| 1. |
- Göransson, Hanna, et al.
(author)
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Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data
- 2009
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In: PloS one. - : Public Library of Science (PLoS). - 1932-6203. ; 4:6, s. e6057-
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Journal article (peer-reviewed)abstract
- BACKGROUND: Technologies based on DNA microarrays have the potential to provide detailed information on genomic aberrations in tumor cells. In practice a major obstacle for quantitative detection of aberrations is the heterogeneity of clinical tumor tissue. Since tumor tissue invariably contains genetically normal stromal cells, this may lead to a failure to detect aberrations in the tumor cells. PRINCIPAL FINDING: Using SNP array data from 44 non-small cell lung cancer samples we have developed a bioinformatic algorithm that accurately models the fractions of normal and tumor cells in clinical tumor samples. The proportion of normal cells in combination with SNP array data can be used to detect and quantify copy number neutral loss-of-heterozygosity (CNNLOH) in the tumor cells both in crude tumor tissue and in samples enriched for tumor cells by laser capture microdissection. CONCLUSION: Genome-wide quantitative analysis of CNNLOH using the CNNLOH Quantifier method can help to identify recurrent aberrations contributing to tumor development in clinical tumor samples. In addition, SNP-array based analysis of CNNLOH may become important for detection of aberrations that can be used for diagnostic and prognostic purposes.
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| 2. |
- Wiklund, Susanne, et al.
(author)
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Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models
- 2008
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In: Analytical Chemistry. - Columbus, OH : American Chemical Society. - 0003-2700 .- 1520-6882. ; 80:1, s. 115-22
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Journal article (peer-reviewed)abstract
- Metabolomics studies generate increasingly complex data tables, which are hard to summarize and visualize without appropriate tools. The use of chemometrics tools, e.g., principal component analysis (PCA), partial least-squares to latent structures (PLS), and orthogonal PLS (OPLS), is therefore of great importance as these include efficient, validated, and robust methods for modeling information-rich chemical and biological data. Here the S-plot is proposed as a tool for visualization and interpretation of multivariate classification models, e.g., OPLS discriminate analysis, having two or more classes. The S-plot visualizes both the covariance and correlation between the metabolites and the modeled class designation. Thereby the S-plot helps identifying statistically significant and potentially biochemically significant metabolites, based both on contributions to the model and their reliability. An extension of the S-plot, the SUS-plot (shared and unique structure), is applied to compare the outcome of multiple classification models compared to a common reference, e.g., control. The used example is a gas chromatography coupled mass spectroscopy based metabolomics study in plant biology where two different transgenic poplar lines are compared to wild type. By using OPLS, an improved visualization and discrimination of interesting metabolites could be demonstrated.
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| 3. |
- Benkestock, Kurt, et al.
(author)
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Electrospray ionization mass spectrometry as a tool for determination of drug binding sites to human serum albumin by noncovalent interaction
- 2005
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In: Rapid Communications in Mass Spectrometry. - : Wiley. - 0951-4198 .- 1097-0231. ; 19:12, s. 1637-1643
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Journal article (peer-reviewed)abstract
- Most proteins in blood plasma bind ligands. Human serum albumin (HSA) is the main transport protein with a very high capacity for binding of endogenous and exogenous compounds in plasma. Many pharmacokinetic properties of a drug depend on the level of binding to plasma proteins. This work reports studies of noncovalent interactions by means of nanoelectrospray ionization mass spectrometry (nanoESI-MS) for determination of the specific binding of selected drug candidates to HSA. Warfarin, iopanoic acid and digitoxin were chosen as site-specific probes that bind to the main sites of HSA. Two drug candidates and two known binders to HSA were analyzed using a competitive approach. The drugs were incubated with the target protein followed by addition of site-specific probes, one at a time. The drug candidates showed predominant affinity to site I (warfarin site). Naproxen and glyburide showed affinity to both sites I and II. The advantages of nanoE-SI-MS for these studies are the sensitivity, the absence of labeled molecules and the short method development time.
