| 1. |
- Aamodt, K., et al.
(författare)
-
The ALICE experiment at the CERN LHC
- 2008
-
Ingår i: Journal of Instrumentation. - 1748-0221. ; 3:S08002
-
Forskningsöversikt (refereegranskat)abstract
- ALICE (A Large Ion Collider Experiment) is a general-purpose, heavy-ion detector at the CERN LHC which focuses on QCD, the strong-interaction sector of the Standard Model. It is designed to address the physics of strongly interacting matter and the quark-gluon plasma at extreme values of energy density and temperature in nucleus-nucleus collisions. Besides running with Pb ions, the physics programme includes collisions with lighter ions, lower energy running and dedicated proton-nucleus runs. ALICE will also take data with proton beams at the top LHC energy to collect reference data for the heavy-ion programme and to address several QCD topics for which ALICE is complementary to the other LHC detectors. The ALICE detector has been built by a collaboration including currently over 1000 physicists and engineers from 105 Institutes in 30 countries, Its overall dimensions are 16 x 16 x 26 m(3) with a total weight of approximately 10 000 t. The experiment consists of 18 different detector systems each with its own specific technology choice and design constraints, driven both by the physics requirements and the experimental conditions expected at LHC. The most stringent design constraint is to cope with the extreme particle multiplicity anticipated in central Pb-Pb collisions. The different subsystems were optimized to provide high-momentum resolution as well as excellent Particle Identification (PID) over a broad range in momentum, up to the highest multiplicities predicted for LHC. This will allow for comprehensive studies of hadrons, electrons, muons, and photons produced in the collision of heavy nuclei. Most detector systems are scheduled to be installed and ready for data taking by mid-2008 when the LHC is scheduled to start operation, with the exception of parts of the Photon Spectrometer (PHOS), Transition Radiation Detector (TRD) and Electro Magnetic Calorimeter (EMCal). These detectors will be completed for the high-luminosity ion run expected in 2010. This paper describes in detail the detector components as installed for the first data taking in the summer of 2008.
|
|
| 2. |
- Yao, W-M, et al.
(författare)
-
Review of Particle Physics
- 2006
-
Ingår i: Journal of Physics G: Nuclear and Particle Physics. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 33:1, s. 1-1
-
Tidskriftsartikel (refereegranskat)
|
|
| 3. |
- Clark, Andrew G., et al.
(författare)
-
Evolution of genes and genomes on the Drosophila phylogeny
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
-
Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
|
|
| 4. |
- Liu, Kui, et al.
(författare)
-
Kallikrein genes are associated with lupus and glomerular basement membrane-specific antibody-induced nephritis in mice and humans
- 2009
-
Ingår i: Journal of Clinical Investigation. - 0021-9738 .- 1558-8238. ; 119:4, s. 911-923
-
Tidskriftsartikel (refereegranskat)abstract
- Immune-mediated nephritis contributes to disease in systemic lupus erythematosus, Goodpasture syndrome (caused by antibodies specific for glomerular basement membrane [anti-GBM antibodies]), and spontaneous lupus nephritis. Inbred mouse strains differ in susceptibility to anti-GBM antibody-induced and spontaneous lupus nephritis. This study sought to clarify the genetic and molecular factors that maybe responsible for enhanced immune-mediated renal disease in these models. When the kidneys of 3 mouse strains sensitive to anti-GBM antibody-induced nephritis were compared with those of 2 control strains using microarray analysis, one-fifth of the underexpressed genes belonged to the kallikrein gene family,which encodes serine esterases. Mouse strains that upregulated renal and urinary kallikreins exhibited less evidence of disease. Antagonizing the kallikrein pathway augmented disease, while agonists dampened the severity of anti-GBM antibody-induced nephritis. In addition, nephritis-sensitive mouse strains had kallikrein haplotypes that were distinct from those of control strains, including several regulatory polymorphisms,some of which were associated with functional consequences. Indeed, increased susceptibility to anti-GBM antibody-induced nephritis and spontaneous lupus nephritis was achieved by breeding mice with a genetic interval harboring the kallikrein genes onto a disease-resistant background. Finally, both human SLE and spontaneous lupus nephritis were found to be associated with kallikrein genes, particularly KLK1 and the KLK3 promoter, when DNA SNPs from independent cohorts of SLE patients and controls were compared. Collectively, these studies suggest that kallikreins are protective disease-associated genes in anti-GBM antibody-induced nephritis and lupus.
|
|
| 5. |
|
|
| 6. |
|
|
| 7. |
- de Bakker, Paul I. W., et al.
(författare)
-
Transferability of tag SNPs in genetic association studies in multiple populations
- 2006
-
Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 38:11, s. 1298-1303
-
Tidskriftsartikel (refereegranskat)abstract
- A general question for linkage disequilibrium-based association studies is how power to detect an association is compromised when tag SNPs are chosen from data in one population sample and then deployed in another sample. Specifically, it is important to know how well tags picked from the HapMap DNA samples capture the variation in other samples. To address this, we collected dense data uniformly across the four HapMap population samples and eleven other population samples. We picked tag SNPs using genotype data we collected in the HapMap samples and then evaluated the effective coverage of these tags in comparison to the entire set of common variants observed in the other samples. We simulated case-control association studies in the non-HapMap samples under a disease model of modest risk, and we observed little loss in power. These results demonstrate that the HapMap DNA samples can be used to select tags for genome-wide association studies in many samples around the world.
|
|
| 8. |
- Ding, Li, et al.
(författare)
-
Somatic mutations affect key pathways in lung adenocarcinoma
- 2008
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 455:7216, s. 1069-1075
-
Tidskriftsartikel (refereegranskat)abstract
- Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers--including NF1, APC, RB1 and ATM--and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
|
|
| 9. |
|
|
| 10. |
- Kjeldsen, Frank, et al.
