Quite a number of important crops have been genetically modified with genes for agronomically important traits, such as insect and viral resistance. As the numbers of genetically modified foods continue to increase on the market, the need for rapid development of GMO detection methods is indispensable. This study was carried out to detect if genetically modified potatoes exist on food market in Turkey. Thirty samples from different places were collected. Using a DNA based PCR method, potato samples were examined for the presence of 35S promoter, Nos terminator, neomycin phosphotransferase (nptII) genes, and synthetic cry3A gene which is the general transgene in all approved Newleaf transgenic potato lines. The experimental design of this study was to detect Newleaf insect resistant lines. In 11 samples at least one genetic element was detected. Sample R from Ankara has shown to be belonging to Newleaf insect resistant lines. Since 35S promoter was not detected in samples M3, 14 and F1, it is proposed that they are belonging to Newleaf virus and insect resistant lines (Newleaf plus or Newleaf Y). Although Nos terminator was not detected in samples H2, Z2 and D, cry3A fragments amplified in those samples have been verified that they are from the synthetic cry3A regions of Newleaf lines. The detected synthetic cry3A gene in GM potatoes was amplified by specific primers, which cannot amplify Bacillus thuringiensis tenebrionis natural cry3A gene. In addition, the authenticity of the synthetic cry3A PCR products were confirmed by both sequencing and restriction digestions. Our results showed that genetically modified Newleaf potatoes exist in food market in Turkey. Further studies by accredited laboratories are strongly recommended.

Background: Malaria is a major public health issue. Artemisinin-based combination therapies are the WHO recommended treatment for uncomplicated malaria. Plasmodium malariae and Plasmodium ovale infections are considered underestimated and the effectiveness of artemisinin-based combination treatments against them is poorly documented. The aim of this study was to evaluate the efficacy of dihydroartemisinin-piperaquine against low parasite density Plasmodium malariae and ovale infections.  Methods: DNA was extracted from dried blood spots on filter papers with Chelex®-100 or a column-based extraction method. Species detection and determination was conducted by SYBR Green quantitative PCR targeting the cytochrome b gene (cytb-qPCR) followed by restriction fragment length polymorphism analyses. In total, 241 samples from 53 patients enrolled in a clinical trial were analysed. The obtained molecular data were compared with the microscopy data of the study. Results: Only 69 out of 143 microscopy-positive samples were confirmed as positive by cytb-qPCR. Ninety-three samples were identified as parasite negative by both microscopy and PCR. None of the 36 microscopy-defined coinfections were detected in the molecular analysis. The cytb-qPCR success rate was 72.9% (CI95% 61.4-82.6), 75.0% (CI95% 34.9-96.8) and 14.8% (CI95% 6.9-26.2) for parasite densities above 1000 parasites/ μL, between 600-1000 parasites/ μL and below 600 parasites/ μL, respectively. The observed poor qPCR success rate is most likely due to sample degradation under poor storage conditions. Conclusions: This study highlights the impact on the preservation and quality of Plasmodium genomic DNA on dried blood spots, when filter papers are stored for more than 3 years in tropical conditions.

The increased honey bee colony losses in the last decade gain a considerable attention of scientists and public. The causes of these losses include a wide range of biotic and abiotic factors, but pathogens and parasites are probably the main ones. Monoxenous trypanosomatids in honey bee gut Lotmaria passim and Crithidia mellificae were neglected for a long time but according to recent studies they seem to participate in those colony declines. Trypanosomatids are widespread parasites, including also the causes of some human illnesses, such as sleeping sickness, Chagas disease and leishmaniasis. The mechanism of the effect on honey bee health is not well understood so far. The aim of this thesis was to verify the occurrence of the trypanosomatids in honey bee samples from two regions in Czech Republic. The methods, based on detection of specific DNA loci, confirm the high prevalence of L. passim, which was founded in majority (71 %) of the samples. On the contrary, no samples were positive to C. mellificae.

