DNA sequencing confirms the involvement of Leishmania (L.) amazonensis in american tegumentary leishmaniasis in the state of São Paulo, Brazil

INTRODUCTION: American tegumentary leishmaniasis (ATL) represents one of the most important public health issues in the world. An increased number of autochthonous cases of ATL in the Northeastern region of São Paulo State has been documented in the last few years, leading to a desire to determine the Leishmania species implicated. METHODS: PCR followed by DNA sequencing was carried out to identify a 120bp fragment from the universal kDNA minicircle of the genus Leishmania in 61 skin or mucosal biopsies from patients with ATL. RESULTS: DNA sequencing permitted the identification of a particular 15bp fragment (5' …GTC TTT GGG GCA AGT... 3') in all samples. Analysis by the neighbor-joining method showed the occurrence of two distinct groups related to the genus Viannia (V) and Leishmania (L), each with two subgroups. Autochthonous cases with identity to a special Leishmania sequence not referenced in Genbank predominated in subgroup V.1, suggesting the possible existence of a subtype or mutation of Leishmania Viannia in this region. In the subgroup L.2, which showed identity with a known sequence of L. (L.) amazonensis, there was a balanced distribution of autochthonous and non-autochthonous cases, including the mucosal and mucocutaneus forms in four patients. The last observation may direct us to new concepts, since the mucosal compromising has commonly been attributed to L. (V.) braziliensis, even though L. (L.) amazonensis is more frequent in the Amazonian region. CONCLUSIONS: These results confirm the pattern of distribution and possible mutations of these species, as well as the change in the clinical form presentation of ATL in the São Paulo State.

Differentially displayed expressed sequence tags in Melipona scutellaris (Hymenoptera, Apidae, Meliponini) development

Nesse estudo nós usamos a técnica de Differential Display Reverse Transcriptase - Polymerase Chain Reaction (DDRT-PCR) para comparamos o perfil de mRNA em Melipona scutellaris durante o desenvolvimento ontogenético pós-embrionário e em operárias adultas, rainha natural e induzida pelo Hormônio Juvenil III. Fragmentos diferencialmente expressos foram detectados usando as seguintes combinações de primers: HT11G-AP05; HT11C-AP05; HT11G-OPF12; HT11G-OPA16. Dos 9 ESTs descrito nesse trabalho, 6 tiveram expressão diferencial nas fases de larva L1 e L2, sugerindo serem mecanismos chave no regulação do desenvolvimento larval em Melipona. A combinação HT11G-AP05 revelou em L1 e L2 um produto com similaridade à proteína tioredoxina redutase de Clostridium sporogenes, uma proteína importante durante os processos de oxidoredução. Esse estudo representa as primeiras evidências moleculares do perfil de expressão durante o desenvolvimento ontogenético em abelhas do gênero Melipona.

Evaluation of gene selection metrics for tumor cell classification

Gene expression profiles contain the expression level of thousands of genes. Depending on the issue under investigation, this large amount of data makes analysis impractical. Thus, it is important to select subsets of relevant genes to work with. This paper investigates different metrics for gene selection. The metrics are evaluated based on their ability in selecting genes whose expression profile provides information to distinguish between tumor and normal tissues. This evaluation is made by constructing classifiers using the genes selected by each metric and then comparing the performance of these classifiers. The performance of the classifiers is evaluated using the error rate in the classification of new tissues. As the dataset has few tissue samples, the leave-one-out methodology was employed to guarantee more reliable results. The classifiers are generated using different machine learning algorithms. Support Vector Machines (SVMs) and the C4.5 algorithm are employed. The experiments are conduced employing SAGE data obtained from the NCBI web site. There are few analysis involving SAGE data in the literature. It was found that the best metric for the data and algorithms employed is the metric logistic.

Racial influence on the prevalence of prostate carcinoma in Brazilian volunteers

PURPOSE: To investigate the prevalence of prostate carcinoma in a sample of volunteers known to have a large proportion of Bantu African ancestors, and the performance of total PSA (tPSA), PSA density (PSAD) and free-to-total PSA ratio (f/tPSA) on the diagnosis. MATERIALS AND METHODS: A total of 473 volunteers (range: 40 - 79 years) were screened for prostate carcinoma. Those with tPSA >2 ng/ml and/or abnormal digital rectal examination were submitted to a transrectal ultrasound-directed biopsy (10 cores). The volunteers were classified as White, Mulatto or Black according to physical characteristics and to ancestors race reference. The following variable number of tandem repeats (VNTR) were analyzed in the blood of 120 volunteers without cancer and in 27 patients with prostate cancer: D4S43, PAH, F13A1, APOB and vW-1. RESULTS: The biopsies performed in 121 volunteers revealed cancer in 27 (5.7 percent of 473). The proportions of cancer in White, Mulatto and Black were respectively: 0.6 percent (1/148), 6.7 percent (6/90) and 8.5 percent (20/235) (p = 0.006). The VNTRs analysis revealed heterogeneity in White, Mulatto and Black anthropologic phenotypes with the following admixture of Caucasian, African and Amerindian gene lineages: 67.5 ± 8 percent, 20.8 ± 8 percent, 11.7 ± 7 percent; 54.8 ± 9 percent, 36.3 ± 5 percent, 8.9 ± 7 percent; and, 45.3 ± 3 percent, 45.9 ± 4 percent, 8.8 ± 7 percent. Such a mixture was 50.5 ± 9 percent, 49 ± 8 percent and 0.5 ± 4 percent in volunteers bearing cancer, and 59.1 ± 7 percent, 31.7 ± 8 percent and 9.2 ± 5 percent in those without cancer. The sensitivity and specificity of tPSA at cut-off levels of 2, 2.5 and 4 ng/ml for volunteers with tPSA <= 10 ng/ml were respectively: 100 percent and 6,6 percent, 100 percent and 36,6 percent, 69,2 percent and 62,2 percent. PSAD at a cut-off level of 0.08 or 0.10, and f/tPSA at a cut-off level of 20 percent were able to increase significantly tPSA specificity without loss on sensitivity. CONCLUSIONS: The tumor prevalence was higher in Non-White than in White phenotype. The association of tPSA at a cut-off level of 2.5 ng/ml with a PSAD of 0.08 or a f/tPSA of 20 percent for biopsy indication deserves further investigations as an alternative to tPSA cut-off level of 4 ng/ml.

Hemoglobinopathies and other hereditary hematological diseases in the brazilian population

The complex history and structure of the Brazilian population, to which contributed a large number of ethnic components that are in a state of increasing miscegenation, are reflected in the diversity, frequency and regional distribution of the more common hereditary diseases. It is interesting to observe that no gene mutation was inherited from the original Amerindian population, which is severely reduced today. Four important group of hereditary hematological diseases are represented in the Brazilian population: Sickle cell anemia and other hemoglobinopathies, the thalassemias, familial hypercholesterolemia and thrombophilia. Sickle cell anemia, hemoglobin C disease and thalassemias are heterogeneously distributed owing to the unevenly proportion of descendants of African blacks and European immigrants in the different regions of the country. The most frequent cause of familiar hypercholesterolemia is a mutation of Arab origin. The mutations that may represent risk factors for thrombophilia have a heterogenous ethnic distribution which may help to explain the differences in the prevalence of thrombotic diseases.