| 1611. |
- Rosenling, Therese, et al.
(författare)
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The Impact of Delayed Storage on the Measured Proteome and Metabolome of Human Cerebrospinal Fluid
- 2011
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Ingår i: Clinical Chemistry. - : Oxford University Press (OUP). - 0009-9147 .- 1530-8561. ; 57:12, s. 1703-1711
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Because cerebrospinal fluid (CSF) is in close contact with diseased areas in neurological disorders, it is an important source of material in the search for molecular biomarkers. However, sample handling for CSF collected from patients in a clinical setting might not always be adequate for use in proteomics and metabolomics studies. METHODS: We left CSF for 0, 30, and 120 min at room temperature immediately after sample collection and centrifugation/removal of cells. After tryptic digestion at 2 laboratories by nanoLC Orbitrap-MS and chipLC QTOF-MS, CSF proteomes were analyzed. Metabolome analysis was performed at 3 laboratories by NMR, GC-MS, and LC-MS. Targeted analyses of cystatin C and albumin were performed by LC-MS/MS in the selected reaction monitoring mode. RESULTS: We did not find significant changes in the measured proteome and metabolome of CSF stored at room temperature after centrifugation, except for 2 peptides and 1 metabolite, 2,3,4-trihydrobutanoic acid, of 5780 identified peptides and 93 identified metabolites. A sensitive protein stability marker, cystatin C, was not affected. CONCLUSIONS: The measured proteome and metabolome of centrifuged, human CSF is stable at room temperature for up to 2 hours. We cannot exclude, however, that changes undetectable with our current methodology, such as denaturation or proteolysis, might occur due to sample handling conditions. The stability we observed gives laboratory personnel at the collection site sufficient time to aliquot samples before freezing and storage at -80 °C.
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| 1612. |
- Rothenbacher, Dietrich, et al.
(författare)
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Contribution of cystatin C- and creatinine-based definitions of chronic kidney disease to cardiovascular risk assessment in 20 population-based and 3 disease cohorts : the BiomarCaRE project
- 2020
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Ingår i: BMC Medicine. - : BioMed Central. - 1741-7015. ; 18:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Chronic kidney disease has emerged as a strong cardiovascular risk factor, and in many current guidelines, it is already considered as a coronary heart disease (CHD) equivalent. Routinely, creatinine has been used as the main marker of renal function, but recently, cystatin C emerged as a more promising marker. The aim of this study was to assess the comparative cardiovascular and mortality risk of chronic kidney disease (CKD) using cystatin C-based and creatinine-based equations of the estimated glomerular filtration rate (eGFR) in participants of population-based and disease cohorts.Methods: The present study has been conducted within the BiomarCaRE project, with harmonized data from 20 population-based cohorts (n = 76,954) from 6 European countries and 3 cardiovascular disease (CVD) cohorts (n = 4982) from Germany. Cox proportional hazards models were used to assess hazard ratios (HRs) for the various CKD definitions with adverse outcomes and mortality after adjustment for the Systematic COronary Risk Evaluation (SCORE) variables and study center. Main outcome measures were cardiovascular diseases, cardiovascular death, and all-cause mortality.Results: The overall prevalence of CKD stage 3-5 by creatinine- and cystatin C-based eGFR, respectively, was 3.3% and 7.4% in the population-based cohorts and 13.9% and 14.4% in the disease cohorts. CKD was an important independent risk factor for subsequent CVD events and mortality. For example, in the population-based cohorts, the HR for CVD mortality was 1.72 (95% CI 1.53 to 1.92) with creatinine-based CKD and it was 2.14 (95% CI 1.90 to 2.40) based on cystatin-based CKD compared to participants without CKD. In general, the HRs were higher for cystatin C-based CKD compared to creatinine-based CKD, for all three outcomes and risk increased clearly below the conventional threshold for CKD, also in older adults. Net reclassification indices were larger for a cystatin-C based CKD definition. Differences in HRs (between the two CKD measures) in the disease cohorts were less pronounced than in the population-based cohorts.Conclusion: CKD is an important risk factor for subsequent CVD events and total mortality. However, point estimates of creatinine- and cystatin C-based CKD differed considerably between low- and high-risk populations. Especially in low-risk settings, the use of cystatin C-based CKD may result in more accurate risk estimates and have better prognostic value.
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| 1613. |
- Ruban, Alexander V, et al.
(författare)
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Plasticity in the composition of the light harvesting antenna of higher plants preserves structural integrity and biological function.
