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Search Results: 1 - 10 of 132072 matches for " Jesper V. Olsen "
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PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
Florian Gnad, Shubin Ren, Juergen Cox, Jesper V Olsen, Boris Macek, Mario Oroshi, Matthias Mann
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-11-r250
Abstract: Protein phosphorylation is a ubiquitous and important post-translational modification, responsible for modulating protein function, localization, interaction and stability [1-4]. High-throughput experimental studies such as our recent large scale analysis of the human phosphoproteome by quantitative mass spectrometry, in which we measured the time courses of more than 6,600 phosphorylation sites in response to growth factor stimulation [5], enable us to study biological systems from a global perspective. Those sites were identified by high resolution mass spectrometry with an estimated false positive rate of less than one percent and constitute an unbiased, in-depth sampling of the in vivo phosphoproteome. In addition, PHOSIDA includes large-scale phosphoproteomes from various eukaryotic and prokaryotic organisms, such as Bacillus subtilis [6] and Escherichia coli, providing information about the evolution of phosphorylation events in the cell.We developed PHOSIDA to retrieve and analyze phosphosites from large-scale and high-confidence quantitative phosphoproteomics experiments, usually studying the response of biological systems to various stimuli by the integration of time course data. Thus, it is the first phosphosite database to explicitly store quantitative data on the relative level of phosphorylation. PHOSIDA also matches kinase motifs to phosphosites. A challenge in mass spectrometry-based phosphosite mapping is the fact that phosphopeptides are measured, which then need to be mapped to one or more corresponding protein sequences. This problem is addressed in PHOSIDA by a many-to-many mapping between phosphopeptide sequences and protein entries in the sequence database. One of the fundamental strengths of PHOSIDA lies in the high quality of the in vivo data contained in the database and in the very large size of its in vivo data sets.In this paper we describe the features and capabilities of PHOSIDA. We also use the analysis tools in PHOSIDA to investigate
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
Jun Adachi, Chanchal Kumar, Yanling Zhang, Jesper V Olsen, Matthias Mann
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-9-r80
Abstract: We employed one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis and reverse phase high-performance liquid chromatography for protein separation and fractionation. Fractionated proteins were digested in-gel or in-solution, and digests were analyzed with the LTQ-FT and LTQ-Orbitrap at parts per million accuracy and with two consecutive stages of mass spectrometric fragmentation. We identified 1543 proteins in urine obtained from ten healthy donors, while essentially eliminating false-positive identifications. Surprisingly, nearly half of the annotated proteins were membrane proteins according to Gene Ontology (GO) analysis. Furthermore, extracellular, lysosomal, and plasma membrane proteins were enriched in the urine compared with all GO entries. Plasma membrane proteins are probably present in urine by secretion in exosomes.Our analysis provides a high-confidence set of proteins present in human urinary proteome and provides a useful reference for comparing datasets obtained using different methodologies. The urinary proteome is unexpectedly complex and may prove useful in biomarker discovery in the future.Urine is formed in the kidney by ultrafiltration from the plasma to eliminate waste products, for instance urea and metabolites. Although the kidney accounts for only 0.5% of total body mass, a large volume of plasma (350-400 ml/100 g tissue/min) flows into the kidney, generating a large amount of ultrafiltrate (150-180 l/day) under normal physiologic conditions [1,2]. Components in the ultrafiltrate such as water, glucose, amino acids, and inorganic salts are selectively reabsorbed, and less than 1% of ultrafiltrate is excreted as urine. Serum proteins are filtered based on their sizes and charges at the glomeruli [3]. After passing through glomeruli, abundant serum proteins such as albumin, immunoglobulin light chain, transferrin, vitamin D binding protein, myoglobin, and receptor-associated protein are reabsorbed, mainly by endocytic recept
The prognostic value of the suPARnostic? ELISA in HIV-1 infected individuals is not affected by uPAR promoter polymorphisms
Uffe V Schneider, Rikke L Nielsen, Court Pedersen, Jesper Eugen-Olsen
BMC Infectious Diseases , 2007, DOI: 10.1186/1471-2334-7-134
