| 1. |
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Bringert, Björn, 1979, et al.
(författare)
-
Student Paper: HaskellDB Improved
- 2004
-
Ingår i: Haskell '04: Proceedings of the ACM SIGPLAN workshop on Haskell. - 1581138504 ; , s. 108-115
-
Konferensbidrag (refereegranskat)abstract
- We present an improved version of the HaskellDB database library. The original version relied on TRex, a Haskell extension supported only by the Hugs interpreter. We have replaced the use of TRex by a record implementation which uses more commonly implemented Haskell extensions. Additionally, HaskellDB now supports two different cross-platform database backends. Other changes include database creation functionality, bounded string support, performance enhancements, fixes to the optimisation logic, transaction support and more fine grained expression types.
|
|
| 5. |
- Andersson, Martin E, et al.
(författare)
-
Structural and mutational studies of the carboxylate cluster in iron-free ribonucleotide reductase R2.
- 2004
-
Ingår i: Biochemistry. - 0006-2960. ; 43:24, s. 7966-72
-
Tidskriftsartikel (refereegranskat)abstract
- The R2 protein of ribonucleotide reductase features a di-iron site deeply buried in the protein interior. The apo form of the R2 protein has an unusual clustering of carboxylate side chains at the empty metal-binding site. In a previous study, it was found that the loss of the four positive charge equivalents of the diferrous site in the apo protein appeared to be compensated for by the protonation of two histidine and two carboxylate side chains. We have studied the consequences of removing and introducing charged residues on the local hydrogen-bonding pattern in the region of the carboxylate cluster of Corynebacterium ammoniagenes and Escherichia coli protein R2 using site-directed mutagenesis and X-ray crystallography. The structures of the metal-free forms of wild-type C. ammoniagenes R2 and the mutant E. coli proteins D84N, S114D, E115A, H118A, and E238A have been determined and their hydrogen bonding and protonation states have been structurally assigned as far as possible. Significant alterations to the hydrogen-bonding patterns, protonation states, and hydration is observed for all mutant E. coli apo proteins as compared to wild-type apo R2. Further structural variations are revealed by the wild-type apo C. ammoniagenes R2 structure. The protonation and hydration effects seen in the carboxylate cluster appear to be due to two major factors: conservation of the overall charge of the site and the requirement of electrostatic shielding of clustered carboxylate residues. Very short hydrogen-bonding distances between some protonated carboxylate pairs are indicative of low-barrier hydrogen bonding.
|
|
| 6. |
- Andersson, Martin, 1971-
(författare)
-
Structural studies and design of Di-iron carboxylate proteins
- 2000
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Di-iron carboxylate proteins perform a wide range of chemical reactions in the cell. These reactions often involve activation of dioxygen to generate highly oxidative species that can be used in catalysis. One member of the di-iron carboxylate family is the enzyme ribonucleotide reductase (RNR). This enzyme is essential for DNA synthesis since it is a key enzyme on the pathway for de-novo synthesis of deoxyribonucleotides, the building blocks of DNA. To perform its catalytic function RNR is dependent on a protein radical. In this thesis I have used x-ray crystallographic methods to investigate the mechanism of O2 activation and radical generation in the R2 subunit of RNR. These structural studies have lead to a proposal of a detailed mechanism, which could be common to most O2 activating di-iron carboxylate proteins. The alternative oxidase is a membrane protein that has been proposed to belong to the di-iron carboxylate family. This protein is a ubiquinol/oxygen oxidoreductase and can act as a terminal electron acceptor in the respiratory chain. I have used homology modelling to make a structural model of this enzyme, which provides new insights into its functions and its relationship to the other di-iron carboxylate proteins.Given the strong oxidative power of the di-iron carboxylate proteins they would be very useful as oxidants in various industrial applications. Another part of my project has been aimed towards the design of a di-iron carboxylate enzyme tailored for industrial and environmental applications using a small and stable di-iron carboxylate protein as a starting framework, namely the bacterioferritin protein. This work has lead to the synthesis of a gene library with many potential enzymatic activities.
|
|
| 7. |
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
- Riess, Tanja, et al.
