Characterization of Hepatitis B virus (HBV) genotypes in patients from Rondônia, Brazil

Abstract Background Hepatitis B virus (HBV) can be classified into nine genotypes (A-I) defined by sequence divergence of more than 8% based on the complete genome. This study aims to identify the genotypic distribution of HBV in 40 HBsAg-positive patients from Rondônia, Brazil. A fragment of 1306 bp partially comprising surface and polymerase overlapping genes was amplified by PCR. Amplified DNA was purified and sequenced. Amplified DNA was purified and sequenced on an ABI PRISM® 377 Automatic Sequencer (Applied Biosystems, Foster City, CA, USA). The obtained sequences were aligned with reference sequences obtained from the GenBank using Clustal X software and then edited with Se-Al software. Phylogenetic analyses were conducted by the Markov Chain Monte Carlo (MCMC) approach using BEAST v.1.5.3. Results The subgenotypes distribution was A1 (37.1%), D3 (22.8%), F2a (20.0%), D4 (17.1%) and D2 (2.8%). Conclusions These results for the first HBV genotypic characterization in Rondônia state are consistent with other studies in Brazil, showing the presence of several HBV genotypes that reflects the mixed origin of the population, involving descendants from Native Americans, Europeans, and Africans.

Studio genetico ed epidemiologico su Erysiphe necator agente eziologico dell'Oidio della vite

The objective was to analyse population structure and to determine genetic diversity of Erysiphe necator (syn. Uncinula necator) populations obtained from some vineyards located in the South-East Po valley (Italy). Powdery mildew is one of the most important fungal diseases of grapes (Vitis vinifera L.) throughout the world. The causal agent is the haploid, heterothallic ascomycete E. necator. It is an obligate biotrophic fungus and it can be found only on green organs of plants belonging to the family Vitaceae. For this pathogen, two sympatric populations (groups A and B) have been described in Europe and Australia. The two genetic groups differ at multiple genetic loci and previous studies reported a lack of interfertility among isolates of the two groups. There are now several well documented examples of plant pathogen species, such as Leptosphaeria maculans, Gaeumannomyces graminis var. tritici, Botrytis cinerea and Erysiphe syringae, which are indeed composed of genetically differentiated clades, that have led to the description of new groups or even new species. Several studies have suggested that genetic E. necator group A and B correlated with ecological features of the pathogen; some researchers proposed that group A isolates over-winter as resting mycelium within dormant buds, and in spring originate infected shoots, known as Flag shoots, while group B isolates would survive as ascospores in overwintering cleistothecia. However, the association between genetic groups and mode of over-wintering has been challenged by recent studies reporting that flag-shoot may be originated indifferently by group A or group B isolate. Previous studies observed a strong association between the levels of disease severity at the end of the growing season and the initial compositions of E. necator populations in commercial vineyards. The frequencies of E. necator genetic groups vary considerably among vineyards, and the two groups may coexist in the same vineyard. This finding suggests that we need more information on the genetics and epidemiology of E. necator for optimize the crop management In this study we monitored E. necator populations in different vineyards in Emilia – Romagna region (Italy), where the pathogen overwinters both as flagshoots and as cleistothecia. During the grape growing season, symptomatic leaves were sampled early in the growing season and both leaves and berries later during the epidemic growth of the disease. From each sample, single-conidial isolate was obtained. Each isolates was grown on V. vinifera leaf cv. Primitivo and after harvesting the mycelium, the DNA was purified and used as template for PCR amplification with SCAR primers (Sequences Characterised Amplified Region ), -tubulin, IGS sequences and Microsatellite markers (SSR). Amplified DNA from b-tubulin and IGS loci was digested with AciI and XhoI restriction enzymes, respectively, to show single-nucleotide polymorphisms specific for the two genetic groups. The results obtained indicated that SCAR primers are not useful to study the epidemiology. of E. necator conversely the b-tubulin IGS sequences and SSR. Summarize the results obtained with b-tubulin, IGS sequences, in treated vineyards we have found individuals of group B along all grape growing season, whereas in the untreated vineyard individuals of the two genetic groups A and B coexisted throughout the season, with no significant change of their frequency. DNA amplified from ascospores of single cleistothecia showed the presence of markers diagnostic for either groups A and B and were seldom observed also the coexistence of both groups within a claistothecium. These results indicate that individuals of the two groups mated in nature and were able to produced ascospores. With SSR we showed the possibility of recombination between A and B groups in field isolates. During winter, cleistothecia were collected repeatedly in the same vineyards sampling leaves fallen on ground, exfoliating bark from trunks, and from soil. From each substrate, was assess the percentage of cleistothecia containing viable ascospores. Our results confirmed that cleisthotecia contained viable ascospores, therefore they have the potential to be an additional and important source of primary inoculum in Emilia-Romagna vineyards.

