| 1. |
- Ericsson, Caroline, et al.
(författare)
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Thermotropic phase behaviour of long-chain alkylmaltosides
- 2005
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9084 .- 1463-9076. ; 7:15, s. 2970-2977
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Tidskriftsartikel (refereegranskat)abstract
- The thermotropic phase behaviour and phase structure of crystalline and non-crystalline n-tetradecyl-beta-D-maltoside (C(14)G(2)) and n-hexadecyl-beta-D-maltoside (C(16)G(2)) have been investigated by means of differential scanning calorimetry and X-ray techniques. Upon lyophilisation, both compounds form a solid, lamellar phase comprising disordered head groups and hexagonally packed alkyl chains that are suggested to be tilted and interdigitated. This ordered lamellar phase melts into a metastable lamellar liquid crystal, which re-crystallises to a high-temperature crystalline polymorph comprising interdigitated, non-tilted alkyl chains. Remarkably, the high-temperature polymorph of C(14)G(2) has the same melting point as that of C(16)G(2), namely 105 degrees C for both surfactants. A low-temperature polymorph of anhydrous C(14)G(2) crystallises from water at room temperature, whereas the hemihydrate of C(14)G(2) crystallises at 6 degrees C from water, or from chloroform containing trace water. X-ray data suggest both these crystalline modifications to comprise interdigitated and tilted alkyl chains.
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| 2. |
- Lindskog, Sven, et al.
(författare)
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Validation of an Algorithm for Chronic Periodontitis Risk Assessment and Prognostication : Analysis of an Inflammatory Reactivity Test and Selected Risk Predictors
- 2010
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Ingår i: Journal of Periodontology. - : American Academy of Periodontology. - 0022-3492 .- 1943-3670. ; 81:6, s. 837-847
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Tidskriftsartikel (refereegranskat)abstract
- Background: Patients with severe forms of chronic periodontitis present with varying degrees of decreased inflammatory reactivity. A previously reported algorithm for chronic periodontitis risk assessment and prognostication is based on the analysis of some 20 risk predictors. One of these predictors is a skin provocation test that assesses the individual patient's reactivity to a lipid A challenge. The aim of this report was to analyze results from validation data for the algorithm with respect to the contribution of results of the skin provocation test as a risk predictor for the progression of chronic periodontitis and to compare these results with the contribution from other predictors, namely smoking, angular bony destruction, furcation involvement, abutment teeth, and endodontic pathology. Methods: Data from a previously reported clinical validation sample were used for the analysis, including the calculation of quality measures and explanatory values using different types of regression analysis and non-parametric testing. Results: Smoking, endodontic pathology, abutment teeth, angular bony destruction, and furcation involvement presented with individual explanatory values for periodontitis progression between 4% and 13% and highly significant parameter estimates. Explanatory values for the results of the skin provocation test ranged between 2.6% and 5.1% depending on the disease severity group, with a positive predictive value of 82% for the identification of high-risk patients. Conclusion: The skin provocation test provided a clinically significant contribution to the quality of analysis with the periodontitis risk and prognostication algorithm, in particular in the selection of high-risk patients for in-depth individual tooth analysis.
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| 3. |
- Lindskog, Sven, et al.
(författare)
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Validation of an Algorithm for Chronic Periodontitis Risk Assessment and Prognostication: Risk Predictors, Explanatory Values, Measures of Quality, and Clinical Use
- 2010
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Ingår i: JOURNAL OF PERIODONTOLOGY. - : American Academy of Periodontology. - 0022-3492 .- 1943-3670. ; 81:4, s. 584-593
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Tidskriftsartikel (refereegranskat)abstract
- Background: The American Academy of Periodontology has recently stated that, "[risk assessment will become] increasingly important in periodontal treatment planning and should be part of every comprehensive dental and periodontal evaluation." (J Periodontol 2006;77:1608). Unaided risk assessment and prognostication show significant variability because chronic periodontitis is a multifactorial disease. This report summarizes the clinical validation of an algorithm for chronic periodontitis risk assessment and prognostication. The algorithm is a Web-based analytic tool that integrates some 20 risk predictors and calculates scores indicating levels of risk for chronic periodontitis for the dentition (Level I) and, if an elevated risk is found, prognosticates disease progression tooth by tooth (Level II). Methods: An independent clinical validation sample was generated in an open, prospective clinical trial and analyzed in a predetermined validation plan. Results: The analyses identified two threshold scores above which significant progression of periodontitis was found. Based on these scores, sufficiently high explanatory values with significant and increasing parameter estimates for increasing risk were established in Level I, justifying detailed analysis tooth by tooth in Level II. Subsequent prognostication of chronic periodontitis in Level II was found to be accompanied by clinically relevant measures of quality in relation to rates of disease progression. Three score intervals representing increasing levels of periodontitis progression were identified corresponding to increasing levels of significant annual marginal bone loss. Conclusions: The predictors included in the algorithm reflect a relevant selection for periodontitis risk assessment. Risk assessment and prognostication with the algorithm provides the clinician with a validated, reliable, consistent, and objective tool supporting treatment planning.