(författare)
-
Bartonella adhesin A mediates a proangiogenic host cell response
- 2004
-
Ingår i: Journal of Experimental Medicine. - : Rockefeller University Press. - 0022-1007 .- 1540-9538. ; 200:10, s. 1267-1278
-
Tidskriftsartikel (refereegranskat)abstract
- Bartonella henselae causes vasculoproliferative disorders in humans. We identified a nonfimbrial adhesin of B. henselae designated as Bartonella adhesin A (BadA). BadA is a 340-kD outer membrane protein encoded by the 9.3-kb badA gene. It has a modular structure and contains domains homologous to the Yersinia enterocolitica nonfimbrial adhesin (Yersinia adhesin A). Expression of BadA was restored in a BadA-deficient transposon mutant by complementation in trans. BadA mediates the binding of B. henselae to extracellular matrix proteins and to endothelial cells, possibly via β1 integrins, but prevents phagocytosis. Expression of BadA is crucial for activation of hypoxia-inducible factor 1 in host cells by B. henselae and secretion of proangiogenic cytokines (e.g., vascular endothelial growth factor). BadA is immunodominant in B. henselae–infected patients and rodents, indicating that it is expressed during Bartonella infections. Our results suggest that BadA, the largest characterized bacterial protein thus far, is a major pathogenicity factor of B. henselae with a potential role in the induction of vasculoproliferative disorders.
|
|
| 11. |
- Sun, Zhengwu, et al.
(författare)
-
Effective treatment of gut barrier dysfunction using an antioxidant, a PAF inhibitor, and monoclonal antibodies against the adhesion molecule PECAM-1.
- 2002
-
Ingår i: Journal of Surgical Research. - : Elsevier BV. - 1095-8673 .- 0022-4804. ; 105:2, s. 220-233
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Oxygen free radicals (OFRs), platelet activating factor (PAF), cell adhesion molecules, and transmigration of polymorphonuclear leukocytes through the gut barrier are probably all essential in the development of gut barrier dysfunction following intestinal ischemia and reperfusion (I/R). Pretreatment and early treatment of I/R with the OFRs-scavenger (NAC), the PAF inhibitor lexipafant, and monoclonal antibodies against the adhesion molecule PECAM-1 (anti-PECAM-1-Mab) have been reported to be effective in the prevention or recovery of gut barrier dysfunction and result in a decrease in cytokine levels. Less is known about the effect of treatment inserted during the late stage of I/R. The objective of this study was to evaluate the potential therapeutic value of single or combination therapy with NAC, lexipafant, and anti-PECAM-1-MAb administered late during intestinal I/R in the rat. METHODS: NAC, lexipafant, and anti-PECAM-1-MAb were administrated, alone or in combination, after 3 h of reperfusion following 40 min of superior mesenteric arterial ischemia in the rat. Intestinal endothelial and epithelial barrier permeability, myeloperoxidase (MPO) activity, interleukin-1 beta (IL-1 beta), and protease inhibitor levels were evaluated after 12 h of reperfusion. RESULTS: Intestinal endothelial and epithelial permeability significantly increased in rats with I/R and saline treatment. Proteolytic activity in plasma was indicated by low levels of the three measured plasma protease inhibitors. Intestinal mucosal MPO content increased significantly. These changes were, to different degrees, reduced by late inserted treatment with NAC, lexipafant, or anti-PECAM-1-MAb. Alterations in systemic levels of IL-1 beta paralleled the changes found in gut barrier permeability and leukocyte trapping. Systemic antithrombin III levels and increased barrier permeability in remote organs were partly restored, especially by multimodal therapy. CONCLUSION: Treatment with NAC, lexipafant, and/or monoclonal antibodies against PECAM-1, inserted at a later stage of I/R, reduced the severity of I/R-associated intestinal dysfunction and decreased the systemic concentrations of IL-1 beta, local leukocyte recruitment (MPO), and partly restored plasma protease inhibitor levels.
|
|
| 12. |
- Alsmark, Cecilia M., et al.
