flavio araujo - Academia.edu (original) (raw)

Papers by flavio araujo

Research paper thumbnail of Depress�o em esquizofrenia

Research paper thumbnail of Qualidade de vida em cuidadores de idosos portadores de demência de Alzheimer

Jornal Brasileiro de Psiquiatria, 2008

Qualidade de vida, cuidadores, demência. rEsumo objetivo: Realizar revisão sistemática da literat... more Qualidade de vida, cuidadores, demência. rEsumo objetivo: Realizar revisão sistemática da literatura acerca da QV dos cuidadores de idosos com DA. métodos: Revisão sistemática de literatura por meio do PubMed e da MedLine entre os anos de 1997 e 2008, utilizando os termos quality of life, caregivers, Alzheimer disease. resultados: Dezesseis estudos entre 274 publicações iniciais e 39 artigos posteriormente incluídos pelas referências bibliográficas foram avaliados. A QV dos cuidadores dos idosos demenciados, na maioria dos estudos, estava comprometida negativamente. Diversos fatores interferem na QV do cuidador, desde a gravidade da doença até alterações comportamentais que esses idosos possam vir a apresentar. Conclusão: É necessária a realização de mais estudos direcionados a esse tema, a fim de buscar estratégias para melhora da QV desse cuidador. aBstraCt Objective: Carry out a systematic bibliographycal review about QL of the caregivers of in the elderly with AD. Methods: A systematic bibliographical review about studies indexed on Pubmed and MedLine, from 1997 to 2008, using as key-words the terms: quality of life, caregivers, Alzheimer Disease. Results: Sixteen of the 274 initial articles and 39 additional papers included in a following phase, based on bibliographical references, were evaluated. A negative impairment in QL of the caregivers of demential in the elderly has been documented in most studies. Several factors affect the caregivers' quality of life, such as severity of the patient's illness and behavior disorders of elderly. Conclusion: Futures studies on this theme will be necessary to look for strategies. Recebido em 22/10/2008 Aprovado em 5/12/2008

Research paper thumbnail of Depressão em esquizofrenia

Revista Brasileira de Psiquiatria, 2002

ABSTRACT Realizou-se uma revisão da literatura acerca da presença de depressão em pacientes esqui... more ABSTRACT Realizou-se uma revisão da literatura acerca da presença de depressão em pacientes esquizofrênicos e, em particular, da depressão pós-esquizofrênica (DPE). A pesquisa foi realizada por meio do Medline, envolvendo os anos de 1966 e 2000, com o objetivo de identificar artigos originais e de revisão. Focalizaram-se os seguintes tópicos: dados históricos, principais estudos, quadro clínico e curso evolutivo, diagnóstico e diagnóstico diferencial, etiopatogenia e prognóstico. Conclui-se que a depressão pós-esquizofrênica tem plena autonomia sindrômica, deve ser considerada uma manifestação clínica das formas delirantes da esquizofrenia e integra o curso evolutivo de um transtorno esquizofrênico.

Research paper thumbnail of Characterization of depressive syndrome in schizophrenic outpatients

Revista Brasileira de Psiquiatria, 2002

ABSTRACT OBJECTIVE: The authors carried out a cross-sectional study with the aim of characterizin... more ABSTRACT OBJECTIVE: The authors carried out a cross-sectional study with the aim of characterizing and describing depressive pictures in schizophrenic patients seen at the Psychiatry Outpatient Clinic of the Federal University of Pernambuco (HC-UFPE). The patients had the diagnosis of schizophrenia confirmed on the basis of the operating criteria of the DSM-IV. METHODS: Those who where in the period of stabilization of the clinical picture were selected for the study defined according the following criteria:the last psychotic episode must be happened two months before at least, and during this period the alterations of the antipsychotics doses had been lower than 5 mg of haloperidol or equivalent doses of others neuroleptics. A total of one hundred and four patients took part. Following the identification of the depressive symptoms using the Calgary Depression Scale for Schizophrenia (CDSS), thirty-one patients (29.8%) fulfilled the diagnostic criteria described in the DSM-IV. Of these, 22.1% had the diagnosis of major depression and 7.7% of minor depression according the DSM-IV. Two groups were constituted: Group A, schizophrenics with a depressive syndrome, and Group B, schizophrenics without such a syndrome. An assessment was made of the distribution of the symptoms of the CDSS scores in both groups, the sociodemographic, clinical and therapeutic variables in relation to the frequency of the depressive syndrome, and the patients clinical course. For the investigation of certain clinical features, the following tools were used: problem list (psychosocial stressors) contained in axis IV of the DSM-IV intended to detect the presence of factors triggering the initial episode of schizophrenia and the Global Assessment of Functioning (GAF -- Axis V -- DSM-IV) to characterize the current functioning of the patients. CONCLUSIONS: The results obtained allowed the authors to draw the following conclusions: all the items that comprise the Brazilian version of the CDSS were statistically significant in characterizing the depressive syndrome; a comparison of the sociodemographic and therapeutic variables revealed no statistically significant differences between the two groups, and this was also the case with the majority of the clinical features. Statistically significant differences, however, were found in relation to the greater frequency of life events (psychosocial stressors) in triggering the first episode of schizophrenia and the higher incidence of affective disorders antecedents in family members (first and second degree) among the depressed patients. The mean duration of the depressive syndrome during follow-up of the patients was 5.30 months. The patients in whom there was a recurrence of the psychotic episode presented a delusional-hallucinatory clinical picture. This study seeks to contribute to the inclusion of the Postpsychotic Depressive Disorder (PSD) of Schizophrenia (DSM-IV), in the group of Schizophrenic Disorders.