Genomisches Imprinting Beckwith-Wiedemann-Syndrom assoziierter Gene

In der vorliegenden Arbeit wurde das Imprinting von Genen der Chromosomenregion 11p15.5 des Menschen und des orthologen murinen Abschnitts 7F5 untersucht. Bei der Analyse der humanen Gene H19, IGF2 und KCNQ1OT1 stand deren Regulation durch differentiell methylierte Regionen (DMR) und die Identifizierung von Methylierungsfehlern bei Patienten mit Verdacht auf Beckwith-Wiedemann Syndrom (BWS) im Vordergrund. Hierzu wurden unmethylierte Cytosinnukleotide durch Bisulfitbehandlung in Uracilnukleotide umgewandelt und PCR-amplifizierte DNA-Fragmente sequenziert. Die elterliche Herkunft der Allele wurde mit Hilfe von Einzelnukleotidpolymorphismen (SNP) bestimmt. Während in der H19-Promotorregion in Lymphozyten eine nur tendenziell allelspezifische Methylierung festgestellt werden konnte, wurde im B1-Repeat der H19/IGF2-Region in allen Kontroll- und 20 Patienten-DNAs eine spezifische Methylierung des väterlichen Allels nachgewiesen. Vier BWS-DNAs zeigten hingegen eine nahezu vollständige Hypomethylierung. In der zwe

Identifizierung biogene Amine bildender Bakterien und Einsatz von Enzymen zur Hemmung ihres Wachstums während der Weinbereitung

Mikroorganismen spielen eine wichtige Rolle in der Weinherstellung. Neben ihren positiven Stoffwechselaktivitäten wie die Bildung von Ethanol während der alkoholischen Gärung sind vor allem Bakterien in der Lage, Weinfehler zu verursachen. Einer dieser Weinfehler ist die Produktion von biogenen Aminen. Diese niedermolekularen Stickstoffverbindungen können zu verschiedenen Gesundheitsproblemen wie Bluthochdruck und Migräne führen. Aufgrund von hohen Ethanolgehalten und dem Vorkommen verschiedener biogener Amine kommt es im Wein zu einer Verstärkung dieser physiologischen Effekte. Um die Bildung dieser Verbindungen zu verhindern, ist es von speziellem Interesse, die verantwortlichen Mikroorganismen zu identifizieren und sie in ihrem Wachstum zu hemmen.In einem Teil der Dissertation stand die Isolierung und Identifizierung biogener Amine produzierender Bakterien aus deutschen Jungweinen und Mosten im Vordergrund. Es konnte gezeigt werden, dass hauptsächlich Milchsäurebakterien als potenzielle Produzenten in Frage kommen. Diese Bakteriengruppe war in hohen Titern in nahezu allen Proben vorhanden und stellt somit eine potentielle Gefahr für die Weinbereitung dar. Zur Identifizierung der Isolate wurden verschiedene molekularbiologische Methoden wie specifically amplified DNA polymorphic-PCR (Fingerprintmethode), Multiplex-PCR oder 16S rDNA-Sequenzierung angewandt. Das Screening bezüglich der Bildung von biogenen Aminen erfolgte mit Hilfe einer im Rahmen dieser Arbeit entwickelten hochauflösenden Dünnschichtchromatographie gefolgt von der Quantifizierung mittels HPLC.Zur Wachstumshemmung dieser Schadbakterien wurden zwei Exoenzyme aus Streptomyces albidoflavus B578 isolieren. Diese Enzyme wurden gereinigt und als eine Muramidase und eine Protease identifiziert. Aktivitätstests konnten zeigen, dass diese Enzyme eine hohe lytische Wirkung gegen weinrelevante Mikroorganismen aufweisen. Ebenso war die Aktivität der Enzyme unter Weinbedingungen sehr stabil. Aufgrund dieser Ergebnisse könnten diese Enzyme eine mögliche Alternative zur Zugabe von Lysozym oder Schwefeldioxid sein, welche konventionell in der Weinbereitung ihren Einsatz finden.