(författare)
-
The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae
- 2004
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 101:26, s. 9716-9721
-
Tidskriftsartikel (refereegranskat)abstract
- We present the complete genomes of two human pathogens, Bartonella quintana (1,581,384 bp) and Bartonella henselae (1,931,047 bp). The two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. A primary difference between the two pathogens is their reservoir ecology. Whereas B. quintana is a specialist, using only the human as a reservoir, B. henselae is more promiscuous and is frequently isolated from both cats and humans. Genome comparison elucidated a high degree of overall similarity with major differences being B. henselae specific genomic islands coding for filamentous hemagglutinin, and evidence of extensive genome reduction in B. quintana, reminiscent of that found in Rickettsia prowazekii. Both genomes are reduced versions of chromosome I from the highly related pathogen Brucella melitensis. Flanked by two rRNA operons is a segment with similarity to genes located on chromosome II of B. melitensis, suggesting that it was acquired by integration of megareplicon DNA in a common ancestor of the two Bartonella species. Comparisons of the vector-host ecology of these organisms suggest that the utilization of host-restricted vectors is associated with accelerated rates of genome degradation and may explain why human pathogens transmitted by specialist vectors are outnumbered by zoonotic agents, which use vectors of broad host ranges.
|
|
| 13. |
|
|
| 14. |
- Andersson, Bo, et al.
(författare)
-
Small x phenomenology: summary and status
- 2002
-
Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 25:1, s. 77-101
-
Forskningsöversikt (refereegranskat)abstract
- The aim of this paper is to summarize the general status of our understanding of small-x physics. It is based on presentations and discussions at an informal meeting OIL this topic held in Lund, Sweden, in March 2001. This document also marks the founding of an informal collaboration between experimentalists and theoreticians with a special interest in small-x physics. This paper is dedicated to the memory of Bo Andersson. who died unexpectedly from a heart attack on March 4th, 2002.
|
|
| 15. |
- Andersson, Carina, et al.
(författare)
-
Understanding software processes through system dynamics simulation: a case study
- 2002
-
Ingår i: Proceedings Ninth Annual IEEE International Conference and Workshop on the Engineering of Computer-Based Systems. - 0769515495 ; , s. 41-48
-
Konferensbidrag (refereegranskat)abstract
- This paper presents a study with the intent to examine the opportunities provided by creating and using simulation models of software development processes. A model of one software development project was created through means of system dynamics, with data collected from documents, interviews and observations. The model was simulated in a commercial simulation tool. The simulation runs indicate that increasing the effort spent on the requirements phase, to a certain extent, will decrease the lead time and increase the quality in similar projects. The simulation model visualizes relations in the software process, and can be used by project managers when planning future projects. The study indicates that this type of simulation is a feasible way of modelling the process dynamically although the study calls for further investigations as to how project or process managers can benefit the most from using system dynamics simulations
|
|
| 16. |
- Andersson, Jan O, 1971-, et al.
(författare)
-
Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes
- 2003
-
Ingår i: Current Biology. - 0960-9822 .- 1879-0445. ; 13:2, s. 94-104
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary mechanism among prokaryotes. The situation in eukaryotes is less clear; the human genome sequence failed to give strong support for any recent transfers from prokaryotes to vertebrates, yet a number of LGTs from prokaryotes to protists (unicellular eukaryotes) have been documented. Here, we perform a systematic analysis to investigate the impact of LGT on the evolution of diplomonads, a group of anaerobic protists.RESULTS: Phylogenetic analyses of 15 genes present in the genome of the Atlantic Salmon parasite Spironucleus barkhanus and/or the intestinal parasite Giardia lamblia show that most of these genes originated via LGT. Half of the genes are putatively involved in processes related to an anaerobic lifestyle, and this finding suggests that a common ancestor, which most probably was aerobic, of Spironucleus and Giardia adapted to an anaerobic environment in part by acquiring genes via LGT from prokaryotes. The sources of the transferred diplomonad genes are found among all three domains of life, including other eukaryotes. Many of the phylogenetic reconstructions show eukaryotes emerging in several distinct regions of the tree, strongly suggesting that LGT not only involved diplomonads, but also involved other eukaryotic groups.CONCLUSIONS: Our study shows that LGT is a significant evolutionary mechanism among diplomonads in particular and protists in general. These findings provide insights into the evolution of biochemical pathways in early eukaryote evolution and have important implications for studies of eukaryotic genome evolution and organismal relationships. Furthermore, "fusion" hypotheses for the origin of eukaryotes need to be rigorously reexamined in the light of these results.
