Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association

The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

Functional and morphometric differences between the early and delayed use of phototherapy in crushed median nerves of rats

This study evaluated the functional and quantitative differences between the early and delayed use of phototherapy in crushed median nerves. After a crush injury, low-level laser therapy (GaAs) was applied transcutaneously at the injury site, 3 min daily, with a frequency of five treatments per week for 2 weeks. In the early group, the first laser treatment started immediately after surgery, and in the delayed group, after 7 days. The grasping test was used for functional evaluation of the median nerve, before, 10, and 21 days after surgery, when the rats were killed. Three segments of the median nerve were analyzed histomorphometrically by light microscopy and computer analysis. The following features were observed: myelinated fiber and axon diameters, myelin sheath area, g-ratio, density and number of myelinated fibers, and area and number of capillaries. In the proximal segment (site of crush), the nerves of animals submitted to early and delayed treatment showed myelinated fiber diameter and myelin sheath area significantly larger compared to the untreated group. In the distal segment, the myelin sheath area was significantly smaller in the untreated animals compared to the delayed group. The untreated, early, and delayed groups presented a 50, 57, and 81% degree of functional recovery, respectively, at 21 days after injury, with a significant difference between the untreated and delayed groups. The results suggest that the nerves irradiated with low-power laser exhibit myelinated fibers of greater diameter and a better recovery of function.

Relationship between Vitamin D Receptor gene polymorphisms and the components of metabolic syndrome

Abstract Background The Vitamin D Receptor gene (VDR) is expressed in many tissues and modulates the expression of several other genes. The purpose of this study was to investigate the association between metabolic syndrome (MetSyn) with the presence of VDR 2228570 C > T and VDR 1544410 A > G polymorphisms in Brazilian adults. Methods Two hundred forty three (243) individuals were included in a cross-sectional study. MetSyn was classified using the criteria proposed by National Cholesterol Educational Program - Adult Treatment Panel III. Insulin resistance and β cell secretion were estimated by the mathematical models of HOMA IR and β, respectively. The VDR 2228570 C > T and VDR 1544410 A > G polymorphisms were detected by enzymatic digestion and confirmed by allele specific PCR or amplification of refractory mutation. Results Individuals with MetSyn and heterozygosis for VDR 2228570 C > T have higher concentrations of iPTH and HOMA β than those without this polymorphism, and subjects with recessive homozygosis for the same polymorphisms presented higher insulin resistance than those with the heterozygous genotype. There is no association among VDR 1544410 A > G and components of MetSyn, HOMA IR and β, serum vitamin D (25(OH)D3) and intact parathormone (iPTH) levels in patients with MetSyn. A significant lower concentration of 25(OH)D3 was observed only in individuals without MetSyn in the VDR 1544410 A > G genotype. Additionally, individuals without MetSyn and heterozygosis for VDR 2228570 C > T presented higher concentration of triglycerides and lower HDL than those without this polymorphism. Conclusions Using two common VDR polymorphism data suggests they may influence insulin secretion, insulin resistance an serum HDL-cholesterol in our highly heterogeneous population. Whether VDR polymorphism may influence the severity of MetSyn component disorder, warrants examination in larger cohorts used for genome-wide association studies.

Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes

Craniofrontonasal syndrome (CFNS), an X-linked disorder caused by loss-of-function mutations of EFNB1, exhibits a paradoxical sex reversal in phenotypic severity: females characteristically have frontonasal dysplasia, craniosynostosis and additional minor malformations, but males are usually more mildly affected with hypertelorism as the only feature. X-inactivation is proposed to explain the more severe outcome in heterozygous females, as this leads to functional mosaicism for cells with differing expression of EPHRIN-B1, generating abnormal tissue boundaries-a process that cannot occur in hemizygous males. Apparently challenging this model, males occasionally present with a more severe female-like CFNS phenotype. We hypothesized that such individuals might be mosaic for EFNB1 mutations and investigated this possibility in multiple tissue samples from six sporadically presenting males. Using denaturing high performance liquid chromatography, massively parallel sequencing and multiplex-ligation-dependent probe amplification (MLPA) to increase sensitivity above standard dideoxy sequencing, we identified mosaic mutations of EFNB1 in all cases, comprising three missense changes, two gene deletions and a novel point mutation within the 5' untranslated region (UTR). Quantification by Pyrosequencing and MLPA demonstrated levels of mutant cells between 15 and 69%. The 5' UTR variant mutates the stop codon of a small upstream open reading frame that, using a dual-luciferase reporter construct, was demonstrated to exacerbate interference with translation of the wild-type protein. These results demonstrate a more severe outcome in mosaic than in constitutionally deficient males in an X-linked dominant disorder and provide further support for the cellular interference mechanism, normally related to X-inactivation in females.

