Identification of protein-coding and intronic noncoding RNAs down-regulated in clear cell renal carcinoma

The clear cell subtype of renal cell carcinoma (RCC) is the most lethal and prevalent cancer of the urinary system. To investigate the molecular changes associated with malignant transformation in clear cell RCC, the gene expression profiles of matched samples of tumor and adjacent non-neoplastic tissue were obtained from six patients. A custom-built cDNA microarray platform was used, comprising 2292 probes that map to exons of genes and 822 probes for noncoding RNAs mapping to intronic regions. Intronic transcription was detected in all normal and neoplastic renal tissues. A subset of 55 transcripts was significantly down-regulated in clear cell RCC relative to the matched nontumor tissue as determined by a combination of two statistical tests and leave-one-out patient cross-validation. Among the down-regulated transcripts, 49 mapped to untranslated or coding exons and 6 were intronic relative to known exons of protein-coding genes. Lower levels of expression of SIN3B, TRIP3, SYNJ2BP and NDE1 (P<0.02), and of intronic transcripts derived from SND1 and ACTN4 loci (P<0.05), were confirmed in clear cell RCC by Real-time RT-PCR. A subset of 25 transcripts was deregulated in additional six nonclear cell RCC samples, pointing to common transcriptional alterations in RCC irrespective of the histological subtype or differentiation state of the tumor. Our results indicate a novel set of tumor suppressor gene candidates, including noncoding intronic RNAs, which may play a significant role in malignant transformations of normal renal cells. (C) 2008 Wiley-Liss, Inc.

Morfoanatomia da flor de cinco espécies de Galipea Aubl. e seu significado na evolução de flores tubulosas entre as Rutaceae neotropicais

A maioria dos gêneros da subtribo neotropical Galipeinae (tribo Galipeeae, Rutoideae) tem flores tubulosas, com várias formas e graus de conação e adnação. Galipea e outros gêneros na subtribo apresentam apenas duas anteras férteis mais cinco ou mais estaminódios, o que é intrigante porque na tribo predominam flores pentâmeras isostêmones. Visando elucidar a condição anatômica dessas características e estabelecer estados acurados para caracteres em análises filogenéticas, um estudo morfoanatômico de flores de cinco espécies de Galipea foi realizado, buscando os padrões de vascularização, posição, e união dos segmentos da flor. Destacam-se os resultados: 1) um tubo floral genuíno se forma no terço basal da flor por conação dos filetes e adnação desse tubo estaminal às pétalas; 2) as pétalas são distalmente coerentes umas às outras e aderentes aos filetes por meio de entrelaçamento de tricomas densos - um caso de pseudossimpetalia; 3) dentre as cinco (às vezes seis) estruturas tratadas como estaminódios, apenas as três externas são de fato homólogas a estames esterilizados, as demais surgem como ramificações adaxiais das pétalas; 4) os carpelos são peltados, congenitalmente conatos axial e lateralmente da base do ovário até o nível das placentas, e no estilete e estigma; na zona mediana e superior do ovário eles são unidos apenas posgenitalmente, com a epiderme diferenciada de carpelos contíguos e suturas evidentes na região ventral de cada carpelo; 5) a vascularização do disco sugere origem receptacular. As implicações desses dados para o entendimento da evolução das flores tubulosas em Galipea e grupos relacionados são discutidas.

The mitochondrial genome of the stingless bee Melipona bicolor (Hymenoptera, Apidae, Meliponini): sequence, gene organization and a unique tRNA translocation event conserved across the tribe Meliponini

