High throughput technologies and statistical analyses have transformed the way biological research is performed. These technologies accomplish tasks that were labeled as science fiction only 20 years ago - identifying millions of genetic variations in a genome, a chip that measures expression levels of all genes, quantifying the concentration of dozens of proteins at a single cell resolution. High-throughput genome-wide approaches allowed us, for the first time, to perform unbiased research that doesn't depend on existing knowledge. Thanks to these new technologies, we now have a much better understanding on what goes awry in cancer, what are the genetic predispositions for numerous diseases, and how to select the best available treatment for each patient based on his/her genetic and genomic features. The emergence of new technologies, however, also introduced many new problems that need to be addressed in order to fully exploit the information within the data. Tasks start with data normalization and artifact identification, continue with how to properly model the data using statistical tools, and end with the suitable ways to translate those statistical results into informative and correct biological insights. A new field - computational biology - was emerged to address those problems and bridge the gap between statistics and biology. Here I present 3 studies on computational modeling of heterogeneity and context-specificity in biological systems. My work focused on the identification of genomic features that can predict or explain a phenotype. In my studies of both yeast and cancer, I found vast heterogeneity between individuals that hampers the prediction power of many statistical models. I developed novel computational models that account for the heterogeneity and discovered that, in most cases, the relationship between the genomic feature and the phenotype is context-specific - genomic features explain, predict or exert influence on the phenotype in only a subset of cases. In the first project I studied the landscape of genetic interactions in yeast using gene expression data. I found that roughly 80% of interactions are context-specific, where genetic mutations influence expression levels only in the context of other mutations. In the second project I used gene expression and copy number data to identify drivers of oncogenesis. By using gene expression as a phenotype, and by accounting for context-specificity, I identified two novel copy number drivers that were validated experimentally. In the third project I studied the transcriptional and phenotypic effects of MAPK pathway inhibition in melanoma. I show that most MAPK targets are context-specific - under the control of the pathway only in a subset of cell lines. A computational model I designed to detect context-specific interactions of the MAPK pathway identified the interferon pathway as a major player in the cytotoxic response of MAPK inhibition. Taken together, my research demonstrates the importance of context-specificity in the analysis of biological systems. Context-specific computational modeling, combined with high-throughput technologies, is a powerful tool for dissecting biological networks.

The translocation of a biopolymer through a narrow pore exists in universal cellular processes, such as the translocations of nascent proteins through ribosome and the degradation of protein by ATP-dependent proteases. However, the molecular details of these translocation processes remain unclear. Using computer simulations we study the translocations of a ubiquitin-like protein into a pore. It shows that the mechanism of co-translocational unfolding of proteins through pores depends on the pore diameter, the magnitude of pulling force and on whether the force is applied at the N- or the C-terminus. Translocation dynamics depends on whether or not polymer reversal is likely to occur during translocation. Although it is of interest to compare the timescale of polymer translocation and reversal, there are currently no theories available to estimate the timescale of polymer reversal inside a pore. With computer simulations and approximate theories, we show how the polymer reversal depends on the pore size, r, and the chain length, N. We find that one-dimensional transition state theory (TST) using the polymer extension along the pore axis as a reaction coordinate adequately predicts the exponentially strong dependence of the reversal rate on r and N. Additionally, we find that the transmission factor (the ratio of the exact rate and the TST rate) has a much weaker power law dependence on r and N. Finite-size effects are observed even for chains with several hundred monomers. If metastable states are separated by high energy-barriers, transitions between them will be rare events. Instead of calculating the relative energy by studying those transitions, we can calculate absolute free energy separately to compare their relative stability. We proposed a method for calculating absolute free energy from Monte Carlo or molecular dynamics data. Additionally, the diffusion of a knot in a tensioned polymer is studied using simulations and it can be modeled as a one-dimensional free diffusion problem. The diffusion coefficient is determined by the number of monomers involved in a knot and its tension dependence shows a maximum due to two dominating factors: the friction from solvents and “local friction” from interactions among monomers in a compact knot. / text

