| 1. |
- Bidartondo, Martin, et al.
(författare)
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Preserving accuracy in GenBank
- 2008
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Ingår i: Science. ; 319:5870
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
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| 3. |
- Anderson, Henrik, 1975-
(författare)
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Development of Electroacoustic Sensors for Biomolecular Interaction Analysis
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Biomolecular interaction analysis to determine the kinetics and affinity between interacting partners is important for the fundamental understanding of biology, as well as for the development of new pharmaceutical substances. A quartz crystal microbalance instrument suitable for kinetics and affinity analyses of interaction events was developed. The functionality of the sensor system was demonstrated by development of an assay for relative affinity determination of lectin-carbohydrate interactions.Sensor surfaces allowing for effective immobilization of one interacting partner is a key functionality of a biosensor. Here, three different surfaces and immobilization methods were studied. First, optimized preparation conditions for sensor surfaces based on carboxyl-terminated self assembled monolayers were developed and were demonstrated to provide highly functional biosensor surfaces with low non-specific binding. Second, a method allowing for immobilization of very acidic biomolecules based on the use of an electric field was developed and evaluated. The electric field made it possible to immobilize the highly acidic C-peptide on a carboxylated surface. Third, a method for antibody immobilization on a carboxyl surface was optimized and the influence of immobilization pH on the immobilization level and antigen binding capacity was thoroughly assessed. The method showed high reproducibility for a set of antibodies and allowed for antibody immobilization also at low pH.Three broadly different strategies to increase the sensitivity of electroacoustic sensors were explored. A QCM sensor with small resonator electrodes and reduced flow cell dimensions was demonstrated to improve the mass transport rate to the sensor surface. The use of polymers on QCM sensor surfaces to enhance the sensor response was shown to increase the response of an antibody-antigen model system more than ten-fold. Moreover, the application of high frequency thin film bulk acoustic resonators for biosensing was evaluated with respect to sensing range from the surface. The linear detection range of the thin film resonator was determined to be more than sufficient for biosensor applications involving, for instance, antibody-antigen interactions. Finally, a setup for combined frequency and resistance measurements was developed and was found to provide time resolved data suitable for kinetics determination.
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| 4. |
- Anderson, Henrik, et al.
(författare)
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Quartz crystal microbalance sensor design : I. Experimental study of sensor response and performance
- 2007
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Ingår i: Sensors and actuators. B, Chemical. - : Elsevier BV. - 0925-4005 .- 1873-3077. ; 123:1, s. 27-34
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Tidskriftsartikel (refereegranskat)abstract
- This paper investigates a novel quartz crystal microbalance (QCM) biosensor with a small and rectangular flow cell along with a correspondingly shaped crystal electrode. The sensor was evaluated with impedance analysis and compared to standard circular sensor crystals and sensor crystals with small circular electrodes. Comparative QCM measurements on an antibody–antigen interaction system were carried out on the rectangular and standard circular sensor systems. Impedance analysis and subsequent data extraction of the three different sensor crystals showed that the smaller sensors had significantly higher Q-values in air, but that liquid load on the electrodes lowered the Q-values radically for all crystals. Under liquid load, Q-values for the standard circular and the rectangular sensors were similar whereas the Q-value for the small circular sensor was 50% higher. QCM experiments showed that the QCM system with rectangular crystal electrodes was fully functional in a liquid environment. The rectangular system showed higher and more rapid responses for series of antibody injections, albeit at a higher noise level than the standard system. The study elucidates a significant potential for improvement of sensor performance by optimising the sensor electrode size and shape together with the flow cell geometry.
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| 5. |
- Anderson, Lars, et al.