At present a complete mtDNA sequence has been reported for only two hymenopterans, the Old World honey bee, Apis mellifera and the sawfly Perga condei. Among the bee group, the tribe Meliponini (stingless bees) has some distinction due to its Pantropical distribution, great number of species and large importance as main pollinators in several ecosystems, including the Brazilian rain forest. However few molecular studies have been conducted on this group of bees and few sequence data from mitochondrial genomes have been described. In this project, we PCR amplified and sequenced 78% of the mitochondrial genome of the stingless bee Melipona bicolor (Apidae, Meliponini). The sequenced region contains all of the 13 mitochondrial protein-coding genes, 18 of 22 tRNA genes, and both rRNA genes (one of them was partially sequenced). We also report the genome organization (gene content and order), gene translation, genetic code, and other molecular features, such as base frequencies, codon usage, gene initiation and termination. We compare these characteristics of M. bicolor to those of the mitochondrial genome of A. mellifera and other insects. A highly biased A+T content is a typical characteristic of the A. mellifera mitochondrial genome and it was even more extreme in that of M. bicolor. Length and compositional differences between M. bicolor and A. mellifera genes were detected and the gene order was compared. Eleven tRNA gene translocations were observed between these two species. This latter finding was surprising, considering the taxonomic proximity of these two bee tribes. The tRNA Lys gene translocation was investigated within Meliponini and showed high conservation across the Pantropical range of the tribe.

Genotype-phenotype correlation in Brazillian Rett syndrome patients

BACKGROUND: Rett syndrome (RS) is a severe neurodevelopmental X-linked dominant disorder caused by mutations in the MECP2 gene. PURPOSE: To search for point mutations on the MECP2 gene and to establish a correlation between the main point mutations found and the phenotype. METHOD: Clinical evaluation of 105 patients, following a standard protocol. Detection of point mutations on the MECP2 gene was performed on peripheral blood DNA by sequencing the coding region of the gene. RESULTS: Classical RS was seen in 68% of the patients. Pathogenic point mutations were found in 64.1% of all patients and in 70.42% of those with the classical phenotype. Four new sequence variations were found, and their nature suggests patogenicity. Genotype-phenotype correlations were performed. CONCLUSION: Detailed clinical descriptions and identification of the underlying genetic alterations of this Brazilian RS population add to our knowledge of genotype/phenotype correlations, guiding the implementation of mutation searching programs.

Molecular markers and genetic diversity of Plasmodium vivax

Enhanced understanding of the transmission dynamics and population genetics for Plasmodium vivax is crucial in predicting the emergence and spread of novel parasite phenotypes with major public health implications, such as new relapsing patterns, drug resistance and increased virulence. Suitable molecular markers are required for these population genetic studies. Here, we focus on two groups of molecular markers that are commonly used to analyse natural populations of P. vivax. We use markers under selective pressure, for instance, antigen-coding polymorphic genes, and markers that are not under strong natural selection, such as most minisatellite and microsatellite loci. First, we review data obtained using genes encoding for P. vivax antigens: circumsporozoite protein, merozoite surface proteins 1 and 3α, apical membrane antigen 1 and Duffy binding antigen. We next address neutral or nearly neutral molecular markers, especially microsatellite loci, providing a complete list of markers that have already been used in P. vivax populations studies. We also analyse the microsatellite loci identified in the P. vivax genome project. Finally, we discuss some practical uses for P. vivax genotyping, for example, detecting multiple-clone infections and tracking the geographic origin of isolates.

Cloning, purification and comparative characterization of two digestive lysozymes from Musca domestica larvae

cDNA coding for two digestive lysozymes (MdL1 and MdL2) of the Musca domestica housefly was cloned and sequenced. MdL2 is a novel minor lysozyme, whereas MdL1 is the major lysozyme thus far purified from M. domestica midgut. MdL1 and MdL2 were expressed as recombinant proteins in Pichia pastoris, purified and characterized. The lytic activities of MdL1 and MdL2 upon Micrococcus lysodeikticus have an acidic pH optimum (4.8) at low ionic strength (μ = 0.02), which shifts towards an even more acidic value, pH 3.8, at a high ionic strength (μ = 0.2). However, the pH optimum of their activities upon 4-methylumbelliferyl N-acetylchitotrioside (4.9) is not affected by ionic strength. These results suggest that the acidic pH optimum is an intrinsic property of MdL1 and MdL2, whereas pH optimum shifts are an effect of the ionic strength on the negatively charged bacterial wall. MdL2 affinity for bacterial cell wall is lower than that of MdL1. Differences in isoelectric point (pI) indicate that MdL2 (pI = 6.7) is less positively charged than MdL1 (pI = 7.7) at their pH optima, which suggests that electrostatic interactions might be involved in substrate binding. In agreement with that finding, MdL1 and MdL2 affinities for bacterial cell wall decrease as ionic strength increases.

