Evaluation of monocot and eudicot divergence using the sugarcane transcriptome(1[w])

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm. functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.

A transcript finishing initiative for closing gaps in the human transcriptome

We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST Clusters, mapped against the genomic sequence. Each pair of EST Clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted Set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.

Searching for larval support for majoid families (Crustacea : Brachyura) with particular reference to Inachoididae Dana, 1851

We re-evaluated the larval support for families within majoids using the Wilcoxon signed-rank test with emphasis on Inachoididae. To accomplish our objectives, we added 10 new taxa, two of which are traditionally assigned to the family of special interest, to a previous larval database for majoids, and re-appraised the larval characters used in earlier studies. Phylogenetic analysis was performed with PAUP* using the heuristic search with 50 replicates or the branch-and-bound algorithm when possible. Multi-state transformation series were considered unordered; initially characters were equally weighted followed by successive weighting, and trees were rooted at the Oregoniidae node. Ten different topological constraints were enforced for families to evaluate tree length under the assumption of monophyly for each taxonomic entity. Our results showed that the tree length of most constrained topologies was not considerably greater than that of unconstrained analysis in which most families nested as paraphyletic taxa. This may indicate that the present larval database does not provide strong support for paraphyly of the taxa in question. For Inachoididae, although the Wilcoxon signed-rank test rejected a significant difference between unconstrained and constrained cladograms, we were unable to provide a single synapomorphy for this clade. Except for the conflicting position of Leurocyclus and Stenorhynchus, the two clades correspond to the traditional taxonomic arrangement. Among inachoidids, the clade (Anasimus (Paradasygyius (Collodes + Pyromaia))) is supported, whereas for inachids, the clade (Inachus (Macropodia + Achaeus)) is one of the most supported clades within majids. As often stated, only additional characters will provide a better test for the monophyly of Inachoididae and other families within Majoidea.

Floral anatomy of Bromeliaceae, with particular reference to the evolution of epigyny and septal nectaries in commelinid monocots

Floral anatomy is described in ten genera of Bromeliaceae, including three members of subfamily Bromelioideae, three Tillandsioideae, and four genera of the polyphyletic subfamily Pitcairnioideae (including Brocchinia, the putatively basal genus of Bromeliaceae). Bromeliaceae are probably unique in the order Poales in possessing septal nectaries and epigynous or semi-epigynous flowers. Evidence presented here from floral ontogeny, vasculature, and the relative positions of nectary and ovules indicates that there could have been one or more reversals to apparent hypogyny in Bromeliaceae, although this hypothesis requires a better-resolved phylogeny. Such evolutionary reversals probably evolved in response to specialist pollinators, and in conjunction with other aspects of floral morphology of Bromeliaceae, such as the petal appendages of some species. The ovary is initiated in an inferior position even in semi-epigynous or hypogynous species. The ovary of all so-called hypogynous Bromeliaceae is actually semi-inferior, because the septal nectary is infralocular; in these species the nectaries have a labyrinthine surface and many vascular bundles. Brocchinia differs from most other fully epigynous species in that each carpel is secretory at the apex and reproductive, rather than secretory, at the base.

Chromosome banding in three species of Hypsiboas (Hylidae, Hylinae), with special reference to a new case of B-chromosome in anuran frogs and to the reduction of the diploid number of 2n=24 to 2n=22 in the genus

The chromosomes of hylids Hypsiboas albopunctatus, H. raniceps, and H. crepitans from Brazil were analyzed with standard and differential staining techniques. The former species presented 2n = 22 and 2n = 23 karyotypes, the odd diploid number is due to the presence of an extra element interpreted as B chromosome. Although morphologically very similar to the small-sized chromosomes of the A complement, the B was promptly recognized, even under standard staining, on the basis of some characteristics that are usually attributed to this particular class of chromosomes. The two other species have 2n = 24, which is the chromosome number usually found in the species of Hypsiboas karyotyped so far. This means that 2n = 22 is a deviant diploid number, resulted from a structural rearrangement, altering the chromosome number of 2n = 24 to 2n = 22. Based on new chromosome data, some possibilities were evaluated for the origin of B chromosome in Hypsiboas albopunctatus, as well as the karyotypic evolution in the genus, leading to the reduction in the diploid number of 2n = 24 to 2n = 22.