Este trabalho apresenta uma proposta para a identificação biométrica de indivíduos através da análise da íris, utilizando uma abordagem baseada em Morfologia Matemática. Algoritmos baseados em operadores morfológicos são utilizados nas diversas etapas de processamento, para segmentação, realçamento de padrões, extração e representação de características. Para avaliar os algoritmos, testes foram realizados utilizando imagens do Banco de Dados de Imagens de Íris da Universidade de Bath - UBIID, da base de dados do Instituto de Automação da Academia Chinesa de Ciências - CASIA, além de imagens adquiridas para compor o Banco de Dados Brasileiro de Pesquisa de Íris - BIRD. A fim de avaliar o desempenho de classificação, o método proposto foi comparado ao método de Daugman (referência). Os resultados obtidos indicam a viabilidade da abordagem proposta para o reconhecimento de íris. Para imagens do UBIID, o desempenho do método proposto foi superior ao do método de referência, alcançando 99,35% de acerto no ponto de erro igual (EER - Equal Error Rate), onde as taxas de falsa aceitação (FAR) e de falsa rejeição (FRR) são iguais. / This paper presents a proposal for biometric identification of individuals by analyzing the iris, using an approach based on Mathematical Morphology. Algorithms based on morphological operators are used in several stages of processing, segmentation, enhancement of patterns, extraction and representation of features. To evaluate the algorithms, tests were performed using images of the University of Bath Iris Image Database - UBIID, of the Chinese Academy of Sciences Institute of Automation - CASIA, and acquired images to compose the Brazilian Iris Research Database - BIRD. In order to assess the performance of classification, the proposed method was compared to Daugman’s method (reference). The results indicate the viability of the proposed approach for iris recognition. For UBIID images, the performance of the proposed method was superior to the reference method, achieving 99.35% accuracy at the point of equal error (EER - Equal Error Rate), where the false acceptance rate (FAR) and false rejection rate (FRR) are equal.

It was suggested that marker and phenotypic information be combined in order to obtain more accurate or earlier genetic evaluations. An improvement in accuracy or time of evaluation due to utilization of marker assisted selection (MAS) increases genetic progress. Fernando and Grossman (1989) suggested including marker information directly into the Animal Model, Best Linear Unbiased Prediction system, but several problems need to be solved before their approach becomes feasible. Other selection indices were suggested but either do not use all the available information or are suitable only for evaluation of the offspring of the sire from which the marker information was established. A selection index combining marker and Animal Model information was developed to allow comparisons involving offspring, grandoffspring and great-grandoffspring of a sire. Marker information was assumed to be a least square estimate of the difference between the average effects of the two quantitative trait loci (QTL) alleles present in a sire (D_p) and the standard error of this estimate (SE(D_p)). Estimates may have been obtained from a daughter or granddaughter design. Comparisons among grandoffspring and great-grandoffspring also require an estimate of the recombination rate (r) between the marker and the QTL. The Animal Model information consists of predicted transmitting ability (PTA) and reliability of PTA. PTA was assumed not to include any marker information. The expected percentage of the gain in accuracy (PGA) due to the inclusion of marker information in the selection indices is affected by the degree of polymorphism at the marker locus. The polymorphism information content (PIC) of a marker locus was computed for the second and third generations and for mates genotyped or not. PGA increased with larger Dos lower SE(D_p), lower r, a smaller number of own and progeny records, and larger PIC. PGA and PIC reduce over generations. Marker information in dairy cattle is likely to be used in generations beyond offspring. Then, only the use of highly polymorphic markers with a large and accurately estimated effect may be economically justified. / Master of Science

Thesis (PhD)--Stellenbosch University, 2015 / ENGLISH ABSTRACT : Diuraphis noxia Kurdjumov (Russian Wheat Aphid; RWA) is a pest of wheat and barley that has spread from its home range in the fertile crescent to most wheat producing countries except Australia. Since its first introduction to South Africa and the USA in the late 20th century, breeding programs for wheat phenotypes resistant to the aphid were put in place. Conventional breeding practices rely on phenotypic screening to verify traits carried by offspring and genetic tools such as marker assisted selection (MAS) have greatly aided this process in speed and accuracy. The size and complexity of the wheat genome, its allopolyploid nature and repetitive elements have, however, posed a challenge to studies on the genetics of this cereal crop. Many studies have focused on chromosome 3B which is the largest of the wheat chromosomes and easily separated from the redundant genomic background by techniques such as flow cytometry. The similarity in size of the remaining chromosomes however, limits the