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| 4. |
- Ahlford, Marianne, et al.
(författare)
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Uppsala Underdogs - A Robot Soccer Project
- 2006
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Rapport (populärvet., debatt m.m.)abstract
- In this paper, we describe the four-legged soccer team Uppsala Underdogs developed by a group of 4th year computer science students at Uppsala University during the fall of 2004. The project is based on the experience from two similar previous projects. This year the emphasis of the project has been on distribution of data and on support for evaluation and reconfiguration of strategies. To support data distribution, a middleware has been developed, which implements a replication algorithm and provides a clean interface for the other software modules (or behaviors). To enable easy reconfiguration of strategies, an automata-based graphical description language has been developed, which can be compiled into code that uses the database and the lower level modules, such as tactics and positioning, to make decisions and control the robot. In addition, a graphical simulator has been developed in which the strategies can be evaluated.
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| 5. |
- All-Ericsson, Charlotta, et al.
(författare)
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c-Kit-dependent growth of uveal melanoma cells : a potential therapeutic target?
- 2004
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Ingår i: Investigative Ophthalmology and Visual Science. - : Association for Research in Vision and Ophthalmology (ARVO). - 0146-0404 .- 1552-5783. ; 45:7, s. 2075-82
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: This study was conducted to investigate the expression and functional impact of the proto-oncogene c-kit in uveal melanoma. METHODS: Based on immunohistochemical (IHC) study of paraffin-embedded specimens from 134 uveal melanomas and Western blot analysis on eight fresh-frozen samples the expression of c-kit in uveal melanoma was studied. Furthermore, the phosphorylation of c-kit and the impact of the tyrosine kinase inhibitor STI571 was examined in the three uveal melanoma cell lines OCM-1, OCM-3, and 92-1. RESULTS: Eighty-four of 134 paraffin-embedded samples and six of eight fresh-frozen samples expressed c-kit. c-Kit was strongly expressed and tyrosine phosphorylated in cultured uveal melanoma cells compared with cutaneous melanoma cells. Moreover, in contrast to cutaneous melanoma cell lines c-kit maintained a high phosphorylation level in serum-depleted uveal melanoma cells. No activation-related mutations in exon 11 of the KIT gene were found. On the contrary, expression of the stem cell growth factor (c-kit ligand) was detected in all three uveal melanoma cell lines, suggesting the presence of autocrine (paracrine) stimulation pathways. Treatment of uveal melanoma cell lines with STI571, which blocks c-kit autophosphorylation, resulted in cell death. The IC(50) of the inhibitory effects on c-kit phosphorylation and cell proliferation was of equal size and less than 2.5 microM. CONCLUSIONS: The results confirm that c-kit is vastly expressed in uveal melanoma, suggest that the c-kit molecular pathway may be important in uveal melanoma growth, and point to its use as a target for therapy with STI571.
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| 6. |
- Banér, Johan, et al.
(författare)
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Microarray-based molecular detection of foot-and-mouth disease, vesicular stomatitis and swine vesicular disease viruses, using padlock probes
- 2007
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Ingår i: Journal of Virological Methods. - : Elsevier BV. - 0166-0934 .- 1879-0984. ; 143:2, s. 200-206
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Tidskriftsartikel (refereegranskat)abstract
- The World Organization for Animal Health (Office International des Epizooties, OIE) includes the diseases caused by foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), and vesicular stomatitis virus (VSV), as "Diseases Notifiable to the OIE". Foot-and-mouth disease (FMD) outbreaks have severe economical as well as social effects and cannot be differentiated from the diseases caused by the other two viruses on the basis of clinical symptoms. Efficient laboratory techniques are therefore required for detection and identification of the viruses causing similar vesicular symptoms in swine. A rapid method is described using padlock probes and microarrays to detect simultaneously and differentiate the three viruses in a single reaction, as well as providing serotype information in cases of VSV infection. The padlock probe/microarray assay detected successfully and identified 39 cDNA samples of different origin representing the three viruses. The results were in complete agreement with identities and serotypes determined previously. This novel virus detection method is discussed in terms of usefulness and further development.