(författare)
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Kinetics and stereochemistry of the Cellulomonas fimi beta-mannanase studied using H-1-NMR
- 2008
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Ingår i: Biocatalysis and Biotransformation. - : Informa UK Limited. - 1024-2422 .- 1029-2446. ; 26:1-2, s. 86-95
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Tidskriftsartikel (refereegranskat)abstract
- Endo-1,4-beta-mannanases (beta-mannanases) randomly hydrolyse the mannosidic bonds within the main chain of various mannans and heteromannans. Some of these polysaccharides are hemicelluloses, a major part of the plant cell-wall. The beta-mannanases have been assigned to family 5 and 26 of the glycoside hydrolase clan A. This work presents a detailed kinetic analysis of the family 26 beta-mannanase CfMan26A from the soil-bacterium Cellulomonas fimi. The full-length enzyme consists of five modules: a family 26 catalytic module, an immunoglobulin-like module, a mannan-binding module, a surface layer homology-module and a module of unknown function. A truncated variant consisting of the catalytic module and the immunoglobulin-like module was used in these studies. The degradation of mannotriose, mannotetraose and mannopentaose was studied by H-1-NMR. First, the mutarotation of one of the hydrolysis products (mannose) was determined to be 1.7 10(-5) s(-1) at 5 degrees C and pH 5.0. As expected for a family 26 glycoside hydrolase, the hydrolysis was shown to proceed with overall retention of the anomeric configuration. Many 'retaining' enzymes can perform transglycosylation reactions. However, no transglycosylation could be detected. Kinetic constants were calculated from progress curves using computer simulation. It was revealed that the -3 subsite had a greater impact on the apparent k(cat)/K-m ratio (the catalytic efficiency) than the +2 subsite. The beta-anomer of mannotriose was hydrolysed 1000-times more efficiently than the alpha-anomer indicating selectivity for the beta- over the alpha-anomer in the +1 subsite. With background information from the previous published 3D-structure of the truncated variant of Man26A, a structural explanation for the observations is discussed.
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| 6. |
- Antov, Mirjana, et al.
(författare)
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Affinity partitioning of a Cellulomonas fimi beta-mannanase with a mannan-binding module in galactomannan/starch aqueous two-phase system
- 2006
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Ingår i: Journal of Chromatography A. - : Elsevier BV. - 0021-9673. ; 1123:1, s. 53-59
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Tidskriftsartikel (refereegranskat)abstract
- A new approach in affinity separations was studied by partitioning of Cellulomonas fimi beta-mannanase (EC 3.2.1.78) containing a mannan-binding module in galactomannan/hydroxypropyl starch aqueous two-phase system. Comparison was made with a truncated version of C. fimi beta-mannanase which lacked the mannan-binding module. Results showed that affinity partitioning of the beta-mannanase was achieved due to biospecificity of the mannan-binding module towards the top phase containing galactomannan. Experiments were conducted at pH 8 to prevent enzyme degradation of the phase containing galactomannan. Removal of the top phase polymer was accomplished by beta-mannanase degradation allowed by shifting to the optimal pH 6. In the combination with the genetic fusion of any given protein to the mannan-binding module, the results envision a general procedure for primary affinity recovery of such fusion proteins.
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| 7. |
- Dunér, Gunnar, et al.
(författare)
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Surface-confined photopolymerization of pH-responsive acrylamide/acrylate brushes on polymer thin films
- 2008
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 24:14, s. 7559-7564
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic acrylamide/acrylate polymeric brushes were synthesized at gold-plated quartz crystal surfaces. The crystals were initially coated with polystyrene-type thin films, derivatized with photolabile iniferter groups, and subsequently subjected to photoinitiated polymerization in acrylamide/acrylate monomer feeds. This surface-confined polymerization method enabled direct photocontrol over the polymerization, as followed by increased frequency responses of the crystal oscillations in a quartz crystal microbalance (QCM). The produced polymer layers were also found to be highly sensitive to external acid/base stimuli. Large oscillation frequency shifts were detected when the brushes were exposed to buffer solutions of different pH. The dynamic behavior of the resulting polymeric brushes was evaluated, and the extent of expansion and contraction of the films was monitored by the QCM setup in situ in real time. The resulting responses were rapid, and the effects were fully reversible. Low pH resulted in full contractions of the films, whereas higher pH yielded maximal expansion in order to minimize repulsion around the charged acrylate centers. The surfaces also proved to be very robust because the responsiveness was reproducible over many cycles of repeated expansion and contraction. Using ellipsometry, copolymer layers were estimated to be similar to 220 nm in a collapsed state and similar to 340 nm in the expanded state, effectively increasing the thickness of the film by 55%.
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| 8. |
- Gustavsson, Malin, 1975, et al.