Abstract: DNA samples were collected retrospectively from 145 Danes infected with HIV-1 with known seroconversion times. In addition, plasma was collected retrospectively from 81 of these participants for use in the suPAR analysis. Survival was analysed using Kaplan Meier analysis.Survival was strongly correlated to suPAR levels (p < 0.001). Levels at or above 6 ng/ml were associated with death in 13 of 27 patients within a two-years period; whereas only one of 54 patients with suPAR levels below 6 ng/ml died during this period. We identified two common uPAR promoter polymorphisms: a G to A transition at -118 and an A to G transition at -465 comparative to the transcription start site. These promoter transitions influenced neither suPAR levels nor patient survival.Plasma suPAR levels, as measured by the suPARnostic? assay, were strongly predictive of survival in ART-na?ve HIV-1 infected patients. Furthermore, plasma suPAR levels were not influenced by uPAR promoter polymorphisms.Patients with HIV infection receive regular clinical follow-up to assess the need for more invasive treatment regimens such as initiation of ART. Currently, this assessment relies on the evaluation of HIV RNA viral load and CD4 cell count; the former of which requires expensive, high technology laboratory facilities. Thus, there is a need for robust, reliable prognostic markers for HIV infection that can also be used in resource-limited settings. Inflammation increases HIV replication and CD4 T cell depletion [1] and markers of inflammation are potential candidates as prognostic markers for HIV. However, the plasma level of these markers should be independent of genetic polymorphisms in order to be reliable biomarkers.An elevated level of suPAR is predictive of negative clinical outcome in a number of different diseases such as HIV-1[2], tuberculosis [3], pneumococcal bacteraemia [4], rheumatoid arthritis [5], multiple sclerosis [6] and certain forms of cancer [7,8]. suPAR is an independent marker of
Comprehensive Identification of SUMO2/3 Targets and Their Dynamics during Mitosis
Julie Schou, Christian D. Kelstrup, Daniel G. Hayward, Jesper V. Olsen, Jakob Nilsson
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0100692
Abstract: During mitosis large alterations in cellular structures occur rapidly, which to a large extent is regulated by post-translational modification of proteins. Modification of proteins with the small ubiquitin-related protein SUMO2/3 regulates mitotic progression, but few mitotic targets have been identified so far. To deepen our understanding of SUMO2/3 during this window of the cell cycle, we undertook a comprehensive proteomic characterization of SUMO2/3 modified proteins in mitosis and upon mitotic exit. We developed an efficient tandem affinity purification strategy of SUMO2/3 modified proteins from mitotic cells. Combining this purification strategy with cell synchronization procedures and quantitative mass spectrometry allowed for the mapping of numerous novel targets and their dynamics as cells progressed out of mitosis. This identified RhoGDIα as a major SUMO2/3 modified protein, specifically during mitosis, mediated by the SUMO ligases PIAS2 and PIAS3. Our data provide a rich resource for further exploring the role of SUMO2/3 modifications in mitosis and cell cycle regulation.
Review of Survey activities 2008: Soil erosion and land-use change during the last six millennia recorded in lake sediments of Gudme S , Fyn, Denmark
Rasmussen, Peter,Olsen, Jesper
Geological Survey of Denmark and Greenland Bulletin , 2009,
Abstract:
Phosphorylation of the Yeast γ-Tubulin Tub4 Regulates Microtubule Function
Tien-chen Lin,Linda Gombos,Annett Neuner,Dominik Sebastian,Jesper V. Olsen,Ajla Hrle,Christian Benda,Elmar Schiebel
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019700
Abstract: The yeast γ-tubulin Tub4 is assembled with Spc97 and Spc98 into the small Tub4 complex. The Tub4 complex binds via the receptor proteins Spc72 and Spc110 to the spindle pole body (SPB), the functional equivalent of the mammalian centrosome, where the Tub4 complex organizes cytoplasmic and nuclear microtubules. Little is known about the regulation of the Tub4 complex. Here, we isolated the Tub4 complex with the bound receptors from yeast cells. Analysis of the purified Tub4 complex by mass spectrometry identified more than 50 phosphorylation sites in Spc72, Spc97, Spc98, Spc110 and Tub4. To examine the functional relevance of the phosphorylation sites, phospho-mimicking and non-phosphorylatable mutations in Tub4, Spc97 and Spc98 were analyzed. Three phosphorylation sites in Tub4 were found to be critical for Tub4 stability and microtubule organization. One of the sites is highly conserved in γ-tubulins from yeast to human.
Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system
Lyris MF de Godoy, Jesper V Olsen, Gustavo A de Souza, Guoqing Li, Peter Mortensen, Matthias Mann
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-6-r50
Abstract: To probe the yeast proteome in depth and determine factors currently preventing complete analysis, we grew yeast cells, extracted proteins and separated them by one-dimensional gel electrophoresis. Peptides resulting from trypsin digestion were analyzed by liquid chromatography mass spectrometry on a linear ion trap-Fourier transform mass spectrometer with very high mass accuracy and sequencing speed. We achieved unambiguous identification of more than 2,000 proteins, including very low abundant ones. Effective dynamic range was limited to about 1,000 and effective sensitivity to about 500 femtomoles, far from the subfemtomole sensitivity possible with single proteins. We used SILAC (stable isotope labeling by amino acids in cell culture) to generate one-to-one pairs of true peptide signals and investigated if sensitivity, sequencing speed or dynamic range were limiting the analysis.Advanced mass spectrometry methods can unambiguously identify more than 2,000 proteins in a single proteome. Complex mixture analysis is not limited by sensitivity but by a combination of dynamic range (high abundance peptides preventing sequencing of low abundance ones) and by effective sequencing speed. Substantially increased coverage of the yeast proteome appears feasible with further development in software and instrumentation.Technological goals of proteomics include the identification and quantification of as many proteins as possible in the proteome to be investigated [1-3]. However, despite spectacular advances in mass spectrometric technology, no cellular or microorganismal proteome has been completely sequenced yet. This has not hindered successful application of proteomics, as most biologically relevant studies have focused on functionally relevant 'subproteomes'. For example, our laboratory has been interested in protein constituents of organelles such as the nucleolus and mitochondria [4-6]. These proteomes have complexities of about a 1,000 proteins and are largely within
Predicting Kinase Activity in Angiotensin Receptor Phosphoproteomes Based on Sequence-Motifs and Interactions
Rikke B?gebo, Heiko Horn, Jesper V. Olsen, Steen Gammeltoft, Lars J. Jensen, Jakob L. Hansen, Gitte L. Christensen
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0094672
Abstract: Recent progress in the understanding of seven-transmembrane receptor (7TMR) signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR) is one of the most studied 7TMRs with respect to selective activation of the β-arrestin dependent signalling. Two complimentary global phosphoproteomics studies have analyzed the complex signalling induced by the AT1aR. Here we integrate the data sets from these studies and perform a joint analysis using a novel method for prediction of differential kinase activity from phosphoproteomics data. The method builds upon NetworKIN, which applies sophisticated linear motif analysis in combination with contextual network modelling to predict kinase-substrate associations with high accuracy and sensitivity. These predictions form the basis for subsequently nonparametric statistical analysis to identify likely activated kinases. This suggested that AT1aR-dependent signalling activates 48 of the 285 kinases detected in HEK293 cells. Of these, Aurora B, CLK3 and PKG1 have not previously been described in the pathway whereas others, such as PKA, PKB and PKC, are well known. In summary, we have developed a new method for kinase-centric analysis of phosphoproteomes to pinpoint differential kinase activity in large-scale data sets.
Corn and Soybean Responses to Two Tillage Systems in a Cool Growing Season  [PDF]
Jesper K. V. Nielsen, Howard J. Woodard
Open Journal of Soil Science (OJSS) , 2015, DOI: 10.4236/ojss.2015.58016
Abstract: A field study in 2014 documented corn and soybean biomass and nutrient responses between conventional-till and no-till tillage systems at Beresford, SD during cooler than normal weather conditions with adequate soil moisture. The overall study was established in 1992. Each treatment plot was monitored weekly from June to August for soil moisture, temperature, and plant growth stages. Biomass was harvested during and at the end of the growing season for yield and nutrient content. Soil moisture measured throughout the early and middle part of the growing season was determined to be sufficient for crop growth, since precipitation was much greater than normal in June (33.2 cm). However, air temperature was below normal early in the growing season and lowered Growing Degree Days (939°C) compared to the 30-year average (139°C). Soil temperatures (5 cm depth) were not significant between tillage treatments in the corn plots during the growing season for 12 observation dates (range 16.3°C - 28.0°C). Plant growth was not significantly different between tillage treatments, reflecting the lack of soil temperature differences (5 cm depth) between tillage treatments. The mid-season plant tissue and crop residue at harvest nutrient content (P, K, and Zn) were not significant between tillage treatments. Corn grain yields were 10.3 T·ha-1 and 10.1 T·ha-1 for conventional tillage and no-till, respectively. Soybean grain yields were 3.9 T·ha-1?and 3.3 T·ha-1 for conventional tillage and no-till, respectively. These results would more than likely have been
Evidence for Widespread AGN Activity among Massive Quiescent Galaxies at z ~ 2
Karen Pardos Olsen,Jesper Rasmussen,Sune Toft,Andrew W. Zirm
Physics , 2012, DOI: 10.1088/0004-637X/764/1/4
Abstract: We quantify the presence of Active Galactic nuclei (AGN) in a mass-complete (M_* >5e10 M_sun) sample of 123 star-forming and quiescent galaxies at 1.5 < z < 2.5, using X-ray data from the 4 Ms Chandra Deep Field-South (CDF-S) survey. 41+/-7% of the galaxies are detected directly in X-rays, 22+/-5% with rest-frame 0.5-8 keV luminosities consistent with hosting luminous AGN (L_0.5-8keV > 3e42 ergs/s). The latter fraction is similar for star-forming and quiescent galaxies, and does not depend on galaxy stellar mass, suggesting that perhaps luminous AGN are triggered by external effects such as mergers. We detect significant mean X-ray signals in stacked images for both the individually non-detected star-forming and quiescent galaxies, with spectra consistent with star formation only and/or a low luminosity AGN in both cases. Comparing star formation rates inferred from the 2-10 keV luminosities to those from rest-frame IR+UV emission, we find evidence for an X-ray excess indicative of low-luminosity AGN. Among the quiescent galaxies, the excess suggests that as many as 70-100% of these contain low- or high-luminosity AGN, while the corresponding fraction is lower among star-forming galaxies (43-65%). The ubiquitous presence of AGN in massive, quiescent z ~ 2 galaxies that we find provides observational support for the importance of AGN in impeding star formation during galaxy evolution.
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