Tipagem molecular, perfis de sensibilidade e caracterização de transcritos diferencialmente expressos durante a infecção de Cryptococcus neoformans

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Hanseniaspora nectarophila sp nov., a yeast species isolated from ephemeral flowers

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Identifizierung, Quantifizierung und Hemmung von ausgewählten Hefen im Wein

Hefen stellen einen großen und wichtigen Teil der Mikrobiota während der Weinbereitung dar, da ohne ihre alkoholische Fermentation die Umwandlung von Most und Wein nicht möglich wäre. Ferner ist es ihre Vielzahl an Stoffwechselprodukten, die dem Aroma des fertigen Weines eine zusätzliche Komplexität verleihen. Auf der anderen Seite steht durch den Metabolismus verschiedenster so genannter Wildhefen die Gefahr von Qualitätsabstufungen der Weine, was allgemein als „Weinfehler“ betrachtet wird. Ziel dieser Arbeit war zum einen die taxonomische Einordnung von Saccharomyces-Spezies, sowie die Quantifizierung und Hemmung von ausgewählten Wildhefen während der Weinbereitung.rnEin Teil dieser Arbeit umfasste die Identifizierung der nahverwandten Mitglieder der Saccharomyces sensu stricto-Gruppe. Durch den Einsatz des DNA-Fingerpinting-Systems SAPD-PCR konnten alle die Gruppe umfassenden Spezies anhand spezifischer Bandenmuster nachgewiesen werden, wodurch eine Einordnung dieser schwer zu differenzierenden Arten möglich war. Die Differenzierung zwischen den einzelnen Spezies war in jedem Fall deutlicher als dies die Sequenzierung der 5.8S rDNA und ihre flankierenden ITS-Regionen vermochte. Die SAPD-PCR zeichnete sich zudem durch eine geringe Muster-Varianz bei verschiedenen Stämmen einer Art aus und konnte zuverlässig unbekannte Stämme bestimmen und bereits hinterlegte Stämme neu klassifizieren. Zudem konnte mit Hilfe dieses Systems Hybride aus Saccharomyces cerevisiae und S. bayanus bzw. S. cerevisiae und S. kudriavzevii detektiert werden, wenn diese Hybride aus relativ gleichen genomischen Anteilen der Eltern bestanden. rnZusätzlich wurde ein quantitatives PCR-System entwickelt, um die Gattungen Saccharomyces, Hanseniaspora und Brettanomyces in Most und Wein detektieren und quantifizieren zu können. Die hierfür entwickelten Primer zeigten sich spezifisch für die untersuchten Arten. Durch die serielle Verdünnung definierter DNA-Mengen konnte für alle drei Systeme eine Kalibrierungskurve erstellt werden, mit Hilfe derer die tatsächlichen Quantifizierungen durchgeführt wurden. Die qPCR-Analyse lieferte ähnliche Zellzahlen wie Lebendzellzahl-Bestimmungen und wurde nicht von anderen Spezies und von Traubensaft gestört. Die maximal detektierbare Zellzahl betrug 2 x 107 Zellen/ml, während die minimale Detektionsgrenze je nach Art zwischen 1 x 102 Zellen/ml und 1 x 103 Zellen/ml lag. Allerdings konnte eine effektive DNA-Isolierung dieser geringen Zellzahlen nur erreicht werden, wenn die Zellzahl durch artfremde Hefen künstlich erhöht wurde. Die Analyse einer Most-Vergärung mit den drei Spezies zeigte schlussendlich, dass die quantitative PCR sicher und schnell Veränderungen und Sukzessionen detektiert und so ein geeignetes Mittel darstellt, um Populationsdynamiken während der Weinherstellung zu beobachten. rnDer letzte Teil dieser Arbeit befasste sich mit der Inhibierung von Schadhefen durch zellwand-hydrolysierende Enzyme. Es konnte hierbei eine endoglykosidisch wirkende β-1,3-Glucanase aus dem Bakterium Delftia tsuruhatensis isoliert werden. Diese besaß eine ungefähre Masse von 28 kDa, einen isolektrischen Punkt von ca. 4,3 und wirkte mit einer spezifischen Aktivität von 10 U/mg Protein gegen das Glucan Laminarin. Zudem zeigte das Enzym ein Temperaturoptimum von 50 °C und ein pH-Optimum bei pH 4,0. Weinparameter wie erhöhte Konzentrationen an Ethanol, Phenolen und Sulfit beeinflussten die Wirkung des Enzyms nicht oder nur wenig. Neben der allgemeinen Wirkung gegen β-1,3-Glucane konnte hier auch gezeigt werden, dass ebenso gut die β-1,3-Glucane in der Zellwand verschiedener Hefen hydrolysiert wurden. Fluoreszenz- und rasterelektronen-mikroskopische Aufnahmen von Hefezellen nach Inkubation mit der β-1,3-Glucanase zeigten zusätzlich die Zerstörung der Zelloberfläche der Hefen. Die lytische Wirkung des Enzyms wurde an verschiedenen weintypischen Hefen getestet. Hierbei zeigten sich stammspezifische Unterschiede in der Sensitivität gegenüber dem Enzym. Außerdem konnte festgestellt werden, dass sowohl Wachstumsphase als auch Medium der Hefen Einfluss auf deren Zellwand hat und somit auch auf die Wirkung des Enzyms.rn

