| 26. |
- Jansson, Jennie L. M., et al.
(författare)
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Conformational Dynamics of Oligosaccharides : NMR Techniques and Computer Simulations
- 2006
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Ingår i: NMR Spectroscopy and Computer Modeling of Carbohydrates. - Washington, DC : American Chemical Society (ACS). - 9780841239531 ; , s. 20-39
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Bokkapitel (refereegranskat)abstract
- NMR spectroscopy techniques in conjunction with molecular dynamics simulations facilitate description of conformation and dynamics of oligosaccharides in solution. Herein we describe approaches based on hetero-nuclear carbon-proton spin-spin coupling constants useful for assessing conformational preferences at the glycosidic linkage, exemplified for á-cyclodextrin. Furthermore, we utilize hetero-nuclear carbon-proton residual dipolar couplings together with molecular dynamics simulations in the analysis of the conformational dynamics of the milk oligosaccharide Lacto-N-neotetraose.
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| 27. |
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| 28. |
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| 29. |
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| 30. |
- Mann, Johannes F. E., et al.
(författare)
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Homocysteine lowering with folic acid and B vitamins in people with chronic kidney disease : results of the renal Hope-2 study
- 2008
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Ingår i: Nephrology, Dialysis and Transplantation. - : Oxford University Press (OUP). - 0931-0509 .- 1460-2385. ; 23:2, s. 645-653
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Elevated plasma homocysteine levels are reported to be associated with higher rates of vascular diseases. Plasma homocysteine increases in chronic kidney disease (CKD) and could contribute to the increased cardiovascular risk in CKD. METHODS: Participants aged 55 years or older with CKD, defined as estimated GFR<60 ml/min and at high cardiovascular risk, were randomly assigned to the combination of folic acid, 2.5 mg, vitamin B6, 50 mg and vitamin B12, 1 mg (n = 307) or placebo (n = 312) daily for 5 years. The primary outcome was a composite of death from cardiovascular causes, myocardial infarction and stroke. RESULTS: Mean baseline plasma homocysteine was 15.9 +/- 7.3 micromol/l in the active treatment group and 15.7 +/- 5.7 micromol/l in placebo group and decreased to 11.9 +/- 3.3 micromol/l (P < 0.001) on active treatment (15.5 +/- 4.5 on placebo). Primary outcome events occurred in 90 participants (29.3%) on active therapy and in 80 (25.6%) on placebo (relative risk, 1.19; 95% confidence interval, 0.88-1.61; P = 0.25). There were no significant treatment benefits on death from cardiovascular causes (1.24; 0.84-1.83), myocardial infarction (1.10; 0.76-1.61) and stroke (1.00; 0.54-1.85). More participants in the active treatment group were hospitalized for heart failure (1.98; 1.21-3.26; P = 0.007) and for unstable angina (1.70; 1.02-2.83; P = 0.04). Incidence of primary outcome increased with decreasing GFR. CONCLUSIONS: Active treatment with B vitamins lowered homocysteine levels in participants with CKD but did not reduce cardiovascular risk.
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| 31. |
- Miro, J M, et al.
(författare)
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Staphylococcus aureus native valve infective endocarditis: report of 566 episodes from the International Collaboration on Endocarditis Merged Database.