Research paper thumbnail of Automatic Detection of Glaucoma Using Disc Optic Segmentation and Feature Extraction

2015 Latin American Computing Conference (CLEI), 2015

Research paper thumbnail of Evaluation of the use of computational intelligence techniques in medical claim processes of a health insurance company

Proceedings of the 26th IEEE International Symposium on Computer-Based Medical Systems, 2013

ABSTRACT Brazil has one of the largest private healthcare markets in the world. However, it appea... more ABSTRACT Brazil has one of the largest private healthcare markets in the world. However, it appears that many indicators of our health insurance companies (including consultations, tests, hospitalizations, etc.) are well above the established international standards. This indicates that many appointments and tests are being carried out without need, generating unnecessary costs on businesses and making the service offered more expensive. In this paper, computational intelligence techniques were used to model the behavior of medical reviewers - professionals who assess whether medical requests should be allowed or not. For the generation of knowledge, a database from a nonprofitable health insurance company containing more than one million records collected since the year 2007 was used. Promising experimental results are presented, indicating that the techniques used can support medical reviewers.

Research paper thumbnail of Evaluation of the toxicokinetics and apoptotic potential of ethanol extract from Echinodorus macrophyllus leaves in vivo

Regulatory toxicology and pharmacology : RTP, Jan 25, 2016

This study evaluates the toxicological, genotoxic, mutagenic and apoptotic potential of an in viv... more This study evaluates the toxicological, genotoxic, mutagenic and apoptotic potential of an in vivo assay from Echinodorus macrophyllus extract (EEM). The acute toxicity test used 02 groups (n = 5) of female Wistar rats: negative control group (saline) and experimental group (2000 mg/kg b.w. EEM), both orally administered (gavage) at single doses and monitored for 14 days. To assess the genotoxic, mutagenic and apoptotic potential, 50 male Swiss mice were divided into 5 groups (n = 10): Group I: negative control (saline solution 0.1 ml/10 g b.w.); Group II: positive control (cyclophosphamide 100 mg/kg b.w.) intraperitoneally administered; groups III-V received EEM at 500, 1000 and 2000 mg/kg b.w., respectively. Groups I, III-V received oral administrations (gavage). The results showed that there was no acute lethality or any signs of acute toxicity, indicating that LD50 is greater than 2000 mg/kg b.w. The groups treated with EEM showed no genotoxic or mutagenic activity and did not i...

Research paper thumbnail of The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases

BMC genomics, Jan 27, 2017

The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the c... more The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools. We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a cor...

Research paper thumbnail of Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance

Mammalian Genome, 2016

In bovines, artificial selection has produced a large number of breeds which differ in production... more In bovines, artificial selection has produced a large number of breeds which differ in production, environmental adaptation, and health characteristics. To investigate the genetic basis of these phenotypical differences, several bovine breeds have been sequenced. Millions of new SNVs were described at every new breed sequenced, suggesting that every breed should be sequenced. Guzerat or Guzerá is an indicine breed resistant to drought and parasites that has been the base for some important breeds such as Brahman. Here, we describe the sequence of the Guzerá genome and the in silico functional analyses of intragenic breed-specific variations. Mate-paired libraries were generated using the ABI SOLiD system. Sequences were mapped to the Bos taurus reference genome (UMD 3.1) and 87% of the reference genome was covered at a 26X. Among the variants identified, 2,676,067 SNVs and 463,158 INDELs were homozygous, not found in any database searched, and may represent true differences between Guzerá and B. taurus. Functional analyses investigated with the NGS-SNP package focused on 1069 new, non-synonymous SNVs, splice-site variants (including acceptor and donor sites, and the conserved regions at both intron borders, referred to here as splice regions) and coding INDELs (NS/SS/I). These NS/SS/I map to 935 genes belonging to cell communication, environmental adaptation, signal transduction, sensory, and immune systems pathways. These pathways have been involved in phenotypes related to health, adaptation to the environment and behavior, and particularly, disease resistance and heat tolerance. Indeed, 105 of these genes are known QTLs for milk, meat and carcass, production, reproduction, and health traits. Therefore, in addition to describing new genetic variants, our approach provided groundwork for unraveling key candidate genes and mutations.

Research paper thumbnail of Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs

Genetics and molecular biology, Jan 31, 2016

This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle devel... more This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myo...

Research paper thumbnail of Draft Genome Sequence of Hydrotalea flava Strain CCUG 51397T

Genome announcements, Jan 9, 2016

We report the draft genome sequence of Hydrotalea flava CCUG 51397(T), the type strain of the gen... more We report the draft genome sequence of Hydrotalea flava CCUG 51397(T), the type strain of the genus Hydrotalea (family Chitinophagaceae), isolated from water samples in southern Sweden.

Research paper thumbnail of FluxNGS: a data management system for next-generation sequencing protocols and data

F1000posters, Nov 1, 2011

DNA sequencing has become an indispensable tool for basic biological research. Modern sequencing ... more DNA sequencing has become an indispensable tool for basic biological research. Modern sequencing methods allowed exponential growth of sequenced DNA data generation leading to the development of the process called Next Generation Sequencing (NGS). The amount of data generated by NGS is not compatible with manual storage and management and computational systems (LIMS) have been developed for data input and flux control. In this work we present FluxNGS, a web based LIMS developed to store and manage protocols and data from sequencing laboratories using the NGS Solid TM technology.

Research paper thumbnail of Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis

PloS one, 2015

Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better compr... more Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40-50%), Bacteroidetes (~15-25%) and Proteobacteria (~5-25%), in addition to ~10-20% of non-classified bacteria. 45-55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vagi...

