Search

This study evaluated the effectiveness of thermocycler temperature control, considering the influence of other determinant factors for the optimization of PCR. The reduction in the number of repeated PCR tests, applied in the diagnosis and prognosis of chronic myeloid leukemia at the National Cancer Institute in Brazil, was used as a measure of effectiveness. This indicator was evaluated using samples obtained before and after the temperature control in the wells of the thermocyclers. There was a reduction of 18.9% in the number of repeated exams in the second sample. A structured interview with laboratory staff indicated that there was no change in the other determinant factors.

Cetacean morbillivirus (CeMV) has caused repeated epizootics and interepizootic fatalities in a variety of cetacean species worldwide. Recently, a novel CeMV strain (GD-CeMV) was linked to a mass die-off of Guiana dolphins (Sotalia guianensis) in Brazil. Southern right whales (SRWs; Eubalaena australis) migrate to the southern Brazilian coast during austral winter and spring (June through November) for breeding and calving. Because unexplained high calf mortality rates have recurrently been documented in SRWs, we hypothesized they could be infected with CeMV. We developed a novel real-time RT-PCR method based on SYBR ® GREEN for detection of CeMV and identified the virus in three out of five stranded SRWs from Santa Catarina state, Brazil. The partial sequences of the morbillivirus phosphoprotein gene suggest that the virus is similar to the GD-CeMV strain. Our results indicate CeMV can infect SRWs and should be considered in the differential aetiologic diagnosis of infectious diseases in this species. It also raises concern for potential conservation implications for this species in its main coastal breeding area off Southern Brazil., (© 2018 Blackwell Verlag GmbH.)

A total of 27 seminal plasma samples from cattle-breeding farms or semen centres located in Minas Gerais, Brazil, previously negative by serological and tested positive for Brucella spp. with primer specific for the amplification of the gene virb5 by polymerase chain reaction (PCR) were analysed for the detection of Brucella abortus DNA by PCR. It was found that nine samples (33.33%) contained B. abortus B19 strain DNA, two (7.40%) contained B. abortus DNA and five (18.51%) contained both DNA. The larger number of samples with B. abortus B19 strain DNA would explained by the environmental contamination by vaccinated females with persistent excretion or some illegal vaccination process. It is first reported of male bovines detected with both DNA., (© 2017 Blackwell Verlag GmbH.)

A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The urge of a simple multiplex-PCR scheme to specify these clones has motivated the present study. The established trilocus sequence-based typing (3LST, for ompA, csuE and blaOXA-51-like genes) multiplex-PCR rapidly identifies international clones I (CC109/1), II (CC118/2) and III (CC187/3). Thus, the system detects only one (CC109/1) out of four main CC in Brazil. We aimed to develop an alternative multiplex-PCR scheme to detect these clones, known to be present additionally in Africa, Asia, Europe, USA and South America. MLST, performed in the present study to complement typing our whole collection of isolates, confirmed that all isolates belonged to the same four CC detected previously. When typed by 3LST-based multiplex-PCR, only 12% of the 163 isolates were classified into groups. By comparative sequence analysis of ompA, csuE and blaOXA-51-like genes, a set of eight primers was designed for an alternative multiplex-PCR to distinguish the five CC 113/79, 103/15, 109/1, 110/25 and 118/2. Study isolates and one CC118/2 isolate were blind-tested with the new alternative PCR scheme; all were correctly clustered in groups of the corresponding CC. The new multiplex-PCR, with the advantage of fitting in a single reaction, detects five leading A. baumannii clones and could help preventing the spread in healthcare settings., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Hantaviruses are members of the family Bunyaviridae and are an emerging cause of disease worldwide with high lethality in the Americas. In Brazil, the diagnosis for hantaviruses is based on immunologic techniques associated with conventional RT-PCR. A novel one-step SYBR Green real-time RT-PCR was developed for the detection and quantitation of Araraquara (ARAV) and Rio Mamore hantavirus (RIOMV). The detection limit of assay was 10 copies/μL of RNA in vitro transcribed of segment S. The specificity of assay was evaluated by melting curve analysis, which showed that the Araraquara virus amplified product generated a melt peak at 80.83 ± 0.89 °C without generating primer-dimers or non-specific products. The assay was more sensitive than conventional RT-PCR and we detected two samples undetected by conventional RT-PCR. The one-step SYBR Green real-time quantitative RT-PCR is specific, sensible and reproducible, which makes it a powerful tool in both diagnostic applications and general research of ARAV and RIOMV and possibly other Brazilian hantaviruses.

