Project description:We report the first data of RNA sequencing from two different banana cultivars from Musa acuminata cv. Mas Kirana (AA group) genome and Musa balbisiana cv. Klutuk (BB group) genome in response to blood disease infection caused by Ralstonia syzygii subsp. celebesensis (Rsc)
Project description:We adopted high-throughput sequencing and mass spectrometry (MS) techniques in this study and carried out an integrative analysis of exosome proteome and DNA methylation data from blood samples of normal and Kidney stone disease patients to screen biomarkers.
Project description:The ability to use blood to predict the outcomes of Parkinson’s disease (PD), including disease progression and development of cognitive and motor complications, would be of enormous clinical value. We undertook deep RNA sequencing from the caudate and putamen of postmortem PD (n=35) and control (n=40) striatum, and compared molecular profiles with clinical features, and samples obtained from antemortem peripheral blood from an independent cohort. Cognitive and motor complications of PD were associated with molecular changes in the caudate (e.g., stress response) and putamen (endothelial pathways) respectively. Later and earlier-onset PD were molecularly distinct, and disease duration was associated with changes in caudate (oligodendrocyte development) and putamen (cellular senescence) respectively. Molecular signatures in the postmortem PD brain were also evident in antemortem peripheral blood, and correlated with clinical disease features. Together, these findings identify molecular signatures in PD patients' brain and blood of potential pathophysiologic and prognostic importance
Project description:We measured abundances of tRNAs by means of hydro-tRNA-seq (Gogakos et al., 2017), a method based on partial alkaline RNA hydrolysis that generates fragments suitable for sequencing, in the genome-reduced bacterium Mycoplasma pneumoniae.
Project description:Rapid, simple and reliable blood tests for Parkinson’s disease (PD) may enable pre-symptomatic diagnosis and facilitate disease-changing treatments. Here, we report escalated elevated levels of angiogenin-cleaved a disease specific group of nuclear genome-originated tRNA fragments (hereafter, PD-tRFs) carrying a unique seven-nucleotide motif in substantia nigra, cerebrospinal fluid and blood of PD patients. A blood test using RNA isolated from whole blood and dual multiplexl qPCR primers for PD-tRFs and mitochondrial-originated tRFs (MT-tRFs) successfully distinguished pre-symptomatic PD patients from controls, outperforming traditional clinical scoring (ROC-AUC of 0.86 vs. 0.73). Indicating relevance to disease symptoms, PD patients carrying GBA, SNCA or LRRK2 mutations presented elevated blood PD/MT-tRF ratios compared to mutations-carrying non-symptomatic individuals which indicates relevance to disease symptoms. Furthermore, PD-tRFs’ potential for ribosomal association predicted translational inhibition. Intriguingly, PD-tRFs levels declined both in patients’ blood following deep brain stimulation andas well as in in depolarized neuroblastoma cells where PD-tRFs presented transientlydepolirization impaired impacted ribosomal associations. Our findings facilitate a sensitive and accurate blood test for early PD.
Project description:Given the facilities for whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now only based on automated prediction. However, errors in terms of gene structure are still frequently reported especially for the correct determination of initiation start codons. Here, we propose a strategy to enrich and detect protein N-termini by mass spectrometry in order to refine genome annotation. After selective protein N-termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPPAc-OSu) as labeling reagent, protein digestion was performed with three proteases in parallel. TMPP-labeled N-terminal-most peptides were further resolved from internal peptides by the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting methodology before analysis with tandem mass spectrometry. We refined the annotation of the genome of a model marine bacterium, Roseobacter denitrificans.
Project description:In order to support our research of chronic myeloid leukemia in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-seq) using chronic myeloid leukemia blood in early disease. We obtained a total of 17.74 million read pairs from blood in early disease.The RNA-seq data derived from the sample illustrated the expreesion genes in chronic myeloid leukemia blood in early disease of human. 1 sample examined: blood in early disease.