Research paper thumbnail of HIV-1 Tropism Determines Different Mutation Profiles in Proviral DNA

PLOS ONE, 2015

In order to establish new infections HIV-1 particles need to attach to receptors expressed on the... more In order to establish new infections HIV-1 particles need to attach to receptors expressed on the cellular surface. HIV-1 particles interact with a cell membrane receptor known as CD4 and subsequently with another cell membrane molecule known as a co-receptor. Two major different co-receptors have been identified: C-C chemokine Receptor type 5 (CCR5) and C-X-C chemokine Receptor type 4 (CXCR4) Previous reports have demonstrated cellular modifications upon HIV-1 binding to its co-receptors including gene expression modulations. Here we investigated the effect of viral binding to either CCR5 or CXCR4 co-receptors on viral diversity after a single round of reverse transcription. CCR5 and CXCR4 pseudotyped viruses were used to infect non-stimulated and stimulated PBMCs and purified CD4 positive cells. We adopted the SOLiD methodology to sequence virtually the entire proviral DNA from all experimental infections. Infections with CCR5 and CXCR4 pseudotyped virus resulted in different patterns of genetic diversification. CCR5 virus infections produced extensive proviral diversity while in CXCR4 infections a more localized substitution process was observed. In addition, we present pioneering results of a recently developed method for the analysis of SOLiD generated sequencing data applicable to the study of viral quasi-species. Our findings demonstrate the feasibility of viral quasi-species evaluation by NGS methodologies. We presented for the first time strong evidence for a host cell driving mechanism acting on the HIV-1 genetic variability under the control of co-receptor stimulation. Additional investigations are needed to further clarify this question, which is relevant to viral diversification process and consequent disease progression.

Research paper thumbnail of Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment

PLOS ONE, 2015

Here, we describe the metagenome and functional composition of a microbial community in a histori... more Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.

Research paper thumbnail of CA88, a nuclear repetitive DNA sequence identified in Schistosoma mansoni, aids in the genotyping of nine Schistosoma species of medical and veterinary importance

Memórias do Instituto Oswaldo Cruz, 2010

CA88 is the first long nuclear repetitive DNA sequence identified in the blood fluke, Schistosoma... more CA88 is the first long nuclear repetitive DNA sequence identified in the blood fluke, Schistosoma mansoni. The assembled S. mansoni sequence, which contains the CA88 repeat, has 8,887 nucleotides and at least three repeat units of approximately 360 bp. In addition, CA88 also possesses an internal CA microsatellite, identified as SmBr18. Both PCR and BLAST analysis have been used to analyse and confirm the CA88 sequence in other S. mansoni sequences in the public database. PCR-acquired nuclear repetitive DNA sequence profiles from nine Schistosoma species were used to classify this organism into four genotypes. Included among the nine species analysed were five sequences of both African and Asian lineages that are known to infect humans. Within these genotypes, three of them refer to recognised species groups. A panel of four microsatellite loci, including SmBr18 and three previously published loci, has been used to characterise the nine Schistosoma species. Each species has been identified and classified based on its CA88 DNA fingerprint profile. Furthermore, microsatellite sequences and intra-specific variation have also been observed within the nine Schistosoma species sequences. Taken together, these results support the use of these markers in studying the population dynamics of Schistosoma isolates from endemic areas and also provide new methods for investigating the relationships between different populations of parasites. In addition, these data also indicate that Schistosoma magrebowiei is not a sister taxon to Schistosoma mattheei, prompting a new designation to a basal clade. CA88, a nuclear repetitive • Diana Bahia et al. 392 Armour JA, Brinkworth MH, Kamischke A 1999. Direct analysis by small-pool PCR of MS205 minisatellite mutation rates in sperm after mutagenic therapies. Mutat Res 445: 73-80. Barker SC, Blair D 1996. Molecular phylogeny of Schistosoma species supports traditional groupings within the genus. J Parasitol 82: 292-298. Benson G 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573-580. Blair L, Webster JP, Barker GC 2001. Isolation and characterization of polymorphic microsatellite markers in Schistosoma mansoni from Africa. Mol Ecol Notes 1: 93-95. Christensen NO, Mutani A, Frandsen F 1983. A review of the biology and transmission ecology of African bovine species of the genus Schistosoma. Z Parasitenkd 69: 551-570. Collins HE, Li H, Inda SE, Anderson J, Laiho K, Tuomilehto J, Seldin MF 2000. A simple and accurate method for determination of microsatellite total allele content differences between DNA pools. Hum Genet 106: 218-226. Dabo A, Durand P, Morand S, Diakite M, Langand J, Imbert-Establet D, Doumbo O, Jourdane J 1997. Distribution and genetic diversity of Schistosoma haematobium within its bulinid intermediate hosts in Mali. Acta Trop 66: 15-26. A comprehensive genetic map of the mouse genome. Nature 380: 149-152. Durand P, Sire C, Théron A 2000. Isolation of microsatellite markers in the digenetic trematode Schistosoma mansoni from Guadeloupe island. Mol Ecol 9: 997-998. Eppert A, Lewis FA, Grzywacz C, Coura-Filho P, Caldas I, Minchella DJ 2002. Distribution of schistosome infections in molluscan hosts at different levels of parasite prevalence. J Parasitol 88: 232-236. Grossman Z, Ram D, Markovics A, Tarrab-Hazdai R, Lantner F, Ziv E, Schechter I 1990. Schistosoma mansoni: stage-specific expression of muscle-specific genes. Exp Parasitol 70: 62-71. Hagelberg E, Gray IC, Jeffreys AJ 1991. Identification of the skeletal remains of a murder victim by DNA analysis. Nature 352: 427-429. Hamada H, Petrino MG, Kakunaga T 1982. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79: 6465-6469. Hamburger J, He-Na, Abbasi I, Ramzy RM, Jourdane J, Ruppel A 2001. Polymerase chain reaction assay based on a highly repeated sequence of Schistosoma haematobium: a potential tool for monitoring schistosome-infested water. Am J Trop Med Hyg 65: 907-911. Huang x, Madan A 1999. CAP3: A DNA sequence assembly pro-CAP3: A DNA sequence assembly program. Genome Res 9: 868-877. Jarne P, Lagoda PJ 1996. Microsatellites, from molecules to popula-Microsatellites, from molecules to populations and back. Trends Ecol Evol 11: 424-429. Kalendar R 2003. Fast PCR: a program for fast design PCR primer, DNA and protein manipulation (version 2.5.59). Institute of Biotechnology, University of Helsinki. Kane RA, Southgate VR, Rollinson D, Littlewood DT, Lockyer AE, Pagès JR, Tchuem Tchuentè LA, Jourdane J 2003. A phylogeny based on three mitochondrial genes supports the division of Schistosoma intercalatum into two separate species. Parasitology 127: 131-137. Lipman DJ, Pearson WR 1985. Rapid and sensitive protein similarity searches. Science 227: 1435-1441. Littlewood DT, Johnston DA 1995. Molecular phylogenetics of the four Schistosoma species groups determined with partial 28S ribosomal RNA gene sequences. Parasitology 111: 167-175.