- 2006
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Ingår i: Journal of Biological Chemistry. - 0021-9258. ; 281:21, s. 14981-90
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Tidskriftsartikel (refereegranskat)abstract
- Arabidopsis plants in which the major trimeric light harvesting complex (LHCIIb) is eliminated by antisense expression still exhibit the typical macrostructure of photosystem II in the granal membranes. Here the detailed analysis of the composition and the functional state of the light harvesting antennae of both photosystem I and II of these plants is presented. Two new populations of trimers were found, both functional in energy transfer to the PSII reaction center, a homotrimer of CP26 and a heterotrimer of CP26 and Lhcb3. These trimers possess characteristic features thought to be specific for the native LHCIIb trimers they are replacing: the long wavelength form of lutein and at least one extra chlorophyll b, but they were less stable. A new population of loosely bound LHCI was also found, contributing to an increased antenna size for photosystem I, which may in part compensate for the loss of the phosphorylated LHCIIb that can associate with this photosystem. Thus, the loss of LHCIIb has triggered concerted compensatory responses in the composition of antennae of both photosystems. These responses clearly show the importance of LHCIIb in the structure and assembly of the photosynthetic membrane and illustrate the extreme plasticity at the level of the composition of the light harvesting system.
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| 1614. |
- Rubio-Moscardo, Fanny, et al.
(författare)
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Rare Variants in Calcium Homeostasis Modulator 1 (CALHM1) Found in Early Onset Alzheimer's Disease Patients Alter Calcium Homeostasis
- 2013
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:9, s. e74203-
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Tidskriftsartikel (refereegranskat)abstract
- Calcium signaling in the brain is fundamental to the learning and memory process and there is evidence to suggest that its dysfunction is involved in the pathological pathways underlying Alzheimer's disease (AD). Recently, the calcium hypothesis of AD has received support with the identification of the non-selective Ca2+-permeable channel CALHM1. A genetic polymorphism (p. P86L) in CALHM1 reduces plasma membrane Ca2+ permeability and is associated with an earlier age-at-onset of AD. To investigate the role of CALHM1 variants in early-onset AD (EOAD), we sequenced all CALHM1 coding regions in three independent series comprising 284 EOAD patients and 326 controls. Two missense mutations in patients (p.G330D and p.R154H) and one (p.A213T) in a control individual were identified. Calcium imaging analyses revealed that while the mutation found in a control (p.A213T) behaved as wild-type CALHM1 (CALHM1-WT), a complete abolishment of the Ca2+ influx was associated with the mutations found in EOAD patients (p.G330D and p.R154H). Notably, the previously reported p. P86L mutation was associated with an intermediate Ca2+ influx between the CALHM1-WT and the p.G330D and p. R154H mutations. Since neither expression of wild-type nor mutant CALHM1 affected amyloid beta-peptide (A beta) production or A beta-mediated cellular toxicity, we conclude that rare genetic variants in CALHM1 lead to Ca2+ dysregulation and may contribute to the risk of EOAD through a mechanism independent from the classical A beta cascade.
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| 1615. |
- Russell, Andrew J.C., et al.
(författare)
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Regulators of male and female sexual development are critical for the transmission of a malaria parasite
- 2023
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Ingår i: Cell Host and Microbe. - : Cell Press. - 1931-3128 .- 1934-6069. ; 31:2, s. 305-319.e10
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Tidskriftsartikel (refereegranskat)abstract
- Malaria transmission to mosquitoes requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei, the transcription factor AP2-G is required and sufficient for this switch, but how a particular sex is determined in a haploid parasite remains unknown. Using a global screen of barcoded mutants, we here identify genes essential for the formation of either male or female sexual forms and validate their importance for transmission. High-resolution single-cell transcriptomics of ten mutant parasites portrays the developmental bifurcation and reveals a regulatory cascade of putative gene functions in the determination and subsequent differentiation of each sex. A male-determining gene with a LOTUS/OST-HTH domain as well as the protein interactors of a female-determining zinc-finger protein indicate that germ-granule-like ribonucleoprotein complexes complement transcriptional processes in the regulation of both male and female development of a malaria parasite.
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| 1616. |
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| 1617. |
- Samain, Louise, et al.
