Occurrence and molecular diversity of the Fit insect toxin locus in plant-beneficial pseudomonads

The application of plant-beneficial pseudomonads provides a promising alternative to chemical pest management in agriculture. The fact that Pseudomonas fluorescens CHA0 and Pf-5, both well-known biocontrol agents of fungal root diseases, exhibit also potent insecticidal activity is of particular interest, as these plant-beneficial bacteria naturally colonize the rhizosphere of important crop plants. Insecticidal activity in these strains depends on a novel locus encoding the production of a protein toxin termed Fit (for P. fluorescens insecticidal toxin). To gain a better understanding of the ecological relevance of the Pseudomonas anti-insect activity, we have begun to investigate the occurrence and molecular diversity of the Fit toxin genes among root-associated pseudomonads. To this end, we have screened a large world-wide collection of fluorescent Pseudomonas sp. isolated from the roots of different plant species using molecular fingerprinting techniques. The strains are already well characterized for exoproduct patterns and disease-suppressive ability and are currently being tested for insecticidal activity in a greater wax moth larvae assay system.

Phenotypic and molecular assessment of seven patients with 6p25 deletion syndrome: relevance to ocular dysgenesis and hearing impairment.

BACKGROUND: Thirty-nine patients have been described with deletions involving chromosome 6p25. However, relatively few of these deletions have had molecular characterization. Common phenotypes of 6p25 deletion syndrome patients include hydrocephalus, hearing loss, and ocular, craniofacial, skeletal, cardiac, and renal malformations. Molecular characterization of deletions can identify genes that are responsible for these phenotypes. METHODS: We report the clinical phenotype of seven patients with terminal deletions of chromosome 6p25 and compare them to previously reported patients. Molecular characterization of the deletions was performed using polymorphic marker analysis to determine the extents of the deletions in these seven 6p25 deletion syndrome patients. RESULTS: Our results, and previous data, show that ocular dysgenesis and hearing impairment are the two most highly penetrant phenotypes of the 6p25 deletion syndrome. While deletion of the forkhead box C1 gene (FOXC1) probably underlies the ocular dysgenesis, no gene in this region is known to be involved in hearing impairment. CONCLUSIONS: Ocular dysgenesis and hearing impairment are the two most common phenotypes of 6p25 deletion syndrome. We conclude that a locus for dominant hearing loss is present at 6p25 and that this locus is restricted to a region distal to D6S1617. Molecular characterization of more 6p25 deletion patients will aid in refinement of this locus and the identification of a gene involved in dominant hearing loss.

Morphological and molecular characterization of Pisolithus in soil under eucalyptus plantations in Brazil

Eighteen Pisolithus basidiomes were collected from Eucalyptus plantations in the state of Minas Gerais, Brazil. These basidiomes were characterized morphologically and molecularly. The basidiomes varied in shape, color and size. One of them was found underground, indicating a hypogeous fungus. The main morphological distinctive characteristic was spore ornamentation, which distinguished two groups. One group with short and erect spines was identified as Pisolithus microcarpus, and the other with long and curved spines as Pisolithus marmoratus, after analyzing the cladogram obtained by phylogenetic relationship based on internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA of these isolates.

Clinical and molecular characterization of Diastrophic Dysplasia in the Portuguese population.

SLC26A2-related dysplasias encompass a spectrum of diseases: from lethal achondrogenesis type 1B (ACG1B; MIM #600972) and atelosteogenesis type 2 (AO2; MIM #256050) to classical diastrophic dysplasia (cDTD; MIM #222600) and recessive multiple epiphyseal dysplasia (rMED; MIM #226900). This study aimed at characterizing clinically, radiologically and molecularly 14 patients affected by non-lethal SLC26A2-related dysplasias and at evaluating genotype-phenotype correlation. Phenotypically, eight patients were classified as cDTD, four patients as rMED and two patients had an intermediate phenotype (mild DTD - mDTD, previously 'DTD variant'). The Arg279Trp mutation was present in all patients, either in homozygosity (resulting in rMED) or in compound heterozygosity with the known severe alleles Arg178Ter or Asn425Asp (resulting in DTD) or with the mutation c.727-1G>C (causing mDTD). The 'Finnish mutation', c.-26+2T>C, and the p.Cys653Ser, both frequent mutations in non-Portuguese populations, were not identified in any of the patients of our cohort and are probably very rare in the Portuguese population. A targeted mutation analysis for p.Arg279Trp and p.Arg178Ter in the Portuguese population allows the identification of approximately 90% of the pathogenic alleles.

