| 1. |
- Hedenas, Henrik, et al.
(författare)
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Changes Versus Homeostasis in Alpine and Sub-Alpine Vegetation Over Three Decades in the Sub-Arctic
- 2012
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Ingår i: Ambio. - : Springer Verlag (Germany). - 0044-7447 .- 1654-7209. ; 41, s. 187-196
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Tidskriftsartikel (refereegranskat)abstract
- Plant species distributions are expected to shift and diversity is expected to decline as a result of global climate change, particularly in the Arctic where climate warming is amplified. We have recorded the changes in richness and abundance of vascular plants at Abisko, sub-Arctic Sweden, by re-sampling five studies consisting of seven datasets; one in the mountain birch forest and six at open sites. The oldest study was initiated in 1977–1979 and the latest in 1992. Total species number increased at all sites except for the birch forest site where richness decreased. We found no general pattern in how composition of vascular plants has changed over time. Three species, Calamagrostis lapponica, Carex vaginata and Salix reticulata, showed an overall increase in cover/frequency, while two Equisetum taxa decreased. Instead, we showed that the magnitude and direction of changes in species richness and composition differ among sites.
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| 2. |
- Ruiz-Pavon, Lorena, et al.
(författare)
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Functionally important amino acids in the Arabidopsis thylakoid phosphate transporter: Homology modeling and site-directed mutagenesis
- 2010
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Ingår i: Biochemistry. - : American Chemical Society. - 0006-2960 .- 1520-4995. ; 49:30, s. 6430-6439
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Tidskriftsartikel (refereegranskat)abstract
- The anion transporter 1 (ANTR1) from Arabidopsis thaliana, homologous to the mammalian members of the solute carrier 17 (SLC17) family, is located in the chloroplast thylakoid membrane. When expressed heterologously in Escherichia coli, ANTR1 mediates a Na+-dependent active transport of inorganic phosphate (Pi). The aim of this study was to identify amino acid residues involved in Pi binding and translocation by ANTR1 and in the Na+ dependence of its activity. A three-dimensional structural model of ANTR1 was constructed using the crystal structure of glycerol 3-phosphate/phosphate antiporter from E. coli as a template. Based on this model and multiple sequence alignments, five highly conserved residues in plant ANTRs and mammalian SLC17 homologues have been selected for site-directed mutagenesis, namely, Arg-120, Ser-124, and Arg-201 inside the putative translocation pathway and Arg-228 and Asp-382 exposed at the cytoplasmic surface of the protein. The activities of the wild-type and mutant proteins have been analyzed using expression in E. coli and radioactive Pi transport assays and compared with bacterial cells carrying an empty plasmid. The results from Pi- and Na+-dependent kinetics indicate the following: (i) Arg-120 and Arg-201 may be important for binding and translocation of the substrate; (ii) Ser-124 may function as a transient binding site for Na+ ions in close proximity to the periplasmic side; (iii) Arg-228 and Asp-382 may participate in interactions associated with protein conformational changes required for full transport activity. Functional characterization of ANTR1 should provide useful insights into the function of other plant and mammalian SLC17 homologous transporters.
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| 3. |
- Ahlner, Alexandra, et al.
(författare)
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PINT: a software for integration of peak volumes and extraction of relaxation rates
- 2013
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Ingår i: Journal of Biomolecular NMR. - : Springer Verlag (Germany). - 0925-2738 .- 1573-5001. ; 56:3, s. 191-202
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Tidskriftsartikel (refereegranskat)abstract
- We present the software Peak INTegration (PINT), designed to perform integration of peaks in NMR spectra. The program is very simple to run, yet powerful enough to handle complicated spectra. Peaks are integrated by fitting predefined line shapes to experimental data and the fitting can be customized to deal with, for instance, heavily overlapped peaks. The results can be inspected visually, which facilitates systematic optimization of the line shape fitting. Finally, integrated peak volumes can be used to extract parameters such as relaxation rates and information about low populated states. The utility of PINT is demonstrated by applications to the 59 residue SH3 domain of the yeast protein Abp1p and the 289 residue kinase domain of murine EphB2.
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| 4. |
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| 5. |
- Asad, Samina, et al.
(författare)
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HTR1A a Novel Type 1 Diabetes Susceptibility Gene on Chromosome 5p13-q13
- 2012
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 7:5
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Tidskriftsartikel (refereegranskat)abstract
- Background: We have previously performed a genome-wide linkage study in Scandinavian Type 1 diabetes (T1D) families. In the Swedish families, we detected suggestive linkage (LOD less than= 2.2) to the chromosome 5p13-q13 region. The aim of our study was to investigate the linked region in search for possible T1D susceptibility genes. Methodology/Principal Findings: Microsatellites were genotyped in the Scandinavian families to fine-map the previously linked region. Further, SNPs were genotyped in Swedish and Danish families as well as Swedish sporadic cases. In the Swedish families we detected genome-wide significant linkage to the 5-hydroxytryptamine receptor 1A (HTR1A) gene (LOD 3.98, pless than9.8x10(-6)). Markers tagging two separate genes; the ring finger protein 180 (RNF180) and HTR1A showed association to T1D in the Swedish and Danish families (pless than0.002, pless than0.001 respectively). The association was not confirmed in sporadic cases. Conditional analysis indicates that the primary association was to HTR1A. Quantitative PCR show that transcripts of both HTR1A and RNF180 are present in human islets of Langerhans. Moreover, immunohistochemical analysis confirmed the presence of the 5-HTR1A protein in isolated human islets of Langerhans as well as in sections of human pancreas. Conclusions: We have identified and confirmed the association of both HTR1A and RFN180, two genes in high linkage disequilibrium (LD) to T1D in two separate family materials. As both HTR1A and RFN180 were expressed at the mRNA level and HTR1A as protein in human islets of Langerhans, we suggest that HTR1A may affect T1D susceptibility by modulating the initial autoimmune attack or either islet regeneration, insulin release, or both.