The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

The genetically modified common bean Embrapa 5.1, developed by Brazilian Agricultural Research Corporation (Embrapa), is the first commercial GM plant produced in Latin America. It presents high resistance to the Bean golden mosaic virus. In this work, primers and probes targeting a taxon-specific reference DNA sequence for the common bean (Phaseolus vulgaris L.) and a construct-specific DNA sequence of Embrapa 5.1 GM common bean were successfully developed. The primers and probes showed high specificity for the target detection. Both methods showed suitable efficiency and performance to be used as an endogenous target for detection of common bean DNA and for construct-specific detection of GM common bean Embrapa 5.1, respectively. Both real-time PCR assays proved to be valuable for future assessment of interlaboratory studies.

We used single primer-based DNA markers to assess genetic variability of the mangrove crab, Ucides cordatus, collected from four different localities from Pará to Santa Catarina States in Brazil (almost 5000 km distant). Five primers were chosen based on the consistency of the amplified bands and the polymorphism of each locus. A total of 78 loci were amplified in 76 samples; high polymorphism rates were detected in the entire sample (80.8%) and within each locality (73.5-79.5%). Analysis of molecular variance demonstrates significant differences between localities (P < 0.001); however, the Φ(ST) value (0.078) indicates a low level of genetic differentiation, which suggests that U. cordatus larvae can spread over large distances. The variation was distributed among the samples, and most of it was attributed to differences among individuals within localities. Cluster analysis, based on the Jaccard similarity coefficient, and the Mantel test gave similar results to the analysis of molecular variance data. Despite the low level of population structuring, these markers could be used for studying U. cordatus diversity, due to the high level of polymorphism.

Background: Genotyping of hepatitis C virus (HCV) has become an essential tool for prognosis and prediction of treatment duration. The aim of this study was to compare two HCV genotyping methods: reverse hybridization line probe assay (LiPA v.1) and partial sequencing of the NS5B region., Methods: Plasma of 171 patients with chronic hepatitis C were screened using both a commercial method (LiPA HCV Versant, Siemens, Tarrytown, NY, USA) and different primers targeting the NS5B region for PCR amplification and sequencing analysis., Results: Comparison of the HCV genotyping methods showed no difference in the classification at the genotype level. However, a total of 82/171 samples (47.9%) including misclassification, non-subtypable, discrepant and inconclusive results were not classified by LiPA at the subtype level but could be discriminated by NS5B sequencing. Of these samples, 34 samples of genotype 1a and 6 samples of genotype 1b were classified at the subtype level using sequencing of NS5B., Conclusions: Sequence analysis of NS5B for genotyping HCV provides precise genotype and subtype identification and an accurate epidemiological representation of circulating viral strains.

Purpose: To verify the frequencies of T34T, E50K, M98K, 691&#95;692insAG, and R545Q variants in the optineurin (OPTN) gene in Brazilian subjects with primary open-angle glaucoma (POAG) and controls., Patients and Methods: Ninety-nine patients with POAG and 100 normal controls were enrolled in this study. The frequency of alterations in the OPTN gene was analyzed by direct sequencing and enzymatic digestion of PCR products., Results: None of the five alterations evaluated was significantly associated with POAG when compared to controls. However, the T34T silent change was present in greater frequency in POAG patients (37.37% vs. 23.00% in controls), while the R545Q change was more prevalent in controls (23.00% vs. 10.10% in POAG). The M98K and 691&#95;692insAG presented with low frequencies in POAG patients (1.01% and 2.02%, respectively) and controls (2.00% and 2.00%, respectively). The E50K substitution was not observed., Conclusion: Our data show no association between the five evaluated variants and POAG in the Brazilian population.

Catuaba (Anemopaegma arvense), a Bignoniaceae species endemic to Cerrado regions, shows anticancer properties and is widely used as a stimulant in traditional medicine. We evaluated the genetic diversity of seven populations found in the State of São Paulo, using random amplified polymorphic DNA markers. After optimization of the amplification reaction, 10 selected primers produced 70 reproducible bands, with 72.8% polymorphism. The greatest genetic diversity was observed within populations (71.72%). Variation estimates, theta(B) (0.2421) and Phi(ST) (0.283), obtained by inter- and intra-populational analysis of genetic variability of catuaba, indicated considerable population structure. However, the r value 0.346 (P = 0.099), calculated by the Mantel test, indicates that the genetic diversity among populations is not strongly structured in geographical space, although there appears to be a tendency towards structuring.