Congenital disorder of glycosylation type Id (CDG Id) : phenotypic, biochemical and molecular characterization of a new patient

Rapport de synthèseLes troubles de la glycosylation (Congenital Disorders of Glycosylation, CDG) regroupent une famille de maladies multi-systémiques héréditaires causées par des défauts dans la synthèse de glycoconjugés. La glycosylation est une réaction enzymatique consistant à lier de façon covalente un glucide à une chaîne peptidique ou une protéine. Il existe deux types de glycosylation. La N-gjycosylation est l'addition de glucides aux chaînes peptidiques en croissance dès leur entrée dans la lumière du réticulum endoplasmique. Elle s'effectue sur les futures glycoprotéines membranaires et conduit à des chaînes de sucres courtes et ramifiées. La O-glycosylation est l'addition de glucides au niveau des résidus hydroxylés des acides aminés sérine et thréonine des chaînes peptidiques déjà présentes dans la lumière de l'appareil de Golgi. Elle est, dans la plupart des cas, effectuée sur îes protéoglycanes et conduit à des chaînes de sucres longues et non ramifiées. La classification des CDG repose sur le niveau de l'étape limitante de la glycosylation. Les CDG de type 1, plus fréquents, regroupent les déficits enzymatiques se situant en amont du transfert de Poligosaccharide sur la chaîne peptidique. Les CDG de type 2 regroupent ceux ayant lieu en aval de ce transfert. Parmi les nombreux différents sous-types de CDG, le CDG de type ld est causé par une anomalie de la mannosyltransferase, enzyme codée par le gène ALG3 (chromosome 3q27). Jusqu'à ce jour, six patients atteints de CDG ld ont été reportés dans la littérature. Notre travail a permis de décrire un septième patient et d'affiner les caractéristiques cliniques, biologiques, neuroradiologiques et moléculaires du CDG ld. Notre patient est notamment porteur d'une nouvelle mutation de type missense sur le gène ALG3. Tous les patients atteints de CDG ld présentent une encéphalopathie progressive avec microcéphalie, retard psychomoteur sévère et épilepsie. Une ostéopénie marquée est présente chez certains patients. Elle est parfois sous diagnostiquée et révélée uniquement lors de fracture pathologique. Les patients atteints de CDG ld présentent également des traits dysmorphiques typiques, mais aucune atteinte multi-systémique ou anomalie biologique spécifique n'est retrouvée telle que dans les autres types de CDG. Le dépistage biochimique des troubles de la glycosylation se fait par une analyse simple et peu coûteuse qui est l'analyse de la transferrine sérique par isoelectrofocusing ou par électrophorèse capillaire. Un tel dépistage devrait être effectué chez tout patient présentant une encéphalopathie d'origine indéterminée, et cela même en l'absence d'atteinte multi- systémique. Notre travail a été publié sous forme d'article de type « short report », peer-reviewed, dans le Journal of Inherited Metabolic Diseases. Le Journal est une révue spécialisée du domaine des erreirs innées du métabolisme. S'agissant d'un seul patient rapporté, l'article ne montre que très synthétiquement le travail effectué, Pour cette raison un complément à l'article avec matériel, méthodes et résultats figure ci-après et concerne la partie de recherche moléculaire de notre travail. La doctorante a non seulement encadré personnellement le patient au niveau clinique et biochimique, mais a plus particulièrement mis au point l'analyse moléculaire du gène ALG3 dans le laboratoire de Pédiatrie Moléculaire pour la première fois ; cela a impliqué l'étude du gène, le choix des oligonucleotides et l'optimisation des réactions d'amplification et séquençage.