(författare)
-
On studying protein phosphorylation patterns using bottom-up LC-MS/MS : the case of human alpha-casein
- 2007
-
Ingår i: The Analyst. - : Royal Society of Chemistry (RSC). - 0003-2654 .- 1364-5528. ; 132:8, s. 768-776
-
Tidskriftsartikel (refereegranskat)abstract
- Most proteomics studies involving mapping post-translational modifications, such as the phosphorylation of serine and threonine, are performed today using the 'bottom-up' approach. This approach involves enzymatic cleavage of proteins, most often by trypsin, with subsequent nano-LC-MS/MS. The occupancy rates of phosphosites in proteins may differ by orders of magnitude, and thus the occupancy rate must be reported for each occupied phosphosite. To highlight potential pitfalls in quantifying the occupancy rates, αs1- casein from human milk was selected as a model molecule representing moderately phosphorylated proteins. For this purpose, human milk from one Caucasian woman in the eighth month of lactation was used. The phosphorylation level of caseins is believed to have major implications for the formation of micelles that are involved in delivering valuable calcium phosphate and other minerals to the new-born. Human αs1-casein has been reported to be much less phosphorylated than ruminant caseins, which may indicate a different function of caseins in humans. Revealing the phosphorylation pattern in human casein can thus shed light on its function. The current study found that the sequence region between the residues Ser70 and Ser76 in human αs1-casein is in fact phosphorylated, contrary to previous knowledge. The site of the most abundant phosphorylation is Ser75, in agreement with the known action of the mammary gland casein kinase. There is evidence for the second phosphorylation in that region, possibly at Ser73. Earlier reported positions of phosphorylations at Ser18 and Ser26 are also confirmed, but not the dominance of Ser18 phosphorylation. The occupancy rates at Ser18, Ser26 and Ser75 are estimated to be (7 ± 2), (20 ± 6) and (27 ± 9)%, respectively. Owing to differences in the ionization efficiency between phosphorylated and unphosphorylated peptides a 30% error margin is added to the occupancy rates. The highlighted pitfalls of the bottom-up strategy include the sensitivity of enzymes to proximal acidic and phosphorylated residues and the presence of multiple isoforms, including unexpected ones, of the tryptic peptides. The utility of the earlier introduced PhosTS_hunter and ModifiComb approaches for evading the latter pitfall is demonstrated.
|
|
| 11. |
|
|
| 12. |
- Rueda, B., et al.
(författare)
-
The STAT4 gene influences the genetic predisposition to systemic sclerosis phenotype
- 2009
-
Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 18:11, s. 2071-2077
-
Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to investigate the possible role of STAT4 gene in the genetic predisposition to systemic sclerosis (SSc) susceptibility or clinical phenotype. A total of 1317 SSc patients [896 with limited cutaneous SSc (lcSSc) and 421 with diffuse cutaneous SSc (dcSSc)] and 3113 healthy controls, from an initial case-control set of Spanish Caucasian ancestry and five independent cohorts of European ancestry (The Netherlands, Germany, Sweden, Italy and USA), were included in the study. The rs7574865 polymorphism was selected as STAT4 genetic marker. We observed that the rs7574865 T allele was significantly associated with susceptibility to lcSSc in the Spanish population [P = 1.9 x 10(-5) odds ratio (OR) 1.61 95% confidence intervals (CI) 1.29-1.99], but not with dcSSc (P = 0.41 OR 0.84 95% CI 0.59-1.21). Additionally, a dosage effect was observed showing individuals with rs7574865 TT genotype higher risk for lcSSc (OR 3.34, P = 1.02 x 10(-7) 95% CI 2.11-5.31). The association of the rs7574865 T allele with lcSSc was confirmed in all the replication cohorts with different effect sizes (OR ranging between 1.15 and 1.86), as well as the lack of association of STAT4 with dcSSc. A meta-analysis to test the overall effect of the rs7574865 polymorphism showed a strong risk effect of the T allele for lcSSc susceptibility (pooled OR 1.54 95% CI 1.36-1.74; P < 0.0001). Our data show a strong and reproducible association of the STAT4 gene with the genetic predisposition to lcSSc suggesting that this gene seems to be one of the genetic markers influencing SSc phenotype.
|
|
| 13. |
- van Meurs, Joyce B, et al.
(författare)
-
Large-scale analysis of association between LRP5 and LRP6 variants and osteoporosis.
- 2008
-
Ingår i: JAMA : the journal of the American Medical Association. - Chicago : American Medical Association (AMA). - 1538-3598 .- 0098-7484. ; 299:11, s. 1277-90
-
Tidskriftsartikel (refereegranskat)abstract
- CONTEXT: Mutations in the low-density lipoprotein receptor-related protein 5 (LRP5) gene cause rare syndromes characterized by altered bone mineral density (BMD). More common LRP5 variants may affect osteoporosis risk in the general population. OBJECTIVE: To generate large-scale evidence on whether 2 common variants of LRP5 (Val667Met, Ala1330Val) and 1 variant of LRP6 (Ile1062Val) are associated with BMD and fracture risk. DESIGN AND SETTING: Prospective, multicenter, collaborative study of individual-level data on 37,534 individuals from 18 participating teams in Europe and North America. Data were collected between September 2004 and January 2007; analysis of the collected data was performed between February and May 2007. Bone mineral density was assessed by dual-energy x-ray absorptiometry. Fractures were identified via questionnaire, medical records, or radiographic documentation; incident fracture data were available for some cohorts, ascertained via routine surveillance methods, including radiographic examination for vertebral fractures. MAIN OUTCOME MEASURES: Bone mineral density of the lumbar spine and femoral neck; prevalence of all fractures and vertebral fractures. RESULTS: The Met667 allele of LRP5 was associated with reduced lumbar spine BMD (n = 25,052 [number of participants with available data]; 20-mg/cm2 lower BMD per Met667 allele copy; P = 3.3 x 10(-8)), as was the Val1330 allele (n = 24,812; 14-mg/cm2 lower BMD per Val1330 copy; P = 2.6 x 10(-9)). Similar effects were observed for femoral neck BMD, with a decrease of 11 mg/cm2 (P = 3.8 x 10(-5)) and 8 mg/cm2 (P = 5.0 x 10(-6)) for the Met667 and Val1330 alleles, respectively (n = 25 193). Findings were consistent across studies for both LRP5 alleles. Both alleles were associated with vertebral fractures (odds ratio [OR], 1.26; 95% confidence interval [CI], 1.08-1.47 for Met667 [2001 fractures among 20 488 individuals] and OR, 1.12; 95% CI, 1.01-1.24 for Val1330 [1988 fractures among 20,096 individuals]). Risk of all fractures was also increased with Met667 (OR, 1.14; 95% CI, 1.05-1.24 per allele [7876 fractures among 31,435 individuals)]) and Val1330 (OR, 1.06; 95% CI, 1.01-1.12 per allele [7802 fractures among 31 199 individuals]). Effects were similar when adjustments were made for age, weight, height, menopausal status, and use of hormone therapy. Fracture risks were partly attenuated by adjustment for BMD. Haplotype analysis indicated that Met667 and Val1330 variants both independently affected BMD. The LRP6 Ile1062Val polymorphism was not associated with any osteoporosis phenotype. All aforementioned associations except that between Val1330 and all fractures and vertebral fractures remained significant after multiple-comparison adjustments. CONCLUSIONS: Common LRP5 variants are consistently associated with BMD and fracture risk across different white populations. The magnitude of the effect is modest. LRP5 may be the first gene to reach a genome-wide significance level (a conservative level of significance [herein, unadjusted P < 10(-7)] that accounts for the many possible comparisons in the human genome) for a phenotype related to osteoporosis.