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| 7. |
- Bauer, Fredric, et al.
(författare)
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Miljöforskare: ”Industrins klimatomställning måste gå snabbare”
- 2021
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Ingår i: Ny teknik. - 0550-8754.
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- DEBATT. Svensk industri tar flera lovande initiativ, men omställningen går alldeles för långsamt – och i vissa branscher märks den knappt alls, skriver sju miljöforskare.
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| 8. |
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| 9. |
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| 10. |
- Conze, Tim, 1977-, et al.
(författare)
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Single molecule analysis of combinatorial splicing
- 2010
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 38:16, s. e163-
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Tidskriftsartikel (refereegranskat)abstract
- Alternative splicing forms diverse mRNA isoform populations from a single ancestral pre-mRNA and thereby enhances complexity of transcript structure and of gene function. We describe a method called spliceotyping, which translates combinatorial mRNA splicing patterns into a library of binary strings of nucleic acid tags, encoding the exon composition of transcripts. The transcript abundance is registered by counts of individual molecules and individual exon inclusion patterns are represented as strings of binary data. The technique is illustrated by analyzing the splicing patterns of the adenovirus early 1A gene and the beta actin reference transcript. The method permits different genes to be analyzed in parallel and will be valuable for elucidating the complex effects of combinatorial splicing.
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| 11. |
- Darmanis, Spyros, et al.
(författare)
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Multiplexed solid-phase proximity ligation assays: Highly specific and parallel protein measurements with DNA sequencing readout
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Identification and validation of protein biomarkers is a very important step towards the understanding of the underlying mechanisms of disease, early diagnosis and efficient patient treatment. To carry out this task, methods are needed that would allow us to mine the proteome with sufficient sensitivity and specificity in large sets of samples. We present herein the development of a Multiplexed Proximity Ligation Assay (MultiPLAy), to facilitate efficient protein profiling in a parallel, sensitive and specific manner. We showed that for the simultaneous analysis of 35 proteins MultiPLAy exhibited an improved sensitivity over conventional sandwich assays as well as a smaller susceptibility to background signal increase in the transition from singleplex to multiplex. We used MultiPLAy to identify putative biomarkers in two separate sample cohorts of colorectal cancer (CRC) and cardiovascular disease (CVD) and with the use a novel multivariate analysis approach were able to identify new, as well as already known diagnostic biomarkers. Furthermore we were able to combine MultiPLAy with the use of next-generation sequencing allowing for the first time digital recording of protein profiles in blood. We demonstrated good reproducibility of MultiPLAy coupled to next-generation sequencing, as well as a satisfactory correlation to standard real-time PCR readout. We conclude that MultiPLAy has great potential as a basis for highly multiplexed protein detection assays that can be utilized for the identification of large numbers of proteins or protein variants. This will allow extensive validation of protein expression patterns in biobanked samples and in prospective studies, and can provide a much-needed platform for efficient validation of diagnostic markers for clinical use.
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| 12. |
- Darmanis, Spyros, et al.
(författare)
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ProteinSeq : high-performance proteomic analyses by proximity ligation and next generation sequencing
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:9, s. e25583-
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Tidskriftsartikel (refereegranskat)abstract
- Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 μl of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use.
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| 13. |
- Darmanis, Spyros, et al.