Description and phylogenetic analysis of the Calycopidina (Lepidoptera, Lycaenidae, Theclinae, Eumaeini): a subtribe of detritivores

Description and phylogenetic analysis of the Calycopidina (Lepidoptera, Lycaenidae, Theclinae, Eumaeini): a subtribe of detritivores. The purpose of this paper is to establish a phylogenetic basis for a new Eumaeini subtribe that includes those lycaenid genera in which detritivory has been recorded. Morphological characters were coded for 82 species of the previously proposed "Lamprospilus Section" of the Eumaeini (19 of these had coding identical to another species), and a phylogenetic analysis was performed using the 63 distinct ingroup terminal taxa and six outgroups belonging to four genera. Taxonomic results include the description in the Eumaeini of Calycopidina Duarte & Robbins new subtribe (type genus Calycopis Scudder, 1876), which contains Lamprospilus Geyer, Badecla Duarte & Robbins new genus (type species Thecla badaca Hewitson), Arzecla Duarte & Robbins new genus (type species Thecla arza Hewitson), Arumecla Robbins & Duarte, Camissecla Robbins & Duarte, Electrostrymon Clench, Rubroserrata K. Johnson & Kroenlein revalidated status, Ziegleria K. Johnson, Kisutam K. Johnson & Kroenlein revalidated status, and Calycopis. Previous "infratribe" names Angulopina K. Johnson & Kroenlein, 1993, and Calycopina K. Johnson & Kroenlein, 1993, are nomenclaturally unavailable and polyphyletic as proposed. New combinations include Badecla badaca (Hewitson), Badecla picentia (Hewitson), Badecla quadramacula (Austin & K. Johnson), Badecla lanckena (Schaus), Badecla argentinensis (K. Johnson & Kroenlein), Badecla clarissa (Draudt), Arzecla arza (Hewitson), Arzecla tarpa (Godman & Salvin), Arzecla canacha (Hewitson), Arzecla calatia (Hewitson), Arzecla tucumanensis (K. Johnson & Kroenlein), Arzecla sethon (Godman & Salvin), Arzecla nubilum (H. H. Druce), Arzecla paralus (Godman & Salvin), Arzecla taminella (Schaus), Arzecla albolineata (Lathy), Electrostrymon denarius (Butler & H.Druce), Electrostrymon guzanta (Schaus), Electrostrymon perisus (H. H. Druce), Rubroserrata mathewi (Hewitson), Rubroserrata ecbatana (Hewitson), Kisutam micandriana (K. Johnson), and Kisutam syllis (Godman & Salvin). The structure of the male genitalia lateral window, labides, and brush organs are described and discussed, as are the female genitalia signa of the corpus bursae and 8th abdominal tergum. Widespread wing pattern sexual dimorphism in the Calycopidina is noted and illustrated, and the presence of alternating dark and light bands on the ventral wings of both sexes is discussed. The evidence for detritivory in Lamprospilus, Badecla, Arzecla, Arumecla, Camissecla, Electrostrymon, Ziegleria, Kisutam, and Calycopis is summarized using the new classification.