application of flow cytometry to their isolation. Databases such as Grain-Genes (http://wheat.pw.usda.gov/GG2/index.shtml) house marker data from various mapping studies for all wheat chromosomes and in 2014 the International Wheat Genome Sequencing Consortium (IWGSC) completed the draft genome sequence of wheat categorized by chromosome. Sources of resistance (Dn resistance genes) against RWA are located on chromosome 7D. but despite the marker and sequence data available currently, mapping studies specific for the Dn resistance genes are few. Additionally, sequence data available is derived from cultivars susceptible to RWA and is not comprehensively annotated and assembled in many cases. In this study, we demonstrate a novel, combined approach to isolate and characterize the Dn resistance genes through the use of a genetic map constructed from Amplified Fragment Length Polymorphism (AFLP), Expressed Sequence Tag (EST) and microsatellite markers and a physical map constructed from Next Generation Sequencing (NGS) data of ditelosomic chromosomes (7DS and 7DL) isolated by microdissection on the PALM microbeam system. A 122.8 cM genetic map was produced from 38 polymorphic AFLP markers and two ESTs with the microsatellite Xgwm111 as anchor to related genetic maps. Through comparison to maps available on GrainGenes the location of the Dn1 resistance gene was narrowed down to a deletion bin (7DS5-0.36-0.62) on the short arm of chromosome 7D with an AFLP marker (E-ACT/M-CTG_0270.84) mapping closely at 3.5 cM and two ESTs mapping at 15.3 cM and 15.9 cM from Dn1. Isolation of individual chromosome arms 7DS and 7DL using the PALM Microbeam system allowed sequencing of the chromosome without the redundancy of the remainder of the hexaploid genome. Through isolating the chromosome arms in this way, a >80-fold reduction in genome size was achieved as well as a major reduction in repetitive elements. Analysis of the sequencing data confirmed that 7DL is the physically shorter arm of the chromosome though it contains the majority of protein coding sequences. / AFRIKAANSE OPSOMMING : Diuraphis noxia Kurdjumov (Russiese koring-luis; RWA) is « pes wat op koring en gars voorkom. Die pes het vanaf sy tuiste in die midde Ooste na meeste koringproduserende lande behalwe Australië versprei. Sedert die eerste bekendstelling van RWA in Suid Afrika en die VSA in die vroeë 20ste eeu is teelprogramme ten gunste van koring lyne met weerstand teen RWA begin. Tradisionele teelprogramme maak op fisieise observasie van die fenotipe staat om te verifieer of plante in die nageslag die gewenste eienskap dra. Genetiese metodes soos merkerondersteunde seleksie (MAS) versnel hierdie selekteringsproses grootliks. Die grootte en kompleksiteit van die koring genoom asook die polyploïde en herhalende natuur daarvan is « groot hindernis vir genetiese studies van hierdie graangewas. Baie studies het op chromosoom 3B gefokus wat die grootste van die koring chromosome is en dus maklik vanaf die res van die oorbodige genomiese agtergond deur tegnieke soos vloeisitometrie geskei word. Die ooreenkoms in grootte tussen die res van die chromosome bemoeilik die toepassing van vloeisitometrie om hulle te isoleer. Databasisse soos GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml) bevat merker data vanaf verskeie karterings-studies vir al die chromosome en in 2014 het die "International Wheat Genome Sequencing Consortium"(IWGSC) die voorlopige basispaarvolgorde van die koring genoom bekendgestel, gekategoriseer volgens chromosoom. Weerstandsbronne (Dn weerstandsgene) teen RWA kom meestal op chromosoom 7D voor. Ten spyte van merker en basispaarvolgorde data tans beskikbaar is karterings-studies spesifiek tot die Dn gene skaars en basispaarvolgorde data is vanaf kultivars afkomstig wat nie weerstandbiedend teen RWA is nie en waarvan die annotasie en samestelling baie keer nie goed is nie. In hierdie studie demonstreer ons « nuwe, gekombineerde aanslag om die Dn weerstandsgene te isoleer en karakteriseer deur van « genetiese kaart opgestel met "Amplified Fragment Length Polymorphism"(AFLP), "Expressed Sequence Tag"(EST) en mikrosatelliet merkers asook « fisiese kaart saamgestel deur die volgende-generasiebasispaarvolgordebepaling van ditelosomiese chromosome (7DS en 7DL) geïsoleer deur mikrodisseksie met die "PALM Microbeam"sisteem gebruik te maak. « Genetiese kaart van 122.8 cM was met 38 polimorfiese AFLP merkers en twee EST merkers geskep. Die mikrosatelliet, Xgwm111, is ook ingesluit en het as anker vir verwante genetiese-kaarte gedien. Deur vergelyking met genetiese-kaarte op GrainGenes is die posisie van die Dn1 weerstandsgeen vernou na « delesie bin (7DS5-0.36-0.62) op die kort arm van chromosoom 7D met « AFLP merker (EACT/ M-CTG_0270.84) wat ongeveer 3.5 cM vanaf die geen karteer. Die twee EST merkers is 15.3 cM en 15.9 cM vanaf die geen gekarteer. Isolering van die individuele chromosoom arms, 7DS en 7DL, deur van die "PALM Microbeam"sisteem gebruik te maak het basispaarvolgordebepaling van die chromosoom toegelaat sonder die oortolligheid van die res van die hexaploïde genoom. Deur die chromosoom so te isoleer is « >80-maal verkleining in genoom grootte bereik insluitend « groot reduksie in herhalende elemente. Analise van die data vanaf basispaarvolgordebepaling het bevestig dat chromosoom 7D die fisiese kleiner chromosoom is maar dat dit die meerderheid van proteïn koderende basispaarvolgordes bevat.