|
|
| 14. |
|
|
| 15. |
- Baroni, Mpma, et al.
(författare)
-
Modeling and gradient pattern analysis of irregular SFM structures of porous silicon
- 2006
-
Ingår i: Microelectronics Journal. - : Elsevier BV. - 0026-2692. ; 37:4, s. 290-294
-
Tidskriftsartikel (refereegranskat)abstract
- Technological applications in opto-electronic devices have increased the interest in characterizing porous silicon structure patterns. Due to its physical properties, solutions from KPZ 2D are adopted to simulate the structure of porous material interface whose spatial characteristics are equivalent to those found in porous silicon samples. The analysis of the simulated and real scanning Force Microscopy (SFM) surfaces was done using the Gradient Pattern Analysis (GPA). We found that the KPZ 2D model presented asymmetry levels compatible with the irregular surfaces observed by means of SFM images of pi-Si.
|
|
| 16. |
- Baroni, M. P. M. A., et al.
(författare)
-
Optical and morphological properties of porous diamond-like-carbon films deposited by magnetron sputtering
- 2006
-
Ingår i: Journal of Non-Crystalline Solids. - : Elsevier BV. - 0022-3093 .- 1873-4812. ; 352:32-35, s. 3734-3738
-
Tidskriftsartikel (refereegranskat)abstract
- Porous diamond-like-carbon (PDLC) thin films obtained on silicon substrate by DC low energy magnetron sputtering have been investigated by photoluminescence, transmission and reflection spectroscopy, photoacoustic and spectroscopic ellipsometry. The absorption features observed for these films show similarities with those of porous silicon (PS) as well as in the performed gradient structural pattern classification of the SFM porosity, by means of the computational GPA-flyby environment on PS and PDLC samples. The dielectric function is also calculated for the bulk diamond-like carbon using the full-potential linearized augmented plane wave method within the framework of local density approximation to density functional theory. From the measurement a low real dielectric constant of about 4.5 at 0.8 eV was found whereas the calculated e(1)(0) for the bulk diamond has a value of 5.5.
|
|
| 17. |
- da Silva, A. Ferreira, et al.
(författare)
-
Growth, Electrical and Optical Properties of SnO2:F on ZnO, Si and Porous Si Structures
- 2009
-
Ingår i: NANOTECH CONFERENCE & EXPO 2009, VOL 1, TECHNICAL PROCEEDINGS. - : CRC PRESS-TAYLOR & FRANCIS GROUP. - 9781439817827 ; , s. 352-
-
Konferensbidrag (refereegranskat)abstract
- In this work we have analyzed the optical absorption of the ZnO and SnO2:F (FTO) films and applied them in porous silicon light-emitting diodes. The absorption and energy gap were calculated by employing the projector augmented wave method [1] within the local density approximation and with a modeled on-site self-interaction-like correction potential within the LDA+U-S/C [2]. Experiment and theory show a good agreement when the optical absorption and optical energy gap are considered. A layer of FTO is deposited by spray pyrolysis on top of porous Si (PSi) or ZnO/(PSi) in order to make the LEDs. The morphology and roughness of the films are analyzed by Atomic Force Microscopy before and after the FTO deposition. The electrical and optical properties are studied by characteristics curves J x V, and electroluminescence intensity versus bias.
|
|
| 18. |
|
|
| 19. |
- Forsman, M., et al.
(författare)
-
Urinary detection times and excretion patterns of flunitrazepam and its metabolites after a single oral dose
- 2009
-
Ingår i: Journal of Analytical Toxicology. - 0146-4760 .- 1945-2403. ; 33:8, s. 491-501
-
Tidskriftsartikel (refereegranskat)abstract
- We investigated the excretion profiles of flunitrazepam metabolites in urine after a single dose. Sixteen volunteers received either 0.5 or 2.0 mg flunitrazepam. Urine samples were collected after 2, 4, 6, 8, 12, 24, 48, 72, 96, 120, 240, and 336 h. Samples were screened using CEDIA (300 µg/L cutoff) and quantitated using liquid chromatography-tandem mass spectrometry. The cutoff was 0.5 µg/L for flunitrazepam, N-desmethylflunitrazepam, 7-aminoflunitrazepam, 7-aminodesmethylflunitrazepam, 7-acetamidoflunitrazepam, and 7-acetamidodesmethylflunitrazepam. None of the subjects receiving 0.5 mg were screened positive, and only 23 of 102 samples from the subjects given 2.0 mg were positive with CEDIA. The predominant metabolites were 7-aminoflunitrazepam and 7-aminodesmethylflunitrazepam. For all subjects given the low dose, 7-aminoflunitrazepam was detected up to 120 h, and for two subjects for more than 240 h. Seven subjects given the high dose were positive up to 240 h for 7-aminoflunitrazepam. We conclude that the ratio 7-aminodesmethylflunitrazepam to 7-aminoflunitrazepam increased with time, independent of dose, and may be used to estimate the time of intake. For some low-dose subjects, the metabolite concentrations in the early samples were low and a chromatographic method may fail to detect the intake. We think laboratories should consider this when advising police and hospitals about sampling as well as when they set up strategies for analysis.
|
|
| 20. |
- Frank, Ari M., et al.