Efetividade de programa de suplementação alimentar no ganho ponderal de crianças

OBJETIVO: Avaliar a efetividade de programa governamental de suplementação alimentar no ganho ponderal de crianças. MÉTODOS: Estudo de coorte com dados secundários de 25.433 crianças de baixa renda com idade entre seis e 24 meses que ingressaram em programa de distribuição de leite fortificado Projeto Vivaleite, realizado no Estado de São Paulo de 2003 a 2008. O ganho ponderal foi medido por meio dos valores de escores z de peso para idade, calculados pelo padrão da Organização Mundial da Saúde (2007), obtidos, na rotina do programa, ao ingressar e a cada quatro meses durante a permanência. As crianças foram divididas em três grupos de escore z ao entrar: sem comprometimento de peso (z > -1); risco de baixo peso (-2 < z < -1) e baixo peso (z < -2). Utilizou-se regressão linear multinível (modelo misto), permitindo a comparação, em cada idade, das médias ajustadas do escore z dos ingressantes e participantes há pelo menos quatro meses, ajustadas para correlação entre medidas repetidas. RESULTADOS: Verificou-se efeito positivo do programa no ganho de peso das crianças, variando em função do estado nutricional ao ingressar; para as que entraram sem comprometimento de peso, o ganho médio ajustado foi 0,183 escore z;entre as que entraram com risco de baixo peso, foi 0,566; e entre as ingressantes com baixo peso, foi 1,005 escore z. CONCLUSÕES: O programa é efetivo para o ganho ponderal de crianças menores de dois anos, com efeito mais pronunciado entre as crianças que entram no programa em condições menos favoráveis de peso.

Saúde gengival de adolescentes e a utilização de serviços odontológicos, Estado de São Paulo

OBJETIVO: Avaliar a associação de condições de saúde gengival com a utilização de serviço odontológico. MÉTODOS: Realizou-se levantamento epidemiológico de saúde bucal de 1.799 adolescentes, em 35 cidades do Estado de São Paulo, em 2002. A saúde gengival foi avaliada pela prevalência de sangramento na gengiva à sondagem e cálculo dentário (índice periodontal comunitário) e oclusão dentária (índice de estética dentária). A utilização de serviços odontológicos foi medida pelo índice de cuidado (O/CPO) para cada cidade. Análise multinível de regressão logística ajustou modelos explicativos para fatores associados aos desfechos de interesse. RESULTADOS: A prevalência de sangramento gengival à sondagem foi 21,5%; de cálculo dentário foi 19,4%. Os participantes do sexo masculino, negros e pardos, moradores em áreas rurais, residentes em domicílios aglomerados e com atraso escolar apresentaram chance significantemente mais elevada para os agravos que seus respectivos pares de comparação. Características de oclusão dentária também associaram com gengiva não-saudável: apinhamento dos segmentos incisais, mordida aberta vertical anterior, relação molar antero-posterior. Cidades com maior utilização de serviço odontológico tiveram menor proporção de adolescentes com sangramento gengival e cálculo. CONCLUSÕES: A utilização de serviços odontológicos foi significativamente associada a melhores condições de saúde gengival (sangramento e cálculo). Essa associação independeu das características sociodemográficas individuais e contextuais, e de oclusão dentária.

Molecular characterization of Cryptosporidium spp. from HIV infected patients from an urban area of Brazil

Cryptosporidium spp. are important cause of enteric disease in humans, but may also infect animals. This study describes the relative frequency of several Cryptosporidium species found in human specimens from HIV infected patients in the São Paulo municipality obtained from January to July 2007. Sequence analysis of the products of nested-PCR based on small subunit rRNA and Cryptosporidium oocyst wall protein coding genes revealed 17 (63.0%) isolates of C. hominis, four (14.8%) C. parvum, five (18.5%) C. felis and one (3.7%) C. canis. These findings suggest that, in urban environments of Brazil, the cat adapted C. felis may play a potential role in the zoonotic transmission of cryptosporidiosis whereas the anthroponotic transmission of cryptosporidiosis caused by C. hominis seems to predominate.

Differentiation of Bovine coronavirus (BCoV) genotypes by a restriction enzyme assay

This article reports the use of the GsuI restriction enzyme to differentiate genotypes of Bovine Coronavirus (BCoV), based on an 18-nucleotide deletion of S1-coding region found in one of the two genotypes. It was concluded that this assay can be used as a rapid tool for BCoV genotypes differentiation.

