| 1. |
- Stella, Roberto, et al.
(författare)
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Relative Quantification of Membrane Proteins in Wild-Type and Prion Protein (PrP)-Knockout Cerebellar Granule Neurons
- 2012
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 11:2, s. 523-536
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Tidskriftsartikel (refereegranskat)abstract
- Approximately 25% of eukaryotic proteins possessing homology to at least two trans membrane domains are predicted to be embedded in biological membranes. Nevertheless, this group of proteins is not usually well represented in proteome-wide experiments due to their refractory nature. Here we present a quantitative mass spectrometry-based comparison of membrane protein expression in cerebellar granule neurons grown in primary culture that were isolated from wild-type mice and mice lacking the cellular prion protein. This protein is a cell-surface glycoprotein that is mainly expressed in the central nervous system and is involved in several neurodegenerative disorders, though its physiological role is unclear. We used a low specificity enzyme a-chymotrypsin to digest membrane proteins preparations that had been separated by SDS-PAGE. The resulting peptides were labeled with tandem mass tags and analyzed by MS. The differentially expressed proteins identified using this approach were further analyzed by multiple reaction monitoring to confirm the expression level changes.
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| 2. |
- Bendz, Maria, et al.
(författare)
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Membrane protein shaving with thermolysin can be used to evaluate topology predictors
- 2013
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Ingår i: Proteomics. - : Wiley. - 1615-9853 .- 1615-9861. ; 13:9, s. 1467-1480
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Tidskriftsartikel (refereegranskat)abstract
- Topology analysis of membrane proteins can be obtained by enzymatic shaving in combination with MS identification of peptides. Ideally, such analysis could provide quite detailed information about the membrane spanning regions. Here, we examine the ability of some shaving enzymes to provide large-scale analysis of membrane proteome topologies. To compare different shaving enzymes, we first analyzed the detected peptides from two over-expressed proteins. Second, we analyzed the peptides from non-over-expressed Escherichia coli membrane proteins with known structure to evaluate the shaving methods. Finally, the identified peptides were used to test the accuracy of a number of topology predictors. At the end we suggest that the usage of thermolysin, an enzyme working at the natural pH of the cell for membrane shaving, is superior because: (i) we detect a similar number of peptides and proteins using thermolysin and trypsin; (ii) thermolysin shaving can be run at a natural pH and (iii) the incubation time is quite short. (iv) Fewer detected peptides from thermolysin shaving originate from the transmembrane regions. Using thermolysin shaving we can also provide a clear separation between the best and the less accurate topology predictors, indicating that using data from shaving can provide valuable information when developing new topology predictors.
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| 3. |
- Carlsson, Christel, et al.
(författare)
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Transport av kemiska bekämpningsmedel samt fastläggnings- och nedbrytningskarakterisering i en vertikal transekt genom mark- och grundvattenzonen i Vemmenhögs tillrinningsområde, södra Sverige
- 2013
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Projektets mål har varit att undersöka förekomst, fastläggning, transport och nedbrytning av kemiska bekämpningsmedel (KB) i djupare grundvatten i ett litet avrinningsområde i Vemmenhög i Skåne. Inom ramen för studien har grundvatten provtagits på varierande djup (5,5-35 m) och analyserats med avseende på 150 olika KB vid fem olika tillfällen utan att några detekterats (undantaget ett enstaka fynd av AMPA). Dessa djupare grundvatten daterades till mellan 40 och >60 år. I grunt grundvatten från området finns fynd av KB och med hjälp av statistisk analys av spridningsdata och data över fynd visades att den enskilt största faktorn som avgör om KB återfinns i grundvattnet eller ej är dosen vid besprutningstillfället. En högre dos ökar sannolikheten för fynd i grundvattnet. En matematisk modellering har genomförts för att förklara förekomst av 6 olika KB i grunt grundvatten. För modelleringen användes bl.a. experimentellt bestämda parametrar för nedbrytning och fastläggning. Modelleringen möjliggjorde att fynd av lågsorberande KB kunde kopplas till spridningen av dessa substanser, medan fynd av de relativt starkt sorberande substanserna inte kunde förklaras.
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| 4. |
- Cifani, Paolo, et al.