Genetic Algorithms (GAs) are a search heuristic modeled on the processes of evolution. They have been used to solve optimisation problems in a wide variety of fields. When applied to the optimisation of intervention schedules for optimal control problems, such as cancer chemotherapy treatment scheduling, GAs have been shown to require more fitness function evaluations than other search heuristics to find fit solutions. This thesis presents extensions to the GA crossover process, termed directed intervention crossover techniques, that greatly reduce the number of fitness function evaluations required to find fit solutions, thus increasing the effectiveness of GAs for problems of this type. The directed intervention crossover techniques use intervention scheduling information from parent solutions to direct the offspring produced in the GA crossover process towards more promising areas of a search space. By counting the number of interventions present in parents and adjusting the number of interventions for offspring schedules around it, this allows for highly fit solutions to be found in less fitness function evaluations. The validity of these novel approaches are illustrated through comparison with conventional GA crossover approaches for optimisation of intervention schedules of bio-control application in mushroom farming and cancer chemotherapy treatment. These involve optimally scheduling the application of a bio-control agent to combat pests in mushroom farming and optimising the timing and dosage strength of cancer chemotherapy treatments to maximise their effectiveness. This work demonstrates that significant advantages are gained in terms of both fitness function evaluations required and fitness scores found using the proposed approaches when compared with traditional GA crossover approaches for the production of optimal control schedules.

Commercialisées depuis 1996, les plantes génétiquement modifiées produisant une toxine insecticide (toxine Cry) dérivée de Bacillus thuringiensis et appelées plantes Bt ciblent certains Lépidoptères ou Coléoptères ravageurs. Au fil des ans, les surfaces cultivées en plantes Bt sont de plus en plus importantes et contrôlent de larges populations d'insectes. Pour limiter le risque de développement de populations résistantes, une stratégie agricole appelée 'Haute Dose / Zone Refuge' est actuellement recommandée aux Etats-Unis par l'Environmental Protection Agency. Cette stratégie préventive nécessite la plantation d'une 'zone refuge' composée de plantes non-Bt utilisables par le ravageur ciblé et plantée à proximité de la 'zone Bt' qui synthétise une haute dose de toxine Cry. <p><p>Mon projet de recherche s’inscrit dans le cadre de l’évaluation de l'efficacité de cette stratégie et s’articule en deux phases :une phase expérimentale et une phase théorique. La première se concentre sur la caractérisation en laboratoire de l'impact des toxines Cry sur la biologie d'un ravageur. Cette phase constitue un support au volet théorique :la mise au point d’un modèle mathématique évaluant l'efficacité de la stratégie HD/R. L'originalité de ce projet repose entre autre sur l'interactivité entre ces deux volets.<p><p>Volet expérimental. Impact des toxines Cry sur la biologie de Plodia interpunctella. Nous évaluons séparément l'impact d'une gamme de concentrations de deux toxines Cry (CryXX et CryYY) sur une série de paramètres comportementaux et biologiques d'un insecte commun des denrées stockées: Plodia interpunctella (Hübner) (Lepidoptera :Pyralidae). Ces paramètres sont sélectionnés car leur variation pourrait avoir un impact sur l'efficacité de la stratégie HD/R dans le contrôle de la résistance. Il est donc pertinent de les quantifier pour intégrer dans le modèle des ordres de grandeur réalistes et générer des résultats qui ne sont pas uniquement basés sur des spéculations théoriques.<p><p>Volet théorique A. Efficacité de la stratégie HD/R pour des plantes Bt synthétisant une ou deux toxines simultanément. La stratégie 'HD/R' a été développée pour prévenir la résistance envers les plantes Bt synthétisant une seule toxine. Or, depuis 2003, de nouvelles variétés de coton Bt synthétisant simultanément deux toxines Cry sont commercialisées (BollgardII® et WidestrikeTM). Nous évaluons, grâce au modèle que nous avons développé, l'efficacité de cette stratégie lors d'une utilisation exclusive de plantes Bt synthétisant une ou deux toxines.