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- Lysholm, Fredrik, 1981-
(författare)
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Bioinformatic methods for characterization of viral pathogens in metagenomic samples
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Virus infections impose a huge disease burden on humanity and new viruses are continuously found. As most studies of viral disease are limited to theinvestigation of known viruses, it is important to characterize all circulating viruses. Thus, a broad and unselective exploration of the virus flora would be the most productive development of modern virology. Fueled by the reduction in sequencing costs and the unbiased nature of shotgun sequencing, viral metagenomics has rapidly become the strategy of choice for this exploration.This thesis mainly focuses on improving key methods used in viral metagenomics as well as the complete viral characterization of two sets of samples using these methods. The major methods developed are an efficient automated analysis pipeline for metagenomics data and two novel, more accurate, alignment algorithms for 454 sequencing data. The automated pipeline facilitates rapid, complete and effortless analysis of metagenomics samples, which in turn enables detection of potential pathogens, for instance in patient samples. The two new alignment algorithms developed cover comparisons both against nucleotide and protein databases, while retaining the underlying 454 data representation. Furthermore, a simulator for 454 data was developed in order to evaluate these methods. This simulator is currently the fastest and most complete simulator of 454 data, which enables further development of algorithms and methods. Finally, we have successfully used these methods to fully characterize a multitude of samples, including samples collected from children suffering from severe lower respiratory tract infections as well as patients diagnosed with chronic fatigue syndrome, both of which presented in this thesis. In these studies, a complete viral characterization has revealed the presence of both expected and unexpected viral pathogens as well as many potential novel viruses.
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| 2. |
- Nahar, Baitun
(författare)
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Effects of Food Supplementation and Psychosocial Stimulation on Growth and Development of Severely Malnourished Children : Intervention Studies in Bangladesh
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Early childhood malnutrition is a global public health problem with serious short- and long-term consequences. The aim of this thesis is to evaluate the effects of psychosocial stimulation (PS) with or without food supplementation (FS) on growth and development of severely malnourished children, quality of home environment, mother’s child-rearing practices and depressive symptoms. The study setting was Dhaka, Bangladesh, and the participants were severely malnourished children, aged 6-24 months, admitted at Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B). A hospital-based study was conducted in Nutrition Rehabilitation Unit of ICDDR,B hospital, where a control group (n=43) was studied initially, followed by an intervention group (n=54). All received standard nutrition rehabilitation care. The intervention group received daily group meetings and play sessions in the hospital, and was thereafter visited at home for 6 months. A community-based randomised trial was conducted including children (n=507) admitted at hospital for initial treatment of an acute infection, and thereafter assigned to PS, FS, PS+FS, clinic control or hospital control groups. PS was delivered at follow-up visits, fortnightly for 6 months at community clinics. FS included distribution of cereal-based food packets (150–300 kcal/day depending on age) for 3 months. All groups received standard medical care and micronutrient supplementation. In the hospital-based study, the intervention group had significantly higher scores in mental (p<0.001, effect size 0.52 SD) and motor development (p=0.047, effect size 0.37 SD), and weight (p=0.03, effect size 0.39 SD), after 6- months intervention. In the community-based trial, there was a significant effect of stimulation after six months of intervention on children’s mental development (group*session interaction p=0.037, effect size=0.37 SD) and weight (group*session interaction p=0.02, effect size=0.26 SD) but no effect on motor development or linear growth. The PS+FS and PS groups differed in total HOME score, two HOME subscales (maternal involvement and play materials), and in mother’s child- rearing practices scores but not in depressive symptoms. PS with or without FS had small improvement on children’s growth and development, quality of home environment and mother’s rearing-practices of severely malnourished children. More intensive interventions with longer duration are therefore recommended.
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| 3. |
- Nelson, Hanna, 1976-
(författare)
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Modelling precipitation and surface complexation reactions in systems with Goethite, Cu(II) and Oxyanions Containing As(V) or P(V)
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aqueous solubility of oxyanion (e.g. phosphates and arsenates), and thereby their mobility, bioavailability (phosphates) and toxicity (arsenates), in soils and sediments is dependent upon their chemical speciation. In complex, multicomponent systems, equilibrium modelling can be a useful tool to predict chemical speciation. When establishing a model, it is essential to understand the interactions between all the components not only in solution but also on mineral surfaces at a molecular level. By applying surface complexation models processes at mineral surfaces can be accounted for. This thesis is a summary of four papers and focuses on surface complexation of the oxyanions arsenate, phosphate and monomethyl phosphate adsorbed onto the surface of goethite (α-FeOOH). Furthermore, adsorption and precipitation of copper(II) arsenates from aqueous solutions has been studied. Solid copper(II) arsenates obtained in precipitation experiments were characterised and five different solid phases with different Cu(II) to As(V) ratio, as well as proton and Na +content, were identified; Cu5Na(HAsO4)(AsO4)3(s), Cu5Na2(AsO4)4(s), Cu3(AsO4)2(s), Cu3(AsO4)(OH)3(s) and Cu2(AsO4)(OH)(s). The adsorption of arsenate and copper(II) to the goethite surface, could not be predicted by only applying the combined model from the two binary systems, arsenate-goethite and copper(II)-goethite. Instead, two ternary copper-arsenate-goethite surface complexes were added. In one of the surface complexes arsenate is bound to goethite surface via a copper(II) ion coordinating to surface hydroxyl groups and in the other surface complex, copper(II) is coordinating arsenate bound to the goethite surface. Surface complexation models, in agreement with macroscopic data and detailed spectroscopic results, were designed for monomethyl phosphate, phosphate and arsenate adsorbed to goethite. The models contain monodentate inner sphere surface complexes stabilized by hydrogen bonding to neighbouring surface sites. The charge distribution of the complexes was assigned according to Pauling’s valence bond theory. The monomethyl phosphate model consists of three singly protonated surface isomers, only differentiated by the location of the proton . In the case of phosphate and arsenate, six surface complexes, including two pair-wise surface isomers, are suggested to form; ≡FeOAsO 32.5-; (≡FeOAsO3; ≡Fe3OH)2-;(≡FeOAsO3H; ≡Fe3O)2-; (≡FeOAsO3H; ≡Fe3OH)1-; (≡FeOAsO3H2; ≡Fe3O)1- and ≡FeOAsO3H20.5-. A combination of structural information from spectroscopic measurements and quantitative data from spectroscopy, potentiometry and adsorption experiments provides a better understanding of the complexity of the coordination chemistry of particle surfaces and forms the basis for equilibrium models with high physical/chemical relevance.
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