(författare)
-
De novo peptide sequencing and identification with precision mass spectrometry
- 2007
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 6:1, s. 114-123
-
Tidskriftsartikel (refereegranskat)abstract
- The recent proliferation of novel mass spectrometers such as Fourier transform, QTOF, and OrbiTrap marks a transition into the era of precision mass spectrometry, providing a 2 orders of magnitude boost to the mass resolution, as compared to low-precision ion-trap detectors. We investigate peptide de novo sequencing by precision mass spectrometry and explore some of the differences when compared to analysis of low-precision data. We demonstrate how the dramatically improved performance of de novo sequencing with precision mass spectrometry paves the way for novel approaches to peptide identification that are based on direct sequence lookups, rather than comparisons of spectra to a database. With the direct sequence lookup, it is not only possible to search a database very efficiently, but also to use the database in novel ways, such as searching for products of alternative splicing or products of fusion proteins in cancer. Our de novo sequencing software is available for download at http://peptide.ucsd.edu/.
|
|
| 21. |
- Frank, Rupert L., et al.
(författare)
-
On the spectrum of partially periodic operators
- 2007
-
Ingår i: Operator Theory, Analysis and Mathematical Physics. - BASEL : BIRKHAUSER VERLAG AG. - 9783764381349 ; , s. 35-50
-
Konferensbidrag (refereegranskat)abstract
- We consider Schrodinger operators H = -Delta + V in L-2 (Omega) where the domain Omega subset of R-+(d+1) and the potential V = V (x, y) are periodic with respect to the variable x is an element of R-d. We assume that Omega is unbounded with respect to the variable y is an element of R and that V decays with respect to this variable. V may contain a singular term supported on the boundary. We develop a scattering theory for H and present an approach to prove absence of singular continuous spectrum. Moreover, we show that certain repulsivity conditions on the potential and the boundary of Omega exclude the existence of surface states. In this case, the spectrum of His purely absolutely continuous and the scattering is complete.
|
|
| 22. |
- Fälth, Maria, et al.
(författare)
-
Analytical utility of small neutral losses from reduced species in electron capture dissociation studied using SwedECD database
- 2008
-
Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 80:21, s. 8089-8094
-
Tidskriftsartikel (refereegranskat)abstract
- Small neutral losses from charge-reduced species [M + nH]((n-1)+center dot) is one of the most abundant fragmentation channels in both electron capture dissociation, ECD, and electron transfer dissociation, ETD. Several groups have previously studied these losses on particular examples. Now, the availability of a large (11491 entries) SwedECD database (http://www.bmms.uu.se/CAD/indexECD.html) of high-resolution ECD data sets on doubly charged tryptic peptides has made possible a systematic study involving statistical evaluation of neutral losses from [M + 2H](+center dot) ions. Several new types of losses are discovered, and 16 specific (>94%) losses are characterized according to their specificity and sensitivity, as well as occurrence for peptides of different lengths. On average, there is more than one specific loss per ECD mass spectrum, and two-thirds of all MS/MS data sets in SwedECD contain at least one specific loss. Therefore, specific neutral losses are analytically useful for improved database searching and de novo sequencing. In particular, N and GG isomeric sequences can be distinguished. The pattern of neutral losses was found to be remarkably dissimilar with the losses from radical z(center dot) fragment ions: e.g., there is no direct formation of w ions from the reduced species. This finding emphasizes the difference in fragmentation behaviors of hydrogen-abundant and hydrogen-deficient species.
|
|
| 23. |
- Fälth, Maria, et al.
(författare)
-
SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides
- 2007
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 6:10, s. 4063-4067
-
Tidskriftsartikel (refereegranskat)abstract
- A database of high-mass accuracy tryptic peptides has been created. The database contains 15897 unique, annotated MS/MS spectra. It is possible to search for peptides according to their mass, number of missed cleavages, and sequence motifs. All of the data contained in the database is downloadable, and each spectrum can be visualized. An example is presented of how the database can be used for studying peptide fragmentation. Fragmentation of different types of missed cleaved peptides has been studied, and the results can be used to improve identification of these types of peptides.
|
|
| 24. |
|
|
| 25. |
- Grigorenko, Elena L., et al.
(författare)
-
Exploring interactive effects on genes and environments in etiology of individual differences in reading comprehension
- 2007
-
Ingår i: Development and Psychopathology. - 0954-5794 .- 1469-2198. ; 19:4, s. 1089-1103
-
Tidskriftsartikel (refereegranskat)abstract
- It is established that reading and reading-related processes are heritable; genes thus play an important role in the foundation of individual differences in reading. In this article, we focus on one facet of reading–comprehension. Comprehension is a higher order cognitive skill that requires many other cognitive processes for it to unfold completely and successfully. One such process is executive functioning, which has been associated with genetic variation in the catechol-O-methyltransferase (COMT) gene. Genotypes and haplotypes of four single nucleotide polymorphisms in COMT were investigated in 179 incarcerated adolescent delinquents. Four hierarchical logistic regression models predicting the presence/absence of comprehension difficulties were fitted to the data; genetic variation in COMT and the presence/absence of maternal rejection were investigated as main effects and as effects acting interactively. Three out of four interaction terms were found to be important predictors of individual differences in comprehension. These findings were supported by the results of the haplotype analyses, in which the four investigated polymorphisms were considered simultaneously.
|
|
| 26. |
- Haeffel, Gerald J., et al.
(författare)
-
Association Between Polymorphisms in the Dopamine Transporter Gene and Depression : Evidence for a Gene-Environment Interaction in a Sample of Juvenile Detainees
- 2008
-
Ingår i: Psychological Science. - : SAGE Publications. - 0956-7976 .- 1467-9280. ; 19:1, s. 62-69
-
Tidskriftsartikel (refereegranskat)abstract
- Previous research has generated examples of how genetic and environmental factors can interact to create risk for psychopathology. Using a gene-by-environment (G × E) interaction design, we tested whether three polymorphisms in the dopamine transporter gene (DAT1, also referred to as SLC6A3, located at 5p15.33) interacted with maternal parenting style to predict first-onset episodes of depression. Participants were male adolescents (N= 176) recruited from a juvenile detention center in northern Russia. As hypothesized, one of the polymorphisms (rs40184) moderated the effect of perceived maternal rejection on the onset of major depressive disorder, as well as on suicidal ideation. Further, this G × E interaction was specific to depression; it did not predict clinically significant anxiety. These results highlight the need for further research investigating the moderating effects of dopaminergic genes on depression.
|
|
| 27. |
- Kotlova, E. R., et al.