<p><p>Volet théorique B. Impact du ralentissement du développement des insectes sur les plantes Bt sur l'efficacité de la stratégie HD/R. Le volet expérimental met en évidence un allongement de la durée du développement des larves se nourrissant sur une diète contaminée en toxine Cry. Ce ralentissement induit une séparation temporelle entre l'émergence des adultes de la zone Bt et de la zone refuge et perturbe une hypothèse principale de la stratégie HD/R: le croisement aléatoire entre adultes, indépendamment du génotype et de la zone d'origine. Dans ce troisième chapitre, nous étudions l'impact de la perturbation du croisement aléatoire sur l'efficacité de la stratégie HD/R. Nous testons également deux options pour optimiser la stratégie en cas d'asynchronie: l'utilisation de plantes Bt synthétisant une faible concentration en toxine (atténuant le décalage entre l'émergence des adultes) ou l'augmentation de la taille de la zone refuge (favorisant la survie des individus porteurs d'allèle de sensibilité et donc optimisant la dilution de la résistance à la génération suivante). <p><p>Ce travail s'intègre dans une problématique actuelle et utilise des outils de biologie théorique (théories de la dynamique et de la génétique des populations) ainsi que le développement d'un modèle mathématique. Il apporte des éléments de réponse et de réflexion sur l'optimisation de la gestion de la résistance des insectes mais c'est aussi une illustration de la complémentarité entre la biologie expérimentale et théorique.<p><p><p>/<p><p>On the market since 1996, genetically modified plants synthesizing an insecticidal toxin (Cry toxin) stemmed from Bacillus thuringiensis, called Bt plants, target several insect pests (Lepidoptera or Coleoptera). Bt crops cover increasingly larger areas and control important pest populations The Insect Resistance Management Strategy (IRM) strategy currently recommended in the U.S.A. to limit the development of resistant populations is the High Dose / Refuge zone (HD/R) strategy. This pre-emptive strategy requires a refuge zone composed by non-Bt plants, usable by the target insect and in close proximity of the Bt zone synthesizing a high toxin concentration.<p><p>My research project contributes to the effectiveness assessment of this HD/R strategy. It is structured on two main parts: an experimental, and a theoretical section. The first part characterizes the impact of Cry toxins on the biology of an insect pest. It is the basis of the theoretical part: the implementation of a mathematical model, which evaluates the effectiveness of the HD/R strategy.<p>The originality of this project is based on the interactivity of these two components.<p><p>Experimental section. Impact of the Cry toxins on the biology of Plodia interpunctella. We assess the impact of a range of concentrations of two Cry toxins (CryXX et CryYY) on several behavioural and biological parameters of a common pest of stored products: Plodia interpunctella (Hübner) (Lepidoptera :Pyralidae). These parameters are selected because their variation could influence the effectiveness of a HD/R strategy. So, it is important to quantify these parameters so that realistic values can be integrated in our model. The results of the model are thus not based on theoretical assumptions alone.<p> <p>Theoretical section A. Effectiveness of a HD/R strategy with Bt plants synthesizing one or two toxins. Initially, the HD/R strategy has been developed to limit the resistance towards Bt plants synthesizing one toxin. However, since 2003, new Bt cotton varieties synthesize two toxins simultaneously (BollgardII® et WidestrikeTM). We assess, with our model, the effectiveness of this strategy for Bt plants synthesizing one or two toxins.<p><p>Theoretical section B. Impact of the slowing down of the insect development reared on Bt plants on the effectiveness of the HD/R strategy. The experimental part demonstrates that larvae reared on a Bt diet have a protracted development duration. The consequence of this is a temporal separation between adult emergence in the two zones (Bt zone and refuge zone). This could affect the main assumption of the HD/R strategy, i. e. random mating independently of the genotype and of the native zone. In this third chapter, we study the impact of random mating disruption on the effectiveness of a HD/R strategy. We test two options to optimise the strategy in case of asynchrony: the use of Bt plants synthesizing a lower toxin concentration (limiting emergence asynchrony) or increasing the refuge zone size (favouring the survival of insect carrying one or two susceptible allele and thus optimising the dilution of resistance at the next generation). <p><p>This work is applied to a current issue. It uses some of the tools of theoretical biology (theories of population dynamics and population genetics) and develops a mathematical model. It provides some responses and some elements of thought about insect resistance management. It is also an illustration of the complementarity between experimental and theoretical biology.<p> / Doctorat en Sciences / info:eu-repo/semantics/nonPublished