L'ambition de cette thèse était de proposer un nouvel élan pour la création variétale chez la vigne, incluant les connaissances et les derniers outils de la recherche. En effet, la viticulture française comme d'autres filières agricoles doit aujourd'hui faire face à 3 grands défis: la réduction des intrants phytosanitaires (plan Ecophyto 2018), les changements climatiques, et de nouveaux concurrents, notamment les pays du Nouveau Monde. La création variétale, qui a été peu exploitée chez la vigne, peut être une des solutions pour répondre à ces défis.S'appuyant sur un génotypage dense, plusieurs outils et concepts innovants – réunis sous le terme de sélection génomique (GS) – ont vu le jour ces dernières années en sélection animale, qui permettent de prédire les phénotypes des individus seulement génotypés.Afin d'atteindre notre but, nous avons évalué et comparé l'efficacité de la GS et de la sélection assistée par marqueur (SAM) « classique », basée sur la génétique d'association « genome-wide » (GWAS) chez la vigne. Le potentiel théorique des deux méthodes a été évalué dans une étude de simulation, puis sur des données réelles.Nous montrons que la GS est plus pertinente que la SAM « classique » pour prédire les phénotypes et ce pour des caractères complexes et / ou structurés. Cependant la GS couplée aux résultats issus de la GWAS semble être une méthode intéressante lorsque le marquage moléculaire est non limitant. Finalement, nous discutons des conditions d'utilisation de la GS en termes économiques et d'efficacité au cours du temps. Nous proposons trois scénarios fonction de l'investissement de départ et des besoins en termes de création variétale. / The aim of this PhD project was to provide a new impulse for grapevine breeding, applying the latest knowledge and research tools on this species. Indeed, French viticulture, as well as various other agricultural sectors, faces today three major challenges: how to reduce phytosanitary inputs (Ecophyto 2018), impact of climatic changes and new competitors on the market, especially New World countries. Plant breeding in grapevine has not been much exploited until today, but could be a solution to these challenges.Several innovative tools and concepts have seen the light in animal breeding in the last decade. Using high density genome-wide marker information and advanced statistical models, phenotypes can be predicted for individuals that were merely genotyped. The method termed genomic selection (GS) is implementing this type of approach.To achieve our aim, we evaluated and compared the efficiency of GS and “classical” marker-assisted selection (MAS), based on genome-wide association study (GWAS) for grapevine. The theoretical potential of the two methods was evaluated in a simulation study but also on real data.We show that GS is more relevant than “classical” MAS to predict phenotypes of complex and / or structured traits. However, the combination of GS with results from GWAS seems to be of particular interest if the number of molecular markers available is adequate. Finally, we discuss GS implementation in terms of economic aspects and efficiency over time; we propose three scenarios differing by the initial investment required and the breeding objectives to be reached.

Des approches traditionnelles en combinaison avec des méthodes moléculaires et biochimiques ont été utilisées pour étudier les communautés zooplanctoniques de la saline de Sfax. Une dizaine d'espèces ont été identifiées dans 4 bassins de salinité croissante. Les copépodes étaient la composante la plus représentative du compartiment zooplanctonique dans les bassins A5, A16 et C41. Le bassin M2 est monozoïque avec une présence exclusive d'Artemia salina.Nous avons montré le rôle crucial de la salinité dans la distribution des espèces mais nous avons souligné également l’influence, quoique plus faible, d’autres facteurs comme le ratio N:P qui pourrait être liée au mode de vie des animaux et directement aux phytoplancton. La composition en acides gras des copépodes et des Artemia est liée aux facteurs physico-chimiques et biologiques. Grâce à leur teneur en acides gras hautement insaturés, les copépodes et les Artemia peuvent être utilisés comme source alimentaire pour les poissons d'élevage. La phylogénie des copépodes est controversée puisque la structuration génétique de ce groupe n’est pas nettement identifiable. L’existence d’espèces cryptiques au sein des Paracartia grani est supposée mais reste à confirmer. Les facteurs abiotiques ne sont pas impliqués dans ces processus de divergence génétique. Chez Artemia salina, la forte teneur en sel, est un facteur de ségrégation des populations, l’adaptation des artémies à cette condition aboutit à des populations génétiquement distinctes. Un clivage génétique est repéré, il met en évidence une séparation entre les populations vivant dans de fortes teneurs en sel et celles en pleine mer. / Zooplankton community of solar saltern of Sfax. A dozen of species were identified in four ponds of increasing salinity. Copepods were the most abundant group in A5, A16 and C41. M2 is monozoic with an exclusive presence of Artemia salina. Salinity have a crucial role in species distribution, whereas, other factors such as N:P ratio have smaller influence. Fatty acids composition of copepods and Artemia depends on physico-chemical and biological parameters. Owing to their Highly unsaturated fatty acids (HUFAs) composition, copepods and Artemia of the saltern of Sfax can be used as food source for cultured fishes. Copepods phylogeny is controversial because their genetic structure is not clearly identifiable. The existence of cryptic species within Paracartia grani is assumed but should be confirmed. Abiotic factors are not involved in processes of genetic divergence. For Artemia salina, the high salinity, is a factor of population segregation, the adaptation of Artemia in such condition leads to distinct, genetically, population. A genetic divide was identified, it highlights a separation between population living in high salinity and those in the sea.