We developed a TaqMan real-time polymerase chain reaction (PCR) assay for the quantitative detection of Theileria equi from the in vitro-cultured parasite and field blood samples collected from horses living in Ghana and Brazil. The detection limit for the assay was determined to be 1.5 parasites/microl per sample, and the quantitative capacity was demonstrated using the in vitro-cultured parasite. For field applications, the real-time PCR assay was compared to a previously established nested PCR assay used as the gold standard for the real-time PCR assay. Of 65 field blood samples, 46 samples were T. equi-positive in the nested PCR assay, while the real-time PCR assay also detected the parasite in all 46 of the nested PCR-positive samples but did not detect T. equi in the remaining 19 negative blood samples. This quantitative real-time PCR assay provides a valuable tool for fast laboratory diagnostic assessment of T. equi infection in horses.

The aim of the present study was the development of a multiplex genotyping panel of eight microsatellite markers of Arapaima gigas, previously described. Specific primer pairs were developed, each one of them marked with either FAM-6, HEX or NED. The amplification conditions using the new primers were standardized for a single reaction. The results obtained demonstrate high heterozygosity (average of 0.69) in a Lower Amazon population. The multiplex system described can thus be considered a fast, efficient and inexpensive method for the investigation of genetic variability in Arapaima populations.

The accurate specific identification of ticks is essential for the study, control and prevention of tick-borne diseases. Herein, we determined ribosomal nucleotide sequences of the second internal transcribed spacer (ITS2) of 15 Neotropical hard tick species of the genus Amblyomma Koch found in Brazil. Most of the studied ticks accidentally parasite humans and potentially act as vectors of zoonoses. Lengths of the ITS2 sequences ranged from 956 to 1,207 bp, whereas GC content varied from 62.4 to 66.9%. A matrix of ITS2 divergence was calculated with the ITS2 sequence data obtained showing divergence levels varying from 1.5 to 28.8%. The analysis indicated that this molecular marker can be useful for Amblyomma-specific identification. Phylogenetic inferences based on the ITS2 sequences were used to assess some issues in subgenus taxonomy.

The horn fly, Haematobia irritans irritans (L.) (Diptera: Muscidae), has become a problem for Brazilian cattle producers even though its introduction into Brazil is relatively recent. Failure to control this cattle pest is becoming a concern, and horn fly populations from several ranches from the state of Mato Grosso do Sul were surveyed for pyrethroid resistance. Susceptibility bioassays revealed that cypermethrin resistance was widespread and reached high levels in horn fly populations throughout the state, with resistance factors (RFs) ranging from 50.4 to 704.8. Synergist bioassays failed to detect a major role for esterases as a pyrethroid resistance mechanism in these populations, except for the highly pyrethroid-resistant Estrela do Oeste population (RF = 704.8). The kdr sodium channel gene mutation was not detected in eight of the 13 populations, but < 7% of individuals from four populations and 50% of the flies from Estrela do Oeste exhibited this mutation. Neither the superkdr sodium channel gene mutation nor a resistance-associated gene mutation in the HialphaE7 carboxylesterase were found in any of the fly populations. Although target site insensitivity (kdr) and esterase-mediated metabolism occur in horn fly populations from Mato Grosso do Sul state, it seems that they are not the major mechanism causing pyrethroid resistance in most of these populations.

This study aimed to determine whether candiduria is associated with the occurrence of nosocomial candidaemia. In the case-control part of the study, 115 cases (nosocomial candidaemia) and 115 controls (nosocomial bacteraemia) were similar in age, severity of condition and time of hospitalisation. There was a significant association of candidaemia with candiduria (OR 9.79; 95% CI 2.14-44.76). In the microbiology part of the study, 23 pairs of Candida-positive urine and blood cultures were obtained from 23 patients. In ten (43%) cases, the urine and blood culture isolates belonged to different species, and molecular typing showed a difference in two of the 13 cases yielding the same species from both specimens. Overall, there was a significant association between candiduria and candidaemia, but the Candida isolates from urine and blood were different for 52% of the patients. Thus, the data indicated that the urinary tract was probably not a source for the candidaemia.