Molecular evidence that the asexual industrial fungus Trichoderma reesei is a clonal derivative of the ascomycete Hypocrea jecorina.

The relationship of the important cellulase producing asexual fungus Trichoderma reesei to its putative teleomorphic (sexual) ancestor Hypocrea jecorina and other species of the Trichoderma sect. Longibrachiatum was studied by PCR-fingerprinting and sequence analyses of the nuclear ribosomal DNA region containing the internal transcribed spacers (ITS-1 and ITS-2) and the 5.8S rRNA gene. The differences in the corresponding ITS sequences allowed a grouping of anamorphic (asexual) species of Trichoderma sect. Longibrachiatum into Trichoderma longibrachiatum, Trichoderma pseudokoningii, and Trichoderma reesei. The sexual species Hypocrea schweinitzii and H. jecorina were also clearly separated from each other. H. jecorina and T. reesei exhibited identical sequences, suggesting close relatedness or even species identity. Intraspecific and interspecific variation in the PCR-fingerprinting patterns supported the differentiation of species based on ITS sequences, the grouping of the strains, and the assignment of these strains to individual species. The variations between T. reesei and H. jecorina were at the same order of magnitude as found between all strains of H. jecorina, but much lower than the observed interspecific variations. Identical ITS sequences and the high similarity of PCR-fingerprinting patterns indicate a very close relationship between T. reesei and H. jecorina, whereas differences of the ITS sequences and the PCR-fingerprinting patterns show a clear phylogenetic distance between T. reesei/H. jecorina and T. longibrachiatum. T. reesei is considered to be an asexual, clonal line derived from a population of the tropical ascomycete H. jecorina.

Isolation and characterization of microorganisms with probiotic potential

Tese de mestrado em Microbiologia Aplicada, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2016

Diversity of new root nodule bacteria from Erythrina velutina Willd., a native legume from the Caatinga dry forest (Northeastern Brazil).

This study aims to evaluate the phenotypical characteristics of bacterial isolates from mulungu (Erythrina velutina Willd.) nodules and determinate their Box-PCR fingerprinting. All bacteria were evaluated by the following phenotypic characteristics: growth rate, pH change, colony color and mucus production. The bacterial isolates able to re-nodulate the original host were also evaluated regarding its tolerance to increased salinity and different incubation temperatures, ability to growth using different carbon sources, intrinsic antibiotic resistance and ?in vitro? auxin biosynthesis. The molecular fingerprints were set up using the Box-PCR technique and the isolates were clustered by their profiles. Among the 22 bacterial isolates obtained, eight were able to re-nodulate the original host. Among the nodule inducing isolates, some were tolerant to 1% of NaCl and 39° C and all of them metabolized the maltose, fructose, glucose, sucrose and arabinose, were resistant to rifampicin and produced auxin. The bacteria showed low genetic similarity among them and reference strains, which indicates the great genetic variability of the isolates. The results of this work are the first reports about the bacterial isolates able to nodulate this species. A more deep study of these bacteria may reveal the existence of isolates tolerant to environmental stresses and suitable as a future mulungu inoculant.

Genetic relationships between sympatric populations of Bacillus cereus and Bacillus thuringiensis, as revealed by rep-PCR genomic fingerprinting

The bacterial strain Bacillus cereus is closely related to Bacillus thuringiensis, although any genetic relationship between the two strains is still in debate. Using rep-PCR genomic fingerprinting, we established the genetic relationships between Brazilian sympatric populations of B. cereus and B. thuringiensis simultaneously collected from two geographically separate sites. We observed the formation of both B. thuringiensis and B. cereus clusters, as well as strains of B. cereus that are more closely related to B. thuringiensis than to other B. cereus strains. In addition, lower genetic variability was observed among B. thuringiensis clusters compared to B. cereus clusters, indicating that either the two species should be categorized as separate or that B. thuringiensis may represent a clone from a B. cereus background.