(författare)
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Crystal structure and high-temperature properties of the Ruddlesden-Popper phases Sr3-xYx(Fe1.25Ni0.75)O7-delta (0 <= x <= 0.75)
- 2015
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Ingår i: Journal of Solid State Chemistry. - : Elsevier BV. - 0022-4596 .- 1095-726X. ; 227, s. 45-54
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Tidskriftsartikel (refereegranskat)abstract
- Ruddlesden-Popper n=2 member phases Sr3-xYxFe1.25Ni0.75O7-delta, 0 <= x <= 0.75, have been investigated by X-ray and neutron powder diffraction, thermogravimetry and Mossbauer spectroscopy. Both samples as-prepared at 1300 degrees C under N-2(g) flow and samples subsequently air-annealed at 900 degrees C were studied. The as-prepared x=0.75 phase is highly oxygen deficient with delta=1, the O1 atom site being vacant, and the Fe3+/Ni2+ ions having a square pyramidal coordination. For as-prepared phases with lower x values, the Mossbauer spectral data are in good agreement with the presence of both 5- and 4-coordinated Fe3+ ions, implying in addition a partial occupancy of the O3 atom sites that form the basal plane of the square pyramid. The air-annealed x=0.75 sample has a delta value of 0.61(1) and the structure has Fe/Ni ions in both square pyramids and octahedra. Mossbauer spectroscopy shows the phase to contain only Fe3+, implying that all Ni is present as Ni3+. Air-annealed phases with lower x values are found to contain both Fe3+ and Fe4+. For both the as-prepared and the air-annealed samples, the Y3+ cations are found to be mainly located in the perovskite block. The high-temperature thermal expansion of as-prepared and air-annealed x=0.75 phases were investigated by high-temperature X-ray diffraction and dilatometry and the linear thermal expansion coefficient determined to be 14.4 ppm K-1. Electrical conductivity measurements showed that the air-annealed samples have higher conductivity than the as-prepared ones.
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| 1618. |
- Sánchez Brotons, Alejandro, et al.
(författare)
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Pipelines and Systems for Threshold-Avoiding Quantification of LC-MS/MS Data
- 2021
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 93:32, s. 11215-11224
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Tidskriftsartikel (refereegranskat)abstract
- The accurate processing of complex liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) data from biological samples is a major challenge for metabolomics, proteomics, and related approaches. Here, we present the pipelines and systems for threshold-avoiding quantification (PASTAQ) LC-MS/MS preprocessing toolset, which allows highly accurate quantification of data-dependent acquisition LC-MS/MS datasets. PASTAQ performs compound quantification using single-stage (MS1) data and implements novel algorithms for high-performance and accurate quantification, retention time alignment, feature detection, and linking annotations from multiple identification engines. PASTAQ offers straightforward parameterization and automatic generation of quality control plots for data and preprocessing assessment. This design results in smaller variance when analyzing replicates of proteomes mixed with known ratios and allows the detection of peptides over a larger dynamic concentration range compared to widely used proteomics preprocessing tools. The performance of the pipeline is also demonstrated in a biological human serum dataset for the identification of gender-related proteins.
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| 1619. |
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| 1620. |
- Sartor, Oliver, et al.
(författare)
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Re-treatment with radium-223 : 2-year follow-up from an international, open-label, phase 1/2 study in patients with castration-resistant prostate cancer and bone metastases
- 2019
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Ingår i: The Prostate. - : Wiley Periodicals. - 0270-4137 .- 1097-0045. ; 79:14, s. 1683-1691
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Tidskriftsartikel (refereegranskat)abstract
- Background: Radium-223 dichloride (radium-223) is approved for patients with castration-resistant prostate cancer (CRPC), symptomatic bone metastases, and no visceral disease using a dosing regimen of 6 injections (55 kBq/kg intravenously; 1 injection every 4 weeks). Early results from international, open-label, phase 1/2 study NCT01934790 showed that re-treatment with radium-223 was well tolerated with favorable effects on disease progression. Here we report safety and efficacy findings from 2-year follow-up of the radium-223 re-treatment study.Methods: Patients with CRPC and bone metastases who completed 6 initial radium-223 injections with no disease progression in bone and later progressed were eligible for radium-223 re-treatment (up to 6 additional radium-223 injections), provided that hematologic parameters were adequate and chemotherapy had not been administered after the initial course of radium-223. Concomitant cytotoxic agents were not allowed during re-treatment but were allowed at the investigator's discretion during follow-up; other concomitant agents for prostate cancer (including abiraterone acetate or enzalutamide) were allowed at investigator's discretion. The primary objective was safety. Exploratory objectives included time to radiographic bone progression, radiographic progression-free survival (rPFS), time to total alkaline phosphatase (tALP), and prostate-specific antigen (PSA) progression, overall survival (OS), time to first symptomatic skeletal event (SSE), and SSE-free survival, all calculated from re-treatment start. Evaluation of safety and exploratory efficacy objectives included active 2-year follow-up. Safety results from active follow-up and updated efficacy are reported.Results: Overall, 44 patients were re-treated with radium-223; 29 (66%) completed all 6 injections, and 34 (77%) entered 2-year active follow-up, during which no new safety concerns and no serious drug-related adverse events were noted. rPFS events (progression or death) occurred in 19 (43%) of 44 patients; median rPFS was 9.9 months. Radiographic bone progression occurred in 5 (11%) of 44 patients. Median OS was 24.4 months. Median times to first SSE and SSE-free survival were 16.7 and 12.8 months, respectively. Median time to tALP progression was not reached; median time to PSA progression was 2.2 months.Conclusions: Re-treatment with radium-223 in this selected patient population was well tolerated, led to minimal hematologic toxicity, and provided continued disease control in bone at 2-year follow-up.
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