Formation of a spatial memory trace : a behavioral, cellular and molecular study

THESIS ABSTRACTThis thesis project was aimed at studying the molecular mechanisms underlying learning and memory formation, in particular as they relate to the metabolic coupling between astrocytes and neurons. For that, changes in the metabolic activity of different mice brain regions after 1 or 9 days of training in an eight-arm radial maze were assessed by (14C) 2-deoxyglucose (2DG) autoradiography. Significant differences in the areas engaged during the behavioral task at day 1 (when animals are confronted for the first time to the learning task) and at day 9 (when animals are highly performing) have been identified. These areas include the hippocampus, the fornix, the parietal cortex, the laterodorsal thalamic nucleus and the mammillary bodies at day 1 ; and the anterior cingulate, the retrosplenial cortex and the dorsal striatum at day 9. Two of these cerebral regions (those presenting the greatest changes at day 1 and day 9: the hippocampus and the retrosplenial cortex, respectively) were microdissected by laser capture microscopy and selected genes related to neuron-glia metabolic coupling, glucose metabolism and synaptic plasticity were analyzed by RT-PCR. 2DG and gene expression analysis were performed at three different times: 1) immediately after the end of the behavioral paradigm, 2) 45 minutes and 3) 6 hours after training. The main goal of this study was the identification of the metabolic adaptations following the learning task. Gene expression results demonstrate that the learning task profoundly modulates the pattern of gene expression in time, meaning that these two cerebral regions with high 2DG signal (hippocampus and retrosplenial cortex) have adapted their metabolic molecular machinery in consequence. Almost all studied genes show a higher expression in the hippocampus at day 1 compared to day 9, while an increased expression was found in the retrosplenial cortex at day 9. We can observe these molecular adaptations with a short delay of 45 minutes after the end of the task. However, 6 hours after training a high gene expression was found at day 9 (compared to day 1) in both regions, suggesting that only one day of training is not sufficient to detect transcriptional modifications several hours after the task. Thus, gene expression data match 2DG results indicating a transfer of information in time (from day 1 to day 9) and in space (from the hippocampus to the retrosplenial cortex), and this at a cellular and a molecular level. Moreover, learning seems to modify the neuron-glia metabolic coupling, since several genes involved in this coupling are induced. These results also suggest a role of glia in neuronal plasticity.RESUME DU TRAVAIL DE THESECe projet de thèse a eu pour but l'étude des mécanismes moléculaires qui sont impliqués dans l'apprentissage et la mémoire et, en particulier, à les mettre en rapport avec le couplage métabolique existant entre les astrocytes et les neurones. Pour cela, des changements de l'activité métabolique dans différentes régions du cerveau des souris après 1 ou 9 jours d'entraînement dans un labyrinthe radial à huit-bras ont été évalués par autoradiographie au 2-désoxyglucose (2DG). Des différences significatives dans les régions engagées pendant la tâche comportementale au jour 1 (quand les animaux sont confrontés pour la première fois à la tâche) et au jour 9 (quand les animaux ont déjà appris) ont été identifiés. Ces régions incluent, au jour 1, l'hippocampe, le fornix, le cortex pariétal, le noyau thalamic laterodorsal et les corps mamillaires; et, au jour 9, le cingulaire antérieur, le cortex retrosplenial et le striatum dorsal. Deux de ces régions cérébrales (celles présentant les plus grands changements à jour 1 et à jour 9: l'hippocampe et le cortex retrosplenial, respectivement) ont été découpées par microdissection au laser et quelques gènes liés au couplage métabolique neurone-glie, au métabolisme du glucose et à la plasticité synaptique ont été analysées par RT-PCR. L'étude 2DG et l'analyse de l'expression de gènes ont été exécutés à trois temps différents: 1) juste après entraînement, 2) 45 minutes et 3) 6 heures après la fin de la tâche. L'objectif principal de cette étude était l'identification des adaptations métaboliques suivant la tâche d'apprentissage. Les résultats de l'expression de gènes démontrent que la tâche d'apprentissage module profondément le profile d'expression des gènes dans le temps, signifiant que ces deux régions cérébrales avec un signal 2DG élevé (l'hippocampe et le cortex retrosplenial) ont adapté leurs « machines moléculaires » en conséquence. Presque tous les gènes étudiés montrent une expression plus élevée dans l'hippocampe au jour 1 comparé au jour 9, alors qu'une expression accrue a été trouvée dans le cortex retrosplenial au jour 9. Nous pouvons observer ces adaptations moléculaires avec un retard court de 45 minutes après la fin de la tâche. Cependant, 6 heures après l'entraînement, une expression de gènes élevée a été trouvée au jour 9 (comparé à jour 1) dans les deux régions, suggérant que seulement un jour d'entraînement ne suffit pas pour détecter des modifications transcriptionelles plusieurs heures après la tâche. Ainsi, les données d'expression de gènes corroborent les résultats 2DG indiquant un transfert d'information dans le temps (de jour 1 à jour 9) et dans l'espace (de l'hippocampe au cortex retrosplenial), et ceci à un niveau cellulaire et moléculaire. D'ailleurs, la tâche d'apprentissage semble modifier le couplage métabolique neurone-glie, puisque de nombreux gènes impliqués dans ce couplage sont induits. Ces observations suggèrent un rôle important de la glie dans les mécanismes de plasticité du système nerveux.