A simple and single-step technique based on multiplex PCR (multiplex polymerase chain reaction) has been developed for simultaneous identification of Brazilian Biomphalaria species, the intermediate hosts of Schistosoma mansoni, and their diagnosis of infection by the trematode. We used species-specific primers directed both to the internal transcribed spacer 2 (ITS2) of ribosomal DNA from 3 of the S. mansoni host species and to the mitochondrial DNA (mtDNA) from the trematode. Those primers were used simultaneously in a single multiplex-PCR reaction, and template DNA was obtained from S. mansoni-infected and noninfected snails. The results were visualized in silver stained polyacrylamide gels, revealing the presence of specific bands. The methodology has shown to be efficient, fast, and reproducible for Biomphalaria species identification and diagnosis of snails infected by S. mansoni during prepatent periods.

Molecular techniques were used to examine the phylogenetic relationships among Hepatozoon species isolated from 13 foxes and 15 opossums from Brazil, and from 15 dogs, 20 foxes, 45 rodents, and 330 domestic cats from Spain. Hemogregarine infection was confirmed by amplification of the 18S rRNA gene and later sequencing. No hemogregarine infections were found in opossums. The prevalence of Hepatozoon in canids ranged from 26.6% (symptomatic domestic dogs) to 90% (Spanish foxes). Four different H. canis genotypes were detected, as well as an H. americanum-related protozoan (97% identical to the USA strain). Two Spanish cats were parasitized by a Hepatozoon species (0.6% prevalence) that showed 96% sequence identity to H. canis. DNA amplification assays performed on Spanish rodents showed 2 bank voles (Clethrionomys glareolus) to be infected by a Hepatozoon species (4.44% prevalence) with 95% sequence identity to Hepatozoon sp. from cats. Phylogenetic analysis showed Hepatozoon to be a monophyletic genus, in which species from carnivorous mammals (Hepatozoon sp. from cats, H. americanum and H. canis) appear as a sister lineage of that of lower vertebrates and rodents. This association suggests that H. americanum evolved in ticks and carnivores (either canids, or felids, or both) rather than in other ectoparasites and other types of mammal.

Background: The purpose of this investigation was to analyze the incidence of clonal evolution in children in Brazil children with acute lymphoblastic leukemia and its interference with the detection of minimal residual disease by polymerase chain reaction using clone-specific primers., Patients and Methods: The authors analyzed DNA samples from 12 children with acute lymphoblastic leukemia at diagnosis and after relapse using polymerase chain reaction and automatic sequencing to determine the presence of T-cell receptor gamma (TCRgamma) gene rearrangements. A clone-specific primer was synthesized based on the sequence obtained at diagnosis for each patient and at relapse for those with clonal evolution for the study of minimal residual disease., Results: A change of the original clone was detected in 3 of 12 patients (25%), involving the same rearrangement detected at diagnosis, suggesting the development of subclones. Minimal residual disease was detected at the end of treatment or before the relapse in all patients who had maintained the same rearrangements detected at diagnosis. Minimal residual disease was investigated at the end of treatment in two of the three patients with clonal evolution and was not detected with the use of clone-specific primers., Conclusions: These data suggest that clonal evolution for TCRgamma gene rearrangements was not a rare event among children in Brazil and, when present, interfered with the detection of minimal residual disease.

Purpose: To determine the distribution of CYP1B1 gene mutations in Brazilian patients with primary congenital glaucoma (PCG)., Methods: PCG diagnosis was established by presence of buphthalmos in at least one affected eye and associated high intraocular pressures before the age of 3 years. CYP1B1 mutation screening of 52 patients with PCG was performed by SSCP and direct sequencing of PCR fragments., Results: Eleven mutations, four of which are novel, were observed in 26 (50%) individuals. A new frameshift mutation (4340delG) was observed in 20.2% of all individuals screened. These individuals had early-onset, bilateral glaucoma that necessitated multiple surgical interventions. CYP1B1 mutations were twice as frequent in affected individuals of European descent as in individuals of African descent. Analysis of six intragenic single nucleotide polymorphisms (SNPs) established 5'-C-C-G-G-T-A-3' as the most common haplotype among the affected Brazilian individuals. A nonsense mutation (W57X) previously reported in an individual with Peters anomaly (compound heterozygote) was also observed in two individuals with PCG but combined with different mutations. A newly developed SSCP assay enabled us to detect all DNA mutations and polymorphisms previously detected by direct sequencing., Conclusions: Our results indicate that CYP1B1 mutations may be responsible for half of cases of PCG in the Brazilian population. The SNP haplotype 5'-C-C-G-G-T-A-3' was associated with the majority of CYP1B1 mutations. This haplotype harbors the high-activity V432 allele, which is emerging as a putative susceptibility factor in several cancers.

