisition, organic matter decomposition and tolerance against biotic and abiotic stresses such as heat, high salt, drought and disease, by regulating plant defense responses. The rhizosphere is a complex micro-ecological zone in the direct vicinity of plant roots and is considered a hotspot of microbial diversity.
View Article and Find Full Text PDFInferring Tripartite Associations of Vector-Borne Plant Pathogens Using a Next-Generation Sequencing Approach.
Pathogens
January 2025
Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA.
Phytoplasmas are a group of plant-pathogenic, cell-wall-less bacteria vectored primarily by leafhoppers (Hemiptera Cicadellidae), one of the most diverse families of insects. Despite the importance of documenting associations between phytoplasmas, their insect vectors, and plant hosts to prevent disease outbreaks, such knowledge is currently highly incomplete and largely neglects the diversity of the system in natural areas. Here, we used anchored hybrid enrichment (AHE) to recover the DNA of five plant genes (, , , , and ) in 58 phloem-feeding leafhoppers from around the world that had previously tested positive for phytoplasma infection.
View Article and Find Full Text PDFIdentification the Cellular Senescence Associated lncRNA LINC01579 in Gastric Cancer.
J Cell Mol Med
January 2025
Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, People's Republic of China.
Cellular senescence is a key promoter of tumorigenesis and malignant progression. This study aimed to develop a predictive model for assessing cellular senescence in gastric cancer (GC) outcomes. We identified senescence-related genes and lncRNAs from 375 stomach adenocarcinoma (STAD) patients and established a prognostic senescence score using multivariate Cox regression, validated in testing, TCGA-STAD and the combined TCGA-COAD and READ cohorts.
View Article and Find Full Text PDFApplication of TRIM58 Gene Methylation-Based Minimal Residual Disease Assays in Non-Small Cell Lung Cancer for Prognosis Prediction and Treatment Decision.
Ann Clin Lab Sci
November 2024
Department of Thoracic Surgery, First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
Objective: To identify key genes associated with the prognosis of non-small cell lung cancer (NSCLC) through bioinformatics analysis and experimental validation, exploring the expression of the TRIM58 gene and its potential effect as a tumor suppressor.
Methods: In this study, differentially expressed genes (DEGs) and differentially methylated genes (DMGs) related to lung adenocarcinoma and lung squamous cell carcinoma were selected from the TCGA dataset, with the Limma package in R software used for further filtering and intersection, followed by the assessment of the relationship between these genes and NSCLC prognosis using log-rank tests and univariate Cox regression analysis. Meanwhile, six clinical NSCLC cancer and adjacent tissue samples were collected, along with the detection of TRIM58 mRNA and protein levels using RT-PCR and Western blot.
Filter-aided extracellular vesicle enrichment (FAEVEr) for proteomics.
Mol Cell Proteomics
January 2025
VIB-UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium. Electronic address:
Extracellular vesicles (EVs), membrane-delimited nanovesicles that are secreted by cells into the extracellular environment, are gaining substantial interest due to their involvement in cellular homeostasis and their contribution to disease pathology. The latter in particular has led to an exponential increase in interest in EVs as they are considered to be circulating packages containing potential biomarkers and are also a possible biological means to deliver drugs in a cell-specific manner. However, several challenges hamper straightforward proteome analysis of EVs as they are generally low abundant and reside in complex biological matrices.
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