The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases

Triacylglycerol lipases (EC 3.1.1.3) catalyze both hydrolysis and synthesis reactions with a broad spectrum of substrates rendering them especially suitable for many biotechnological applications. Most lipases used today originate from mesophilic organisms and are susceptible to thermal denaturation whereas only few possess high thermotolerance. Here, we report on the identification and characterization of two novel thermostable bacterial lipases identified by functional metagenomic screenings. Metagenomic libraries were constructed from enrichment cultures maintained at 65 to 75°C and screened resulting in the identification of initially 10 clones with lipolytic activities. Subsequently, two ORFs were identified encoding lipases, LipS and LipT. Comparative sequence analyses suggested that both enzymes are members of novel lipase families. LipS is a 30.2 kDa protein and revealed a half-life of 48 h at 70°C. The lipT gene encoded for a multimeric enzyme with a half-life of 3 h at 70°C. LipS had an optimum temperature at 70°C and LipT at 75°C. Both enzymes catalyzed hydrolysis of long-chain (C12 and C14) fatty acid esters and additionally hydrolyzed a number of industry-relevant substrates. LipS was highly specific for (R)-ibuprofen-phenyl ester with an enantiomeric excess (ee) of 99%. Furthermore, LipS was able to synthesize 1-propyl laurate and 1-tetradecyl myristate at 70°C with rates similar to those of the lipase CalB from Candida antarctica. LipS represents the first example of a thermostable metagenome-derived lipase with significant synthesis activities. Its X-ray structure was solved with a resolution of 1.99 Å revealing an unusually compact lid structure

Adaptive threshold optimisation for colour-based lip segmentation in automatic lip-reading systems

A thesis submitted to the Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, in ful lment of the requirements for the degree of Doctor of Philosophy. Johannesburg, September 2016Having survived the ordeal of a laryngectomy, the patient must come to terms with the resulting loss of speech. With recent advances in portable computing power, automatic lip-reading (ALR) may become a viable approach to voice restoration. This thesis addresses the image processing aspect of ALR, and focuses three contributions to colour-based lip segmentation. The rst contribution concerns the colour transform to enhance the contrast between the lips and skin. This thesis presents the most comprehensive study to date by measuring the overlap between lip and skin histograms for 33 di erent colour transforms. The hue component of HSV obtains the lowest overlap of 6:15%, and results show that selecting the correct transform can increase the segmentation accuracy by up to three times. The second contribution is the development of a new lip segmentation algorithm that utilises the best colour transforms from the comparative study. The algorithm is tested on 895 images and achieves percentage overlap (OL) of 92:23% and segmentation error (SE) of 7:39 %. The third contribution focuses on the impact of the histogram threshold on the segmentation accuracy, and introduces a novel technique called Adaptive Threshold Optimisation (ATO) to select a better threshold value. The rst stage of ATO incorporates -SVR to train the lip shape model. ATO then uses feedback of shape information to validate and optimise the threshold. After applying ATO, the SE decreases from 7:65% to 6:50%, corresponding to an absolute improvement of 1:15 pp or relative improvement of 15:1%. While this thesis concerns lip segmentation in particular, ATO is a threshold selection technique that can be used in various segmentation applications.MT201

Selected Works in Bioinformatics

This book consists of nine chapters covering a variety of bioinformatics subjects, ranging from database resources for protein allergens, unravelling genetic determinants of complex disorders, characterization and prediction of regulatory motifs, computational methods for identifying the best classifiers and key disease genes in large-scale transcriptomic and proteomic experiments, functional characterization of inherently unfolded proteins/regions, protein interaction networks and flexible protein-protein docking. The computational algorithms are in general presented in a way that is accessible to advanced undergraduate students, graduate students and researchers in molecular biology and genetics. The book should also serve as stepping stones for mathematicians, biostatisticians, and computational scientists to cross their academic boundaries into the dynamic and ever-expanding field of bioinformatics

Improved facial feature fitting for model based coding and animation

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Novel system of pavement cracking detection algorithms using 1mm 3D surface data

Pavement cracking is one of the major concerns for pavement design and management. There have been rapid developments of automated pavement cracking detection in recent years. However, none of them has been widely accepted so far due to lack of capability of maintaining consistently high detection accuracy for various pavement surfaces. Using 1mm 3D data collected by WayLink Digital Highway Data Vehicle (DHDV), an entire system of algorithms, which consists of Fully Automated Cracking Detection Subsystem, Interactive Cracking Detection Subsystem and Noisy Pattern Detection Subsystem, is proposed in this study for improvements in adaptability, reliability and interactivity of pavement cracking detection.The Fully Automated Cracking Detection Subsystem utilizes 3D Shadow Simulation to find lower areas in local neighborhood, and then eliminates noises by subsequent noise suppressing procedures. The assumption behind 3D Shadow Simulation is that local lower areas will be shadowed under light with a certain projection angle. According to the Precision-Recall Analysis on two real pavement segments, the fully automated subsystem can achieve a high level of Precision and Recall on both pavement segments.The Interactive Cracking Detection Subsystem implements an interactive algorithm proposed in this study, which is capable of improving its detection accuracy by adjustments based on the operator's feedback, to provide a slower but more flexible as well as confident approach to pavement cracking detection. It is demonstrated in the case study that the interactive subsystem can retrieve almost 100 percent of cracks with nearly no noises.The Noisy Pattern Detection Subsystem is proposed to exclude pavement joints and grooves from cracking detection so that false-positive errors on rigid pavements can be reduced significantly. This subsystem applies Support Vector Machines (SVM) to train the classifiers for the recognition of transverse groove, transverse joint, longitudinal groove and longitudinal joint respectively. Based on the trained classifiers, pattern extraction procedures are developed to find the exact locations of pavement joints and grooves.Non-dominated Sorting Genetic Algorithm II (NSGA-II), which is one of multi objective genetic algorithms, is employed in this study to optimize parameters of the fully automated subsystem for the pursuing of high Precision and high Recall simultaneously. In addition to NSGA-II, an Auxiliary Prediction Model (APM) is proposed in this study to assist NSGA-II for faster convergence and better diversity.Finally, CPU-based and GPU-based Parallel Computing Techniques, including MultiGPU, GPU streaming, Multi-Core and Multi-Threading are combined in this study to increase the processing speed for all computational tasks that can be synchronous

