A5054449714- Advanced Proteomics Techniques and Applications
- RNA modifications and cancer
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- RNA and protein synthesis mechanisms
- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Histiocytic Disorders and Treatments
- Plant Disease Resistance and Genetics
- Bioinformatics and Genomic Networks
- Monoclonal and Polyclonal Antibodies Research
- Muscle Physiology and Disorders
- Extracellular vesicles in disease
- Amino Acid Enzymes and Metabolism
- RNA Research and Splicing
- Autoimmune Bullous Skin Diseases
- Melamine detection and toxicity
- Reproductive System and Pregnancy
- Nutrition and Health in Aging
- Sarcoma Diagnosis and Treatment
- Peptidase Inhibition and Analysis
- Ubiquitin and proteasome pathways
- Estrogen and related hormone effects
ETH Zurich
2011-2020
University College Dublin
2017-2020
University of Alberta
2008-2014
Simon Fraser University
2005-2009
Plant Industry
2005
Freie Universität Berlin
2003
Franklin University
2003
University of British Columbia
1999-2002
Friedrich Schiller University Jena
2000-2001
Schiller International University
2001
We report the complete sequence of an extreme halophile, Halobacterium sp. NRC-1, harboring a dynamic 2,571,010-bp genome containing 91 insertion sequences representing 12 families and organized into large chromosome 2 related minichromosomes. The NRC-1 codes for 2,630 predicted proteins, 36% which are unrelated to any previously reported. Analysis shows presence pathways uptake utilization amino acids, active sodium-proton antiporter potassium systems, sophisticated photosensory signal...
Abstract Mass spectrometry is the method of choice for deep and reliable exploration (human) proteome. Targeted mass reliably detects quantifies pre-determined sets proteins in a complex biological matrix used studies that rely on quantitatively accurate reproducible measurement across multiple samples. It requires one-time, priori generation specific assay each targeted protein. SWATH-MS spectrometric combines data-independent acquisition (DIA) data analysis vastly extends throughput can be...
The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa Arabidopsis thaliana . A deeper division the plants is defined radiation gymnosperms, with latter comprising commercially important conifers. conifers are expected to provide information regarding evolution highly conserved small regulatory RNAs. Deep sequencing provides means characterize quantitatively profile in understudied these....
In eukaryotes, dozens of posttranscriptional modifications are directed to specific nucleotides in ribosomal RNAs (rRNAs) by small nucleolar (snoRNAs). We identified homologs snoRNA genes both branches the Archaea. Eighteen sno-like (sRNAs) were cloned from archaeon Sulfolobus acidocaldarius coimmunoprecipitation with archaeal fibrillarin and NOP56, eukaryotic snoRNA-associated proteins. trained a probabilistic model on these sRNAs search for more genomic sequences. Over 200 additional seven...
The genomes of hyperthermophilic Archaea encode dozens methylation guide, C/D box small RNAs that guide 2′-O-methylation ribose to specific sites in rRNA and various tRNAs. genes encoding the Sulfolobus homologues eukaryotic proteins are known be present nucleolar ribonucleoprotein (snoRNP) complexes were cloned, (aFIB, aNOP56, aL7a) expressed purified. purified along with an vitro transcript sR1 RNA reconstituted , into RNP complex. order assembly three onto was aL7a, aFIB. complex active...
Accurate classification of breast tumors is vital for patient management decisions and enables more precise cancer treatment. Here, we present a quantitative proteotyping approach based on sequential windowed acquisition all theoretical fragment ion spectra (SWATH) mass spectrometry establish key proteins tumor classification. The study 96 tissue samples representing five conventional subtypes. SWATH proteotype patterns largely recapitulate these subtypes; however, they also reveal varying...
RNA silencing is an evolutionarily conserved process in eukaryotes that represses gene expression by using 21- to 24-nt guide RNAs mediate mRNA cleavage or translational inhibition. Plants have two distinct groups of silencing-associated small (smRNAs): the micro (miRNAs) and interfering (siRNAs). A recent report Yu et al. [Yu, B., Yang, Z., Li, J., Minakhina, S., M., Padgett, R. W., Steward, & Chen, X. (2005) Science 307, 932-935] has shown plant miRNAs are modified at their 3′ termini...
Rationale. Obesity is a risk factor for atherothrombosis and various cancers. However, the mechanisms are not yet completely clarified. Objectives. We aimed to verify whether microparticles (MPs) released from thrombin-activated platelets differed in obese nonobese women number, size, proteomics cargo capacity modulate vitro expression of (i) genes related epithelial mesenchymal transition (EMT) endothelial (EndMT), (ii) cyclooxygenase(COX)-2 involved production angiogenic inflammatory...
Cancer cachexia (cancer-induced muscle wasting) is found in a subgroup of cancer patients leaving the with poor prognosis for survival due to lower tolerance chemotherapeutic drug. The cause wasting these not fully understood, and no predictive biomarker exists identify early on. Skeletal loss an inevitable consequence advancing age. As frequently occurs old age, identifying differentiating molecular mechanisms mediating vs. age-related sarcopenia are challenge. However, ability distinguish...