Research paper thumbnail of Genetic variability in the 5' UTR and NS5A regions of hepatitis C virus RNA isolated from non-responding and responding patients with chronic HCV genotype 1 infection

Memórias do Instituto Oswaldo Cruz, 2008

isolates has adaptive significance and reflects the modes and intensities of selection mechanisms... more isolates has adaptive significance and reflects the modes and intensities of selection mechanisms operating on the virus. In this work, we sought to investigate using classical population genetics parameters, the genetic variability of HCV genotype 1 using the 5` UTR and NS5A regions from treatment non-responding and responding groups of patients. Both regions showed low genetic variability and the 5` UTR showed neutral deviation. No differences were observed in the nonsynonymous/synonymous nucleotide substitution ratio among groups for NS5A. The analysis of molecular variance test of the 5` UTR region showed an 11.94% variation among groups. Phylogenetic analysis showed no correlation between sequence variations and therapeutic responses.

Research paper thumbnail of Sequence and structural analysis of the 5′ noncoding region of hepatitis C virus in patients with chronic infection

Journal of Medical Virology, 2009

Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well ... more Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5 0 noncoding region (5 0 NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5 0 NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5 0 NCR structure. The heterogeneous sequence observed on 5 0 NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed.

Research paper thumbnail of Xerostomia, hyposalivation and sialadenitis in patients with chronic hepatitis C are not associated with the detection of HCV RNA in saliva or salivary glands

Journal of Clinical Pathology, 2010

Salivary gland disorders in patients with chronic hepatitis C (CHC) have been considered oral ext... more Salivary gland disorders in patients with chronic hepatitis C (CHC) have been considered oral extrahepatic manifestations, reinforcing the hepatitis C virus (HCV) as a sialotropic virus. Hence, the authors investigated the prevalence of HCV RNA in saliva and salivary glands and its possible association with xerostomia, hyposalivation and sialadenitis in patients with CHC. In 65 patients with confirmed CHC, the HCV RNA was investigated by nested RT-PCR in saliva samples and minor salivary glands. Xerostomia, hyposalivation, clinical and histopathological evidence of sialadenitis were also evaluated. Univariate and multivariate analyses were employed to verify associations. HCV RNA was detected in the saliva of 26/65 (40.0%) patients and in 12/65 (18.5%) salivary glands. Xerostomia was reported by 23/65 (35.4%) patients, and hyposalivation was diagnosed in 13/65 (20.0%) patients. Sialadenitis was confirmed by histopathological features in 31/65 (47.7%) patients. Twelve (38.7%) of the 31 patients with sialadenitis presented HCV RNA in saliva and 2/31 (6.5%) in salivary glands. No associations were found between xerostomia, hyposalivation or sialadenitis and the detection of HCV RNA in saliva or in salivary glands. Although xerostomia, hyposalivation and sialadenitis are frequent findings in CHC patients, our study did not confirm the association between the detection of HCV RNA in saliva or salivary glands with these salivary gland disorders. However, an indirect role of HCV by immune-mediated virus mechanisms in the pathogenesis of salivary gland disorders in this group of patients cannot be ruled out.

Research paper thumbnail of Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient

Journal of Bacteriology, 2012

Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that ... more Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that causes human gastroenteritis. Here, we report the draft genome sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative genomic analysis unveiled three strain-specific genomic islands that potentially confer the multidrug resistance and virulence of the strain.