(författare)
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Sensitive plasma protein analysis by microparticle-based proximity ligation assays
- 2010
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 9:2, s. 327-335
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Tidskriftsartikel (refereegranskat)abstract
- Detection of proteins released in the bloodstream from tissues damaged by disease can promote early detection of pathological conditions, differential diagnostics, and follow-up of therapy. Despite these prospects and a plethora of candidate biomarkers, efforts in recent years to establish new protein diagnostic assays have met with limited success. One important limiting factor has been the challenge of detecting proteins present at trace levels in complex bodily fluids. To achieve robust, sensitive, and specific detection, we have developed a microparticle-based solid-phase proximity ligation assay, dependent on simultaneous recognition of target proteins by three antibody molecules for added specificity. After capture on a microparticle, solid-phase pairs of proximity probes are added followed by washes, enabling detection and identification of rare protein molecules in blood while consuming small amounts of sample. We demonstrate that single polyclonal antibody preparations raised against target proteins of interest can be readily used to establish assays where detection depends on target recognition by three individual antibody molecules, recognizing separate epitopes. The assay was compared with state-of-the-art sandwich ELISAs for detection of vascular endothelial growth factor, interleukin-8 and interleukin-6, and it was found to be superior both with regard to dynamic range and minimal numbers of molecules detected. Furthermore, the assays exhibited excellent performance in undiluted plasma and serum as well as in whole blood, producing comparable results for nine different antigens. We thus show that solid-phase proximity ligation assay is suitable for validation of a variety of protein biomarkers over broad dynamic ranges in clinical samples.
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| 14. |
- Ericsson, Caroline, et al.
(författare)
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Aggregate morphology and flow behaviour of micellar alkylglycoside solutions
- 2005
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Ingår i: Colloid and Polymer Science. - : Springer Science and Business Media LLC. - 0303-402X. ; 283:12, s. 1313-1320
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Tidskriftsartikel (refereegranskat)abstract
- Solutions of n-nonyl-beta-D-glucoside (C(9)G(1)), n-decyl-beta-D-glucoside (C(10)G(1)), n-dodecyl-beta-D-maltoside (C(12)G(2)) n-tetradecyl-beta-D-maltoside (C(14)G(2)) and C(9)G(1)/C(10)G(1) mixtures have been characterised by capillary viscometry and rheology in H2O and D2O, in order to map the influence of surfactant characteristics on micellisation over a wide concentration range. For the maltosides, the micellar solutions are shear thinning with a zero-shear viscosity that scales with concentration according to a power law with an exponent of about 5.8. In contrast, solutions of the glucosides C(9)G(1), C(10)G(1) and their mixtures show Newtonian flow behaviour and a much lower scaling exponent (< 2.4). In C(9)G(1)/C(10)G(1) mixtures, the scaling exponent decreases monotonously with increasing C(10)G(1) content. The flow behaviour correlates with the packing requirements of the various surfactants, and are compatible with the idea that the maltosides form worm-like micelles, whereas the glucosides form branched, interconnected micelles (C(9)G(1)) and space-filling micellar networks (C(10)G(1)).
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| 15. |
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| 16. |
- Ericsson, Caroline, et al.
(författare)
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Effects of temperature, salt, and deuterium oxide on the self-aggregation of alkylglycosides in dilute solution. 2. n-Tetradecyl-beta-D-maltoside
- 2005
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 21:4, s. 1507-1515
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Tidskriftsartikel (refereegranskat)abstract
- The effects of salt, temperature, and deuterium oxide on the self-aggregation of n-tetradecyl-beta-D-maltoside (C(14)G(2)) in dilute solution have been investigated by static light scattering, dynamic light scattering (DLS), small-angle neutron scattering (SANS), tensiometry, and capillary viscometry. SANS data show that the micelles can be described as relatively flexible polymer-like micelles with an elliptical cross section, at least at temperatures between 35 and 50 degreesC. The micelles grow in one dimension with increasing temperature and concentration. DLS and viscometry data suggest that the micelle size reaches a maximum at 60-70 degreesC. Comparison of DLS data in D2O and H2O shows that the micelles are larger in the former case. The effect of salt on the micelle size was found to follow the Hofmeister series. Thus, at constant salt concentration, the micelle size decreases according to the sequence SO42- > Cl (-)> NO3 > I- > SCN-, where I- and SCN- act as salting-in anions. From tensiometric data, it can be concluded that the temperature effects on micelle morphology do not correlate directly with those on unimer solubility. Rather, the temperature effect on the hydrocarbon chain conformation seems to be decisive for the micelle morphology. At constant temperature, on the other hand, the effect of salt and deuterium isotope is attributable to changes in effective headgroup area, including intermolecular interactions and water of hydration.
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| 17. |
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| 18. |
- Ericsson, Olle, et al.