Homozygous Cys542-->Arg substitution in GPIIIa in a Swiss patient with type I Glanzmann's thrombasthenia

Glanzmann's thrombasthenia (GT) arises from a qualitative or quantitative defect in the GPIIb-IIIa complex (integrin alphaIIbbeta3), the mediator of platelet aggregation. We describe a patient in whom clinical and laboratory findings typical of type I GT were found together with a second pathology involving neurological and other complications symptomatic of tuberous sclerosis. Analysis of platelet proteins by Western blotting revealed trace amounts of normally migrating GPIIb and equally small amounts of GPIIIa of slightly slower than normal migration. Flow cytometry confirmed a much decreased binding to platelets of monoclonal antibodies to GPIIb, GPIIIa or GPIIb-IIIa, and an antibody to the alphav subunit also showed decreased binding. Nonradioactive PCR single-strand conformation polymorphism analysis followed by direct sequencing of PCR-amplified DNA fragments showed a homozygous point mutation (T to C) at nucleotide 1722 of GPIIIa cDNA and which led to a Cys542-->Arg substitution in the GPIIIa protein. The mutation gave rise to a HinP1 I restriction site in exon 11 of the GPIIIa gene and allele-specific restriction enzyme analysis of family members confirmed that a single mutated allele was inherited from each parent. This amino acid substitution presumably changes the capacity for disulphide bond formation within the cysteine-rich core region of GPIIIa and its study will provide new information on GPIIb-IIIa and alphavbeta3 structure and biosynthesis.

Molecular characterisation of BSR4, a novel bradyzoite-specific gene from Neospora caninum

Here we present the identification and cloning of the NcBSR4 gene, the putative Neospora caninum orthologue to the Toxoplasma gondii TgBSR4 gene. To isolate NcBSR4, genome walking PCR was performed on N. caninum genomic DNA using the expressed sequence tag NcEST3c28h02.y1 sequence, which shares a 44% identity with the TgBSR4 gene, as a framework. Nucleotide sequencing of amplified DNA fragments revealed a single uninterrupted 1227 bp open reading frame that encodes a protein of 408 amino acids with 66% similarity to the TgBSR4 antigen. A putative 39-residue signal peptide was found at the NH2-terminus, followed by a hydrophilic region. At the COOH-terminus, a potential site for a glycosylphosphatidylinositol anchor was identified at amino acid 379. A polyclonal serum against recombinant NcBSR4 protein was raised in rabbits, and immunolabelling demonstrated stage-specific expression of the NcBSR4 antigen in N. caninum bradyzoites produced in vitro and in vivo. Furthermore, RT-PCR analysis showed a slight increase of NcBSR4 transcripts in bradyzoites generated during in vitro tachyzoite-to-bradyzoite stage-conversion, suggesting that this gene is specifically expressed at the bradyzoite stage and that its transcription relies on the switch to this stage.

