Inference of biomolecular interactions from sequence data

This thesis describes our work on the inference of biomolecular interactions from sequence data. In particular, the first part of the thesis focuses on proteins and describes computational methods that we have developed for the inference of both intra- and inter-protein interactions from genomic data. The second part of the thesis centers around protein-RNA interactions and describes a method for the inference of binding motifs of RNA-binding proteins from high-throughput sequencing data. The thesis is organized as follows. In the first part, we start by introducing a novel mathematical model for the characterization of protein sequences (chapter 1). We then show how, using genomic data, this model can be successfully applied to two different problems, namely to the inference of interacting amino acid residues in the tertiary structure of protein domains (chapter 2) and to the prediction of protein-protein interactions in large paralogous protein families (chapters 3 and 4). We conclude the first part by a discussion of potential extensions and generalizations of the methods presented (chapter 5). In the second part of this thesis, we first give a general introduction about RNA- binding proteins (chapter 6). We then describe a novel experimental method for the genome-wide identification of target RNAs of RNA-binding proteins and show how this method can be used to infer the binding motifs of RNA-binding proteins (chapter 7). Finally, we discuss a potential mechanism by which KH domain-containing RNA- binding proteins could achieve the specificity of interaction with their target RNAs and conclude the second part of the thesis by proposing a novel type of motif finding algorithm tailored for the inference of their recognition elements (chapter 8)

The gravity of modern amplitudes: using on-shell scattering amplitudes to probe gravity

In this thesis, we explore the use of on-shell scattering amplitudes as a way to understand various gravitational phenomena. We show that amplitudes are a viable way of studying certain aspects of gravity and showcase three such novel results here. First is the computation of the deflection angle of both light and gravitational waves due to a massive static body. We compute this from a purely on-shell amplitude perspective and find that the result is in complete agreement with the corresponding calculation in General Relativity. The second is the ability to derive classical results from the amplitudes. In this section we use on-shell scattering amplitudes to derive the perturbative metric of a rotating black hole in a generic form of Einstein gravity that has additional terms cubic in the Riemann tensor. We show that the metric we derive reduces to correct static metric in the zero angular momentum limit. We show that at first order in the coupling, the classical potential can be written to all orders in spin as a differential operator acting on the non-rotating potential. Further we compute the classical impulse and scattering angle of such a black hole. The third is the resolution of a classical discontinuity in N = 1 super gravity. Here we use on-shell methods for massive particles and use them to compute the supersymmetric version of the van Damme-Veltman-Zakharov (vDVZ) discontinuity. We construct the amplitudes of massive gravitinos (the superpartner of massive gravitons) and show that in the massless limit of the gravitinos there is the same discontinuity as found in massive gravity. This method sheds light on intricacies of the discontinuity that is obscured when handled classically

Biological effects of cigarette smoke in cultured human retinal pigment epithelial cells.

The goal of the present study was to determine whether treatment with cigarette smoke extract (CSE) induces cell loss, cellular senescence, and extracellular matrix (ECM) synthesis in primary human retinal pigment epithelial (RPE) cells. Primary cultured human RPE cells were exposed to 2, 4, 8, and 12% of CSE concentration for 24 hours. Cell loss was detected by cell viability assay. Lipid peroxidation was assessed by loss of cis-parinaric acid (PNA) fluorescence. Senescence-associated ß-galactosidase (SA-ß-Gal) activity was detected by histochemical staining. Expression of apolipoprotein J (Apo J), connective tissue growth factor (CTGF), fibronectin, and laminin were examined by real-time PCR, western blot, or ELISA experiments. The results showed that exposure of cells to 12% of CSE concentration induced cell death, while treatment of cells with 2, 4, and 8% CSE increased lipid peroxidation. Exposure to 8% of CSE markedly increased the number of SA-ß-Gal positive cells to up to 82%, and the mRNA expression of Apo J, CTGF, and fibronectin by approximately 3-4 fold. Treatment with 8% of CSE also increased the protein expression of Apo J and CTGF and the secretion of fibronectin and laminin. Thus, treatment with CSE can induce cell loss, senescent changes, and ECM synthesis in primary human RPE cells. It may be speculated that cigarette smoke could be involved in cellular events in RPE cells as seen in age-related macular degeneration

The black silicon method II: the effect of mask material and loading on the reactive ion etching of deep silicon trenches

Very deep trenches in Si with smooth controllable profiles are etched using a fluorine-based Reactive Ion Etcher(RIE). The effect of various mask materials and loading on the profile is examined using the Black Silicon Method. It is found that most metal layers have an almost infinite selectivity. When the aspect ratio of the trenches is beyond five, RIE lag is found to be an important effect. Evidence is found that this effect is caused by the bowing of incoming ions by the electrical field

Novel microstructures and technologies applied in chemical analysis techniques

Novel glass and silicon microstructures and their application in chemical analysis are presented. The micro technologies comprise (deep) dry etching, thin layer growth and anodic bonding. With this combination it is possible to create high resolution electrically isolating silicon dioxide structures with aspect ratio's similar to those possible in silicon. Main applications are chemical separation methods such as high performance liquid chromatography (HPLC) or electrophoresis (HPCE). Beside these channel structures, a capillary connector with very low dead and mixing volume has been designed and fabricated for use in (correlation) electrophoresis, and tested by means of precision of consecutive single injection

Miniaturised friction force measuring system for tribological research on magnetic storage devices

In this paper a silicon head slider suspension with integrated piezoresistive friction force sensors is presented. This device can be used for tribological research on magnetic rigid disk storage devices. Both the tangential and radial friction forces between the slider and disk, as well as a friction induced moment, can be measured simultaneously. Furthermore the normal load on the head slider can be measured. The paper focusses on design considerations and the realisation process of the suspension. Friction measurements are included to illustrate the feasibility of the system

Die stand en ontwikkeling van geloofsleierskap in die V.G.K. gemeente Springbok

Thesis (MTh)--Stellenbosch University, 2001.ENGLISH ABSTRACT: No abstract availableAFRIKAANSE OPSOMMING: Geen opsommin