Agrobacterium are Alphaproteobacteria common in most soils that closely interact with plants in two respects. Firstly, they are rhizospheric bacteria saprophytically living in the rhizosphere of numerous plants and they are likely beneficial to plants. Secondly, when they harbor a dispensable Ti plasmid (i.e. tumor inducing plasmid), agrobacteria are plant pathogens able to cause the crown gall disease to most dicots and gymnosperms and some monocots. An epidemiological survey of crown gall thus also requires expert determination of the Agrobacterium taxonomy. In this thesis we evaluated the usefulness of MALDI-TOF MS technique as a high throughput tool to determine and classify agrobacteria. Then we set up a recA-based PCR method to accurately and exhaustively assess agrobacterial diversity either of isolated agrobacteria or directly in various biotopes. We applied standard biochemical, recA-based and Ti plasmid-based identification methods to study the prevalence of pathogenic and non-pathogenic agrobacteria at the country and local scales. Finally, we tested whether analyzing the internal composition of recA amplicons could be a way to directly assess the micro-diversity of agrobacterial populations using cloning sequencing or pyrosequencing approaches. The later methodology was applied to establish the actual field diversity of Agrobacterium and to evaluate whether plant genotypes differentially select agrobacteria in their root systems, providing first data upon biotic factors shaping the population structure of agrobacteria

Les bactéries du genre Agrobacterium forment un ensemble taxonomiquement diversifié composé de nombreuses espèces, présent dans la plupart des sols et des rhizosphère. Les agrobactéries sont le plus souvent anodines voire stimulatrices de la croissance des plantes. Par contre, celles qui hébergent un plasmide Ti induisent la maladie de la galle du collet à de nombreuses plantes d'intérêt agronomique. Dans ce contexte, nous avons d'une part donné l'état actuel des connaissances sur la taxonomie du genre Agrobacterium, et nous avons fait une revue des méthodes d'isolement et de typage de ces bactéries. D'autre part, nous avons cherché à mettre au point des méthodes d'identification rapides et fiables des différentes espèces d'agrobactérie. La méthode de MALDI-TOF MS a permis d'identifier les espèces mais elle n'était pas assez résolutive pour typer des souches et encore moins la présence de plasmides Ti dans les isolats. Nous avons alors développé des amorces de PCR spécifiques de 17 espèces, du genre Agrobacterium et de la famille Rhizobiaceae. Ces amorces se sont révélées efficaces pour identifier les bactéries cultivées et aussi pour détecter leur présence dans des communautés microbiennes. Nous avons utilisé ces outils pour étudier la répartition des agrobactéries à l'échelle d'un pays, d'une station et entre sols nus et sols rhizosphériques en utilisant soit des isolats soit des ADN extraits des différents environnements. Enfin, nous avons montré que le clonage-séquençage ou le séquençage à haut débit d'amplicons obtenus à partir d’ADN de communautés microbiennes nous permettaient de connaître la diversité des populations d'agrobactéries / Agrobacterium are Alphaproteobacteria common in most soils that closely interact with plants in two respects. Firstly, they are rhizospheric bacteria saprophytically living in the rhizosphere of numerous plants and they are likely beneficial to plants. Secondly, when they harbor a dispensable Ti plasmid (i.e. tumor inducing plasmid), agrobacteria are plant pathogens able to cause the crown gall disease to most dicots and gymnosperms and some monocots. An epidemiological survey of crown gall thus also requires expert determination of the Agrobacterium taxonomy. In this thesis we evaluated the usefulness of MALDI-TOF MS technique as a high throughput tool to determine and classify agrobacteria. Then we set up a recA-based PCR method to accurately and exhaustively assess agrobacterial diversity either of isolated agrobacteria or directly in various biotopes. We applied standard biochemical, recA-based and Ti plasmid-based identification methods to study the prevalence of pathogenic and non-pathogenic agrobacteria at the country and local scales. Finally, we tested whether analyzing the internal composition of recA amplicons could be a way to directly assess the micro-diversity of agrobacterial populations using cloning sequencing or pyrosequencing approaches. The later methodology was applied to establish the actual field diversity of Agrobacterium and to evaluate whether plant genotypes differentially select agrobacteria in their root systems, providing first data upon biotic factors shaping the population structure of agrobacteria