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| 4. |
- Botling, Johan, et al.
(author)
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Impact of thawing on RNA integrity and gene expression analysis in fresh frozen tissue
- 2009
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In: Diagnostic molecular pathology (Print). - 1052-9551 .- 1533-4066. ; 18:1, s. 44-52
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Journal article (peer-reviewed)abstract
- Biobanks of fresh, unfixed human tissue represent a valuable source for gene expression analysis in translational research and molecular pathology. The aim of this study was to evaluate the impact of thawing on RNA integrity and gene expression in fresh frozen tissue specimens. Portions of snap frozen tonsil tissue, unfixed or immersed in RNAlater, were thawed at room temperature for 0 minute, 5 minutes, 30 minutes, 45 minutes, 1 hour, 3 hours, 6 hours, and 16 hours before RNA extraction. Additionally, tonsil tissue underwent repetitive freezing and thawing cycles. RNA integrity was analyzed by microchip gel electrophoresis and gene expression by quantitative real-time polymerase chain reaction for selected genes (FOS, TGFB1, HIF1A, BCL2, and PCNA). Minimal RNA degradation was detected after 30 minutes of thawing in unfixed samples. This degradation was accompanied by relevant changes in gene expression for FOS and BCL2 at 45 minutes. Modified primer design or the use of different housekeeping genes could not rectify the changes for FOS. Repetitive thawing cycles had similar effects on RNA integrity. The incubation of the tissue in RNAlater efficiently prevented RNA degradation. In conclusion, degradation of RNA in frozen tissue occurs first after several minutes of thawing. Already minimal decrease in RNA quality may result in significant changes in gene expression patterns in clinical tissue samples.
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| 5. |
- Carlström, Mattias, et al.
(author)
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Role of nitric oxide deficiency in the development of hypertension in hydronephrotic animals
- 2008
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In: American Journal of Physiology - Renal Physiology. - : American Physiological Society. - 0363-6127 .- 1522-1466 .- 1931-857X. ; 294:2, s. 362-370
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Journal article (peer-reviewed)abstract
- Hydronephrotic animals develop renal injury and hypertension, which is associated with an abnormal tubuloglomerular feedback (TGF). The TGF sensitivity is coupled to nitric oxide (NO) in the macula densa. The involvement of reduced NO availability in the development of hypertension in hydronephrosis was investigated. Hydronephrosis was induced by ureteral obstruction in young rats. Blood pressure and renal excretion were measured in adulthood, under different sodium conditions, and before and after chronic administration of either N-G- nitro-L-arginine methyl ester (L-NAME) or L-arginine. Blood samples for ADMA, SDMA, and L-arginine analysis were taken and the renal tissue was used for histology and determination of NO synthase (NOS) proteins. TGF characteristics were determined by stop-flow pressure technique before and after administration of 7-nitroindazole (7-NI) or L-arginine. Hydronephrotic animals developed salt-sensitive hypertension, which was associated with pressure natriuresis and diuresis. The blood pressure response to L-NAME was attenuated and L-arginine supplementation decreased blood pressure in hydronephrotic animals, but not in the controls. Under control conditions, reactivity and sensitivity of the TGF response were greater in the hydronephrotic group. 7-NI administration increased TGF reactivity and sensitivity in control animals, whereas, in hydronephrotic animals, neuronal NOS (nNOS) inhibition had no effect. L-Arginine attenuated TGF response more in hydronephrotic kidneys than in controls. The hydronephrotic animals displayed various degrees of histopathological changes. ADMA and SDMA levels were higher and the renal expressions of nNOS and endothelial NOS proteins were lower in animals with hydronephrosis. Reduced NO availability in the diseased kidney in hydronephrosis, and subsequent resetting of the TGF mechanism, plays an important role in the development of hypertension.