Genetic removal of tri-unsaturated fatty acids suppresses developmental and molecular phenotypes of an Arabidopsis tocopherol-deficient mutant. Whole-body mapping of malondialdehyde pools in a complex eukaryote.

Malondialdehyde (MDA) is a small, ubiquitous, and potentially toxic aldehyde that is produced in vivo by lipid oxidation and that is able to affect gene expression. Tocopherol deficiency in the vitamin E2 mutant vte2-1 of Arabidopsis thaliana leads to massive lipid oxidation and MDA accumulation shortly after germination. MDA accumulation correlates with a strong visual phenotype (growth reduction, cotyledon bleaching) and aberrant GST1 (glutathione S-transferase 1) expression. We suppressed MDA accumulation in the vte2-1 background by genetically removing tri-unsaturated fatty acids. The resulting quadruple mutant, fad3-2 fad7-2 fad8 vte2-1, did not display the visual phenotype or the aberrant GST1 expression observed in vte2-1. Moreover, cotyledon bleaching in vte2-1 was chemically phenocopied by treatment of wild-type plants with MDA. These data suggest that products of tri-unsaturated fatty acid oxidation underlie the vte2-1 seedling phenotype, including cellular toxicity and gene regulation properties. Generation of the quadruple mutant facilitated the development of an in situ fluorescence assay based on the formation of adducts of MDA with 2-thiobarbituric acid at 37 degrees C. Specificity was verified by measuring pentafluorophenylhydrazine derivatives of MDA and by liquid chromatography analysis of MDA-2-thiobarbituric acid adducts. Potentially applicable to other organisms, this method allowed the localization of MDA pools throughout the body of Arabidopsis and revealed an undiscovered pool of the compound unlikely to be derived from trienoic fatty acids in the vicinity of the root tip quiescent center.

In vitro susceptibility of Actinobaculum schaalii to 12 antimicrobial agents and molecular analysis of fluoroquinolone resistance.

OBJECTIVES: To assess the in vitro susceptibility of Actinobaculum schaalii to 12 antimicrobial agents as well as to dissect the genetic basis of fluoroquinolone resistance. METHODS: Forty-eight human clinical isolates of A. schaalii collected in Switzerland and France were studied. Each isolate was identified by 16S rRNA sequencing. MICs of amoxicillin, ceftriaxone, gentamicin, vancomycin, clindamycin, linezolid, ciprofloxacin, levofloxacin, moxifloxacin, co-trimoxazole, nitrofurantoin and metronidazole were determined using the Etest method. Interpretation of results was made according to EUCAST clinical breakpoints. The quinolone-resistance-determining regions (QRDRs) of gyrA and parC genes were also identified and sequence analysis was performed for all 48 strains. RESULTS: All isolates were susceptible to amoxicillin, ceftriaxone, gentamicin, clindamycin (except three), vancomycin, linezolid and nitrofurantoin, whereas 100% and 85% were resistant to ciprofloxacin/metronidazole and co-trimoxazole, respectively. Greater than or equal to 90% of isolates were susceptible to the other tested fluoroquinolones, and only one strain was highly resistant to levofloxacin (MIC ?32 mg/L) and moxifloxacin (MIC 8 mg/L). All isolates that were susceptible or low-level resistant to levofloxacin/moxifloxacin (n?=?47) showed identical GyrA and ParC amino acid QRDR sequences. In contrast, the isolate exhibiting high-level resistance to levofloxacin and moxifloxacin possessed a unique mutation in GyrA, Ala83Val (Escherichia coli numbering), whereas no mutation was present in ParC. CONCLUSIONS: When an infection caused by A. schaalii is suspected, there is a risk of clinical failure by treating with ciprofloxacin or co-trimoxazole, and ?-lactams should be preferred. In addition, acquired resistance to fluoroquinolones more active against Gram-positive bacteria is possible.