- 2005
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Ingår i: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. - : Oxford University Press (OUP). - 1537-6591. ; 41:4, s. 507-14
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Staphylococcus aureus native valve infective endocarditis (SA-NVIE) is not completely understood. The objective of this investigation was to describe the characteristics of a large, international cohort of patients with SA-NVIE. METHODS: The International Collaboration on Endocarditis Merged Database (ICE-MD) is a combination of 7 existing electronic databases from 5 countries that contains data on 2212 cases of definite infective endocarditis (IE). RESULTS: Of patients with native valve IE, 566 patients [corrected] had IE due to S. aureus, and 1074 patients had IE due to pathogens other than S. aureus (non-SA-NVIE). Patients with S. aureus IE were more likely to die (20% vs. 12%; P < .001), to experience an embolic event (61% [corrected] vs. 31%; P < .001), or to have a central nervous system event (21% [corrected] vs. 13%; P < .001) and were less likely to undergo surgery (26% vs. 39%; P < .001) than were patients with non-SA-NVIE. Multivariate analysis of prognostic factors of mortality identified age (odds ratio [OR], 1.4; 95% confidence interval [CI], 1.1-1.7), periannular abscess (OR, 2.4; 95% CI, 1.0 [corrected] -5.6), heart failure (OR, 3.9; 95% CI, 2.3-6.7), and absence of surgical therapy (OR, 2.3; 95% CI, 1.3-4.2) as variables that were independently associated with mortality in patients with SA-NVIE. After adjusting for patient-, pathogen-, and treatment-specific characteristics by multivariate analysis, geographical region was also found to be associated with mortality in patients with SA-NVIE (P < .001). CONCLUSIONS: S. aureus is an important and common cause of IE. The outcome of SA-NVIE is worse than that of non-SA-NVIE. Several clinical parameters are independently associated with mortality for patients with SA-NVIE. The clinical characteristics and outcome of SA-NVIE vary significantly by geographic region, although the reasons for such regional variations in outcomes of SA-NVIE are unknown and are probably multifactorial. A large, prospective, multinational cohort study of patients with IE is now under way to further investigate these observations.
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| 32. |
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| 33. |
- Naidoo, Kevin J., et al.
(författare)
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Glucose orientation and dynamics in α-, β-, and γ-cyclodextrins
- 2008
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Ingår i: The Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1089-5647 .- 1520-6106 .- 1520-5207. ; 112:47, s. 15151–15157-
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Tidskriftsartikel (refereegranskat)abstract
- We investigate, using molecular dynamics (MD) computer simulations, the conformational behavior of α-, β-, and γ-cyclodextrins (CDs). Our analysis of a 30 ns trajectory of CD solution dynamics reveals the underlying conformational behaviours of the CDs that explain their relative flexibility. The distributions of the torsion angles related to the glycosidic linkages, P(ϕ,ψ) were calculated for the three CDs. Most noticeable is the limited range in ϕ torsion rotations compared with ψ rotations for all the CDs. This difference between the three CDs is amplified in the motion and dynamics of their glucose monomers when we monitor their orientational and librational positions relative to the macrocyclic mean plane. The relaxation times of the monomers to their equilibrium orientations follow the pattern γ-CD > α-CD > β-CD. The root-mean-square deviations of the motion of the monomer centers of mass from the mean macrocyclic planes exhibit the same trend.
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| 34. |
- Replogle, Kirstin, et al.
(författare)
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The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
- 2008
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 9:131
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Tidskriftsartikel (refereegranskat)abstract
- Background: Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts. Results: We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA: Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing similar to 22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations. Conclusion: Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.
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| 35. |
- Thiele, Christina M., et al.
(författare)
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On the Treatment of Conformational Flexibility when Using Residual Dipolar Couplings for Structure Determination
- 2009
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Ingår i: Angewandte Chemie International Edition. - Weinheim : WILEY-VCH Verlag GmbH & Co. KGaA. - 1433-7851 .- 1521-3773. ; 48:36, s. 6708-6712
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Tidskriftsartikel (refereegranskat)abstract
- Mission possible! The motional averaging of NMR spectroscopic data complicates the determination of conformation and relative configuration in flexible organic molecules. Two alternative routes are discussed for the treatment of conformational equilibrium in a moderately flexible compound (see the superposition of the two conformers of the butyrolactone studied) when residual dipolar couplings are used.
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| 36. |
- Thiele, Christina M., et al.
(författare)
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Use of Local Alignment Tensors for the Determination of Relative Configurations in Organic Compounds
- 2009
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 131:36, s. 12878-12879
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Tidskriftsartikel (refereegranskat)abstract
- In this proof of principle the use of local alignment tensors for the determination of relative configurations in moderately flexible molecules is demonstrated. These tensors are derived from residual dipolar couplings. Two methods for the analysis of partly linearly dependent RDCs in a rigid molecular fragment are also presented.