Purpose: Axenfeld-Rieger syndrome is a genetically heterogeneous, autosomal dominant disorder that is characterized by anterior segment defects, glaucoma, and extraocular anomalies. This study examined the two genes known to cause Rieger syndrome, PITX2 and FOXC1, for mutations in five Brazilian families with Axenfeld-Rieger syndrome., Methods: Five families with a total of 23 persons affected by Axenfeld-Rieger syndrome were recruited for this study. A sequencing-based mutation screen was undertaken for the PITX2 and FOXC1 genes. Linkage analysis was used to study one large family for which no mutations were detected in the PITX2 or FOXC1 genes., Results: Two of the five families harbored mutations in the PITX2 gene, but none of the families had a detectable FOXC1 mutation. Haplotypic analysis of three Rieger syndrome regions in a large family with Axenfeld-Rieger syndrome excluded linkage to the 4q25 (PITX2), 6p25 (FOXC1), and 13q14 (RIEG2) regions., Conclusions: It appears that the PITX2 gene is responsible for a significant portion of Axenfeld-Rieger syndrome in the Brazilian population. Furthermore, there is also evidence for the presence of genetic heterogeneity of the disorder within the Brazilian population. Finally, a large family with Axenfeld-Rieger syndrome has been identified that does not appear to harbor any of the three known loci. Axenfeld-Rieger syndrome gene segregation in this family likely represents a novel locus.

Canine parvovirus (CPV) was first isolated in 1978 in the USA. Analysis of CPV isolates by monoclonal antibodies and restriction enzymes have shown that after the first emergence of CPV (CPV-2) it evolved to give rise to new antigenic types, which were designated CPV type 2a and type 2b. These new types have replaced the original CPV type 2, although the proportions of each of the new antigenic types vary in different countries. In Brazil, CPV-like infections were first observed in 1979, however, there has been no information concerning the antigenic types of CPV prevailing in South America. In this study, we designed a PCR assay to type canine parvovirus strains in fecal samples collected from symptomatic dogs during 1980 through 1986 and 1990 through 1995. Our data showed that the CPV epizootic in Brazil followed the same pattern observed in the USA of emergence of CPV-2 followed by replacement by the variants CPV-2a and 2b. The predominant strain found during 1980 was CPV-2a, which was substantially replaced by CPV-2b from 1990 to 1995.

One to three accessions of 22 Alstroemeria species, an interspecific hybrid (A. aurea x A. inodora), and single accessions of Bomarea salsilla and Leontochir ovallei were evaluated using the AFLP-marker technique to estimate the genetic diversity within the genus Alstroemeria. Three primer combinations generated 716 markers and discriminated all Alstroemeria species. The dendrogram inferred from the AFLP fingerprints supported the conjecture of the generic separation of the Chilean and Brazilian Alstroemeria species. The principal co-ordinate plot showed the separate allocation of the A. ligtu group and the allocation of A. aurea, which has a wide range of geographical distribution and genetic variation, in the middle of other Alstroemeria species. The genetic distances, based on AFLP markers, determined the genomic contribution of the parents to the interspecific hybrid.

We used a reverse transcription-polymerase chain reaction (RT-PCR) to obtain the genotypes of circulating hepatitis C virus (HCV) in patients from a Gastro-Hepatology Unit in the city of Salvador (Bahia State) in northeastern Brazil. Viral RNA was detected in 83 (65.4%) of 127 anti-HCV seropositive serum samples. Positivity was significantly associated with alterations in levels of aspartate aminotransferase and alanine aminotransferase (P < 0.05). Genotyping of HCV was performed by RT-PCR using genotype-specific primers from the core region: 24.1% were infected with subtype 1a, 38.6% with 1b, 3.6% with 2, 21.7% with 3a, and 12.0% with a mixed genotype. There was no difference in genotype distribution when compared with results from other Brazilian locations. Surprisingly, the high frequency of genotype 3 in Brazilian samples continues to be different from that reported around the world and warrants further investigation.