La résistance aux agents de biocontrôle est un problème majeur dans les cultures du monde entier. Ainsi, le carpocapse du pommier, Cydia pomonella, a développé des résistances contre des traitements répétés au Cydia pomonella granulovirus (CpGV) dans plusieurs pays d’Europe. Ces résistances posent la question de la durabilité de ce type de lutte contre les ravageurs. Ce travail porte sur l’étude de plusieurs aspects des interactions granulovirus/hôtes : en premier lieu, sur l’étude des différences de sensibilité au CpGV entre des colonies d’insectes de laboratoire afin de mieux cerner les mécanismes d’apparition de résistances. Concernant le virus, le génome complet de cinq isolats viraux utilisés au cours de ces travaux a été séquencé et une analyse des gènes positivement sélectionnés a été conduite afin de découvrir de nouveaux gènes potentiellement importants pour la valeur sélective du virus. L’adaptabilité du CpGV à un hôte C. pomonella résistant ainsi qu’à un hôte d’une espèce proche, Cydia molesta a également été étudiée. Enfin, l’efficacité, sur différentes colonies d’insectes, de populations de génotypes viraux mélangées ainsi que de leurs générations successives ont été analysés. Ces études nous ont permis de mettre en évidence une diversité génétique très étendue chez le CpGV ainsi que des phénomènes de co-infections d’une même cellule et de recombinaison. Ainsi, s’il semble impossible de certifier une méthode de biocontrôle d’une efficacité constante, il apparait que les capacités évolutives des virus permettront de supporter des phénomènes de résistance des hôtes. Un suivi annuel afin de permettre une évolution dirigée du virus sera toutefois obligatoire. / Resistance to biocontrol agents is a critical issue worldwide in orchards. Thereby the codling moth Cydia pomonella developed resistances under repeated treatments with Cydia pomonella granulovirus (CpGV) in several European countries. These resistances raise the issue of the durability of such a pest control. This work aims to investigate various aspects of granulovirus/host interactions: first by studying the susceptibility variations to CpGV infection between different laboratory insect colonies in order to assess the mechanisms of resistances apparition; to investigate the virus diversity, complete genomes of five viral isolates used over this work have been sequenced and an analysis of the positively selected genes has been carried out as to come up with new genes potentially important for the fitness of the virus. The adaptability of CpGV to a resistant C. pomonella host as well as to a related specie, Cydia molesta has also been studied. Finally, the efficiency, on different insect colonies, of mixed populations of viral genotypes as well as their successive offspring have been analyzed. These studies allowed highlighting a wide genetic diversity among CpGVs, together with co-infection within cell and recombination phenomenon. Thus, if it seems impossible to certify a biocontrol method with constant efficacy, it appears that the evolutive capacities of viruses will allow overcoming host resistance phenomenon. However, one will need to keep one step ahead from the virus, which means an annual survey to permit a directed evolution of the virus.