Research paper thumbnail of Depress�o em esquizofrenia

Research paper thumbnail of Qualidade de vida em cuidadores de idosos portadores de demência de Alzheimer

Jornal Brasileiro de Psiquiatria, 2008

Qualidade de vida, cuidadores, demência. rEsumo objetivo: Realizar revisão sistemática da literat... more Qualidade de vida, cuidadores, demência. rEsumo objetivo: Realizar revisão sistemática da literatura acerca da QV dos cuidadores de idosos com DA. métodos: Revisão sistemática de literatura por meio do PubMed e da MedLine entre os anos de 1997 e 2008, utilizando os termos quality of life, caregivers, Alzheimer disease. resultados: Dezesseis estudos entre 274 publicações iniciais e 39 artigos posteriormente incluídos pelas referências bibliográficas foram avaliados. A QV dos cuidadores dos idosos demenciados, na maioria dos estudos, estava comprometida negativamente. Diversos fatores interferem na QV do cuidador, desde a gravidade da doença até alterações comportamentais que esses idosos possam vir a apresentar. Conclusão: É necessária a realização de mais estudos direcionados a esse tema, a fim de buscar estratégias para melhora da QV desse cuidador. aBstraCt Objective: Carry out a systematic bibliographycal review about QL of the caregivers of in the elderly with AD. Methods: A systematic bibliographical review about studies indexed on Pubmed and MedLine, from 1997 to 2008, using as key-words the terms: quality of life, caregivers, Alzheimer Disease. Results: Sixteen of the 274 initial articles and 39 additional papers included in a following phase, based on bibliographical references, were evaluated. A negative impairment in QL of the caregivers of demential in the elderly has been documented in most studies. Several factors affect the caregivers' quality of life, such as severity of the patient's illness and behavior disorders of elderly. Conclusion: Futures studies on this theme will be necessary to look for strategies. Recebido em 22/10/2008 Aprovado em 5/12/2008

Research paper thumbnail of Depressão em esquizofrenia

Revista Brasileira de Psiquiatria, 2002

ABSTRACT Realizou-se uma revisão da literatura acerca da presença de depressão em pacientes esqui... more ABSTRACT Realizou-se uma revisão da literatura acerca da presença de depressão em pacientes esquizofrênicos e, em particular, da depressão pós-esquizofrênica (DPE). A pesquisa foi realizada por meio do Medline, envolvendo os anos de 1966 e 2000, com o objetivo de identificar artigos originais e de revisão. Focalizaram-se os seguintes tópicos: dados históricos, principais estudos, quadro clínico e curso evolutivo, diagnóstico e diagnóstico diferencial, etiopatogenia e prognóstico. Conclui-se que a depressão pós-esquizofrênica tem plena autonomia sindrômica, deve ser considerada uma manifestação clínica das formas delirantes da esquizofrenia e integra o curso evolutivo de um transtorno esquizofrênico.

Research paper thumbnail of Characterization of depressive syndrome in schizophrenic outpatients

Revista Brasileira de Psiquiatria, 2002

ABSTRACT OBJECTIVE: The authors carried out a cross-sectional study with the aim of characterizin... more ABSTRACT OBJECTIVE: The authors carried out a cross-sectional study with the aim of characterizing and describing depressive pictures in schizophrenic patients seen at the Psychiatry Outpatient Clinic of the Federal University of Pernambuco (HC-UFPE). The patients had the diagnosis of schizophrenia confirmed on the basis of the operating criteria of the DSM-IV. METHODS: Those who where in the period of stabilization of the clinical picture were selected for the study defined according the following criteria:the last psychotic episode must be happened two months before at least, and during this period the alterations of the antipsychotics doses had been lower than 5 mg of haloperidol or equivalent doses of others neuroleptics. A total of one hundred and four patients took part. Following the identification of the depressive symptoms using the Calgary Depression Scale for Schizophrenia (CDSS), thirty-one patients (29.8%) fulfilled the diagnostic criteria described in the DSM-IV. Of these, 22.1% had the diagnosis of major depression and 7.7% of minor depression according the DSM-IV. Two groups were constituted: Group A, schizophrenics with a depressive syndrome, and Group B, schizophrenics without such a syndrome. An assessment was made of the distribution of the symptoms of the CDSS scores in both groups, the sociodemographic, clinical and therapeutic variables in relation to the frequency of the depressive syndrome, and the patients clinical course. For the investigation of certain clinical features, the following tools were used: problem list (psychosocial stressors) contained in axis IV of the DSM-IV intended to detect the presence of factors triggering the initial episode of schizophrenia and the Global Assessment of Functioning (GAF -- Axis V -- DSM-IV) to characterize the current functioning of the patients. CONCLUSIONS: The results obtained allowed the authors to draw the following conclusions: all the items that comprise the Brazilian version of the CDSS were statistically significant in characterizing the depressive syndrome; a comparison of the sociodemographic and therapeutic variables revealed no statistically significant differences between the two groups, and this was also the case with the majority of the clinical features. Statistically significant differences, however, were found in relation to the greater frequency of life events (psychosocial stressors) in triggering the first episode of schizophrenia and the higher incidence of affective disorders antecedents in family members (first and second degree) among the depressed patients. The mean duration of the depressive syndrome during follow-up of the patients was 5.30 months. The patients in whom there was a recurrence of the psychotic episode presented a delusional-hallucinatory clinical picture. This study seeks to contribute to the inclusion of the Postpsychotic Depressive Disorder (PSD) of Schizophrenia (DSM-IV), in the group of Schizophrenic Disorders.

Research paper thumbnail of Automatic Detection of Glaucoma Using Disc Optic Segmentation and Feature Extraction

2015 Latin American Computing Conference (CLEI), 2015

Research paper thumbnail of Evaluation of the use of computational intelligence techniques in medical claim processes of a health insurance company

Proceedings of the 26th IEEE International Symposium on Computer-Based Medical Systems, 2013

ABSTRACT Brazil has one of the largest private healthcare markets in the world. However, it appea... more ABSTRACT Brazil has one of the largest private healthcare markets in the world. However, it appears that many indicators of our health insurance companies (including consultations, tests, hospitalizations, etc.) are well above the established international standards. This indicates that many appointments and tests are being carried out without need, generating unnecessary costs on businesses and making the service offered more expensive. In this paper, computational intelligence techniques were used to model the behavior of medical reviewers - professionals who assess whether medical requests should be allowed or not. For the generation of knowledge, a database from a nonprofitable health insurance company containing more than one million records collected since the year 2007 was used. Promising experimental results are presented, indicating that the techniques used can support medical reviewers.