Partition coefficient and molecular flexibility: the concept of lipophilicity space.

The rationale of this study was to investigate molecular flexibility and its influence on physicochemical properties with a view to uncovering additional information on the fuzzy concept of dynamic molecular structure. Indeed, it is now known that computed molecular interaction fields (MIFs) such as molecular electrostatic potentials (MEPs) and lipophilicity potentials (MLPs) are conformation-dependent, as are dipole moments. A database of 125 compounds was used whose conformational space was explored, while conformation-dependent parameters were computed for each non-redundant conformer found in the conformational space of the compounds. These parameters were the virtual log P (log P(MLP), calculated by a MLP approach), the apolar surface area (ASA), polar surface area (PSA), and solvent-accessible surface (SAS). For each compound, the range taken by each parameter (its property space) was divided by the number of rotors taken as an index of flexibility, yielding a parameter termed 'molecular sensitivity'. This parameter was poorly correlated with others (i.e., it contains novel information) and showed the compounds to fall into two broad classes. 'Sensitive' molecules are those whose computed property ranges are markedly sensitive to conformational effects, whereas 'insensitive' (in fact, less sensitive) molecules have property ranges which are comparatively less affected by conformational fluctuations. A pharmacokinetic application is presented.

The genetic structure of metapopulations and conservation biology.

A range of models describing metapopulations is surveyed and their implications for conservation biology are described. An overview of the use of both population genetic elements and demographic theory in metapopulation models is given. It would appear that most of the current models suffer from either the use of over-simplified demography or the avoidance of selectively important genetic factors. The scale for which predictions are made by the various models is often obscure. A conceptual framework for describing metapopulations by utilising the concept of fitness of local populations is provided and some examples are given. The expectation that any general theory, such as that of metapopulations, can make useful predictions for particular problems of conservation is examined and compared with the prevailing 'state of the art' recommendations.

Chronic norovirus gastroenteritis in a double hematopoietic stem cell and lung transplant recipient.

N. Boillat Blanco, R. Kuonen, C. Bellini, O. Manuel, C. Estrade, J. Mazza-Stalder, J.D. Aubert, R. Sahli, P. Meylan. Chronic norovirus gastroenteritis in a double hematopoietic stem cell and lung transplant recipient. Transpl Infect Dis 2011: 13: 213-215. All rights reserved.

Discovery and molecular characterization of an ambisense densovirus from South American populations of Solenopsis invicta

In an effort to discover viruses as classical biological control agents, a metatranscriptomics/pyrosequencing approach was used to survey native Solenopsis invicta collected exclusively in Argentina. A new virus was discovered with characteristics consistent with the family Parvoviridae, subfamily Densovirinae. The virus, tentatively named Solenopsis invicta densovirus (SiDNV), represents the first DNA virus discovered in ants (Formicidae) and the first densovirus in a hymenopteran insect. The ambisense genome was 5280 nucleotides in length and the termini possessed asymmetrically positioned inverted terminal repeats, formed hairpin loops, and had transcriptional regulatory elements including CAAT and TATA sites. Phylogenetic analysis revealed that SiDNV belongs to a group that includes two other densoviruses found in insects (Acheta domestica densovirus and Planococcus citri densovirus). SiDNV was prevalent in fire ants from Argentina but completely absent in fire ants found in the USA indicating that this virus has potential for biological control of introduced S. invicta.

Dpp/BMP signaling in flies: From molecules to biology.

Decapentaplegic (Dpp), the fly homolog of the secreted mammalian BMP2/4 signaling molecules, is involved in almost all aspects of fly development. Dpp has critical functions at all developmental stages, from patterning of the eggshell to the determination of adult intestinal stem cell identity. Here, we focus on recent findings regarding the transcriptional regulatory logic of the pathway, on a new feedback regulator, Pentagone, and on Dpp's roles in scaling and growth of the Drosophila wing.