(författare)
-
Alterations in the composition of membrane glycero-and sphingolipids in the course of Flammulina velutipes surface culture development
- 2009
-
Ingår i: Microbiology (Mikrobiologija). - 0026-2617 .- 1608-3237. ; 78:2, s. 193-201
-
Tidskriftsartikel (refereegranskat)abstract
- Qualitative and quantitative characteristics of the alterations in the lipid composition of the membrane of the basidial fungus Flammulina velutipes in the course of surface culture development were investigated. Modifications of the lipid composition were shown to be timed to specific ontogeny stages, such as changes in the growth rate of the colonies, the appearance of differentiated vegetative cells, and the formation of generative structures. A slowdown of growth correlated with an alteration in the ratio of major classes of phospholipids, namely, with a decrease of phosphatidylcholine relative content and an increase in phosphatidylethanolamines. The differentiation of vegetative cells of the mycelium proceeded along with modifications of molecular composition of glycoceramides. In the course of the first week of growth, the surface culture of F. velutipes produced monohexosylceramides with epoxidized methyl sphingadienine as a sphingoid base. Later on, along with culture growth and specialization of mycelium cells, molecular species with methyl sphingadienine, common for basidiomycetes, start to prevail among the fungal glycoceramides. The formation of fruit bodies is accompanied by enrichment of molecules of phospholipids, mainly, the phosphatidylcholines, with unsaturated fatty acids.
|
|
| 28. |
- Köcher, Thomas, et al.
(författare)
-
PhosTShunter : A fast and reliable tool to detect phosphorylated peptides in liquid chromatography Fourier transform tandem mass spectrometry data sets
- 2006
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 5:3, s. 659-668
-
Tidskriftsartikel (refereegranskat)abstract
- A database independent search algorithm for the detection of phosphopeptides is described. The program interrogates the tandem mass spectra of LC-MS/MS data sets regarding the presence of phosphorylation specific signatures. To achieve maximum informational content, the complementary fragmentation techniques electron capture dissociation (ECD) and collisionally activated dissociation (CAD) are used independently for peptide fragmentation. Several criteria characteristic for peptides phosphorylated on either serine or threonine residues were evaluated. The final algorithm searches for product ions generated by either the neutral loss of phosphoric acid or the combined neutral loss of phosphoric acid and water. Various peptide mixtures were used to evaluate the program. False positive results were not observed because the program utilizes the parts-per-million mass accuracy of Fourier transform ion cyclotron resonance mass spectrometry. Additionally, false negative results were not generated owing to the high sensitivity of the chosen criteria. The limitations of database dependent data interpretation tools are discussed and the potential of the novel algorithm to overcome these limitations is illustrated.
|
|
| 29. |
- Lerner, Mikael, et al.
(författare)
-
The RBCC gene RFP2 (leu5) encodes a novel transmembrane E3 ubiquitin ligase involved in ERAD
- 2007
-
Ingår i: Molecular Biology of the Cell. - 1059-1524 .- 1939-4586. ; 18:5, s. 1670-1682
-
Tidskriftsartikel (refereegranskat)abstract
- RFP2, a gene frequently lost in various malignancies, encodes a protein with RING finger, B-box, and coiled-coil domains that belongs to the RBCC/TRIM family of proteins. Here we demonstrate that Rfp2 is an unstable protein with auto-polyubiquitination activity in vivo and in vitro, implying that Rfp2 acts as a RING E3 ubiquitin ligase. Consequently, Rfp2 ubiquitin ligase activity is dependent on an intact RING domain, as RING deficient mutants fail to drive polyubiquitination in vitro and are stabilized in vivo. Immunopurification and tandem mass spectrometry enabled the identification of several putative Rfp2 interacting proteins localized to the endoplasmic reticulum (ER), including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). Importantly, we also show that Rfp2 regulates the degradation of the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein), establishing Rfp2 as a novel E3 ligase involved in ERAD. Finally, we show that Rfp2 contains a C-terminal transmembrane domain indispensable for its localization to the ER and that Rfp2 colocalizes with several ER-resident proteins as analyzed by high-resolution immunostaining. In summary, these data are all consistent with a function for Rfp2 as an ERAD E3 ubiquitin ligase.
|
|
| 30. |
- Nielsen, Michael L., et al.
(författare)
-
Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics
- 2006
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 5:12, s. 2384-2391
-
Tidskriftsartikel (refereegranskat)abstract
- The complexity of the uman proteome, already enormous at the organism level, increases further in the course of the proteome analysis due to in vitro sample evolution. Most of in vitro alterations can also occur in vivo as post-translational modifications. These two types of modifications can only be distinguished a posteriori but not in the process of analysis, thus rendering necessary the analysis of every molecule in the sample. With the new software tool ModifiComb applied to MS/MS data, the extent of modifications was measured in tryptic mixtures representing the full proteome of human cells. The estimated level of 8-12 modified peptides per each unmodified tryptic peptide present at ≥1 % level is approaching one modification per amino acid on average. This is a higher modification rate than was previously thought, posing an additional challenge to analytical techniques. The solution to the problem is seen in improving sample preparation routines, introducing dynamic range-adjusted thresholds for database searches, using more specific MS/MS analysis using high mass accuracy and complementary fragmentation techniques, and revealing peptide families with identification of additional proteins only by unfamiliar peptides. Extensive protein separation prior to analysis reduces the requirements on speed and dynamic range of a tandem mass spectrometer and can be a viable alternative to the shotgun approach.
|
|
| 31. |
- Nielsen, Michael L, et al.