(författare)
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A dual-tag microarray platform for high-performance nucleic acid and protein analyses
- 2008
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 36:8, s. e45-
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Tidskriftsartikel (refereegranskat)abstract
- DNA microarrays serve to monitor a wide range of molecular events, but emerging applications like measurements of weakly expressed genes or of proteins and their interaction patterns will require enhanced performance to improve specificity of detection and dynamic range. To further extend the utility of DNA microarray-based approaches we present a high-performance tag microarray procedure that enables probe-based analysis of as little as 100 target cDNA molecules, and with a linear dynamic range close to 10(5). Furthermore, the protocol radically decreases the risk of cross-hybridization on microarrays compared to current approaches, and it also allows for quantification by single-molecule analysis and real-time on-chip monitoring of rolling-circle amplification. We provide proof of concept for microarray-based measurement of both mRNA molecules and of proteins, converted to tag DNA sequences by padlock and proximity probe ligation, respectively.
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| 19. |
- Ericsson, Olle, 1978-
(författare)
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Biomolecular Analysis by Dual-Tag Microarrays and Single Molecule Amplification
- 2008
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Padlock probes and proximity ligation are two powerful molecular tools for detection of nucleic acids and proteins, respectively. Both methods result in the formation of DNA reporter molecules upon recognition of specific target molecules. These reporter molecules can be designed to include tag sequences that can be analyzed by techniques for nucleic acid analysis. Herein, I present a dual-tag microarray (DTM) platform that is suitable for high-performance analyses of DNA reporter molecule libraries, generated by padlock and proximity probing reactions. The DTM platform was applied for analysis of mRNA transcripts using padlock probes, and of cytokines using proximity ligation. The platform drastically improved specificity of detection, and it allowed precise measurements of proteins and nucleic acids over wide dynamic ranges.The thesis also presents two techniques for multi-probe analyses of biomolecules: the triple-specific proximity ligation assay (3PLA) for protein analyses, and the spliceotyping assay for mRNA analyses. 3PLA allows highly specific measurements of as little as hundreds of target protein molecules by interrogating three target epitopes simultaneously. In spliceotyping the exon composition of individual transcripts are represented as a series of tag sequences in DNA reporter molecules, via a series of target-dependent ligation reactions. Next, the splicing patterns along individual transcripts can be revealed by amplified single molecule detection and step-wise decoding.
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| 20. |
- Ericsson, Olle, et al.
(författare)
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Clinical validation of a novel automated cell-free DNA screening assay for trisomies 21, 13, and 18 in maternal plasma.
- 2019
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Ingår i: Prenatal diagnosis. - : Wiley. - 1097-0223 .- 0197-3851. ; 39:11, s. 1011-1015
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Tidskriftsartikel (refereegranskat)abstract
- To evaluate clinical performance of a new automated cell-free (cf)DNA assay in maternal plasma screening for trisomies 21, 18, and 13, and to determine fetal sex.Maternal plasma samples from 1200 singleton pregnancies were analyzed with a new non-sequencing cfDNA method, which is based on imaging and counting specific chromosome targets. Reference outcomes were determined by either cytogenetic testing, of amniotic fluid or chorionic villi, or clinical examination of neonates.The samples examined included 158 fetal aneuploidies. Sensitivity was 100% (112/112) for trisomy 21, 89% (32/36) for trisomy 18, and 100% (10/10) for trisomy 13. The respective specificities were 100%, 99.5%, and 99.9%. There were five first pass failures (0.4%), all in unaffected pregnancies. Sex classification was performed on 979 of the samples and 99.6% (975/979) provided a concordant result.The new automated cfDNA assay has high sensitivity and specificity for trisomies 21, 18, and 13 and accurate classification of fetal sex, while maintaining a low failure rate. The study demonstrated that cfDNA testing can be simplified and automated to reduce cost and thereby enabling wider population-based screening.
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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Ghorai, Sagar, et al.