Phylogenetic placement of the enigmatic parasite, Polypodium hydriforme, within the Phylum Cnidaria

Background: Polypodium hydriforme is a parasite with an unusual life cycle and peculiar morphology, both of which have made its systematic position uncertain. Polypodium has traditionally been considered a cnidarian because it possesses nematocysts, the stinging structures characteristic of this phylum. However, recent molecular phylogenetic studies using 18S rDNA sequence data have challenged this interpretation, and have shown that Polypodium is a close relative to myxozoans and together they share a closer affinity to bilaterians than cnidarians. Due to the variable rates of 18S rDNA sequences, these results have been suggested to be an artifact of long-branch attraction ( LBA). A recent study, using multiple protein coding markers, shows that the myxozoan Buddenbrockia, is nested within cnidarians. Polypodium was not included in this study. To further investigate the phylogenetic placement of Polypodium, we have performed phylogenetic analyses of metazoans with 18S and partial 28S rDNA sequences in a large dataset that includes Polypodium and a comprehensive sampling of cnidarian taxa. Results: Analyses of a combined dataset of 18S and partial 28S sequences, and partial 28S alone, support the placement of Polypodium within Cnidaria. Removal of the long-branched myxozoans from the 18S dataset also results in Polypodium being nested within Cnidaria. These results suggest that previous reports showing that Polypodium and Myxozoa form a sister group to Bilateria were an artifact of long-branch attraction. Conclusion: By including 28S rDNA sequences and a comprehensive sampling of cnidarian taxa, we demonstrate that previously conflicting hypotheses concerning the phylogenetic placement of Polypodium can be reconciled. Specifically, the data presented provide evidence that Polypodium is indeed a cnidarian and is either the sister taxon to Hydrozoa, or part of the hydrozoan clade, Leptothecata. The former hypothesis is consistent with the traditional view that Polypodium should be placed in its own cnidarian class, Polypodiozoa.

Diffractive phase-shift lithography photomask operating in proximity printing mode

A phase shift proximity printing lithographic mask is designed, manufactured and tested. Its design is based on a Fresnel computer-generated hologram, employing the scalar diffraction theory. The obtained amplitude and phase distributions were mapped into discrete levels. In addition, a coding scheme using sub-cells structure was employed in order to increase the number of discrete levels, thus increasing the degree of freedom in the resulting mask. The mask is fabricated on a fused silica substrate and an amorphous hydrogenated carbon (a:C-H) thin film which act as amplitude modulation agent. The lithographic image is projected onto a resist coated silicon wafer, placed at a distance of 50 mu m behind the mask. The results show a improvement of the achieved resolution - linewidth as good as 1.5 mu m - what is impossible to obtain with traditional binary masks in proximity printing mode. Such achieved dimensions can be used in the fabrication of MEMS and MOEMS devices. These results are obtained with a UV laser but also with a small arc lamp light source exploring the partial coherence of this source. (C) 2010 Optical Society of America

Geographic Information Systems (GIS) in Assessing Dental Health

The present study investigated the distribution profile of dental caries and its association with areas of social deprivation at the individual and contextual level. The cluster sample consisted of 1,002 12-year-old schoolchildren from Piracicaba, SP, Brazil. The DMFT Index was used for dental caries and the Care Index was used to determine access to dental services. On the individual level, variables were associated with a better oral status. On the contextual level, areas were not associated with oral status. However, maps enabled determining that the central districts have better social and oral conditions than the deprived outlying districts.

Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region

Intergenic spacers of chloroplast DNA (cpDNA) are very useful in phylogenetic and population genetic studies of plant species, to study their potential integration in phylogenetic analysis. The non-coding trnE-trnT intergenic spacer of cpDNA was analyzed to assess the nucleotide sequence polymorphism of 16 Solanaceae species and to estimate its ability to contribute to the resolution of phylogenetic studies of this group. Multiple alignments of DNA sequences of trnE-trnT intergenic spacer made the identification of nucleotide variability in this region possible and the phylogeny was estimated by maximum parsimony and rooted with Convolvulaceae Ipomoea batalas, the most closely related family. Besides, this intergenic spacer was tested for the phylogenetic ability to differentiate taxonomic levels. For this purpose, species from four other families were analyzed and compared with Solanaceae species. Results confirmed polymorphism in the trnE-trnT region at different taxonomic levels.