Analysis of 16S rRNA and mxaF genes reveling insights into Methylobacterium niche-specific plant association

The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.

Oral leucine supplementation is sensed by the brain but neither reduces food intake nor induces an anorectic pattern of gene expression in the hypothalamus

Leucine activates the intracellular mammalian target of the rapamycin (mTOR) pathway, and hypothalamic mTOR signaling regulates food intake. Although central infusion of leucine reduces food intake, it is still uncertain whether oral leucine supplementation is able to affect the hypothalamic circuits that control energy balance. We observed increased phosphorylation of p70s6k in the mouse hypothalamus after an acute oral gavage of leucine. We then assessed whether acute oral gavage of leucine induces the activation of neurons in several hypothalamic nuclei and in the brainstem. Leucine did not induce the expression of Fos in hypothalamic nuclei, but it increased the number of Fos-immunoreactive neurons in the area postrema. In addition, oral gavage of leucine acutely increased the 24 h food intake of mice. Nonetheless, chronic leucine supplementation in the drinking water did not change the food intake and the weight gain of ob/ob mice and of wild-type mice consuming a low- or a high-fat diet. We assessed the hypothalamic gene expression and observed that leucine supplementation increased the expression of enzymes (BCAT1, BCAT2 and BCKDK) that metabolize branched-chain amino acids. Despite these effects, leucine supplementation did not induce an anorectic pattern of gene expression in the hypothalamus. In conclusion, our data show that the brain is able to sense oral leucine intake. However, the food intake is not modified by chronic oral leucine supplementation. These results question the possible efficacy of leucine supplementation as an appetite suppressant to treat obesity

A Galactic ring of minimum stellar density near the solar orbit radius

We analyse the secular effects of a long-lived Galactic spiral structure on the stellar orbits with mean radii close to the corotation resonance. By test-particle simulations and different spiral potential models with parameters constrained on observations, we verified the formation of a minimum with amplitude ∼30–40 per cent of the background disc stellar density at corotation. Such a minimum is formed by the secular angular momentum transfer between stars and the spiral density wave on both sides of corotation. We demonstrate that the secular loss (gain) of angular momentum and decrease (increase) of mean orbital radius of stars just inside (outside) corotation can counterbalance the opposite trend of exchange of angular momentum shown by stars orbiting the librational points L4/5 at the corotation circle. Such secular processes actually allow steady spiral waves to promote radial migration across corotation. We propose some pieces of observational evidence for the minimum stellar density in the Galactic disc, such as its direct relation to the minimum in the observed rotation curve of the Galaxy at the radius r ∼ 9 kpc (for R0 = 7.5 kpc), as well as its association with a minimum in the distribution of Galactic radii of a sample of open clusters older than 1Gyr. The closeness of the solar orbit adius to the corotation resonance implies that the solar orbit lies inside a ring of minimum surface density (stellar + gas). This also implies a correction to larger values for the estimated total mass of the Galactic disc, and consequently, a greater contribution of the disc componente to the inner rotation curve of the Galaxy.