(författare)
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Site-specific atomic substitution in a giant magnetocaloric Fe2P-type system
- 2023
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 107:10
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Tidskriftsartikel (refereegranskat)abstract
- Giant magnetocaloric (GMC) materials constitute a requirement for near room temperature magnetic refrigeration. (Fe,Mn)2(P,Si) is a GMC compound with strong magnetoelastic coupling. The main hindrance towards application of this material is a comparably large temperature hysteresis, which can be reduced by metal site substitution with a nonmagnetic element. However, the (Fe,Mn)2(P,Si) compound has two equally populated metal sites, the tetrahedrally coordinated 3f and the pyramidally coordinated 3g sites. The magnetic and magnetocaloric properties of such compounds are highly sensitive to the site specific occupancy of the magnetic atoms. Here we have attempted to study separately the effect of 3f and 3g site substitution with equal amounts of vanadium. Using formation energy calculations, the site preference of vanadium and its influence on the magnetic phase formation are described. A large difference in the isothermal entropy change (as high as 44\%) with substitution in the 3f and 3g sites is observed. The role of the lattice parameter change with temperature and the strength of the magnetoelastic coupling on the magnetic properties are highlighted.
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| 25. |
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| 26. |
- Hammond, Maria, et al.
(författare)
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Profiling cellular protein complexes by proximity ligation with dual tag microarray readout
- 2012
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:7, s. e40405-
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Tidskriftsartikel (refereegranskat)abstract
- Patterns of protein interactions provide important insights in basic biology, and their analysis plays an increasing role in drug development and diagnostics of disease. We have established a scalable technique to compare two biological samples for the levels of all pairwise interactions among a set of targeted protein molecules. The technique is a combination of the proximity ligation assay with readout via dual tag microarrays. In the proximity ligation assay protein identities are encoded as DNA sequences by attaching DNA oligonucleotides to antibodies directed against the proteins of interest. Upon binding by pairs of antibodies to proteins present in the same molecular complexes, ligation reactions give rise to reporter DNA molecules that contain the combined sequence information from the two DNA strands. The ligation reactions also serve to incorporate a sample barcode in the reporter molecules to allow for direct comparison between pairs of samples. The samples are evaluated using a dual tag microarray where information is decoded, revealing which pairs of tags that have become joined. As a proof-of-concept we demonstrate that this approach can be used to detect a set of five proteins and their pairwise interactions both in cellular lysates and in fixed tissue culture cells. This paper provides a general strategy to analyze the extent of any pairwise interactions in large sets of molecules by decoding reporter DNA strands that identify the interacting molecules.
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| 27. |
- He, Mingyue, et al.
(författare)
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Printing protein arrays from DNA arrays
- 2008
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 5:2, s. 175-177
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Tidskriftsartikel (refereegranskat)abstract
- We describe a method, DNA array to protein array (DAPA), which allows the 'printing' of replicate protein arrays directly from a DNA array template using cell-free protein synthesis. At least 20 copies of a protein array can be obtained from a single DNA array. DAPA eliminates the need for separate protein expression, purification and spotting, and also overcomes the problem of long-term functional storage of surface-bound proteins.
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| 28. |
- Johansson, Henrik, et al.
(författare)
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Targeted resequencing of candidate genes using Selector Probes
- 2011
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 39:2, s. e8-
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Tidskriftsartikel (refereegranskat)abstract
- Targeted genome enrichment is a powerful tool for making use of the massive throughput of novel DNA-sequencing instruments. We herein present a simple and scalable protocol for multiplex amplification of target regions based on the Selector technique. The updated version exhibits improved coverage and compatibility with next-generation-sequencing (NGS) library-construction procedures for shotgun sequencing with NGS platforms. To demonstrate the performance of the technique, all 501 exons from 28 genes frequently involved in cancer were enriched for and sequenced in specimens derived from cell lines and tumor biopsies. DNA from both fresh frozen and formalin-fixed paraffin-embedded biopsies were analyzed and 94 specificity and 98 coverage of the targeted region was achieved. Reproducibility between replicates was high (R 2=0, 98) and readily enabled detection of copy-number variations. The procedure can be carried out in <24 h and does not require any dedicated instrumentation.
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| 29. |
- Karlsson, Magnus, et al.