Application of real-time fluorescent PCR for quantitative assessment of Neospora caninum infections in organotypic slice cultures of rat central nervous system tissue

The previously described Nc5-specific PCR test for the diagnosis of Neospora caninum infections was used to develop a quantitative PCR assay which allows the determination of infection intensities within different experimental and diagnostic sample groups. The quantitative PCR was performed by using a dual fluorescent hybridization probe system and the LightCycler Instrument for online detection of amplified DNA. This assay was successfully applied for demonstrating the parasite proliferation kinetics in organotypic slice cultures of rat brain which were infected in vitro with N. caninum tachyzoites. This PCR-based method of parasite quantitation with organotypic brain tissue samples can be regarded as a novel ex vivo approach for exploring different aspects of cerebral N. caninum infection.

NRAS and BRAF mutations in primary cutaneous melanoma: A comparison of mutation rates between radial and vertical growth phases in individual tumors

Primary cutaneous melanoma is a cancer arising from melanocytes in the skin. In recent decades the incidence of this malignancy has increased significantly. Mortality rates are high for patients with tumors measuring over a few millimeters in thickness. Response rates to conventional radiation and chemotherapy are very low in patients with metastatic melanoma. New therapies targeting melanoma’s aberrant cell signaling pathways such as the MAP Kinase pathway are being developed. Mutations of NRAS and BRAF genes are quite common in cutaneous melanoma and lead to constitutive activation of the MAP Kinase pathway. This study tests the hypothesis that NRAS and BRAF mutations increase as a tumor progresses from the noninvasive radial growth phase (RGP) to the invasive vertical growth phase (VGP). Laser capture microdissection was used to obtain separate, pure tumor DNA samples from the RGP and VGP of thirty primary cutaneous melanomas. PCR was used to amplify NRAS exon 2 and BRAF exon 15 tumor DNA. The amplified DNA was sequenced and analyzed for mutations. An overall mutation rate of 74% was obtained for the twenty-three melanomas in which there were complete sequence results. With the exception of one melanoma NRAS and BRAF mutations were mutually exclusive. All seven NRAS exon 2 mutations involved codon 61. Three of these melanomas had mutations in both the RGP and VGP. The remaining four tumors were wild type for NRAS exon 2 in the RGP but mutated in the VGP. Of the fifteen BRAF exon 15 mutated melanomas all but one involved codon 600. Twelve of the fifteen BRAF exon 15 mutations were the T1799A type. Nine of the fifteen BRAF mutated tumors had the same mutation in both the RGP and VGP. Five of fifteen melanomas had wild type RGP DNA and BRAF exon 15 mutated VGP DNA. A single melanoma had BRAF exon 15 mutated DNA in the RGP and wild type DNA in the VGP. Overall, these results suggest a trend toward the acquisition of NRAS and BRAF mutations as cutaneous melanomas change from a noninvasive to an invasive, potentially deadly cancer.^

Effectiveness of AFLPs and retrotransposon-based markers for the identification of portuguese grapevine cultivars and clones

Grapevine germplasm, including 38 of the main Portuguese cultivars and three foreign cultivars, Pinot Noir, Pinot Blanc and Chasselas, used as a reference, and 37 true-to-type clones from the Alvarinho, Arinto, Loureiro, Moscatel Galego Branco, Trajadura and Vinhão cultivars were studied using AFLP and three retrotransposon-based molecular techniques, IRAP, REMAP and SSAP. To study the retrotransposon-based polymorphisms, 18 primers based on the LTR sequences of Tvv1, Gret1 and Vine-1 were used. In the analysis of 41 cultivars, 517 IRAP, REMAP, AFLP and SSAP fragments were obtained, 83% of which were polymorphic. For IRAP, only the Tvv1Fa primer amplified DNA fragments. In the REMAP analysis, the Tvv1Fa-Ms14 primer combination only produced polymorphic bands, and the Vine-1 primers produced mainly ISSR fragments. The highest number of polymorphic fragments was found for AFLP. Both AFLP and SSAP showed a greater capacity for identifying clones, resulting in 15 and 9 clones identified, respectively. Together, all of the techniques allowed for the identification of 54% of the studied clones, which is an important step in solving one of the challenges that viticulture currently faces.