Research paper thumbnail of Evaluation of the toxicokinetics and apoptotic potential of ethanol extract from Echinodorus macrophyllus leaves in vivo

Regulatory toxicology and pharmacology : RTP, Jan 25, 2016

This study evaluates the toxicological, genotoxic, mutagenic and apoptotic potential of an in viv... more This study evaluates the toxicological, genotoxic, mutagenic and apoptotic potential of an in vivo assay from Echinodorus macrophyllus extract (EEM). The acute toxicity test used 02 groups (n = 5) of female Wistar rats: negative control group (saline) and experimental group (2000 mg/kg b.w. EEM), both orally administered (gavage) at single doses and monitored for 14 days. To assess the genotoxic, mutagenic and apoptotic potential, 50 male Swiss mice were divided into 5 groups (n = 10): Group I: negative control (saline solution 0.1 ml/10 g b.w.); Group II: positive control (cyclophosphamide 100 mg/kg b.w.) intraperitoneally administered; groups III-V received EEM at 500, 1000 and 2000 mg/kg b.w., respectively. Groups I, III-V received oral administrations (gavage). The results showed that there was no acute lethality or any signs of acute toxicity, indicating that LD50 is greater than 2000 mg/kg b.w. The groups treated with EEM showed no genotoxic or mutagenic activity and did not i...

Research paper thumbnail of The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases

BMC genomics, Jan 27, 2017

The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the c... more The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools. We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a cor...

Research paper thumbnail of Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance

Mammalian Genome, 2016

In bovines, artificial selection has produced a large number of breeds which differ in production... more In bovines, artificial selection has produced a large number of breeds which differ in production, environmental adaptation, and health characteristics. To investigate the genetic basis of these phenotypical differences, several bovine breeds have been sequenced. Millions of new SNVs were described at every new breed sequenced, suggesting that every breed should be sequenced. Guzerat or Guzerá is an indicine breed resistant to drought and parasites that has been the base for some important breeds such as Brahman. Here, we describe the sequence of the Guzerá genome and the in silico functional analyses of intragenic breed-specific variations. Mate-paired libraries were generated using the ABI SOLiD system. Sequences were mapped to the Bos taurus reference genome (UMD 3.1) and 87% of the reference genome was covered at a 26X. Among the variants identified, 2,676,067 SNVs and 463,158 INDELs were homozygous, not found in any database searched, and may represent true differences between Guzerá and B. taurus. Functional analyses investigated with the NGS-SNP package focused on 1069 new, non-synonymous SNVs, splice-site variants (including acceptor and donor sites, and the conserved regions at both intron borders, referred to here as splice regions) and coding INDELs (NS/SS/I). These NS/SS/I map to 935 genes belonging to cell communication, environmental adaptation, signal transduction, sensory, and immune systems pathways. These pathways have been involved in phenotypes related to health, adaptation to the environment and behavior, and particularly, disease resistance and heat tolerance. Indeed, 105 of these genes are known QTLs for milk, meat and carcass, production, reproduction, and health traits. Therefore, in addition to describing new genetic variants, our approach provided groundwork for unraveling key candidate genes and mutations.

Research paper thumbnail of Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs

Genetics and molecular biology, Jan 31, 2016

This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle devel... more This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myo...

Research paper thumbnail of Draft Genome Sequence of Hydrotalea flava Strain CCUG 51397T

Genome announcements, Jan 9, 2016

We report the draft genome sequence of Hydrotalea flava CCUG 51397(T), the type strain of the gen... more We report the draft genome sequence of Hydrotalea flava CCUG 51397(T), the type strain of the genus Hydrotalea (family Chitinophagaceae), isolated from water samples in southern Sweden.

Research paper thumbnail of FluxNGS: a data management system for next-generation sequencing protocols and data

F1000posters, Nov 1, 2011

DNA sequencing has become an indispensable tool for basic biological research. Modern sequencing ... more DNA sequencing has become an indispensable tool for basic biological research. Modern sequencing methods allowed exponential growth of sequenced DNA data generation leading to the development of the process called Next Generation Sequencing (NGS). The amount of data generated by NGS is not compatible with manual storage and management and computational systems (LIMS) have been developed for data input and flux control. In this work we present FluxNGS, a web based LIMS developed to store and manage protocols and data from sequencing laboratories using the NGS Solid TM technology.

Research paper thumbnail of Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis

PloS one, 2015

Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better compr... more Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40-50%), Bacteroidetes (~15-25%) and Proteobacteria (~5-25%), in addition to ~10-20% of non-classified bacteria. 45-55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vagi...