(författare)
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Hunting for Protein Markers of Hypoxia by Combining Plasma Membrane Enrichment with a New Approach to Membrane Protein Analysis
- 2011
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 10:4, s. 1645-1656
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Tidskriftsartikel (refereegranskat)abstract
- Nontransient hypoxia is strongly associated with malignant lesions, resulting in aggressive behavior and resistance to treatment. We present an analysis of mRNA and protein expression changes in neuroblastoma cell lines occurring upon the transition from normoxia to hypoxia. The correlation between mRNA and protein level changes was poor, although some known hypoxia-driven genes and proteins correlated well. We present previously undescribed membrane proteins expressed under hypoxic conditions that are candidates for evaluation as biomarkers.
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| 5. |
- Göransson, Gunnel, et al.
(författare)
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Mass transport of contaminated soil released into surface water by landslides (Göta River, SW Sweden)
- 2012
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Ingår i: Hydrology and Earth System Sciences. - : Copernicus GmbH. - 1607-7938. ; 16:7, s. 1879-1893
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Tidskriftsartikel (refereegranskat)abstract
- Landslides of contaminated soil into surface water represent an overlooked exposure pathway that has not been addressed properly in existing risk analysis for landslide hazard, contaminated land, or river basin management. A landslide of contaminated soil into surface water implies an instantaneous exposure of the water to the soil, dramatically changing the prerequisites for the mobilisation and transport of pollutants. In this study, an analytical approach is taken to simulate the transport of suspended matter released in connection with landslides into rivers. Different analytical solutions to the advection-dispersion equation (ADE) were tested against the measured data from the shallow rotational, retrogressive landslide in clayey sediments that took place in 1993 on the Göta River, SW Sweden. The landslide encompassed three distinct events, namely an initial submerged slide, followed by a main slide, and a retrogressive slide. These slides generated three distinct and non-Gaussian peaks in the online turbidity recordings at the freshwater intake downstream the slide area. To our knowledge, this registration of the impact on a river of the sediment release from a landslide is one of few of its kind in the world and unique for Sweden. Considering the low frequency of such events, the data from this landslide are highly useful for evaluating how appropriate the ADE is to describe the effects of landslides into surface water. The results yielded realistic predictions of the measured variation in suspended particle matter (SPM) concentration, after proper calibration. For the three individual slides it was estimated that a total of about 0.6% of the total landslide mass went into suspension and was transported downstream. This release corresponds to about 1 to 2% of the annual suspended sediment transport for that river stretch. The studied landslide partly involved an industrial area, and by applying the analytical solution to estimate the transport of metals in the sediments, it was found that landslides may release a significant amount of pollutants if large contaminated areas are involved. However, further studies are needed to develop more detailed descriptions of the transport processes. There is also a need to increase the knowledge on possible environmental consequences in the near and far field, in a short- and long-time perspective. In summary, the release of pollutants should not be neglected in landslide risk assessments.
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| 6. |
- Kreuger, Jenny, et al.
(författare)
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Modelling pesticide transport in a shallow groundwater catchment using tritium and helium-3 data
- 2014
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Ingår i: Applied Geochemistry. - : Elsevier BV. - 0883-2927. ; 50, s. 231-239
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Tidskriftsartikel (refereegranskat)abstract
- Using tritium and helium-3 data for calibration, a 2-D transport model was set up to explain the occurrence of bentazone, dichlorprop, glyphosate, isoproturon, MCPA and metamitron in a small groundwater catchment in southern Sweden. The model was parameterised with site-specific degradation and sorption data to enable transport simulations. Local climatological data and a 21-year record of agricultural pesticide use within the study area were used as boundary conditions. Model output was evaluated against a 7-year long pesticide monitoring data-series from two monitoring wells within the study area. The model successfully predicts observed breakthrough of bentazone, dichlorprop, isoproturon and MCPA. However, it fails to simulate observed occurrences of glyphosate and metamitron. Glyphosate and metamitron exhibit relatively high sorption potential, and their occurrence is suggested to be the result of non-equilibrium preferential flow paths which the model cannot reproduce due the conceptualisation of the system as homogenous and isotropic. The results indicate a promising methodological approach applicable to groundwater contamination risk assessment, and demonstrate the potential for transport model calibration by means of tritium and helium-3 data. Main constraints of the study relate to the relatively simple system conceptualisation, indicating a need for further consideration of physical and chemical heterogeneity. (C) 2014 Elsevier Ltd. All rights reserved.
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