Orientador: Vera Nisaka Solferini / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T01:41:48Z (GMT). No. of bitstreams: 1 Ramos_RafaelFlora_M.pdf: 2299855 bytes, checksum: 943dfb31cd7db5f4dcc0508ca7f17c91 (MD5) Previous issue date: 2013 / Resumo: Euterpe edulis é uma palmeira tropical ameaçada de extinção que no passado era abundante na Mata Atlântica, desde a planície costeira até 1.000 metros acima do nível do mar. O objetivo deste estudo foi avaliar a diversidade e a estrutura genética em populações naturais de E. edulis distribuídas em diferentes altitudes dentro de um contínuo florestal. O estudo foi conduzido em uma área de proteção ambiental da Serra do Mar, no litoral norte do estado de São Paulo, onde foram amostrados 300 adultos em seis localidades, denominadas subpopulações. Cada indivíduo foi genotipado com sete locos microssatélite. O número total de alelos foi alto (140) e o número médio de alelos não variou entre as subpopulações. A heterozigosidade total esperada foi de 0,867, variando entre 0,782 e 0,859 entre subpopulações. O índice de fixação foi baixo para todas as subpopulações, concordando com o sistema de reprodução cruzada da espécie. A estruturação espacial genética foi ausente ou muito baixa nas subpopulações analisadas separadamente ou agrupadas. A estrutura genética foi alta (?' = 0,26) considerando a distância máxima de 32 km entre as subpopulações amostradas. Foram definidos quatro grupos genéticos mais prováveis de acordo com o teste de atribuição dos indivíduos, e cinco grupos de acordo com a AMOVA (Análise de Variância Molecular). O teste de Mantel parcial correlacionou à estrutura genética entre pares de subpopulações com a distância geográfica (r = 0,8; p < 0,05) e ainda com a diferença altitudinal excluído o efeito da distância geográfica (r = 0,5; p < 0,05). Se estas diferenças são causadas pelo fluxo gênico reduzido ou por adaptações locais ainda precisa ser testado em estudos futuros. Este padrão de diferenciação genética em distâncias reduzidas é inesperado dentro de um contínuo florestal, destacando a importância de abordagens em pequena escala para a compreensão das dinâmicas complexas nos sistemas tropicais / Abstract: Euterpe edulis is an endangered tropical palm, once abundant throughout the Atlantic Forest from the coastal plain up to 1000 meters above sea level. The main purpose of this study was to evaluate the genetic diversity and structure in natural populations of E. edulis distributed in different altitudes within a continuous forest. The study was conducted in a protected area of Serra do Mar, at the north coast of São Paulo State, where we sampled 300 adults from six locations. Each individual was genotyped with seven microsatellite loci. The total allele number was high (140) and the mean allele number did not vary between samples. The total expected heterozygosity was 0.867, ranging from 0.782 to 0.859 among samples. The inbreeding coefficient was low in all samples, in accordance with the outcrossing breeding system. The spatial genetic structure was absent or weak at populations analyzed individually or grouped. The genetic structure was high (?' = 0.26) considering that the maximum distance of 32 km between samples. Four most likely genetic groups were defined according to the assignment test, and five groups according to AMOVA (Analysis of Molecular Variance). A partial Mantel test correlated the pairwise genetic structure with the geographical distance (r = 0.8; p < 0.05) and also with the pairwise altitudinal differences without the effect of the geographic distances (r = 0.5; p < 0.05). Whether those differences are mainly due to reduced gene flow or to local adaptation remains to be tested in future studies. This pattern of genetic differentiation at short distances is unexpected within a continuous rainforest, highlighting the importance of small scale approaches to understanding the complex dynamics of tropical systems / Mestrado / Ecologia / Mestre em Ecologia