(författare)
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Hypoxic preconditioning confers long-term reduction of brain injury and improvement of neurological ability in immature rats
- 2005
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Ingår i: Pediatr Res. ; 57:2, s. 305-9
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Tidskriftsartikel (refereegranskat)abstract
- Exposure to preconditioning (PC) hypoxia 24 h before a severe hypoxic-ischemic (HI) insult reduces development of injury in the immature brain. Several protective regimens have proved effective in the short-term but not in the long-term perspective. The aim of the present study, therefore, was to evaluate the PC effect on long-term morphologic and neurologic outcome in the developing brain. Six-day-old rats were subjected to hypoxia (36 degrees C, 8.0% O2; PC/HI group) and sham controls to normoxia (36 degrees C; HI group) for 3 h. Twenty-four hours later, all rats were exposed to cerebral HI produced by unilateral carotid artery occlusion combined with 1 h, 15 min of hypoxia (36 degrees C, 7.7% O2). A cylinder test was used to evaluate forelimb asymmetry to determine sensorimotor function at 4, 6, and 8 wk of age. Spatial/cognitive ability was assessed by Morris water maze trials at 7 wk of recovery. Neuropathologic analysis was performed 8 wk after insult. Brain damage was reduced (p<0.0001) in PC/HI (45.0+/-11.1 mm3) in comparison with HI (159.3+/-12.2 mm3) rats. A bias for using the ipsilateral forelimb in wall movements was observed in the cylinder test in HI compared with PC/HI rats at 4 (p<0.001), 6 (p<0.01), and 8 (p<0.0001) wk of age. Results of the Morris water maze test revealed differences (p<0.0001) in average path length between groups on the third and fourth day of trials. Hypoxic PC before HI reduced brain injury by 72% at 8 wk after the insult and provided long-term improvement of sensorimotor and spatial/cognitive functions.
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| 9. |
- Jönsson, Mats, et al.
(författare)
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Quartz crystal microbalance biosensor design: II. Simulation of sample transport
- 2007
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Ingår i: Sensors and actuators. B, Chemical. - : Elsevier BV. - 0925-4005 .- 1873-3077. ; 123:1, s. 21-26
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Tidskriftsartikel (refereegranskat)abstract
- The influence of flow cell geometry on sample dispersion in a quartz crystal microbalance (QCM) biosensor system was investigated. A circular and a rectangular flow cell and corresponding sensor electrodes were studied experimentally and modelled using a coupled Navier-Stokes and convection-diffusion model. Finite element simulations showed that dispersion phenomena in a flow cell can be significantly reduced with the rectangular flow cell compared to a circular system. Experimental results from measurement of the time-dependent viscosity change of a model sample indicate that the sample delivery system has a predominant effect on the dispersion of the whole sensor system. Consequently, improvement of the sensor flow cell should be accompanied with improvement of the sample delivery system. With reference to kinetic studies of biological interactions, the current dispersion should have little effect on the results for studies of interaction pairs with relatively slow to normal binding rates such as antibody-antigen interactions. Incentive for further development of the flow cell and sample delivery system exists primarily for applications with high reaction rates such as for certain receptor ligand interactions.
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| 10. |
- Karlsson, Elinor K., et al.
(författare)
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Efficient mapping of mendelian traits in dogs through genome-wide association
- 2007
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 39:11, s. 1321-1328
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Tidskriftsartikel (refereegranskat)abstract
- With several hundred genetic diseases and an advantageous genome structure, dogs are ideal for mapping genes that cause disease. Here we report the development of a genotyping array with |[sim]|27,000 SNPs and show that genome-wide association mapping of mendelian traits in dog breeds can be achieved with only |[sim]|20 dogs. Specifically, we map two traits with mendelian inheritance: the major white spotting (S) locus and the hair ridge in Rhodesian ridgebacks. For both traits, we map the loci to discrete regions of <1 Mb. Fine-mapping of the S locus in two breeds refines the localization to a region of |[sim]|100 kb contained within the pigmentation-related gene MITF. Complete sequencing of the white and solid haplotypes identifies candidate regulatory mutations in the melanocyte-specific promoter of MITF. Our results show that genome-wide association mapping within dog breeds, followed by fine-mapping across multiple breeds, will be highly efficient and generally applicable to trait mapping, providing insights into canine and human health.
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