Chromatin Remodeling by BRG1 and SNF2H : Biochemistry and Function

Chromatin is a highly dynamic, regulatory component in the process of transcription, repair, recombination and replication. The BRG1 and SNF2H proteins are ATP-dependent chromatin remodeling proteins that modulate chromatin structure to regulate DNA accessibility for DNA-binding proteins involved in these processes. The BRG1 protein is a central ATPase of the SWI/SNF complexes involved in chromatin remodeling associated with regulation of transcription. SWI/SNF complexes are biochemically hetero-geneous but little is known about the unique functional characteristics of the various forms. We have shown that SWI/SNF activity in SW13 cells affects actin filament organization dependent on the RhoA signaling pathway. We have further shown that the biochemical composition of SWI/SNF complexes qualitatively affects the remodeling activity and that the composition of biochemically purified SWI/SNF complexes does not reflect the patterns of chromatin binding of individual subunits. Chromatin binding assays (ChIP) reveal variations among subunits believed to be constitutive, suggesting that the plasticity in SWI/SNF complex composition is greater than suspected. We have also discovered an interaction between BRG1 and the splicing factor Prp8, linking SWI/SNF activity to mRNA processing. We propose a model whereby parts of the biochemical heterogeneity is a result of function and that the local chromatin environment to which the complex is recruited affect SWI/SNF composition. We have also isolated the novel B-WICH complex that contains WSTF, SNF2H, the splicing factor SAP155, the RNA helicase II/Guα, the transcription factor Myb-binding protein 1a, the transcription factor/DNA repair protein CSB and the RNA processing factor DEK. The formation of this complex is dependent on active transcription and links chromatin remodeling by SNF2H to RNA processing. By linking chromatin remodeling complexes with RNA processing proteins our work has begun to build a bridge between chromatin and RNA, suggesting that factors in chromatin associated assemblies translocate onto the growing nascent RNA.

Clinicopathological and molecular characterization of gastroesophageal junction (GEJ) adenocarcinoma before age of 40 years

Gastroesophageal junction (GEJ) adenocarcinoma are uncommon before age of 40 years. While certain clinical, pathological and molecular features of GEJ adenocarcinoma in older patients have been extensively studied, these characteristics in the younger population remain to be determined. In the recent literature, a high sensitivity and specificity for the detection of dysplasia and esophageal adenocarcinoma was demonstrated by using multicolor fluorescence in situ hybridization (FISH) DNA probe set specific for the locus specific regions 9p21 (p16), 20q13.2 and Y chromosome. We evaluated 663 patients with GEJ adenocarcinoma and further divided them into 2 age-groups of or= 50 years, rispectively. FISH with selected DNA probe for Y chromosome, locus 9p21 (p16), and locus 20q13.2 was investigated with formalin fixed and parassin embedded tissue from surgical resections of 17 younger and 11 older patients. Signals were counted in > 100 cells with each given histopathological category. The chromosomal aberrations were then compared in the 2 age-groups with the focus on uninvolved squamous and columnar epithelium, intestinal metaplasia (Barrett's mucosa), glandular dysplasia, and adenocarcinoma. Comparisons were performed by the X2 test, Fisher's exact test, Student's t-test and Mann-Whitney U-test as appropriate. Survival was estimated by the Kaplan-Meier method with univariate analysis by the log-rank. Significance was taken at the 5% level. There was no difference in the surgical technique applied in both age groups and most patients underwent Ivor Lewis esophagectomy. Among clinical variables there was a higher incidence of smocking history in older patient group. We identified a progressive loss of Y chromosome from benign squamos epithelium to Barrett's mucosa and glandular dysplasia, and, ultimately, to a near complete loss in adenocarcinoma in both age groups. The young group revealed significantly more losses of 9p21 in both benign and neoplastic cells when compared to the older patients group. In addition, we demonstrated an increase in the percentage of cells showing gain of locus 20q13.2 with progression from benign epithelium through dysplasia to adenocarcinoma with almost the same trend in both the young and the older patients. When compared with the older age-group, younger patients with GEJ adenocarcinoma possess similar known demographics, environmental factors, clinical, and pathologic characteristics. The most commonly detected genetic aberrations of progressive Y chromosomal loss, 9p21 locus loss, and 20q13 gains were similar in the younger and older patients. However the rate of loss of 9p21 is significantly higher in young patients, in both the benign and the neoplastic cells. The loss of 9p21, and possibly, the subsequent inactivation of p16 gene may be one of the molecular mechanisms responsible for the accelerated neoplastic process in young patients.