(författare)
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Kostnadseffektivitet i åtgärder mot övergödning i Östersjön - Fallstudie Gävle fjärdar
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- I detta projekt har kostnadseffektivitetet och resursförbrukning i samband med olika åtgärder studerats i syfte att minska effekter av övergödning i kustzonen i Östersjön. Som studieområde valdes Gävle fjärdar, ett relativt inneslutet kustområde med tillförsel av näringsämnen från olika källor och med en vattenkvalitet som visar på näringsrika förhållanden. Studien har fokuserat på olika åtgärder för att minska tillförseln av fosfor. De landbaserade källor som undersökts är utsläpp från cellulosaindustrin Korsnäsverken och utsläpp från det kommunala reningsverket i Gävle. Därutöver har åtgärder i form av aluminiumbehandling av sedimenten, reduktionsfiske av vitfiskbestånd och syresättning av bottenvattnet utvärderats. För att klarlägga hur fosfor omsätts i det aktuella kustområdet genomfördes massbalansmodelleringar samt en kartering av fosforförrådet i fjärdarnas bottensediment. Det konstaterades att området återhämtat sig från en tidigare period med syrgasbrist och att sedimenten innehöll relativt stora mängder av fosfor. Med modellen simulerades hur olika reduktioner av fosfortillförseln påverkar de ekologiska förhållandena. En minskning av fosfortillförseln med cirka 15 ton/år identifierades som nödvändig för att åstadkomma en reell förändring av miljöförhållandena. Vid detta scenario skulle produktionen av växtplankton minska med storleksordningen 20 % och siktdjupet öka med cirka en halvmeter. Följderna av detta skulle sannolikt bli att utbredningen av påväxtalger ökar i vertikalled och att beståndet av gös skulle minska något till förmån för gädda och abborre. Potentialen och kostnaden för olika åtgärder har beräknats översiktligt. Den specifika kostnaden varierar mellan 400 och 10 000 kr/kg avskiljd fosfor. Den mest kostnadseffektiva åtgärden bedöms vara åtgärder för att förbättra fosforavskiljningen i det kommunala reningsverket. Störst potential för att minska fosfortillförseln har identifierates vid Korsnäsverken men där är också de specifika kostnaderna som högst. Både aluminiumbehandling av sediment och reduktionsfiske bedöms som relativt kostnadseffektiva åtgärder. Vid reduktionsfiske kan dessutom ytterligare positiva effekter tillkomma genom att näringsväven manipuleras på ett gynnsamt sätt. Aluminiumbehandling skulle permanent fastlägga betydande mängder av eljest mobil fosfor. Syresättning bedöms däremot inte vara något alternativ i det studerade fallet eftersom syrgasförhållandena i dagsläget är goda. Kostnadsnyttokalkylen för elektriskt drivna pumpar som transporterar ned ytvatten till botten indikerar emellertid att åtgärden i de fall syrgasbrist föreligger skulle vara en effektiv metod. För att åstadkomma en reduktion motsvarande det föreslagna lokala miljömålet fordras att flera åtgärder genomförs parallellt och den sammanlagda årliga kostnaden beräknas uppgå till cirka 60 Mkr. För att bedöma den potentiella miljöbelastningen som olika åtgärder ger upphov till genomförs en översiktlig livscykelanalys där koldioxidemissioner från respektive åtgärd uppskattas. Störst koldioxidemission erhålls vid kemisk fällning vid Korsnäsverken. Detta förklaras av hög kemikalieförbrukning och att metoden genererar stora mängder slam som förbrukar resurser vid kvittblivning. Reduktionsfiske ger en potentiell koldioxidbesparing om fångsten rötas till biogas.
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| 30. |
- Landegren, Ulf, et al.
(författare)
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Molecular tools for a molecular medicine : analyzing genes, transcripts and proteins using padlock and proximity probes
- 2004
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Ingår i: Journal of Molecular Recognition. - : Wiley. - 0952-3499 .- 1099-1352. ; 17:3, s. 194-7
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Tidskriftsartikel (refereegranskat)abstract
- Procedures and reagents are needed to specifically detect all the macromolecules that are being identified in the course of genome projects. We discuss how this challenge may be met using a set of ligation-based reagents termed padlock probes and proximity ligation probes. These probes include elements with affinity for specific nucleic acid and protein molecules, respectively, along with unique identifier DNA sequence elements that encode the identity of the recognized target molecules. The information content of DNA strands that form in the detection reactions are recorded after amplification, allowing the recognized target molecules to be identified. The procedures permit highly specific solution-phase or localized analyses of large sets of target molecules as required in future molecular analyses.
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| 31. |
- Landegren, Ulf, et al.