ИНТЕЛЛЕКТУАЛЬНЫЙ числовым программным ДЛЯ MIMD-компьютер

For most scientific and engineering problems simulated on computers the solving of problems of the computational mathematics with approximately given initial data constitutes an intermediate or a final stage. Basic problems of the computational mathematics include the investigating and solving of linear algebraic systems, evaluating of eigenvalues and eigenvectors of matrices, the solving of systems of non-linear equations, numerical integration of initial- value problems for systems of ordinary differential equations.Для більшості наукових та інженерних задач моделювання на ЕОМ рішення задач обчислювальної математики з наближено заданими вихідними даними складає проміжний або остаточний етап. Основні проблеми обчислювальної математики відносяться дослідження і рішення лінійних алгебраїчних систем оцінки власних значень і власних векторів матриць, рішення систем нелінійних рівнянь, чисельного інтегрування початково задач для систем звичайних диференціальних рівнянь.Для большинства научных и инженерных задач моделирования на ЭВМ решение задач вычислительной математики с приближенно заданным исходным данным составляет промежуточный или окончательный этап. Основные проблемы вычислительной математики относятся исследования и решения линейных алгебраических систем оценки собственных значений и собственных векторов матриц, решение систем нелинейных уравнений, численного интегрирования начально задач для систем обыкновенных дифференциальных уравнений

Genome analysis of an entomopathogenic nematode belonging to the genus Oscheius and its insect pathogenic bacterial endosymbiont

A thesis submitted to the Faculty of Science under the school of Molecular and Cell Biology in fulfilment for requirements for Doctor of Philosophy Degree. February 2016The use of synthetic chemical pesticides has several negative implications for the Agricultural industry, which include the development of resistance to the insecticides, crop contamination and the killing of non-target insects. This has brought many scientists in the field of nematology and entomology to investigate biological control agents which can help solve identified challenges and these biocontrol agents have also included entomopathogenic nematodes. The majority of entomopathogenic nematodes species that have been isolated belong to Heterorhabditids and Steinernematids which act as vectors for insect pathogenic bacteria species belonging to the genera, Photorhabdus and Xenorhabdus, respectively. However, other species of nematodes, one of which includes a strain of Caenorhabditis briggsae, have also been shown to act as a vector for an insect pathogenic strain of Serratia marcescens. Oscheius sp. TEL-2014 EPNs have been observed to act as vectors for insect pathogenic bacteria belonging to the genus Serratia. In this study a novel insect pathogenic Serratia sp. strain TEL was isolated from the gut of infective juveniles belonging to a species of Oscheius sp. TEL-2014. Next generation sequencing of the bacteria was conducted by generating genomic DNA paired-end libraries with the Nextera DNA sample preparation kit (Illumina) and indexed using the Nextera index kit (Illumina). Paired-end (2 × 300 bp) sequencing was performed on a MiSeq Illumina using the MiSeq reagent kit v3 at the Agricultural Research Council Biotechnology Platform. Quality control and adapter trimming was performed and the genome was assembled using SPADES. 19 contigs were generated with an average length of 301767 bp and N50 of 200,110 bp. The genome of the Serratia sp. TEL was found to be 5,000,541 bp in size, with a G+C content of 59.1%, which was similar to that of other Serratia species previously identified. Furthermore, the contigs were annotated using NCBI Prokaryotic Genome Automatic Annotation Pipeline. Features of the annotated genome included protein encoding sequence or genes, rRNA encoding genes, tRNA encoding genes, ncRNA sequences and repeat regions. 4,647 genes were found and 4,495 were protein-coding sequences (CDS). The genome contains 36 pseudo genes, 2 CRISPR arrays, 13 rRNA genes with five operons (5S, 16S, 23S), 88 tRNAs genes, 15 ncRNA sequences and 9 frameshifted genes. Several genes involved in virulence, disease, defense, stress response, cell division, motility and chemotaxis were identified. This genome sequence will allow for the investigation of identified genes and that will be critical in furthering the understanding of the insect pathogenicity of Serratia sp. strain TEL. Furthermore, it will provide additional genomic insights about the insect-nematode interactions and thus help us improve their ability to be used as biological control agents in agricultural industries. Oscheius sp. TEL-2014 was tested for its entomopathogenicity and it was found that this species was able to infect and kill two model insects Galleria mellonella and Tenebrio molitor. This new nematode species brought 100% mortality within 72 h post-exposure in G. mellonella and whereas, within 96 hours in T. molitor. Following morphometrics analysis of Oscheius sp. TEL-2014 it was concluded that this nematode is described as a novel entomopathogenic nematode species based on its morphometrics and 18S rRNA gene sequence originality. Whole genome sequencing of Oscheius sp. TEL-2014 inbred lines (7 and 13) was performed using Illumina Hiseq sequencing system and paired ends library preparation protocol. Sequencing reads assembled on Velvet resulted in generation of 75965 contigs (line 7) and 53190 contigs (line 13). Gene prediction tools showed that proteins involved in gene expression and DNA replication are present in Oscheius sp. TEL-2014. The draft genome of Oscheius nematodes will support the improvement and initiation of further studies intended to help us understand the molecular and metabolic processes in this genus