Investigating the role of single point mutations in the human proteome: a computational study

In the post genomic era with the massive production of biological data the understanding of factors affecting protein stability is one of the most important and challenging tasks for highlighting the role of mutations in relation to human maladies. The problem is at the basis of what is referred to as molecular medicine with the underlying idea that pathologies can be detailed at a molecular level. To this purpose scientific efforts focus on characterising mutations that hamper protein functions and by these affect biological processes at the basis of cell physiology. New techniques have been developed with the aim of detailing single nucleotide polymorphisms (SNPs) at large in all the human chromosomes and by this information in specific databases are exponentially increasing. Eventually mutations that can be found at the DNA level, when occurring in transcribed regions may then lead to mutated proteins and this can be a serious medical problem, largely affecting the phenotype. Bioinformatics tools are urgently needed to cope with the flood of genomic data stored in database and in order to analyse the role of SNPs at the protein level. In principle several experimental and theoretical observations are suggesting that protein stability in the solvent-protein space is responsible of the correct protein functioning. Then mutations that are found disease related during DNA analysis are often assumed to perturb protein stability as well. However so far no extensive analysis at the proteome level has investigated whether this is the case. Also computationally methods have been developed to infer whether a mutation is disease related and independently whether it affects protein stability. Therefore whether the perturbation of protein stability is related to what it is routinely referred to as a disease is still a big question mark. In this work we have tried for the first time to explore the relation among mutations at the protein level and their relevance to diseases with a large-scale computational study of the data from different databases. To this aim in the first part of the thesis for each mutation type we have derived two probabilistic indices (for 141 out of 150 possible SNPs): the perturbing index (Pp), which indicates the probability that a given mutation effects protein stability considering all the “in vitro” thermodynamic data available and the disease index (Pd), which indicates the probability of a mutation to be disease related, given all the mutations that have been clinically associated so far. We find with a robust statistics that the two indexes correlate with the exception of all the mutations that are somatic cancer related. By this each mutation of the 150 can be coded by two values that allow a direct comparison with data base information. Furthermore we also implement computational methods that starting from the protein structure is suited to predict the effect of a mutation on protein stability and find that overpasses a set of other predictors performing the same task. The predictor is based on support vector machines and takes as input protein tertiary structures. We show that the predicted data well correlate with the data from the databases. All our efforts therefore add to the SNP annotation process and more importantly found the relationship among protein stability perturbation and the human variome leading to the diseasome.

Generierung und Charakterisierung von rekombinanten Cytomegaloviren mit Punktmutationen in antigenen Peptiden