(författare)
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Padlock and proximity probes for in situ and array-based analyses : tools for the post genomic era
- 2003
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Ingår i: Comparative and functional genomics. - : Hindawi Limited. - 1531-6912 .- 1532-6268. ; 4:5, s. 525-30
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Tidskriftsartikel (refereegranskat)abstract
- Highly specific high-throughput assays will be required to take full advantage of the accumulating information about the macromolecular composition of cells and tissues, in order to characterize biological systems in health and disease. We discuss the general problem of detection specificity and present the approach our group has taken, involving the reformatting of analogue biological information to digital reporter segments of genetic information via a series of DNA ligation assays. The assays enable extensive, coordinated analyses of the numbers and locations of genes, transcripts and protein.
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| 32. |
- Malmaeus, Mikael, et al.
(författare)
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Effekter av ytterligare reningssteg vid skogsindustrier
- 2010
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- I denna studie har konsekvenser av utbyggnad av ett tredje reningssteg vid två svenska massafabriker utvärderats ur olika aspekter. Beräkningar av utsläppsminskningar och kostnader för membranfiltrering, kemisk fällning respektive sandfilter har genomförts. Resultaten skiljer sig en del såväl mellan de två fabrikerna som mellan val av reningssteg. Analysen av de nya reningsstegens sammanlagda miljöpåverkan visar att de totala utsläppen av närsalter till miljön minskar i samtliga fall. Emellertid ökar miljöpåverkan i alla övriga undersökta påverkanskategorier till följd av bland annat ökad energiförbrukning och kemikalieanvändning vid drift och tillverkning och ökade slammängder vid de nya reningsanläggningarna. Ingen av de metoder som använts i denna studie för att jämföra olika påverkanskategorier ger något entydigt svar på frågan om nyttan är större än kostnaden, men enligt de flesta testade scenarier verkar de nya reningsstegen orsaka ungefär lika mycket miljöpåverkan i vissa avseenden som de gör nytta i andra. Tolkningen försvåras delvis av att den kompletterande reningens effekt på toxicitet inte kunnat bedömas. Resultaten visar emellertid att det är långt ifrån självklart att de nya reningsstegen leder till miljöförbättringar. En slutsats är därmed att tydligare ställningstaganden kring samhälleliga värderingar av olika miljömål efterfrågas
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| 33. |
- Schallmeiner, Edith, et al.
(författare)
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Sensitive protein detection via triple-binder proximity ligation assays
- 2007
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 4:2, s. 135-137
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Tidskriftsartikel (refereegranskat)abstract
- The detection of weakly expressed proteins and protein complexes in biological samples represents a fundamental challenge. We have developed a new proximity-ligation strategy named 3PLA that uses three recognition events for the highly specific and sensitive detection of as little as a hundred molecules of the vascular endothelial growth factor (VEGF), the biomarkers troponin I, and prostate-specific antigen (PSA) alone or in complex with an inhibitor--demonstrating the versatility of 3PLA.
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| 34. |
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| 35. |
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| 36. |
- Wadenberg, Marie-Louise, et al.
(författare)
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Suppression of conditioned avoidance behavior by the local application of (-)sulpiride into the ventral, but not the dorsal, striatum of the rat.
- 1990
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Ingår i: Biological Psychiatry. - 0006-3223 .- 1873-2402. ; 28:4, s. 297-307
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Tidskriftsartikel (refereegranskat)abstract
- The local application of (−)sulpiride, 200 ng side−1, into the nucleus accumbens produced a suppression of conditioned avoidance behavior in male rats, 10 and 90 min after injection. The decrease in avoidance behavior was accompained by a decrease in motor activity, as evidenced by changes in the number of intertrial crosses. When injected into the dorsolateral neostriatum, or the amygdala, (−)sulpiride produced a suppression of conditioned avoidance behavior at the 90-min time interval only. Considering diffusion from the injection site, as indicated by an increase in local dopamine turnover [(DO-PAC+HVA) DA−1], the effects obtained in the dorsolateral neostriatum, and possibly also the amygdala, 90 min after injection could be due to diffusion to the nucleus accumbens. The local application of (-) sulpiride into the posterior neostriatum, or into the prefrontal cortex, produced no statistically significant effect on conditioned avoidance behavior 10 or 90 min after injection. It is concluded that the performance of conditioned avoidance behavior in the rat is critically dependent on an intact dopaminergic neurotransmission in the nucleus accumbens or adjacent areas of the ventral striatum.
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| 37. |
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