Fluorescence images combined to statistic test for fingerprinting of citrus plants after bacterial infection

The citrus greening (or huanglongbing) disease has caused serious problems in citrus crops around the world. An early diagnostic method to detect this malady is needed due to the rapid dissemination of Candidatus Liberibacter asiaticus (CLas) in the field. This analytical study investigated the fluorescence responses of leaves from healthy citrus plants and those inoculated with CLas by images from a stereomicroscope and also evaluated their potential for the early diagnosis of the infection caused by this bacterium. The plants were measured monthly, and the evolution of the bacteria on inoculated plants was monitored by real-time quantitative polymerase chain reaction (RT-qPCR) amplification of CLas sequences. A statistical method was used to analyse the data. The selection of variables from histograms of colours (colourgrams) of the images was optimized using a paired Student's t-test. The intensity of counts for green colours from images of fluorescence had clearly minor variations for healthy plants than diseased ones. The darker green colours were the indicators of healthy plants and the light colours for the diseased. The method of fluorescence images is novel for fingerprinting healthy and diseased plants and provides an alternative to the current method represented by PCR and visual inspection. A new, non-subjective pattern of analysis and a non-destructive method has been introduced that can minimize the time and costs of analyses.

A DNA fingerprinting procedure for ultra high-throughput genetic analysis of insects

Existing procedures for the generation of polymorphic DNA markers are not optimal for insect studies in which the organisms are often tiny and background molecular Information is often non-existent. We have used a new high throughput DNA marker generation protocol called randomly amplified DNA fingerprints (RAF) to analyse the genetic variability In three separate strains of the stored grain pest, Rhyzopertha dominica. This protocol is quick, robust and reliable even though it requires minimal sample preparation, minute amounts of DNA and no prior molecular analysis of the organism. Arbitrarily selected oligonucleotide primers routinely produced similar to 50 scoreable polymorphic DNA markers, between individuals of three Independent field isolates of R. dominica. Multivariate cluster analysis using forty-nine arbitrarily selected polymorphisms generated from a single primer reliably separated individuals into three clades corresponding to their geographical origin. The resulting clades were quite distinct, with an average genetic difference of 37.5 +/- 6.0% between clades and of 21.0 +/- 7.1% between individuals within clades. As a prelude to future gene mapping efforts, we have also assessed the performance of RAF under conditions commonly used in gene mapping. In this analysis, fingerprints from pooled DNA samples accurately and reproducibly reflected RAF profiles obtained from Individual DNA samples that had been combined to create the bulked samples.

Fingerprinting of cell lines by directed amplification of minisatellite-region DNA (DAMD)

The development of in vitro propagation of cells has been an extraordinary technical advance for several biological studies. The correct identification of the cell line used, however, is crucial, as a mistaken identity or the presence of another contaminating cell may lead to invalid and/or erroneous conclusions. We report here the application of a DNA fingerprinting procedure (directed amplification of minisatellite-region DNA), developed by Heath et al. [Nucleic Acids Research (1993) 21: 5782-5785], to the characterization of cell lines. Genomic DNA of cells in culture was extracted and amplified by PCR in the presence of VNTR core sequences, and the amplicons were separated by agarose gel electrophoresis. After image capture with a digital camera, the banding profiles obtained were analyzed using a software (AnaGel) specially developed for the storage and analysis of electrophoretic fingerprints. The fingerprints are useful for construction of a data base for identification of cell lines by comparison to reference profiles as well as comparison of similar lines from different sources and periodic follow-up of cells in culture.

RAPD genomic fingerprinting differentiates Thiobacillus ferrooxidans strains

The PCR-based technique, involving the random amplification of polymorphic DNA (RAPD), was optimized and used for assessing genomic variability among eight Thiobacillus ferrooxidans strains. RAPD fingerprints presented variation for the thirty primers used, giving a total of 269 polymorphic bands. Similarity coefficients between the strains were calculated, and UPGMA cluster analysis was used to generate a dendrogram showing relationships among them. Most primers divided T. ferrooxidans strains in two distinct groups - Group 1: S, SSP, V3, AMF and Group 2: CMV, FG-460, I-35, LR. We observed that the T. ferrooxidans strains used in this work have a high degree of genomic diversity and that RAPD is a powerful method to differentiate them.