Die Kontrolle der produktiven Cytomegalovirus- (CMV) Infektion ist von der effizienten Rekonstitution antiviraler CD8 T-Zellen abhängig. Dies führt jedoch nicht zur vollständigen Eliminierung des viralen Genoms aus den Zielorganen, sondern das Virus verbleibt in einem nicht-replikativen Zustand: der Latenz. Es ist bekannt, dass während der Latenz nur ein geringer Anteil latenter mCMV-Genome in der Lunge die Major Immediate Early (MIE) Gene ie1 und ie2 exprimiert, die Latenz aber dennoch bestehen bleibt, weil das differentielle Splicing des primären IE1/3-Transkripts zum Transaktivator-Transkript IE3 nicht erfolgt. Damit war neben der Initiation der IE-Genexpression am MIE-Promotor-Enhancer das IE1/3-Splicing als zweiter molekularer Latenz-Kontrollpunkt identifiziert. Parallel zur Latenz-assoziierten IE1-Genexpression sind in der Lunge aktivierte CD62L-low CD8 T-Zellen mit Spezifität für das immundominante IE1-Peptid 168-YPHFMPTNL-176 angereichert. Dies legte die Hypothese nahe, dass neben der molekularen Kontrolle der Latenz auch eine immunologische Kontrolle, beispielsweise durch IE1-Epitop-spezifische CD8 T-Zellen besteht. Zur Evaluierung dieser Hypothese wurde in der vorliegenden Arbeit mittels BAC-Mutagenese erstmals ein rekombinantes mCMV generiert, in dem das IE1-Peptid durch Punktmutation der C-terminalen MHC-Ankeraminosäure L176A zerstört ist. Dazu musste zunächst die Technik der BAC-Mutagenese herpesviraler Genome (in Anlehnung an die publizierten Arbeiten von Messerle et al., 1997; Borst et al., 1999, 2004; Wagner et al., 1999) in der Arbeitsgruppe etabliert werden. Neben der Funktionsverlust-Mutante (mCMV-IE1-L176A) wurden zur Kontrolle zwei Revertanten (mCMV-IE1-A176L und mCMV-IE1-A176L*) generiert. In letzterer, als Wobble-Revertante bezeichnet, wird wieder die authentische MHC-Ankeraminosäure L eingesetzt, es verbleibt aber ein singulärer Nukleotidaustausch A->T in der Wobble-Position des Codons als Marker zur Unterscheidung zum WT-mCMV zurück. Der immunologische Phänotyp der Funktionsverlust-Mutante, also die funktionelle Auslöschung des antigenen IE1-Peptids im Priming einer CD8 T-Zell-Antwort, entsprach der Erwartung. Entsprechend konnte nach Infektion mit der Funktionsverlust-Mutante keine Reaktivität gegen das IE1-Peptid nachgewiesen werden. In den Revertanten hingegen war die Erkennung des IE1-Peptids wieder hergestellt. Die Ergebnisse dieser Arbeit zeigen weiter, dass die Funktionsverlust-Mutante sowie die Revertanten ohne signifikante Beeinflussung in vitro in permissiven Fibroblasten und in vivo in verschiedenen Geweben replizieren. Wie aktuelle Daten nach Knochenmarktransplantation und Infektion mit der Funktionsverlust-Mutante im Vergleich zu den Revertanten zeigen, ist die Frequenz Latenz-assoziierter IE1-Transkriptionsereignisse bei der Funktionsverlust-Mutante signifikant erhöht. Damit konnte erstmalig der Beweis für eine Kontrolle der Latenz-assoziierten IE1-Genexpression durch IE1-Epitop-spezifische CD8 T-Zellen und damit für eine Präsentation des IE1-Peptids während der Latenz erbracht werden.

Cis- und trans-Regulation bei Drosophila-T-Box-Genen

Die räumliche und zeitliche Organisation von Genexpression ist für die Entwicklung und das Funktionieren eines jeden Lebewesens von immenser Bedeutung. Dazu laufen eine Vielzahl von Regulationsprozessen auf unterschiedlichen Ebenen ab. In dieser Arbeit wurden im ersten Teil Untersuchungen zur Genregulation des Drosophila optomotor-blind Genes und zur Funktion des Omb Proteins durchgeführt. Eine Mutante, der ein großer Teil der upstream regulatory region (URR) fehlt wurde erzeugt, aus einer Vielzahl von Linien isoliert und molekular charakterisiert. Die biologischen Auswirkungen dieser Deletion werden in Shen et al. (2008) beschrieben. Plasmide zur Erzeugung transgener Fliegen, mit deren Hilfe eine bereits von Sivasankaran et al. (2000) durchgeführte Enhancer-reporter-Analyse vervollständigt werden sollte, wurden hergestellt. Die bereits bekannte Inversion In(1)ombH31 wurde molekular kartiert. Eine Reihe von Konstrukten mit Punktmutationen in der Omb T-Domäne wurden generiert, die unter anderem über deren Funktion hinsichtlich DNA-Protein Interaktion und einer potentiellen Metallionenbindefähigkeit (ATCUN) hin Aufschluss geben sollen. Des Weiteren wurde eine Reihe von P-Element-Deletionslinien auf den Verlust eines alternativen omb Transkriptionsstartpunktes hin untersucht, mit dem Ziel eine vollständige Protein-Nullmutante zur Verfügung zu haben. Der zweite Abschnitt dieser Arbeit befasste sich mit der Erzeugung von Dpp-GFP-Fusionskonstrukten, mit deren Hilfe weitere Erkenntnisse über den Dpp-Langstreckentransport erhofft werden. Es wurde außerdem damit begonnen bei einem weitern Drosophila T-Box Transkriptionsfaktor, Optomotor-blind related gene-1 (Org-1), eine Reihe von Varianten mit homopolymeren polyAlanin und polyGlutamin Expansionen unterschiedlicher Länge herzustellen. Durch Experimente mit diesen Konstrukten soll Aufschluss darüber gewonnen werden, ob Glutamin-Expansionen, wie in der Literatur vorgeschlagen, aktivierend und Alanin-Expansionen in Transkriptionsfaktoren vielleicht reprimierend auf Genaktivität wirken. Letztlich wurden in dieser Arbeit im Rahmen des DROSDEL Projektes (Ryder et al., 2004, 2007) Deletionen in der distalen Hälfte des Chromosomenarms 3R hergestellt. Der DROSDEL Deletionskit, der durch eine Kooperation europäischer Labore entstand stellt der Drosophila Forschung einen umfassenden Satz molekular basengenau definierter Defizienzen zur Verfügung.