The papillomatosis is an infectious disease caused by papillomaviruses which belongs to the Papillomaviridae family. In dogs, Canis familiaris papillomavirus (CPV) species is the causative agent of the disease and it has so far twenty identified types. These viruses can lead to benign neoplastic lesions of the skin and mucosal epithelium that are exophytic and endophytic papilloma and pigmented plaques which may occur progression to carcinoma squamous cell (SCCs) cancer. The pathogenicity of the virus related to the types, subtypes and variants can influence deafferents lesions on the animal. Thus, there is a need to identify and characterize the existing virus to a better understanding of the disease and adoptions of both preventive measures as treatment. In this study, the general objective is to analyze the genetic diversity of canine papillomavirus present in infected dogs in the state of Sergipe - Brazil. We used diagnostic strategies for the identification of canine papillomavirus; wherein the histopathology was used to the characterization of the lesion as papilloma and the PCR with electrophoresis for confirm the viral DNA, then sequencing performed for subsequent genotyping of samples and bioinformatics tools was used for analysis of the nucleotide and amino acid sequences of the L1 gene. As a result, eighteen samples of possible papillomatous lesions were collected and nine samples had the presence of CPV DNA with oral and cutaneous exophytic lesions confirmed by histopathology. It was possible observe in one sample the presence of oral SCCs. The Canine papillomavirus type 1 (CPV1) was identified in nine samples of this study. Eight samples were CPV1 variants with 100% identity with the already described variants and one sample was identified as a new CPV1 variant having a difference of 0.8% when compared with the reference sequence of the CPV1 L1 gene and a difference of 0.2% with the existing CPV1 variant. The mutations of the variants and the change in stability of the protein structure were analyzed and it was observed that the V204A mutation of the new variant of isolate eight is highly destabilizing with alteration of protein function. This study corroborates the characterization of CPV1 as the main cause of oral papillomatosis in dogs, observing the genetic variability of CPV1 with variants of different pathogenic potentials, with a putative new variant associated with cancer with a mutation that can destabilize the L1 protein structure of CPV1 altering its function. / A papilomatose é uma doença infecciosa causada pelos papilomavírus pertencentes a família Papillomaviridae. Em cães, a espécie Canis familiaris papilomavírus (CPV) é o agente etiológico da doença e possui até o momento vinte tipos identificados. Estes vírus podem levar a lesões neoplásicas benignas na pele e epitélio da mucosa, que são os papilomas exofíticos, endofíticos e as placas pigmentadas, podendo ocorrer a progressão para o câncer carcinoma de células escamosas (CCEs). A patogenicidade do vírus relacionada aos tipos, subtipos e variantes pode influenciar diferentes tipos de lesões nos animais. Com isso, percebe-se que há uma necessidade de identificar e caracterizar os vírus existentes para um melhor entendimento da doença e adoções de medidas tanto preventivas quanto de tratamento. Nesse estudo o objetivo geral é analisar a diversidade genética de papilomavírus canino presentes em cães infectados no estado de Sergipe - Brasil. Estratégias de diagnóstico foram utilizadas para a identificação de papilomavírus canino, em que o exame histopatológico foi utilizado para a caracterização da lesão e o PCR juntamente com a eletroforese para a confirmação da presença do DNA viral, depois foi realizado o sequenciamento para subsequente genotipagem das amostras e ferramentas de bioinformática foram utilizadas para análise das sequências de nucleotídeos e aminoácidos do gene L1. Como resultado, dezoito amostras de possíveis lesões papilomatosas foram coletadas, nove amostras tiveram a presença do DNA de CPV, com lesões exofíticas orais e uma cutânea, confirmadas pelo histopatológico. Foi possível observar na amostra oito a presença de CCEs oral. O CPV1 foi identificado em nove amostras deste estudo. Oito amostras eram variantes de CPV1 com 100% de identidade com uma variante já descrita e uma amostra foi identificada como uma nova variante de CPV1, possuindo uma diferença de 0,8% quando comparada com a sequência do gene L1 de referência de CPV1 e uma diferença de 0,2% com a variante já existente de CPV1. As mutações das variantes e a alteração na estabilidade da estrutura proteína foram analisadas e pôde-se observar que a mutação V204A da nova variante do isolado oito é altamente desestabilizadora com alteração de função da proteína. Esse estudo corrobora com a caracterização do CPV1 como o principal causador da papilomatose oral em cães, observando-se a variabilidade genética de CPV1 com variantes de diferentes potenciais patogênicos, com uma putativa nova variante associada ao câncer com uma mutação que pode desestabilizar a estrutura proteica de L1 de CPV1 alterando sua função. / São Cristóvão, SE

Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2016-07-11T23:39:34Z No. of bitstreams: 1 Tese-Ronaldo SOliveira_2015.pdf: 1819214 bytes, checksum: da69b4c584e3e9304788bb2b45091d51 (MD5) / Made available in DSpace on 2016-07-11T23:39:34Z (GMT). No. of bitstreams: 1 Tese-Ronaldo SOliveira_2015.pdf: 1819214 bytes, checksum: da69b4c584e3e9304788bb2b45091d51 (MD5) Previous issue date: 2015-01-31 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / The aim of this work was to organize a Forage Germplasm Bank in the State University of Feira de Santana-BA (BGF-UEFS), to carry out a survey of the occurrence of species of Stylosanthes and do pre-breeding studies in a sample of accessions collected in the Semiarid of Bahia from 2008 and 2014. Five collection expeditions in different Semiarid regions of the State was done as an attempt to rescue the maximum genetic variability available. For the pre-breeding work, 25 accessions of Stylosanthes plus a control were utilized. The methods of analysis of variance (ANOVA) and Restricted Maximum Likelihood/Best Linear Unbiased Prediction (REML/BLUP) were used. The genetic parameters were estimated in order to choose the most precise method to select the best individuals for a breeding program. Finally, it was studied the genetic diversity in order to choose the best combinations to develop segregating populations in a breeding program of Stylosanthes. In total, 225 accessions of Stylosanthes spp. were rescued in the state of Bahia, being 61 from de Northeast of the state, 58 from the Mid North, 59 from S?o Francisco Valley, 24 from the Mid South and 23 from the Far West. The estimates of the genetic parameters showed that the methods (ANOVA and REML/BLUP) presented divergent values. The REML/BLUP estimated the genetic values with better accuracy, increased the efficiency of selection and therefore decreased the cost of a given breeding program that has the objective to increase the mass production in Stylosanthes. In a sample of the analyzed accessions, four species were found (S. scabra, S. humilis, S. viscosa and S. capitata). Genetic variability among the accessions and the clusters of Tocher and UPGMA were basically defined by the botanical species and some of them were superior for mass production (BGF08-16 and BGF06-15) and for forage quality (BGF08- 006 and BGF08-007). / O objetivo deste trabalho foi organizar um Banco de Germoplasma de Forrageiras da Universidade Estadual de Feira de Santana, BA (BGF-UEFS), realizar o levantamento da ocorr?ncia de esp?cies do g?nero Stylosanthes e conduzir um estudo de Pr?-melhoramento em uma amostra de acessos coletados no Semi?rido baiano entre os anos de 2008 a 2014. Foram realizadas cinco expedi??es de coleta em diferentes regi?es do Estado procurando resgatar o m?ximo da variabilidade gen?tica dispon?vel. Para os estudos de pr?-melhoramento foram utilizados 25 acessos de Stylosanthes mais uma testemunha. Por meio dos m?todos de an?lise de vari?ncia (ANOVA) e M?xima Verossimilhan?a Restrita/Melhor Predi??o Linear n?o Viesada (REML/BLUP) foram estimados os par?metros gen?ticos, procurando indicar qual o m?todo mais preciso na sele??o dos melhores indiv?duos para um programa de melhoramento. Por fim, realizou-se o estudo da diversidade gen?tica no intuito de indicar as melhores combina??es para formar as popula??es segregantes do programa de melhoramento gen?tico dessa forrageira. Foram resgatados 225 acessos de Stylosanthes spp. de cinco mesorregi?es da Bahia, dos quais 61 foram do Nordeste baiano, 58 do Centro Norte baiano, 59 oriundos do Vale S?o Franciscano da Bahia, 24 resgatados no Centro Sul Baiano e 23 acessos no extremo Oeste Baiano. A estimativa dos par?metros gen?ticos mostrou que os m?todos (ANOVA e REML/BLUP) apresentaram valores divergentes sendo que o REML/BLUP estima os valores gen?ticos com maior acur?cia, aumenta a efici?ncia da sele??o e consequentemente diminui os custos dos programas de melhoramento gen?tico que objetivam aumentar a produ??o de massa em Stylosanthes. Em uma amostra de acessos analisada foram identificadas quatro esp?cies (S. scabra, S. humilis, S. viscosa e S. capitata). Foi observada variabilidade gen?tica entre os acessos avaliados e os agrupamentos de Tocher e UPGMA foram definidos quase que pela identifica??o bot?nica das esp?cies, sendo que os acessos BGF08-16 e BGF06-15 se mostraram superiores para produ??o de massa e os acessos BGF08- 006 e BGF08-007 para a qualidade de forragem.