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| 37. |
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| 38. |
- von Arnold, Karin, et al.
(författare)
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Fluxes of CO2, CH4 and N2O from drained coniferous forests on organic soils
- 2005
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127. ; 210:1-3, s. 239-254
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Tidskriftsartikel (refereegranskat)abstract
- Fluxes of CO2, CH4 and N2O were measured during two to three years at four sites, located within an area of 9 km](2) in southern Sweden, using dark static chamber techniques. Three of the sites were drained coniferous forests on moist organic soils that differed in forest productivity and tree species. The fourth site was an undrained tall sedge mire. Although the drained sites were all moist, with average groundwater levels between 17 and 27 cm below the soil surface, the mean annual dark forest floor CO2 release rate was significantly higher at the drained sites, (0.9-1.9 kg m(-2) y(-1)) than at the undrained mire site (0.8 to 1.2 kg m(-2) y(-1)). CH4 emissions were significantly lower from the drained sites than from the undrained mire (0.0 to 1.6 g m(-2) y(-1), compared to 10.6 to 12.2 g m(-2) y(-1)), while NO emissions were significantly lower from the undrained site than from the drained sites (20 to 30 mg m(-2) y(-1), compared to 30 to 90 mg m(-2) y(-1)). There were no clear effects of site productivity or tree species on the soil fluxes of any of the gases. The annual pet primary production of the forests was modeled. All drained sites were net sinks, while the undrained mire was a net source of greenhouse gases. The estimated net greenhouse gas exchange of the drained sites was correlated with productivity: the most productive site was the largest net sink and the least productive the smallest net sink for greenhouse gases. The results indicate that, to mitigate the increase of atmospheric greenhouse gases, drained forest sites, which have been unsuccessfully drained or rewetted due to subsidence, should be managed in a way that keeps the groundwater level at a steady state. (c) 2005 Elsevier B.V. All rights reserved.
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| 39. |
- von Arnold, Karin, et al.
(författare)
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Fluxes of CO2, CH4 and N2O from drained organic soils in deciduous forests
- 2005
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Ingår i: Soil Biology & Biochemistry. - : Elsevier BV. - 0038-0717. ; 37:6, s. 1059-1071
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Tidskriftsartikel (refereegranskat)abstract
- We examined net greenhouse gas exchange at the soil surface in deciduous forests on soils with high organic contents. Fluxes Of CO2, CH4 and N2O were measured using dark static chambers for two consecutive years in three different forest types; (i) a drained and medium productivity site dominated by birch, (ii) a drained and highly productive site dominated by alder and (iii) an undrained and highly productive site dominated by alder. Although the drained sites had shallow mean groundwater tables (15 and 18 cm, respectively) their average annual rates of forest floor CO2 release were almost twice as high compared to the undrained site (1.9 +/- 0.4 and 1.7 +/- 0.3, compared to 1.0 +/- 0.2 kg CO2 m(-2) yr(-1)). The average annual CH4 emission was almost 10 times larger at the undrained site (7.6 +/- 3.1 compared to 0.9 +/- 0.5 g CH4 m(-2) yr(-1) for the two drained sites). The average annual N2O emissions at the undrained site (0.1 +/- 0.05 g N2O m(-2) yr(-1)) were lower than at the drained sites, and the emissions were almost five times higher at the drained alder site than at the drained birch site (0.9 +/- 0.35 compared to 0.2 +/- 0.11 g N2O m(-2)yr(-1)). The temporal variation in forest floor CO2 release could be explained to a large extent by differences in groundwater table and air temperature, but little of the variation in the CH4 and N2O fluxes could be explained by these variables. The measured soil variables were only significant to explain for the within-site spatial variation in CH4 and N2O fluxes at the undrained swamp, and dark forest floor CO2 release was not explained by these variables at any site. The between-site spatial variation was attributed to variations in drainage, groundwater level position, productivity and tree species for all three gases. The results indicate that N2O emissions are of greater importance for the net greenhouse gas exchange at deciduous drained forest sites than at coniferous drained forest sites. (c) 2004 Elsevier Ltd. All rights reserved.
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