Allelic diversity at the Plasmodium vivax merozoite surface protein-3alpha (PvMsp-3alpha) locus was investigated using a combined polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) protocol. Symptomatic patient isolates from global geographic origins showed a high level of polymorphism at the nucleotide level. These samples were used to validate the sensitivity, specificity, and reproducibility of the PCR/RFLP method. It was then used to investigate PvMsp3alpha diversity in field samples from children living in a single village in a malaria-endemic region of Papua New Guinea, with the aim of assessing the usefulness of this locus as an epidemiologic marker of P. vivax infections. Eleven PvMsp-3alpha alleles were distinguishable in 16 samples with single infections, revealing extensive parasite polymorphism within this restricted area. Multiple infections were easily detected and accounted for 5 (23%) of 22 positive samples. Pairs of samples from individual children provided preliminary evidence for high turnover of P. vivax populations.

Sixty-six isolates of Staphylococcus aureus obtained from milk samples of dairy cows suffering from subclinical mastitis in southern Brazil were analysed by five different molecular typing methods. These included the analysis of plasmid profiles, the analysis of coagulase (coa) gene polymorphisms by PCR amplification of the 3' terminal region of the coa gene, the PCR-based detection of polymorphisms in the X region of the protein A gene (spa), the PCR-directed analysis of variations in the spacer region between 16S and 23S rRNA, and the comparison of pulsed-field gel electrophoretically separated genomic SmaI fragment patterns. The molecular typing methods were supplemented with the biochemical characterization of the isolates and the determination of their in-vitro susceptibility to 14 different antibiotics. All genotypic and phenotypic typing methods were analyzed for their ability to discriminate between the isolates. Macrorestriction analysis proved to be the most discriminatory single method (D = 0.96) followed by rRNA spacer typing (D = 0.85), coa PCR (D = 0.82), and spa PCR (D = 0.80).

Thirty one Escherichia coli strains isolated from pigs with urinary tract infections were investigated for presence of virulence factors and plasmid DNA profile. The most frequent virulence factors presented by these strains were mannose-resistant fimbriae, including P. fimbriae (54.8%) and aerobactin production (45.2%). The pap) operon, detected by PCR, was found in 54.8% of the strains, which is similar to its frequency in human strains. Other characteristics such as the presence of mannose-sensitive hemagglutinin (16.1%), indicative of type 1 pili, and production of hemolysin (25.8%), colicin (38.7%) and toxins (22.6% for LT and for VT) were less frequent. No strains were positive for STa production. Plasmid profiles were variable among isolates from either the same or different farms.

To resolve the population genetic structure and phylogeography of the West Indian manatee (Trichechus manatus), mitochondrial (mt) DNA control region sequences were compared among eight locations across the western Atlantic region. Fifteen haplotypes were identified among 86 individuals from Florida, Puerto Rico, the Dominican Republic, Mexico, Columbia, Venezuela, Guyana and Brazil. Despite the manatee's ability to move thousands of kilometers along continental margins, strong population separations between most locations were demonstrated with significant haplotype frequency shifts. These findings are consistent with tagging studies which indicate that stretches of open water and unsuitable coastal habitats constitute substantial barriers to gene flow and colonization. Low levels of genetic diversity within Florida and Brazilian samples might be explained by recent colonization into high latitudes or bottleneck effects. Three distinctive mtDNA lineages were observed in an intraspecific phylogeny of T. manatus, corresponding approximately to: (i) Florida and the West Indies; (ii) the Gulf of Mexico to the Caribbean rivers of South America; and (iii) the northeast Atlantic coast of South America. These lineages, which are not concordant with previous subspecies designations, are separated by sequence divergence estimates of d = 0.04-0.07, approximately the same level of divergence observed between T. manatus and the Amazonian manatee (T. inunguis, n = 16). Three individuals from Guyana, identified as T. manatus, had mtDNA haplotypes which are affiliated with the endemic Amazon form T. inunguis. The three primary T. manatus lineages and the T. inunguis lineage may represent relatively deep phylogeographic partitions which have been bridged recently due to changes in habitat availability (after the Wisconsin glacial period, 10 000 B P), natural colonization, and human-mediated transplantation.

A sample population of Rio de Janeiro, Brazil, was tested for D6S132, D7S467, and D17S26 VNTR loci to determine the fixed-bin frequencies of alleles. RFLP analysis was obtained by HaeIII-digested genomic DNA. The three VNTR loci meet Hardy-Weinberg expectations, and there is no evidence for association of alleles between the VNTR loci. The frequency data can be used in forensic analysis, in paternity tests and to estimate the frequency of a DNA profile in the general Brazilian population.