(författare)
-
Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry
- 2005
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:6, s. 835-845
-
Tidskriftsartikel (refereegranskat)abstract
- Identification of proteins by MS/MS is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein data base. The search engine assigns each spectrum a score indicating how well the experimental data complies with the expected one; a higher score means increased confidence in the identification. One problem is the false-positive identifications, which arise from incomplete data as well as from the presence of misleading ions in experimental mass spectra due to gas-phase reactions, stray ions, contaminants, and electronic noise. We employed a novel technique of reduction of false positives that is based on a combined use of orthogonal fragmentation techniques electron capture dissociation (ECD) and collisionally activated dissociation (CAD). Since ECD and CAD exhibit many complementary properties, their combined use greatly increased the analysis specificity, which was further strengthened by the high mass accuracy (approximately 1 ppm) afforded by Fourier transform mass spectrometry. The utility of this approach is demonstrated on a whole cell lysate from Escherichia coli. Analysis was made using the data-dependent acquisition mode. Extraction of complementary sequence information was performed prior to data base search using in-house written software. Only masses involved in complementary pairs in the MS/MS spectrum from the same or orthogonal fragmentation techniques were submitted to the data base search. ECD/CAD identified twice as many proteins at a fixed statistically significant confidence level with on average a 64% higher Mascot score. The confidence in protein identification was hereby increased by more than 1 order of magnitude. The combined ECD/CAD searches were on average 20% faster than CAD-only searches. A specially developed test with scrambled MS/MS data revealed that the amount of false-positive identifications was dramatically reduced by the combined use of CAD and ECD.
|
|
| 32. |
- Roman, L. S., et al.
(författare)
-
Optical band-edge absorption of oxide compound SnO2
- 2006
-
Ingår i: Applied Surface Science. - : Elsevier BV. - 0169-4332 .- 1873-5584. ; 252:15, s. 5361-5364
-
Tidskriftsartikel (refereegranskat)abstract
- Tin oxide (SnO2) is an important oxide for efficient dielectrics, catalysis, sensor devices, electrodes and transparent conducting coating oxide technologies. SnO2 thin film is widely used in glass applications due to its low infra-red heat emissivity. In this work, the SnO2 electronic band-edge structure and optical properties are studied employing a first-principle and fully relativistic full-potential linearized augmented plane wave (FPLAPW) method within the local density approximation (LDA). The optical band-edge absorption alpha(omega) of intrinsic SnO2 is investigated experimentally by transmission spectroscopy measurements and their roughness in the light of the atomic force microscopy (AFM) measurements. The sample films were prepared by spray pyrolysis deposition method onto glass substrate considering different thickness layers. We found for SnO2 qualitatively good agreement of the calculated optical band-gap energy as well as the optical absorption with the experimental results.
|
|
| 33. |
- Ruchkin, Vladislav V, et al.
(författare)
-
Platelet MAO-B, personality, and psychopathology
- 2005
-
Ingår i: Journal of Abnormal Psychology. - 0021-843X .- 1939-1846. ; 114:3, s. 477-482
-
Tidskriftsartikel (refereegranskat)abstract
- The article investigates the relationships between platelet monoamine oxidase-B (MAO-B) activity, personality, and psychopathology (Diagnostic and Statistical Manual of Mental Disorders [4th ed.; American Psychiatric Association, 1994] diagnoses. These relationships were assessed in 178 incarcerated male juvenile delinquents. Even after controlling for smoking, the authors found that both Internalizing and Externalizing Psychopathology were negatively related to MAO-B activity. In the final reduced model, novelty seeking fully mediated the relationships between MAO-B and Externalizing Psychopathology but not between MAO-B and Internalizing Psychopathology. It was hypothesized that low platelet MAO-B activity does not directly predispose individuals to psychopathology but is related to specific personality traits, which in turn represent a vulnerability factor for psychopathology. Future studies should help clarify the nature of the relationships between personality, biological markers, and psychopathology.
|
|
| 34. |
|
|
| 35. |
- Rueda, B., et al.
(författare)
-
A large multicentre analysis of CTGF - 2945 promoter polymorphism does not confirm association with systemic sclerosis susceptibility or phenotype
- 2009
-
Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 68:10, s. 1618-1620
-
Tidskriftsartikel (refereegranskat)abstract
- Objective: To conduct a replication study to investigate whether the 2945 CTGF genetic variant is associated with systemic sclerosis (SSc) susceptibility or specific SSc phenotype. Methods: The study population comprised 1180 patients with SSc and 1784 healthy controls from seven independent case-control sets of European ancestry (Spanish, French, Dutch, German, British, Swedish and North American). The 2945 CTGF genetic variant was genotyped using a Taqman 59 allelic discrimination assay. Results: An independent association study showed in all the case-control cohorts no association of the CTGF 2945 polymorphism with SSc susceptibility. These findings were confirmed by a meta-analysis giving a pooled OR=1.12 (95% CI 0.99 to 1.25), p=0.06. Investigation of the possible contribution of the 2945 CTGF genetic variant to SSc phenotype showed that stratification according to SSc subtypes (limited or diffuse), selective autoantibodies (anti-topoisomerase I or anticentromere) or pulmonary involvement reached no statistically significant skewing. Conclusion: The results do not confirm previous findings and suggest that the CTGF 2945 promoter polymorphism does not play a major role in SSc susceptibility or clinical phenotype.
|
|
| 36. |
- Samgina, T. Yu., et al.
(författare)
-
Electrospray ionization tandem mass spectrometry sequencing of novel skin peptides from Ranid frogs containing disulfide bridges
- 2007
-
Ingår i: European journal of mass spectrometry. - : SAGE Publications. - 1469-0667 .- 1751-6838. ; 13:2, s. 155-163
-
Tidskriftsartikel (refereegranskat)abstract
- Tandem mass spectrometry sequencing, as well as Edman sequencing of peptides belonging to the Rana genus, represents a difficult task due to the presence of a disulfide bridge at the C-terminus and their rather high molecular masses (over 2000Da). The present study throws light upon the sequence of three rather long peptides (more than 20 amino acid residues each) isolated from the skin secretion of Russian frogs, Rana ridibunda and Rana arvalis. This novel aspect involves the fact that the sequences (including two sequences established de novo) were determined exclusively by means of mass spectrometry. A combination of electron capture dissociation (ECD) and collision-induced dissociaiton (CID) data accompanied by exact mass measurements (LTQ Fourier transform ion cyclotron resonance mass spectrometer) facilitated reaching the goal. To overcome the difficulty dealing with disulphide bridges ("Rana box"), reduction of the S-S bond with dithiotreitol followed by derivatization of Cys residues with iodoacetamide was used. The sequence was determined using combined spectral data on y and b series of fragment ions. A multiple mass spectrometry (MS') experiment was also used to elucidate the sequence inside the "Rana box" after cysteine derivatization. Exact mass measurements were used to differentiate between Lys and Gln residues, while characteristic losses of 29 and 43 Da (d and w fragment ions) in CID and ECD experiments allowed us to distinguish between Ile and Leu isomeric acids.
|
|
| 37. |
- Savitski, Mikhail, et al.