Le VIH-1 groupe O (VIH-1/O) est un groupe divergent de VIH-1, endémique au Cameroun, 140 cas ont été identifiés en France depuis 1990. L’objectif de ce travail était d’évaluer l’impact de la diversité du VIH-1/O sur les caractéristiques épidémiologiques, l’évolution naturelle de l’infection et sur la réponse immuno-virologique aux traitements.En France, le recueil de données de suivi uniques portant sur 101 patients ont permis de mettre en évidence que l’évolution naturelle des VIH-1/O était intermédiaire entre celle des VIH-1/M et celle des VIH-2. La résistance aux INNTI des patients VIH-1/O a été confirmée in vivo. La réponse immuno-virologique aux traitements a été comparée entre les VIH-1/O et les VIH-1/M suivis dans des cohortes en France et dans le cadre d’un essai clinique au Cameroun.Une des caractéristiques des VIH-1/O est une CVp significativement plus faible que celle des VIH-1/M avant l’initiation du traitement. Cela n’a pas d’impact sur la survenue de l’indétectabilité, qui est similaire dans les deux groupes après un an de traitement. La réponse immunologique des patients VIH-1/O est globalement proche de celle des patients VIH-1/M en France. Cependant, la comparaison entre deux populations appariés suivis au Cameroun a montré une réponse immuno-virologique plus faible des patients VIH-1/O, sans que cela ait d’impact clinique.La prise en charge des patients VIH-1/O suivant les recommandations mises en place pour les VIH-1/M est donc efficace si elle ne comporte pas d’INNTI. / HIV-1 group O (HIV-1/O) is genetically distinct from HIV-1/M and is endemic in Cameroon while in France 140 HIV-1/O were diagnoses since 1990. The aim of this work was to characterize HIV-1/O epidemiological characteristics, infection natural evolution and immuno-virological response to treatment.In France, based on a large series of 101 HIV-1/O patients, we demonstrated that the natural evolution of HIV-1/O was in between the evolution of HIV-2 and HIV-1/M, but closer to HIV-1/M. We also confirmed in vivo HIV-1/O natural resistance to INNTI treatment. Then, we compared HIV-1/O and HIV-1/M immune-virological response to ARV treatment. In France, we compared data from two cohorts and a clinical trial was performed in Cameroun. One of the HIV-1/O characteristic is the lower CVp before treatment compared to HIV-1/M in naïve patient. This difference had no impact on the virological responses to cART. The proportion of patients with an undetectable pVL was similar between the two groups one year after the beginning of the treatment. Immunological response was close between HIV-1/O and HIV-1/M in France. But when the two populations were compared in Cameroon, the immunological response to cART was lower for HIV-1/O patients than for HIV-1/M patients, although this diffence didn’t had clinical consequences.HIV-1/O medical care based on HIV-1/M guidelines is highly efficient if the treatment doesn’t include NNRTI treatment.