Computational Modeling of Cardiac Excitation-Contraction Coupling in Physiological and Pathological Conditions

The cardiomyocyte is a complex biological system where many mechanisms interact non-linearly to regulate the coupling between electrical excitation and mechanical contraction. For this reason, the development of mathematical models is fundamental in the field of cardiac electrophysiology, where the use of computational tools has become complementary to the classical experimentation. My doctoral research has been focusing on the development of such models for investigating the regulation of ventricular excitation-contraction coupling at the single cell level. In particular, the following researches are presented in this thesis: 1) Study of the unexpected deleterious effect of a Na channel blocker on a long QT syndrome type 3 patient. Experimental results were used to tune a Na current model that recapitulates the effect of the mutation and the treatment, in order to investigate how these influence the human action potential. Our research suggested that the analysis of the clinical phenotype is not sufficient for recommending drugs to patients carrying mutations with undefined electrophysiological properties. 2) Development of a model of L-type Ca channel inactivation in rabbit myocytes to faithfully reproduce the relative roles of voltage- and Ca-dependent inactivation. The model was applied to the analysis of Ca current inactivation kinetics during normal and abnormal repolarization, and predicts arrhythmogenic activity when inhibiting Ca-dependent inactivation, which is the predominant mechanism in physiological conditions. 3) Analysis of the arrhythmogenic consequences of the crosstalk between β-adrenergic and Ca-calmodulin dependent protein kinase signaling pathways. The descriptions of the two regulatory mechanisms, both enhanced in heart failure, were integrated into a novel murine action potential model to investigate how they concur to the development of cardiac arrhythmias. These studies show how mathematical modeling is suitable to provide new insights into the mechanisms underlying cardiac excitation-contraction coupling and arrhythmogenesis.

Study of Venturia inaequalis sensitivity to fungicides through molecular and biological methodologies

This study was aimed to correlate the results of relative germination from in vitro tests by trifloxystrobin with those of qPCR on a wide range of V. inaequalis populations and monoconidial isolates. Samples were collected in Italian and Turkish distinct locations from orchards with different scab management. In this study, an allele-specific qPCR with primer sets designed was successfully developed to quantitatively determine the frequency of QoI-resistant allele G143A in populations and monoconidial isolates of V. inaequalis. qPCR followed a similar pattern to that obtained using in vitro conidial germination test in very sensitive and very resistant populations. However, the variability between two test results was observed in hetereogenous populations. Therefore, the results of correlations between in vitro and qPCR showed a positive but not very high correlation for Venturia inaequalis populations (R2=0.70). On the contrary, this correlation between two assessment methods was very high for monoconidial isolates (R2=0.92). Results obtained in quantitative PCR and from traditional spore germination assay differed for the same fungal population and in some cases, it is difficult to assess the resistance in the field by only qPCR. It was concluded that it is not always possible to correlate the frequency of detection of the mutation with biological assessment. In such situations, monitoring by molecular techniques must be supported by standard in vitro resistance assessments and observation of field performance in order to have correct conclusions.