Research paper thumbnail of HIV-1 Tropism Determines Different Mutation Profiles in Proviral DNA

PLOS ONE, 2015

In order to establish new infections HIV-1 particles need to attach to receptors expressed on the... more In order to establish new infections HIV-1 particles need to attach to receptors expressed on the cellular surface. HIV-1 particles interact with a cell membrane receptor known as CD4 and subsequently with another cell membrane molecule known as a co-receptor. Two major different co-receptors have been identified: C-C chemokine Receptor type 5 (CCR5) and C-X-C chemokine Receptor type 4 (CXCR4) Previous reports have demonstrated cellular modifications upon HIV-1 binding to its co-receptors including gene expression modulations. Here we investigated the effect of viral binding to either CCR5 or CXCR4 co-receptors on viral diversity after a single round of reverse transcription. CCR5 and CXCR4 pseudotyped viruses were used to infect non-stimulated and stimulated PBMCs and purified CD4 positive cells. We adopted the SOLiD methodology to sequence virtually the entire proviral DNA from all experimental infections. Infections with CCR5 and CXCR4 pseudotyped virus resulted in different patterns of genetic diversification. CCR5 virus infections produced extensive proviral diversity while in CXCR4 infections a more localized substitution process was observed. In addition, we present pioneering results of a recently developed method for the analysis of SOLiD generated sequencing data applicable to the study of viral quasi-species. Our findings demonstrate the feasibility of viral quasi-species evaluation by NGS methodologies. We presented for the first time strong evidence for a host cell driving mechanism acting on the HIV-1 genetic variability under the control of co-receptor stimulation. Additional investigations are needed to further clarify this question, which is relevant to viral diversification process and consequent disease progression.

Research paper thumbnail of Metagenome of a Microbial Community Inhabiting a Metal-Rich Tropical Stream Sediment

PLOS ONE, 2015

Here, we describe the metagenome and functional composition of a microbial community in a histori... more Here, we describe the metagenome and functional composition of a microbial community in a historically metal-contaminated tropical freshwater stream sediment. The sediment was collected from the Mina Stream located in the Iron Quadrangle (Brazil), one of the world&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#39;s largest mining regions. Environmental DNA was extracted and was sequenced using SOLiD technology, and a total of 7.9 Gbp was produced. A taxonomic profile that was obtained by comparison to the Greengenes database revealed a complex microbial community with a dominance of Proteobacteria and Parvarcheota. Contigs were recruited by bacterial and archaeal genomes, especially Candidatus Nitrospira defluvii and Nitrosopumilus maritimus, and their presence implicated them in the process of N cycling in the Mina Stream sediment (MSS). Functional reconstruction revealed a large, diverse set of genes for ammonium assimilation and ammonification. These processes have been implicated in the maintenance of the N cycle and the health of the sediment. SEED subsystems functional annotation unveiled a high degree of diversity of metal resistance genes, suggesting that the prokaryotic community is adapted to metal contamination. Furthermore, a high metabolic diversity was detected in the MSS, suggesting that the historical arsenic contamination is no longer affecting the prokaryotic community. These results expand the current knowledge of the microbial taxonomic and functional composition of tropical metal-contaminated freshwater sediments.

Research paper thumbnail of CA88, a nuclear repetitive DNA sequence identified in Schistosoma mansoni, aids in the genotyping of nine Schistosoma species of medical and veterinary importance

Memórias do Instituto Oswaldo Cruz, 2010

CA88 is the first long nuclear repetitive DNA sequence identified in the blood fluke, Schistosoma... more CA88 is the first long nuclear repetitive DNA sequence identified in the blood fluke, Schistosoma mansoni. The assembled S. mansoni sequence, which contains the CA88 repeat, has 8,887 nucleotides and at least three repeat units of approximately 360 bp. In addition, CA88 also possesses an internal CA microsatellite, identified as SmBr18. Both PCR and BLAST analysis have been used to analyse and confirm the CA88 sequence in other S. mansoni sequences in the public database. PCR-acquired nuclear repetitive DNA sequence profiles from nine Schistosoma species were used to classify this organism into four genotypes. Included among the nine species analysed were five sequences of both African and Asian lineages that are known to infect humans. Within these genotypes, three of them refer to recognised species groups. A panel of four microsatellite loci, including SmBr18 and three previously published loci, has been used to characterise the nine Schistosoma species. Each species has been identified and classified based on its CA88 DNA fingerprint profile. Furthermore, microsatellite sequences and intra-specific variation have also been observed within the nine Schistosoma species sequences. Taken together, these results support the use of these markers in studying the population dynamics of Schistosoma isolates from endemic areas and also provide new methods for investigating the relationships between different populations of parasites. In addition, these data also indicate that Schistosoma magrebowiei is not a sister taxon to Schistosoma mattheei, prompting a new designation to a basal clade. CA88, a nuclear repetitive • Diana Bahia et al. 392 Armour JA, Brinkworth MH, Kamischke A 1999. Direct analysis by small-pool PCR of MS205 minisatellite mutation rates in sperm after mutagenic therapies. Mutat Res 445: 73-80. Barker SC, Blair D 1996. Molecular phylogeny of Schistosoma species supports traditional groupings within the genus. J Parasitol 82: 292-298. Benson G 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27: 573-580. Blair L, Webster JP, Barker GC 2001. Isolation and characterization of polymorphic microsatellite markers in Schistosoma mansoni from Africa. Mol Ecol Notes 1: 93-95. Christensen NO, Mutani A, Frandsen F 1983. A review of the biology and transmission ecology of African bovine species of the genus Schistosoma. Z Parasitenkd 69: 551-570. Collins HE, Li H, Inda SE, Anderson J, Laiho K, Tuomilehto J, Seldin MF 2000. A simple and accurate method for determination of microsatellite total allele content differences between DNA pools. Hum Genet 106: 218-226. Dabo A, Durand P, Morand S, Diakite M, Langand J, Imbert-Establet D, Doumbo O, Jourdane J 1997. Distribution and genetic diversity of Schistosoma haematobium within its bulinid intermediate hosts in Mali. Acta Trop 66: 15-26. A comprehensive genetic map of the mouse genome. Nature 380: 149-152. Durand P, Sire C, Théron A 2000. Isolation of microsatellite markers in the digenetic trematode Schistosoma mansoni from Guadeloupe island. Mol Ecol 9: 997-998. Eppert A, Lewis FA, Grzywacz C, Coura-Filho P, Caldas I, Minchella DJ 2002. Distribution of schistosome infections in molluscan hosts at different levels of parasite prevalence. J Parasitol 88: 232-236. Grossman Z, Ram D, Markovics A, Tarrab-Hazdai R, Lantner F, Ziv E, Schechter I 1990. Schistosoma mansoni: stage-specific expression of muscle-specific genes. Exp Parasitol 70: 62-71. Hagelberg E, Gray IC, Jeffreys AJ 1991. Identification of the skeletal remains of a murder victim by DNA analysis. Nature 352: 427-429. Hamada H, Petrino MG, Kakunaga T 1982. A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79: 6465-6469. Hamburger J, He-Na, Abbasi I, Ramzy RM, Jourdane J, Ruppel A 2001. Polymerase chain reaction assay based on a highly repeated sequence of Schistosoma haematobium: a potential tool for monitoring schistosome-infested water. Am J Trop Med Hyg 65: 907-911. Huang x, Madan A 1999. CAP3: A DNA sequence assembly pro-CAP3: A DNA sequence assembly program. Genome Res 9: 868-877. Jarne P, Lagoda PJ 1996. Microsatellites, from molecules to popula-Microsatellites, from molecules to populations and back. Trends Ecol Evol 11: 424-429. Kalendar R 2003. Fast PCR: a program for fast design PCR primer, DNA and protein manipulation (version 2.5.59). Institute of Biotechnology, University of Helsinki. Kane RA, Southgate VR, Rollinson D, Littlewood DT, Lockyer AE, Pagès JR, Tchuem Tchuentè LA, Jourdane J 2003. A phylogeny based on three mitochondrial genes supports the division of Schistosoma intercalatum into two separate species. Parasitology 127: 131-137. Lipman DJ, Pearson WR 1985. Rapid and sensitive protein similarity searches. Science 227: 1435-1441. Littlewood DT, Johnston DA 1995. Molecular phylogenetics of the four Schistosoma species groups determined with partial 28S ribosomal RNA gene sequences. Parasitology 111: 167-175.