Background: Due to its continuous exposure to food antigens and microbes, the gastrointestinal tract (GIT) is in a constant state of low level immune activation and contains an abundance of activated CCR5+CD4+ T lymphocytes, the primary target HIV-1. As a result, the GIT is a site of intense viral replication and severe CD4+ T cell depletion, a process that begins during primary HIV-1 infection and continues at a reduced rate during chronic infection in association with increased production of pro-inflammatory cytokines, a breakdown in the epithelial barrier, microbial translocation, systemic immune activation and the continued recruitment and infection of new target cells. AntiRetroviral Therapy (ART) is only partially effective in reversing these pathogenic changes. Despite the importance of the GIT in HIV-1 pathogenesis, and as a reservoir of persistent virus during ART, little is known about the diversity of HIV-1 in the GIT, or how different tissues in the GIT respond to ART. Objectives: Primary objectives of this thesis were to: 1) characterize the diversity of HIV-1 RNA variants in different parts of the GIT; 2) determine whether there is compartmentalized evolution of HIV-1 RNA variants in the GIT and whether these variants are likely to have different biological properties; 3) investigate the impact of ART on immune restoration in the GIT. Methods: A prospective study of the duodenum, jejunum, ileum and colon of African AIDS patients with chronic diarrhea and/or weight loss, sampled before and during 6 months of ART. RNA extracted from gut biopsies was reverse transcribed and PCR amplified. Env and gag PCR fragments were cloned, sequenced and subjected to extensive phylogenetic analysis; pol PCR fragments were analyzed for drug resistance. CD4+, CD8+ and CD38+CD8+ T cells levels in biopsies collected at baseline (duodenum, jejunum, ileum and colon) and after 3 (duodenum) and 6 (duodenum and colon) months of ART were quantified by flow cytometry and immunohistochemistry, plasma and tissue VL by the Nuclisens assay. Results: Viral diversity varied in different regions of the GIT with env HIV-1 RNA variants being significantly more diverse than gag variants. Gag HIV-1 RNA variants were widely dispersed among all tissue compartments. Some env variants formed tight monophyletic clusters of closely related viral quasispecies, especially in the colon, a finding that is suggestive of compartmentalized viral replication and adaptive evolution. CD4+ T cell and VL levels were significantly lower, while CD8+ including activated CD38+CD8+ T cell levels were higher in the duodenum and jejunum versus the colon. After 6 months of ART, a significant but incomplete recovery of CD4+ T cells was observed in the colon but not in the duodenum. Failed restoration of CD4+ T cells in the duodenum was associated with non-specific enteritis and CD8+ T cell activation. Conclusions: These results advance our understanding of the GIT as a host-pathogen interface by providing new insights into the diversity, evolution and dissemination of HIV-1 variants in the GIT. Strategies aimed at decreasing immune activation, especially in the small intestine, may be highly beneficial in enhancing the therapeutic efficacy of ART. / Thesis (PhD)--University of Pretoria, 2014. / lk2014 / Immunology / PhD / Unrestricted

The Dinaric karst region in the Balkans is one of the hot spots of biodiversity with a high number of endemic freshwater fish. The major cause of the high degree of endemism are numerous paleoclimatic and geological events that have affected the formation of the entire area. Flows of karst poljes represent a specific ecosystem to which some fishes have adapted. The poljes have been periodically flooded and these floods may activate different underground channels, which lead to interconnection of poljes. These fish species spend a part of the year in surface water and a part in groundwater and they may use the underground flows between poljes for migration. The aim of this thesis is to evaluate the genetic variability of two endemic fish species of the genus Telestes living in karst poljes in the region of eastern Herzegovina, and to detect a possible current gene flow between populations of these species due to the connection of underground flows. For this purpose, the DNA from 102 individuals from five different localities was isolated. The mitochondrial marker cytochrom b and 16 microsatellite loci were used for the analyses. The results point to very low variability between species and populations. Based on mitochondrial marker analysis, no link between populations of the species was detected,...

Habitat fragmentation can adversely affect species populations due to reduced genetic diversity and increased population differentiation due to habitat isolation, reduced population size, and disruption of gene flow. Many species suffer from habitat fragmentation and isolation, and Campanula glomerata is a good example of a species that is noticeably declining in many places due to changes in landscape management. The question is how the model species responds to these changes and whether is the change are reflected in genetic diversity and population structure. The aim of this work is to determine the degree of genetic diversity and to reveal the genetic structure of populations of the model species C. glomerata on a small regional scale in the White Carpathians. This system will allow us to compare populations from two different regions that have been affected to varying degrees by agricultural intensification and fragmentation in the last century. It is a southwestern and northeastern part of the region, which differs from each other in the history of management in the landscape, but also in the continuity of meadows, species composition and environmental conditions. For this purpose, I developed and optimized a total of 16 usable microsatellite markers, 4 of which come from related species of...