Die Interaktion von VHL und PTEN bei der Tumorinitiation und Progression

Das VHL-Syndrom umfasst Erkrankungen, die mit einem Funktionsverlust von VHL einhergehen. Das Tumorspektrum umfasst retinale und zerebrale Hämangioblastome, Nierenzysten und klarzellige Nierenkarzinome, Zysten und Tumore des Pankreas, Phäochromocytome, Adenome der Hoden und Tumore des Mittelohrs. Obwohl aufgrund klinischer Studien bekannt ist, welche VHL-Mutation mit welchen Neoplasien assoziiert werden können, konnte bisher kein VHL-Mausmodell das Krankheitsbild des VHL-Syndroms widerspiegeln. Daher ist vermutlich eine zusätzliche Fehlregulation weiterer Gene nötig ist, um die Tumorgenese in den verschiedenen Geweben zu induzieren. In mehreren klarzelligen Nierenkarzinomen konnte bereits eine PTEN-Defizienz nachgewiesen werden, der Verlust von PTEN wird außerdem auch mit der Tumorgenese von Phäochromocytomen assoziiert. Möglicherweise wirken VHL und PTEN also in der Tumorsuppression in der Niere und der Nebenniere zusammen.rnIm Rahmen dieser Arbeit konnte erstmals eine VHL-vermittelte Stabilisierung der PTEN-Konzentration sowohl in embryonalen als auch in Tumor-Zellen der Niere nachgewiesen werden. Die Analyse des Regulationsmechanismus ergab erstens eine Hypoxie-abhängige Abnahme der Transkription von PTEN. Des Weiteren konnte eine VHL-vermittelte Ubiquitinylierung von NEDD4-1, welches als E3-Ligase von PTEN dessen Degradation und Kerntransport reguliert, ermittelt werden. rnIn Nierenkarzinom-Zellen wurde weiterhin eine VHL- bzw. PTEN-Restitution induziert, um die Auswirkungen der beiden Tumorsuppressoren auf das Zellverhalten in vitro und in vivo zu untersuchen. Sowohl VHL als auch PTEN hatten dieselben Effekte lediglich in unterschiedlicher Intensität auf das Verhalten der Zellen. So konnte VHL- und PTEN-abhängig eine Verstärkung der Adhäsion, eine Inhibierung der Migration und eine Verminderung der Überlebens- und Metastasierungsfähigkeit nachgewiesen werden. Des Weiteren wurden Mausmodelle mit einem ubiquitären, heterozygoten Pten-Verlust generiert, die teilweise eine zusätzliche Haploinsuffizienz von Vhl bzw. eine heterozygote VHL Typ II-Mutation (V2B oder V2C) trugen. Sporadisch entwickelten diese Mäuse Vhl-abhängig Lebertumore und Pten-abhängig Lymphome und Ovarialkarzinome. Einige Mäuse mit einer kombinierten Vhl- und Pten-Defizienz bildeten zusätzlich Nierenzysten aus, die teilweise das gesamte Volumen der Niere einnahmen. Besonders häufig entstanden in Pten-haploinsuffizienten Mäusen Phäochromocytome, die durch eine zusätzliche V2B- oder V2C-Mutation in gleichaltrigen Mäusen deutlich weiterentwickelt waren. Demnach induziert erst der gemeinsame Verlust von Vhl und Pten die Bildung von Nierenzysten und Phäochromocytomen, welche dem Krankheitsbild des VHL-Syndroms zugeordnet werden.rnDie Untersuchungen innerhalb dieser Arbeit zeigen erstmalig die Interaktion und Kooperation von VHL und PTEN in der Tumorsuppression. Die Resultate bieten außerdem die Grundlage für weitere Analysen der Auswirkung der VHL-vermittelten PTEN-Stabilisierung und für detailliertere Untersuchungen der durch die kombinierte Vhl- und Pten-Defizienz induzierten Neoplasien der Niere und der Nebennieren-Tumore in in vivo Mausmodellen.rn