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| 6. |
- Babu Moparthi, Satish, et al.
(författare)
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Transient conformational remodeling of folding proteins by GroES - Individually and in concert with GroEL
- 2014
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Ingår i: Journal of chemical biology. - : Springer Berlin/Heidelberg. - 1864-6158 .- 1864-6166. ; 7:1, s. 1-15
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Forskningsöversikt (refereegranskat)abstract
- The commonly accepted dogma of the bacterial GroE chaperonin system entails protein folding mediated by cycles of several ATP-dependent sequential steps where GroEL interacts with the folding client protein. In contrast, we herein report GroES-mediated dynamic remodeling (expansion and compression) of two different protein substrates during folding: the endogenous substrate MreB and carbonic anhydrase (HCAII), a well-characterized protein folding model. GroES was also found to influence GroEL binding induced unfolding and compression of the client protein underlining the synergistic activity of both chaperonins, even in the absence of ATP. This previously unidentified activity by GroES should have important implications for understanding the chaperonin mechanism and cellular stress response. Our findings necessitate a revision of the GroEL/ES mechanism.
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| 7. |
- Baca, Dejan, et al.
(författare)
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Agile development with security engineering activities
- 2011
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Konferensbidrag (refereegranskat)abstract
- Agile software development has been used by industry to create a more flexible and lean software development process, i.e making it possible to develop software at a faster rate and with more agility during development. There are however concerns that the higher development pace and lack of documentation are creating less secure software. We have therefore looked at three known Security Engineering processes, Microsoft SDL, Cigatel touchpoints and Common Criteria and identified what specific security activities they performed. We then compared these activities with an Agile development process that is used in industry. Developers, from a large telecommunication manufacturer, were interviewed to learn their impressions on using these security activities in an agile development process. We produced a security enhanced Agile development process that we present in this paper. This new Agile process use activities from already established security engineering processes that provide the benefit the developers wanted but did not hinder or obstruct the Agile process in a significant way.
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| 8. |
- Baca, Dejan, et al.
(författare)
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Improving software security with static automated code analysis in an industry setting
- 2013
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Ingår i: Software, practice & experience. - : Wiley. - 0038-0644 .- 1097-024X. ; 43:3, s. 259-279
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Tidskriftsartikel (refereegranskat)abstract
- Software security can be improved by identifying and correcting vulnerabilities. In order to reduce the cost of rework, vulnerabilities should be detected as early and efficiently as possible. Static automated code analysis is an approach for early detection. So far, only few empirical studies have been conducted in an industrial context to evaluate static automated code analysis. A case study was conducted to evaluate static code analysis in industry focusing on defect detection capability, deployment, and usage of static automated code analysis with a focus on software security. We identified that the tool was capable of detecting memory related vulnerabilities, but few vulnerabilities of other types. The deployment of the tool played an important role in its success as an early vulnerability detector, but also the developers perception of the tools merit. Classifying the warnings from the tool was harder for the developers than to correct them. The correction of false positives in some cases created new vulnerabilities in previously safe code. With regard to defect detection ability, we conclude that static code analysis is able to identify vulnerabilities in different categories. In terms of deployment, we conclude that the tool should be integrated with bug reporting systems, and developers need to share the responsibility for classifying and reporting warnings. With regard to tool usage by developers, we propose to use multiple persons (at least two) in classifying a warning. The same goes for making the decision of how to act based on the warning.
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| 9. |
- Barkefors, Annea
(författare)
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Linear Quadratic Gaussian Controllers for Feedforward Active Noise Control : Pushing Performance and Moving Towards Adaptive Control
- 2014
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Active noise control is a research area focused on using destructive interference of sound fields to attenuate undesired noise. Methods for active noise control are best suited for low frequency noise, as the complexity of the problem grows rapidly with frequency. Coincidentally, passive means of damping have the opposite quality in that they work better for higher frequencies and become bulky and impractical for low frequencies. Applications for active noise control range from fan noise in ducts, noise-cancelling headphones and noise in cars to propeller induced aircraft cabin noise. In this comprehensive summary, the underlying principles of active noise control are presented and the control problem is discussed. Several aspects of the control system are introduced to give an introduction to the research papers that are the basis of this licentiate thesis. The work behind the thesis is focused on a Multiple-Input Multiple-Output (MIMO) Minimal Mean Square Error (MMSE) Linear Quadratic Gaussian (LQG) feedforward controller. This controller is shown to achieve uniform damping in an extended region in space and push the upper frequency that can be controlled. The influence of different design variables has been investigated, and the properties of the control path analyzed with consideration of its ability to suppress noise of prescribed spectral properties over an extended region. In this context, it has been shown how to use the reproducibility of the primary noise path by the control path as an indication of achievable performance for a given control system. Finally, the controller has been adapted to follow changes in the primary noise statistics, an approach that seems promising to considerably raise the performance of the controller.
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| 10. |
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