Analysis of genomic alterations in benign, atypical, and anaplastic meningiomas: Toward a genetic model of meningioma progression

Nineteen benign [World Health Organization (WHO) grade I; MI], 21 atypical (WHO grade II; MII), and 19 anaplastic (WHO grade III; MIII) sporadic meningiomas were screened for chromosomal imbalances by comparative genomic hybridization (CGH). These data were supplemented by molecular genetic analyses of selected chromosomal regions and genes. With increasing malignancy grade, a marked accumulation of genomic aberrations was observed; i.e., the numbers (mean ± SEM) of total alterations detected per tumor were 2.9 ± 0.7 for MI, 9.2 ± 1.2 for MII, and 13.3 ± 1.9 for MIII. The most frequent alteration detected in MI was loss on 22q (58%). In MII, aberrations most commonly identified were losses on 1p (76%), 22q (71%), 14q (43%), 18q (43%), 10 (38%), and 6q (33%), as well as gains on 20q (48%), 12q (43%), 15q (43%), 1q (33%), 9q (33%), and 17q (33%). In MIII, most of these alterations were found at similar frequencies. However, an increase in losses on 6q (53%), 10 (68%), and 14q (63%) was observed. In addition, 32% of MIII demonstrated loss on 9p. Homozygous deletions in the CDKN2A gene at 9p21 were found in 4 of 16 MIII (25%). Highly amplified DNA sequences were mapped to 12q13–q15 by CGH in 1 MII. Southern blot analysis of this tumor revealed amplification of CDK4 and MDM2. By CGH, DNA sequences from 17q were found to be amplified in 1 MII and 8 MIII, involving 17q23 in all cases. Despite the high frequency of chromosomal aberrations in the MII and MIII investigated, none of these tumors showed mutations in exons 5–8 of the TP53 gene. On the basis of the most common aberrations identified in the various malignancy grades, a model for the genomic alterations associated with meningioma progression is proposed.

Identification of a new calcitonin gene in the salmon Oncorhynchus gorbuscha.

Three isoforms of calcitonin (CT) exist in salmonids. Isohormones I and II are expressed in the pink salmon Oncorhynchus gorbuscha. We report here the existence in this species of a CT gene and of its transcripts, which encode for a fourth isohormone, the salmon CT (sCT) IV. This new CT gene was identified by PCR from genomic DNA and by sequencing the amplified DNA. The expression of this CT gene was established in ultimobranchial body and brain, by reverse transcription-PCR, hybridization and sequencing. The sCT IV gene, like the sCT I gene, is a complex transcription unit, containing exons encoding for a CT as a calcitonin gene-related peptide (CGRP) molecule. The predicted peptide, sCT IV, has a greater homology with the eel CT and the sCT II than with the sCT I. Alignment of the sCT IV with other fish and chicken CT showed amino acid modifications in similar positions as those found during evolution. The predicted salmon CGRP IV peptide is highly homologous to the known CGRP molecules in other species, confirming the high conservation of the molecule during evolution. This identification of a new salmon CT gene is interesting both for the therapeutic potential represented by the new molecules encoded by this gene and for phylogenetic studies.

Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination.

The life history of Candida albicans presents an enigma: this species is thought to be exclusively asexual, yet strains show extensive phenotypic variation. To address the population genetics of C. albicans, we developed a genetic typing method for codominant single-locus markers by screening randomly amplified DNA for single-strand conformation polymorphisms. DNA fragments amplified by arbitrary primers were initially screened for single-strand conformation polymorphisms and later sequenced using locus-specific primers. A total of 12 single base mutations and insertions were detected from six out of eight PCR fragments. Patterns of sequence-level polymorphism observed for individual strains detected considerable heterozygosity at the DNA sequence level, supporting the view that most C. albicans strains are diploid. Population genetic analyses of 52 natural isolates from Duke University Medical Center provide evidence for both clonality and recombination in C. albicans. Evidence for clonality is supported by the presence of several overrepresented genotypes, as well as by deviation of genotypic frequencies from random (Hardy-Weinberg) expectations. However, tests for nonrandom association of alleles across loci reveal less evidence for linkage disequilibrium than expected for strictly clonal populations. Although C. albicans populations are primarily clonal, evidence for recombination suggests that sexual reproduction or some other form of genetic exchange occurs in this species.