Allele alphaLELY is a low-expression allele of the erythroid spectrin alpha-chain that is characterized by a C --> G mutation at position alpha1857 in exon 40 and a C --> T (nt -12) mutation in intron 45. This second mutation is probably responsible for the partial skipping of exon 46. This exon is essential for the nucleation of the alpha-chains by the beta-chains during erythropoeisis. Although allele alphaLELY remains asymptomatic in both heterozygotes and homozygotes, it enhances the expression of deleterious alpha-alleles that occur and, as such, has clinical importance. In this study, the frequency of allele alphaLELY was estimated in two ethnically different Brazilian populations: a random sample of blood donors from Campinas, a city located in São Paulo State, in the southeastern region of Brazil, and a sample of Parakanã Indians (Tupi tribe), a very isolated population with a high degree of inbreeding. The frequency of allele alphaLELY in the blood donor's sample (n = 54) was 24.1% whereas in the indigenous sample (n = 41), it was 15.9%. These frequencies were not significantly different at the 5% level (chi2 = 1.931). Similarly, when the frequencies of our samples were compared with those of the four ethnic groups studied by Maréchal et al. [Br J Haematol 90:553-556, 1995], no significant differences were found at the 5% level (chi2 = 6.686). These results suggest that allele alphaLELY is a very ancient allele since it occurs with a relatively uniform and high frequency in all human ethnic groups studied so far. These findings confirm the importance of allele alphaLELY in influencing the expression of deleterious alpha-spectrin alleles. To our knowledge, these are the first data concerning allele alphaLELY in native Americans.

Thirty six stocks of Trypanosoma cruzi isolated from sylvatic mammals (32 Didelphis marsupialis and one Philander opossum) and triatomine bugs (Rhodnius robustus and one unidentified bug) in the Amazonian forest by Carajas, Brazil were characterized by isoenzyme and random amplified polymorphic DNA (RAPD) analysis as belonging to principal zymodeme '1 (Z1). Two different homozygous phenotypes and the corresponding heterozygous phenotype were found for phosphoglucomutase with an observed frequency almost identical with that predicted by the theoretical Hardy-Weinberg distribution. Parental and hybrid profiles were also suggested by RAPD analysis, which allowed exclusion of mixed parental strains from the hybrids: isoenzyme and RAPD profiles of biological clones were also indistinguishable from those of uncloned stocks. Trypanosoma cruzi stocks from widely separated geographic origins in Central and South America gave similar RAPD profiles that allowed them to be recognized as being Z1. These results indicate that genetic exchange could contribute to the generation of genetic diversity during the sylvatic cycle of T. cruzi, and this may have epidemiologic and taxonomic implications.

All examined Haemophilus influenzae biogroup aegyptius isolates of the clone associated with Brazilian purpuric fever (the BPF clone) produced type 2 immunoglobulin A1 (IgA1) proteases encoded by identical iga genes that were distinct from the iga genes of other Brazilian H. influenzae biogroup aegyptius isolates. A partial nucleotide sequence analysis revealed close similarities to the iga genes of H. influenzae serotype c and one noncapsular H. influenzae biotype III strain isolated from a case of conjunctivitis in Tunisia, suggesting an evolutionary relationship. Epitopes recognized by neutralizing antibodies differed for the IgA1 proteases of the BPF clone and of other H. influenzae strains, including Brazilian H. influenzae biogroup aegyptius isolates from patients with noninvasive conjunctivitis. The low probability of developing cross-reacting neutralizing antibodies to the IgA1 protease of the BPF clone may contribute to the pathogenic potential of this virulent phenotype in Brazil.

Leishmania (Viannia) braziliensis isolates from two different geographic areas in Brazil were studied by DNA fingerprinting with the 33.15 multilocal probe and PCR with arbitrary primers (random amplification of polymorphic DNA-RAPD). The genetic distance of strains was measured by band sharing. The results showed that the strains isolated in Minas Gerais, southeastern Brazil, are very different from those isolated in Pará, northern Brazil. Strains from Minas Gerais constituted a relatively homogeneous group, presenting DNA fingerprint patterns with 76% of shared bands and RAPD profiles with 93% of shared bands. In contrast, strains from Pará showed higher genetic variability, with only 17 and 45% of shared bands in DNA fingerprint and RAPD patterns, respectively. This study suggests that genetic differences between L. braziliensis from both areas might have an epidemiological significance.