Abstract The manner by which genetic diversity within a population generates individual phenotypes is fundamental question of biology. To advance the understanding genotype–phenotype relationships towards level biochemical processes, we perform proteome-wide association study (PWAS) complex quantitative phenotype. We quantify variation wing imaginal disc proteomes in Drosophila reference panel (DGRP) lines using SWATH mass spectrometry. In spite very large (1/36 bp) between lines, proteome...
Abstract Background Micro(mi)RNAs are short RNA sequences, ranging from 16 to 35 nucleotides (miRBase; http://www.mirbase.org ). The majority of the identified sequences 21 or 22 in length. Despite range sequence lengths for different miRNAs, individual miRNAs were thought have a specific particular A recent report describing longer variant previously miRNA Arabidopsis thaliana prompted this investigation variations length other miRNAs. Results In paper, we demonstrate that fifth annotated...
Selected or multiple reaction monitoring is a targeted mass spectrometry method ( S / MRM ‐ MS ), in which many peptides are simultaneously and consistently analyzed during single liquid chromatography‐mass LC ) measurement. These capabilities make an attractive to monitor consistent set of proteins over various experimental conditions. To increase throughput for it advantageous use scheduled methods unfractionated protein extracts. Here, we established the practically measurable dynamic...
MicroiRNAs are genome encoded small double stranded RNAs that regulate expression of homologous mRNAs. With approximately 2500 human miRNAs and each having hundreds potential mRNA targets, miRNA based gene regulation is quite pervasive in both development disease. While there numerous studies investigating miRNA:mRNA miRNA:protein target correlations, relatively few miRNA:miRNA co-expression. Here we report on our analysis co-expression using data from the atlas Landgraf et al. Our indicates...
Current bovine pregnancy detection methods are not reliable until at least day 28 post artificial insemination (AI). The estrous cycle is approximately 21 days; consequently, producers miss an opportunity to rebreed the next event. Therefore, commercial interest exists for discovery of novel biomarkers which could reliably detect status or before pregnancy. objective present study was use liquid chromatography tandem mass spectrometry (LC-MS/MS) perform a global, label-free, proteomics on...
A specific form of endometrial cancer (EC) can develop in breast patients previously treated with tamoxifen (ET), an antagonist estrogen receptor (ER) that inhibits proliferation ER positive cancer. ET tumors have a different phenotype than tumors, which typically de novo without previous exposure to (EN). Here we aimed identify protein markers could serve as molecular targets either phenotype. set total 45 formalin-fixed paraffin-embedded (FFPE) tumor tissues and adjacent myometrium tissue...
Relating protein concentration to cell-type-specific responses is one of the remaining challenges for obtaining a quantitative systems level understanding mammalian signaling. Here we used mass-spectrometry (MS)- and antibody-based proteomic approaches measure abundances 75% hand-curated reconstructed ErbB network 198 proteins, in two established cell types (HEK293 MCF-7) primary keratinocyte cells. Comparison with other studies allowed building set proteins expressed all cells another which...
In the United States alone one in five newly diagnosed cancers men are prostate carcinomas (PCa). Androgen receptor (AR) status and PI3K-AKT-mTOR signal transduction pathway critical PCa. After initial response to single drugs targeting these pathways resistance often emerges, indicating need for combination therapy. Here, we address question of efficacy drug combinations development mechanisms targeted therapy by a systems pharmacology approach. We combine perturbation with detailed...
Aminoacyl-tRNA protein transferases catalyze the post-translational addition of amino acids to proteins. The eubacterial leucyl/phenylalanyl-tRNA-protein transferase (L/F transferase) catalyzes transfer leucine or phenylalanine from their respective aminoacylated tRNAs N-termini substrate proteins possessing an N-terminal lysine arginine acid. Conventional assays quantify L/F activity involve measuring radioactive acid incorporation into We have developed a quantitative matrix assisted laser...
Tandem mass (MS/MS) spectra generated by collision-induced dissociation (CID) typically lack redundant peptide sequence information in the form of e.g. b- and y-ion series due to frequent use sequence-specific endopeptidases cleaving C- or N-terminal Arg Lys residues.Here we introduce arginyl-tRNA protein transferase (ATE, EC 2.3.2.8) for proteomics. ATE recognizes acidic amino acids oxidized Cys at N-terminus a substrate conjugates an arginine from aminoacylated tRNA(Arg) onto peptide. This...
During ribosome biogenesis in the hyperthermophilic archaeon Sulfolobus acidocaldarius, at least three separate precursor endonucleolytic cleavages occur within 144-nucleotide-long 5' external transcribed spacer (5' ETS) region of rRNA operon primary transcript. The ETS sequence contains regions very stable helical structure. One cleavage to position -98) is single-stranded between and central domains; a second -31) 3' third ETS-16S junction +1). sites share common consensus around cleavage....