Research paper thumbnail of Genetic variability in the 5' UTR and NS5A regions of hepatitis C virus RNA isolated from non-responding and responding patients with chronic HCV genotype 1 infection

Memórias do Instituto Oswaldo Cruz, 2008

isolates has adaptive significance and reflects the modes and intensities of selection mechanisms... more isolates has adaptive significance and reflects the modes and intensities of selection mechanisms operating on the virus. In this work, we sought to investigate using classical population genetics parameters, the genetic variability of HCV genotype 1 using the 5` UTR and NS5A regions from treatment non-responding and responding groups of patients. Both regions showed low genetic variability and the 5` UTR showed neutral deviation. No differences were observed in the nonsynonymous/synonymous nucleotide substitution ratio among groups for NS5A. The analysis of molecular variance test of the 5` UTR region showed an 11.94% variation among groups. Phylogenetic analysis showed no correlation between sequence variations and therapeutic responses.

Research paper thumbnail of Sequence and structural analysis of the 5′ noncoding region of hepatitis C virus in patients with chronic infection

Journal of Medical Virology, 2009

Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well ... more Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5 0 noncoding region (5 0 NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5 0 NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5 0 NCR structure. The heterogeneous sequence observed on 5 0 NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed.

Research paper thumbnail of Xerostomia, hyposalivation and sialadenitis in patients with chronic hepatitis C are not associated with the detection of HCV RNA in saliva or salivary glands

Journal of Clinical Pathology, 2010

Salivary gland disorders in patients with chronic hepatitis C (CHC) have been considered oral ext... more Salivary gland disorders in patients with chronic hepatitis C (CHC) have been considered oral extrahepatic manifestations, reinforcing the hepatitis C virus (HCV) as a sialotropic virus. Hence, the authors investigated the prevalence of HCV RNA in saliva and salivary glands and its possible association with xerostomia, hyposalivation and sialadenitis in patients with CHC. In 65 patients with confirmed CHC, the HCV RNA was investigated by nested RT-PCR in saliva samples and minor salivary glands. Xerostomia, hyposalivation, clinical and histopathological evidence of sialadenitis were also evaluated. Univariate and multivariate analyses were employed to verify associations. HCV RNA was detected in the saliva of 26/65 (40.0%) patients and in 12/65 (18.5%) salivary glands. Xerostomia was reported by 23/65 (35.4%) patients, and hyposalivation was diagnosed in 13/65 (20.0%) patients. Sialadenitis was confirmed by histopathological features in 31/65 (47.7%) patients. Twelve (38.7%) of the 31 patients with sialadenitis presented HCV RNA in saliva and 2/31 (6.5%) in salivary glands. No associations were found between xerostomia, hyposalivation or sialadenitis and the detection of HCV RNA in saliva or in salivary glands. Although xerostomia, hyposalivation and sialadenitis are frequent findings in CHC patients, our study did not confirm the association between the detection of HCV RNA in saliva or salivary glands with these salivary gland disorders. However, an indirect role of HCV by immune-mediated virus mechanisms in the pathogenesis of salivary gland disorders in this group of patients cannot be ruled out.

Research paper thumbnail of Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient

Journal of Bacteriology, 2012

Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that ... more Salmonella enterica serovar Typhimurium is one of the most prevalent serovars of Salmonella that causes human gastroenteritis. Here, we report the draft genome sequence of the S. Typhimurium multidrug-resistant strain ST1660/06. Comparative genomic analysis unveiled three strain-specific genomic islands that potentially confer the multidrug resistance and virulence of the strain.