|
|
| 17. |
|
|
| 18. |
|
|
| 19. |
|
|
| 20. |
- Andersson, Martin, et al.
(författare)
-
A novel reconfigurable pipelined A/D conversion technique for multistandard wideband receivers
- 2004
-
Ingår i: Proceedings of the IASTED International Conference on Circuits, Signals, and Systems. - 0889864551 ; , s. 199-204
-
Konferensbidrag (refereegranskat)abstract
- This paper presents a low complexity, yet power efficient technique to boost the flexibility of a pipelined ADC. It also presents an implementation proposal with simulated results for a reconfigurable pipelined ADC. The proposed ADC architecture is a combination of the conventional pipelined ADC and the cyclic ADC, giving it a very low level of complexity, a high level of component reuse and substantial power savings in low speed low accuracy modes.
|
|
| 21. |
|
|
| 22. |
|
|
| 23. |
- Andersson, Martin, et al.
(författare)
-
Anharmonic resonances in the C-H stretch region of ethoxy adsorbed on W(110): vibrational spectroscopy and calculations
- 2003
-
Ingår i: Surface Science. - 0039-6028. ; 532-535, s. 221-226
-
Tidskriftsartikel (refereegranskat)abstract
- We show that it is possible to understand and interpret the complex and rich C-H stretch region in the vibrational spectrum of ethoxy adsorbed on W(110) in terms of fundamental C-H stretch modes in Fermi resonance with C-H deformation overtones and combinations. The mode assignment is based on calculated C-13 isotopic shifts for an ethoxy-Cu-5 cluster. The coupling constants have been derived from calculated energy third derivatives of free ethanol and the coupling was implemented by an effective Hamiltonian matrix. The agreement with experiments is very good.
|
|
| 24. |
- Andersson, Martin
(författare)
-
Bending the Kuznets Curve - Wrenching and Levelling Forces during Agricultural Transformation in Taiwan and Chile
- 2003
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- What are the effects of growth on equality in a long-term perspective? What are the effects of different patterns of equality on subsequent growth? And why are these questions relevant for the understanding of economic development? These are the overriding questions posed in the dissertation. They are addressed in the context of long-term change from economic backwardness to modern economic growth by examining the processes of agricultural transformation of two successful growth achievers -- Taiwan and Chile. In recent day empirical examinations of the growth-equality relationship, the so-called Kuznets-curve - that inequality initially increases before it declines - has been rejected on the grounds that the relationship does not appear in such systematic fashion. In assessing this latter-day comprehension, the author argues that the thrust of the Kuznets-curve is not its shape but the underlying forces at play during structural change. Such an approach then concentrates on the forces that wrench and level income distribution during structural change. As far as Taiwan and Chile are concerned, such forces have been, to different degrees, in constant struggle during their agricultural transformations. In the initially relatively equal income distribution in Taiwan, the dynamics of homogenous demand eased the wrenching forces of structural change despite population pressure and forceful industrialisation. Chile, on the other hand, starting from a wrenched situation, experienced aggravated wrenching and delayed dynamic change due to its lack of universal access to markets. When dynamic change eventually took place - after decades of forced institutional change - levelling forces outpaced the wrenching forces. The study proposes a causal analytical framework in which wrenching and levelling forces during long-term structural change may be identified and grasped. The framework includes the initial distribution of income as its organising principle . Since reliable longitudinal data of personal income distribution is unavailable, a wide range of variables, indicative of economic change in general and agricultural performance in particular, is put to use.
|
|
| 25. |
|
|