Nonculture-based identification of bacteria in milk by protein fingerprinting

Traditional methods for bacterial identification include Gram staining, culturing, and biochemical assays for phenotypic characterization of the causative organism. These methods can be time-consuming because they require in vitro cultivation of the microorganisms. Recently, however, it has become possible to obtain chemical profiles for lipids, peptides, and proteins that are present in an intact organism, particularly now that new developments have been made for the efficient ionization of biomolecules. MS has therefore become the state-of-the-art technology for microorganism identification in microbiological clinical diagnosis. Here, we introduce an innovative sample preparation method for nonculture-based identification of bacteria in milk. The technique detects characteristic profiles of intact proteins (mostly ribosomal) with the recently introduced MALDI SepsityperTM Kit followed by MALDI-MS. In combination with a dedicated bioinformatics software tool for databank matching, the method allows for almost real-time and reliable genus and species identification. We demonstrate the sensitivity of this protocol by experimentally contaminating pasteurized and homogenized whole milk samples with bacterial loads of 10(3)-10(8) colony-forming units (cfu) of laboratory strains of Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus. For milk samples contaminated with a lower bacterial load (104 cfu mL-1), bacterial identification could be performed after initial incubation at 37 degrees C for 4 h. The sensitivity of the method may be influenced by the bacterial species and count, and therefore, it must be optimized for the specific application. The proposed use of protein markers for nonculture-based bacterial identification allows for high-throughput detection of pathogens present in milk samples. This method could therefore be useful in the veterinary practice and in the dairy industry, such as for the diagnosis of subclinical mastitis and for the sanitary monitoring of raw and processed milk products.

Genetic diversity analysis of isolates belonging to the Photobacterium phosphoreum species group collected from salmon products using AFLP fingerprinting

An accurate amplified fragment length polymorphism (AFLP) method, including three primer sets for the selective amplification step, was developed to display the phylogenetic position of Photobacterium isolates collected from salmon products. This method was efficient for discriminating the three species Photobacterium phosphoreum, Photobacterium iliopiscarium and Photobacterium kishitanii, until now indistinctly gathered in the Photobacterium phosphoreum species group known to be strongly responsible for seafood spoilage. The AFLP fingerprints enabled the isolates to be separated into two main clusters that, according to the type strains, were assigned to the two species P. phosphoreum and P. iliopiscarium. P. kishitanii was not found in the collection. The accuracy of the method was validated by using gyrB-gene sequencing and luxA-gene PCR amplification, which confirmed the species delineation. Most of the isolates of each species were clonally distinct and even those that were isolated from the same source showed some diversity. Moreover, this AFLP method may be an excellent tool for genotyping isolates in bacterial communities and for clarifying our knowledge of the role of the different members of the Photobacterium species group in seafood spoilage.

Post Hoc Analysis Of The Patricia Randomized Trial Of The Efficacy Of Human Papillomavirus Type 16 (hpv-16)/hpv-18 As04-adjuvanted Vaccine Against Incident And Persistent Infection With Nonvaccine Oncogenic Hpv Types Using An Alternative Multiplex Type-specific Pcr Assay For Hpv Dna.

The efficacy of the human papillomavirus type 16 (HPV-16)/HPV-18 AS04-adjuvanted vaccine against cervical infections with HPV in the Papilloma Trial against Cancer in Young Adults (PATRICIA) was evaluated using a combination of the broad-spectrum L1-based SPF10 PCR-DNA enzyme immunoassay (DEIA)/line probe assay (LiPA25) system with type-specific PCRs for HPV-16 and -18. Broad-spectrum PCR assays may underestimate the presence of HPV genotypes present at relatively low concentrations in multiple infections, due to competition between genotypes. Therefore, samples were retrospectively reanalyzed using a testing algorithm incorporating the SPF10 PCR-DEIA/LiPA25 plus a novel E6-based multiplex type-specific PCR and reverse hybridization assay (MPTS12 RHA), which permits detection of a panel of nine oncogenic HPV genotypes (types 16, 18, 31, 33, 35, 45, 52, 58, and 59). For the vaccine against HPV types 16 and 18, there was no major impact on estimates of vaccine efficacy (VE) for incident or 6-month or 12-month persistent infections when the MPTS12 RHA was included in the testing algorithm versus estimates with the protocol-specified algorithm. However, the alternative testing algorithm showed greater sensitivity than the protocol-specified algorithm for detection of some nonvaccine oncogenic HPV types. More cases were gained in the control group than in the vaccine group, leading to higher point estimates of VE for 6-month and 12-month persistent infections for the nonvaccine oncogenic types included in the MPTS12 RHA assay (types 31, 33, 35, 45, 52, 58, and 59). This post hoc analysis indicates that the per-protocol testing algorithm used in PATRICIA underestimated the VE against some nonvaccine oncogenic HPV types and that the choice of the HPV DNA testing methodology is important for the evaluation of VE in clinical trials. (This study has been registered at ClinicalTrials.gov under registration no. NCT00122681.).