(författare)
-
Hydrogen Rearrangement to and from Radical z Fragments in Electron Capture Dissociation of Peptides
- 2007
-
Ingår i: Journal of the American Society for Mass Spectrometry. - : American Chemical Society (ACS). - 1044-0305 .- 1879-1123. ; 18:1, s. 113-120
-
Tidskriftsartikel (refereegranskat)abstract
- Hydrogen rearrangement is an important process in radical chemistry. A high degree of H· rearrangement to and from z· ionic fragments (combined occurrence frequency 47% compared with that of z·) is confirmed in analysis of 15,000 tandem mass spectra of tryptic peptides obtained with electron capture dissociation (ECD), including previously unreported double H· losses. Consistent with the radical character of H· abstraction, the residue determining the formation rate of z′ = z· + H· species is found to be the N-terminal residue in z· species. The size of the complementary cm′ fragment turned out to be another important factor, with z′ species dominating over z· ions for m ≤ 6. The H· atom was found to be abstracted from the side chains as well as from α-carbon groups of residues composing the c′ species, with Gln and His in the c′ fragment promoting H· donation and Asp and Ala opposing it. Ab initio calculations of formation energies of ·A radicals (A is an amino acid) confirmed that the main driving force for H· abstraction by z· is the process exothermicity. No valid correlation was found between the N{single bond}Cα bond strength and the frequency of this bond cleavage, indicating that other factors than thermochemistry are responsible for directing the site of ECD cleavage. Understanding hydrogen attachment to and loss from ECD fragments should facilitate automatic interpretation ECD mass spectra in protein identification and characterization, including de novo sequencing.
|
|
| 38. |
- Savitski, Mikhail M., et al.
(författare)
-
Backbone carbonyl group basicities are related to gas-phase fragmentation of peptides and protein folding
- 2007
-
Ingår i: Angewandte Chemie International Edition. - : Wiley. - 1433-7851 .- 1521-3773. ; 46:9, s. 1481-1484
-
Tidskriftsartikel (refereegranskat)abstract
- A strong correlation is found between the propensity of individual amino acids to induce peptide-bond cleavage in the gas phase (PAA-XX) and their structure-forming propensity (PS, red) and H-bond-accepting propensity (PH, blue). Thus, the same fundamental parameter, carbonyl group basicity, governs the formation of secondary protein structures in solution and directs fragmentation in the gas phase. (Graph Presented).
|
|
| 39. |
- Savitski, Mikhail M., et al.
(författare)
-
ModifiComb : New proteomics tool for mapping substochiometric post-translational modifications, finding novel types of modifications and fingerprinting complex protein mixtures.
- 2006
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 5:5, s. 935-948
-
Tidskriftsartikel (refereegranskat)abstract
- A major challenge in proteomics is to fully identify and characterize the post-translational modification (PTM) patterns present at any given time in cells, tissues, and organisms. Here we present a fast and reliable method ("ModifiComb") for mapping hundreds types of PTMs at a time, including novel and unexpected PTMs. The high mass accuracy of Fourier transform mass spectrometry provides in many cases unique elemental composition of the PTM through the difference DeltaM between the molecular masses of the modified and unmodified peptides, whereas the retention time difference DeltaRT between their elution in reversed-phase liquid chromatography provides an additional dimension for PTM identification. Abundant sequence information obtained with complementary fragmentation techniques using ion-neutral collisions and electron capture often locates the modification to a single residue. The (DeltaM, DeltaRT) maps are representative of the proteome and its overall modification state and may be used for database-independent organism identification, comparative proteomic studies, and biomarker discovery. Examples of newly found modifications include +12.000 Da (+C atom) incorporation into proline residues of peptides from proline-rich proteins found in human saliva. This modification is hypothesized to increase the known activity of the peptide.
|
|
| 40. |
- Savitski, Mikhail M., et al.
(författare)
-
New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques
- 2005
-
Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:8, s. 1180-1188
-
Tidskriftsartikel (refereegranskat)abstract
- The Mascot score (M-score) is one of the conventional validity measures in data base identification of peptides and proteins by MS/MS data. Although tremendously useful, M-score has a number of limitations. For the same MS/MS data, M-score may change if the protein data base is expanded. A low M-value may not necessarily mean poor match but rather poor MS/MS quality. In addition M-score does not fully utilize the advantage of combined use of complementary fragmentation techniques collisionally activated dissociation (CAD) and electron capture dissociation (ECD). To address these issues, a new data base-independent scoring method (S-score) was designed that is based on the maximum length of the peptide sequence tag provided by the combined CAD and ECD data. The quality of MS/MS spectra assessed by S-score allows poor data (39% of all MS/MS spectra) to be filtered out before the data base search, speeding up the data analysis and eliminating a major source of false positive identifications. Spectra with below threshold M-scores (poor matches) but high S-scores are validated. Spectra with zero M-score (no data base match) but high S-score are classified as belonging to modified sequences. As an extension of S-score, an extremely reliable sequence tag was developed based on complementary fragments simultaneously appearing in CAD and ECD spectra. Comparison of this tag with the data base-derived sequence gives the most reliable peptide identification validation to date. The combined use of M- and S-scoring provides positive sequence identification from >25% of all MS/MS data, a 40% improvement over traditional M-scoring performed on the same Fourier transform MS instrumentation. The number of proteins reliably identified from Escherichia coli cell lysate hereby increased by 29% compared with the traditional M-score approach. Finally S-scoring provides a quantitative measure of the quality of fragmentation techniques such as the minimum abundance of the precursor ion, the MS/MS of which gives the threshold S-score value of 2.
|
|
| 41. |
- Savitski, Mikhail M., et al.