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| 6. |
- Nilsson, Maria, et al.
(author)
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Extracting rules from expert operators to support situation awareness in maritime surveillance
- 2008
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In: Proceedings of the 11th International Conference on Information Fusion (FUSION 2008). - : IEEE Press. - 9783000248832 - 9783800730926 ; , s. 908-915
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Conference paper (peer-reviewed)abstract
- In maritime surveillance, supporting operators’ situation awareness is a very important issue for enabling the possibility to detect anomalous behaviour. We present a user study which conceptualises knowledge to be implemented in a rulebased application aiming at supporting situation awareness. Participatory observations were used as a method for extracting operators’ knowledge. The result of the user study is in the form of a number of identified rules emerging from organisational factors, group thinking and individual experience. A description of the rule-based prototype is presented a long with the result from the user study. This is also discussed together with the applicability of rule based systems and how to support situation awareness.
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| 7. |
- Raberg, U., et al.
(author)
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Testing and evaluation of natural durability of wood in above ground conditions in Europe - an overview
- 2005
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In: Journal of Wood Science. - : Springer Science and Business Media LLC. - 1435-0211 .- 1611-4663. ; 51:5, s. 429-440
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Research review (peer-reviewed)abstract
- Natural durability of wood is determined by the European standard EN 252 for specimens in ground contact and EN 113 for basidiomycetes in the laboratory, but no test exists for above ground conditions. For above ground conditions, the European prestandard ENV 12037 and EN 330 are used to determine the durability of treated wood. The most important factors for fungal establishment on the surface and within wood are the moisture content, the surrounding temperature, and the relative humidity. Strength tests are the most sensitive for decay detection, but neither strength tests nor identification of fungi responsible for the decay are included in the standards of above ground durability in field tests. To detect decay, visual examination , pick or splinter tests, and mass loss determination are used. Identifying fungi with traditional methods, e.g., growth on solid medium, is time consuming and complicated. Molecular methods like polymerase chain reaction and sequencing do not require mycological skill for identification to species level, and furthermore the methods do not depend on the subjective judgement like most traditional methods, but are based on the objective information of the target organism (e.g., nucleotide sequences). The next generation of standard field tests will probably consider the drawbacks of standard tests today and be rapid and include both quality tests like molecular identification and nondestructive quantitative tests, e.g., acoustic tests. Laboratory tests can be improved by using fungi identified from field trials and by combining different fungi in the same test and thus simulate degradation in practice.
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| 8. |
- Skog, Johan, et al.
(author)
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Adenoviruses 16 and CV23 efficiently transduce human low-passage brain tumor and cancer stem cells
- 2007
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In: Molecular Therapy. - : Elsevier BV. - 1525-0016 .- 1525-0024. ; 15:12, s. 2140-5
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Journal article (peer-reviewed)abstract
- Most clinical protocols involving adenovirus (Ad) vectors for gene therapy use a vector based on serotype 5 (Ad5). We believe that this serotype is not suitable for all gene therapy applications and that alternative vectors based on other serotypes should be developed. We have compared the ability of Ad5, Ad11p, Ad16p, and a chimpanzee Ad (CV23) to infect human low-passage brain tumor cells as well as primary glioma cells sorted into a CD133(+) and CD133(-) population. Cancer stem cells have been shown to reside in the CD133(+) population of cells in human glioma tumors and they are of considerable interest in glioma therapy. Ad16p and CV23 infected the low-passage brain tumor cell lines and also the CD133(+) and CD133(-) primary tumor cells most efficiently. Interestingly, as the passage number of the cells increased, the infection capacity of Ad5 increased significantly, whereas this was not seen for CV23. To ensure the therapeutic effect of Ad vectors on brain tumors, the vector must be capable of addressing both the CD133(+) cancer stem cells and the CD133(-) cells of the tumor. In particular, Ad16 and CV23 are meeting this challenge.
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