Genetic diversity revealed in the apomictic fruit species Garcinia mangostana L. (mangosteen)

The novel molecular marker technique Randomly Amplified DNA Fingerprinting (RAF) was used to survey genetic relationships between 37 accessions of the tropical fruit G. mangostana (mangosteen) and among 11 accessions from eight other Garcinia species. Although mangosteen is believed to reproduce exclusively through apomixis, our results show that considerable genetic diversity exists within G. mangostana and between other Garcinia species. Among the 37 G. mangostana accessions examined, nine different genotypes were identified which clustered into three distinct groups based on correspondence analysis (reciprocal averaging). For 26 (70%) of the accessions no marker variation was detected over 530 loci screened. A further eight (22%) accessions exhibited very low levels of variation (0.2-1%) suggesting at least one well conservedm angosteen genotype. The remaining three accessions (8%) showed extensive variation (22-31%) compared with the majority of accessions. The three mangosteen groups were 63-70% dissimilar to the other Garcinia species investigated. The genetic diversity identified in this research will assist in the conservation of Garcinia germplasm and provides a valuable framework for the genetic improvement of mangosteen.

Fine mapping of the tomato I-3 gene for fusarium wilt resistance and elimination of a co-segregating resistance gene analogue as a candidate for I-3

The I-3 gene from the wild tomato species Lycopersicon pennellii confers resistance to race 3 of the devastating vascular wilt pathogen Fusarium oxysporum f. sp. lycopersici. As an initial step in a positional cloning strategy for the isolation of I-3, we converted restriction fragment length polymorphism and conserved orthologue set markers, known genes and a resistance gene analogue (RGA) mapping to the I-3 region into PCR-based sequence characterised amplified region (SCAR) and cleaved amplified polymorphic sequence (CAPS) markers. Additional PCR-based markers in the I-3 region were generated using the randomly amplified DNA fingerprinting (RAF) technique. SCAR, CAPS and RAF markers were used for high-resolution mapping around the I-3 locus. The I-3 gene was localised to a 0.3-cM region containing a RAF marker, eO6, and an RGA, RGA332. RGA332 was cloned and found to correspond to a putative pseudogene with at least two loss-of-function mutations. The predicted pseudogene belongs to the Toll interleukin-1 receptor-nucleotide-binding site-leucine-rich-repeat sub-class of plant disease resistance genes. Despite the presence of two RGA332 homologues in L. esculentum, DNA gel blot and PCR analysis suggests that no other homologues are present in lines carrying I-3 that could be alternative candidates for the gene.

A comparison of molecular markers for genetic analysis of macadamia

Various marker systems exist for genetic analysis of horticultural species. Isozymes were first applied to the woody perennial nut crop, macadamia, in the early 1990s. The advent of DNA markers saw the development, for macadamia, of STMS (sequence-tagged microsatellite site), RAPD (randomly amplified polymorphic DNA), and RAF (randomly amplified DNA fingerprinting). The RAF technique typically generates dominant markers, but within the dominant marker profiles, certain primers also amplify multi-allelic co-dominant markers that are suspected to be microsatellites. In this paper, we confirm this for one such marker, and describe how RAF primers can be chosen that amplify one or more putative microsatellites. This approach of genotyping anonymous microsatellite markers via RAF is designated RAMiFi (randomly amplified microsatellite fingerprinting). Several marker systems were compared for the type, amount, and cost-efficiency of the information generated, using data from published studies on macadamia. The markers were also compared for the way they clustered a common set of accessions. The RAMiFi approach was identified as the most efficient and economical. The availability of such a versatile tool offers many advantages for the genetic characterisation of horticultural species.