(författare)
-
Proteomics-grade De Novo sequencing approach
- 2005
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 4:6, s. 2348-2354
-
Tidskriftsartikel (refereegranskat)abstract
- The conventional approach in modern proteomics to identify proteins from limited information provided by molecular and fragment masses of their enzymatic degradation products carries an inherent risk of both false positive and false negative identifications. For reliable identification of even known proteins, complete de novo sequencing of their peptides is desired. The main problems of conventional sequencing based on tandem mass spectrometry are incomplete backbone fragmentation and the frequent overlap of fragment masses. In this work, the first proteomics-grade de novo approach is presented, where the above problems are alleviated by the use of complementary fragmentation techniques CAD and ECD. Implementation of a high-current, large-area dispenser cathode as a source of low-energy electrons provided efficient ECD of doubly charged peptides, the most abundant species (65-80%), in a typical trypsin-based proteomics experiment. A new linear de novo algorithm is developed combining efficiency and speed, processing on a conventional 3 GHz PC, 1000 MS/MS data sets in 60 s. More than 6% of all MS/MS data for doubly charged peptides yielded complete sequences, and another 13% gave nearly complete sequences with a maximum gap of two amino acid residues. These figures are comparable with the typical success rates (5-15%) of database identification. For peptides reliably found in the database (Mowse score > or = 34), the agreement with de novo-derived full sequences was >95%. Full sequences were derived in 67% of the cases when full sequence information was present in MS/MS spectra. Thus the new de novo sequencing approach reached the same level of efficiency and reliability as conventional database-identification strategies.
|
|
| 42. |
- Savitski, Mikhail M., et al.
(författare)
-
Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation
- 2007
-
Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 6:7, s. 2669-2673
-
Tidskriftsartikel (refereegranskat)abstract
- Analysis of a database containing over 20 000 high-resolution collision-activation mass spectra of tryptic peptide dications was employed to study the relative specificity of neutral losses from backbone fragments. The high resolution of the FTMS instrument allowed for the first time the first isotope of the water loss and the monoisotope of the ammonia loss to be distinguished. Contrary to a popular belief, water losses from y' ions are not specific enough to rely upon for detecting the presence of amino acids with oxygen in the side chains. At the same time, ammonia loss from b ions is sufficiently specific (> 95%) to detect the presence of amino acids Gln, Asn, His, Lys, and Arg. This feature will be useful for de novo algorithms for high-resolution MS data. Clear trends were observed when the effect of amino acids proximate to the cleavage site on the rate of loss formation was studied. These trends turned out to be different for losses from b and y ions.
|
|
| 43. |
- Savitski, Mikhail M., et al.
(författare)
-
Side-chain losses in electron capture dissociation to improve peptide identification
- 2007
-
Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 79:6, s. 2296-2302
-
Tidskriftsartikel (refereegranskat)abstract
- Analysis of a database of some 20 000 conventional electron-capture dissociation (ECD) mass spectra of doubly charged ions belonging to tryptic peptides revealed widespread appearance of w ions and related u ions that are due to partial side chain losses from radical z. ions. Half of all z. ions that begin with Leu or Ile produce w ions in conventional one-scan ECD mass spectra, which differentiates these isomeric residues with >97% reliability. Other residues exhibiting equally frequent side chain losses are Gln, Glu, Asp, and Met (cysteine was not included in this work). Unexpectedly, Asp lost not a radical group like other amino acids but a molecule CO2, thus giving rise to a radical w. ion with the possibility of a radical cascade. Losses from amino acids as distant as seven residues away from the cleavage site were detected. The mechanism of such losses seems to be related to radical migration from the original site at the αCn atom in a Zn. ion to other αC and βC atoms. The side chain losses confirm sequence assignment, improve the database matching score, and can be useful in de novo sequencing.
|
|
| 44. |
|
|
| 45. |
|
|
| 46. |
- Uitterlinden, André G, et al.
(författare)
-
The association between common vitamin D receptor gene variations and osteoporosis : a participant-level meta-analysis
- 2006
-
Ingår i: Annals of Internal Medicine. - 0003-4819. ; 145:4, s. 255-264
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Polymorphisms of the vitamin D receptor (VDR) gene have been implicated in the genetic regulation of bone mineral density (BMD). However, the clinical impact of these variants remains unclear.OBJECTIVE: To evaluate the relation between VDR polymorphisms, BMD, and fractures.DESIGN: Prospective multicenter large-scale association study.SETTING: The Genetic Markers for Osteoporosis consortium, involving 9 European research teams.PARTICIPANTS: 26,242 participants (18,405 women).MEASUREMENTS: Cdx2 promoter, FokI, BsmI, ApaI, and TaqI polymorphisms; BMD at the femoral neck and the lumbar spine by dual x-ray absorptiometry; and fractures.RESULTS: Comparisons of BMD at the lumbar spine and femoral neck showed nonsignificant differences less than 0.011 g/cm2 for any genotype with or without adjustments. A total of 6067 participants reported a history of fracture, and 2088 had vertebral fractures. For all VDR alleles, odds ratios for fractures were very close to 1.00 (range, 0.98 to 1.02) and collectively the 95% CIs ranged from 0.94 (lowest) to 1.07 (highest). For vertebral fractures, we observed a 9% (95% CI, 0% to 18%; P = 0.039) risk reduction for the Cdx2 A-allele (13% risk reduction in a dominant model).LIMITATIONS: The authors analyzed only selected VDR polymorphisms. Heterogeneity was detected in some analyses and may reflect some differences in collection of fracture data across cohorts. Not all fractures were related to osteoporosis.CONCLUSIONS: The FokI, BsmI, ApaI, and TaqI VDR polymorphisms are not associated with BMD or with fractures, but the Cdx2 polymorphism may be associated with risk for vertebral fractures.
|
|
| 47. |
- Zubarev, Roman A., et al.
(författare)
-
Identification of dominant signaling pathways from proteomics expression data
- 2008
-
Ingår i: Journal of Proteomics. - : Elsevier BV. - 1874-3919. ; 71:1, s. 89-96
-
Tidskriftsartikel (refereegranskat)abstract
- The availability of the results of high-throughput analyses coming from 'omic' technologies has been one of the major driving forces of pathway biology. Analytical pathway biology strives to design a 'pathway search engine', where the input is the 'omic' data and the output is the list of activated or dominant pathways in a given sample. Here we describe the first attempt to design and validate such a pathway search engine using as input expression proteomics data. The engine represents a specific workflow in computational tools developed originally for mRNA analysis (BMC Bioinformatics 2006, 7 (Suppl 2), S13). Using our own datasets as well as data from recent proteomics literature we demonstrate that different dominant pathways (EGF, TGF(beta), stress, and Fas pathways) can be correctly identified even from limited datasets. Pathway search engines can find application in a variety of proteomics-related fields, from fundamental molecular biology to search for novel types of disease biomarkers.
|
|