Human T cell lymphotropic virus type 1 (HTLV-1) is endemic in South America and the Caribbean basin. To clarify the genetic and phylogenetic relationship between an HTLV-1 strain isolated from a Brazilian woman with adult T cell leukemia and viral isolates from elsewhere in South America and from other geographic regions, selected regions of the gag, pol, env, and pX genes were amplified and directly sequenced. The overall sequence similarities between the Brazil-R-1 strain and the Japanese prototype ATK strain were 98.7% based on 1,295 nucleotides and 99.1% based on 429 amino acids. Phylogenetic analysis indicated that strain Brazil-R-1 clustered with other Brazilian and South American HTLV-1 isolates and was more closely related to Caribbean isolates from Martinique and Guadeloupe than to virus strains from other geographic regions. These data suggest a common source of HTLV-1 infection in the Caribbean basin and South America.

The feasibility of using DNA amplification by the polymerase chain reaction (PCR) for specific detection of Trypanosoma cruzi in human blood specimens was investigated. One hundred blood samples were collected in an endemic area of Minas Gerais, Brazil. They were submitted to DNA extraction and PCR amplification with kinetoplast DNA-specific primers using a simplified boiling procedure that linearized most minicircle molecules without the aid of chemical reagents. Samples that gave negative results were checked for possible inhibition of amplification using primers derived from a human-specific sequence, and those showing some level of inhibition were retested after a new DNA extraction. Of 86 patients previously diagnosed as chagasic by serologic techniques, 83 were positive in our PCR test (sensitivity = 96.5%), including all the xenodiagnosis-positive patients and 21 (87.5%) of 24 xenodiagnosis-negative individuals. In addition, four of six patients with doubtful serologic results were confirmed as positive by PCR. Our results suggest that the PCR may be a useful complement to serology in the diagnosis of Chagas' disease, and that it is the most powerful technique available for parasite detection in patients with chronic disease.

To examine the extent of genetic variation in Biomphalaria glabrata, the intermediate host of Schistosoma mansoni, specimens from seven Brazilian isolates were studied. Regions of genomic DNA were amplified using short, arbitrarily selected oligonucleotide primers under low-stringency conditions (random amplified polymorphic DNAs--RAPDs) and analyzed by polyacrylamide gel electrophoresis followed by silver staining. The RAPD profiles of snails of the same isolate were relatively homogeneous, with the majority of bands being common to all individuals studied. In contrast, the profiles of snails from different isolates were quite distinct, with less than 10% of amplified DNA fragments being common to all of the specimens studied. This was found to be true irrespective of the primer, indicating that B. glabrata is remarkably genetically heterogeneous. The data are consistent with the view that genetic drift plays a major role in the genetic structure of populations of B. glabrata due to their ability to reconstitute populations from very small numbers of individuals by self-fertilization. The great variety of polymorphic genetic markers identified in this restricted survey indicates that RAPD analysis may make a major contribution to the study of the genetics of Biomphalaria.

We have characterized the circumsporozoite (CS) gene sequences of Plasmodium malariae China-1 CDC, isolated recently from a person who was infected 50 years ago in China, and P. vivax Chesson, isolated 48 years ago from a patient who had returned from New Guinea. These protein sequences were compared with the CS protein sequences of recently isolated P. vivax and P. malariae parasites. In a similar manner, we compared the previously characterized CS protein gene of P. falciparum clone 7G8, derived from a Brazilian isolate collected in 1980, with the CS protein genes of recent P. falciparum field isolates. In the case of the P. malariae CS protein gene, with the exception of an additional copy of major (NAAG) and minor (NDAG) repeat sequences and the presence of one copy of NDEG sequence, the China-1 CDC P. malariae parasite is similar to the Uganda-1 CDC isolate of 1982. In the nonrepeat region, changes were noted in two amino acid residues, one of which is also seen in a closely related monkey malaria parasite, P. brasilianum. In the case of P. vivax CS proteins, the nonrepeat region of the protein in Chesson strain shares identity with nearly 71% of the CS clones characterized from field isolates. In the P. falciparum CS proteins, the 7G8 CS protein sequence is identical to 75% of the genes of recent field isolates in the Th1R-N1 region. In the Th2R and Th3R regions, 34% and 55% of the CS clones analyzed, respectively, had changes at two amino acid residues.(ABSTRACT TRUNCATED AT 250 WORDS)