Burrowing behavior of Dermatonotus muelleri (Anura, Microhylidae) with reference to the origin of the burrowing behavior of Anura

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Ichthyofauna of two streams (silted and reference) in the Upper Paraná river basin, Southeastern Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identification of reference genes for expression analysis by real-time quantitative PCR in drought-stressed soybean

O objetivo deste trabalho foi validar, pela técnica de PCR quantitativo em tempo real (RT-qPCR) genes para serem utilizados como referência em estudos de expressão gênica em soja, em ensaios de estresse hídrico. Foram avaliados quatro genes comumente utilizados em soja: Gmβ-actin, GmGAPDH, GmLectin e GmRNAr18S. O RNA total foi extraído de seis amostras: três amostras de raízes em sistema de hidroponia com diferentes intensidades de déficit hídrico (0, 25, 50, 75 e 100 minutos de estresse hídrico), e três amostras de folhas de plantas cultivadas em areia com diferentes umidades do solo (15, 5 e 2,5% de umidade gravimétrica). Os dados brutos do intervalo cycle threshold (Ct) foram analisados, e a eficiência de cada iniciador foi calculada para uma analise da Ct entre as diferentes amostras. A aplicação do programa GeNorm foi utilizada para a avaliação dos melhores genes de referência, de acordo com a estabilidade. O GmGAPDH foi o gene menos estável, com o maior valor médio de estabilidade de expressão (M), e os genes mais estáveis, com menor valor de M, foram o Gmβ-actin e GmRNAr18S, tanto nas amostras de raízes como nas de folhas. Estes genes podem ser usados em RT-qPCR como gens de referência para análises de expressão gênica.

Phytophthora parasitica transcriptome, a new concept in the understanding of the citrus gummosis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Demographic determinants of survival of people living with HIV attending an outpatient reference unit in the city of Três Lagoas, state of Mato Grosso do Sul, Brazil, in the period 1984-2009

,,,,,,,,,, While the incidence of HIV infection and AIDS is increasing in small Brazilian cities, epidemiological studies are often conducted in large urban centers. ,,,,,,,,,,,,,,,,,, Our group conducted a retrospective analysis of survival determinants among 358 patients who attended a reference unit in a small city.,,,,,,,,,,,,,,,,,,,,,,,Death risk was lower among men that had sex with men, patients with an HIV-seropositive partner, and those admitted after highly active antiretroviral therapy (HAART) was available. ,,,,,,,,,,,,,,,,,, The study documents the striking beneficial effect of HAART. The finding of other groups with improved survival may aid in the development of programmatic strategies.,,,,

NEST REUSE AND COMMUNAL NESTING IN MICROTHURGE-CORUMBAE (HYMENOPTERA, MEGACHILIDAE), WITH SPECIAL REFERENCE TO NEST DEFENSE

Observations on the nesting activities of Microthurge corumbae, carried out at the University Campus of Ribeirao Preto, São Paulo, Brazil, from 1977 to 1981, indicated that 61.9% of nests were re-used by succeeding generations. Re-use by one generation was more frequent than by two generations, and re-use by a third was observed only once. Nests were re-used by one or several females. Single females were more frequently in the first re-use. In these cases nest re-use did not differ essentially from the solitary foundation of a new nest, except for the adoption of a pre-existing nest without excavation. In multifemale nests, analysis of relative age (wing wear), ovarian and spermathecal conditions of associated females and the content of nests at excavation indicated that the social pattern in such colonies is communal. There is some evidence that the associated females are relatives. The chalcidoid wasp Leucospis was the principal nest parasite, and ants of the genus Crematogaster were nest predators. In multifemale nests, the rate of parasitism was significantly lower than in solitary nests, indicating that nest-sharing resulted in improved nest defense. on the other hand. The absence of predation on immatures of the first generation of M. corumbue in multifemale nests suggests that such nests are also more resistant to attack by predators.

Transcriptome profiling of Paracoccidioides brasiliensis yeast-phase cells recovered from infected mice brings new insights into fungal response upon host interaction

Paracoccidioides brasiliensis is a fungal human pathogen with a wide distribution in Latin America. It causes paracoccidioidomycosis, the most widespread systemic mycosis in Latin America. Although gene expression in P. brasiliensis had been studied, little is known about the genome sequences expressed by this species during the infection process. To better understand the infection process, 4934 expressed sequence tags (ESTs) derived from a non-normalized cDNA library from P. brasiliensis (isolate Pb01) yeast-phase cells recovered from the livers of infected mice were annotated and clustered to a UniGene (clusters containing sequences that represent a unique gene) set with 1602 members. A large-scale comparative analysis was performed between the UniGene sequences of P. brasiliensis yeast-phase cells recovered from infected mice and a database constructed with sequences of the yeast-phase and mycelium transcriptome (isolate Pb01) (https://dna.biomol.unb.br/Pb/), as well as with all public ESTs available at GenBank, including sequences of the P. brasiliensis yeast-phase transcriptome (isolate Pb18) (http:// www.ncbi.nlm.nih.gov/). The focus was on the overexpressed and novel genes. From the total, 3184 ESTs (64.53%) were also present in the previously described transcriptome of yeast-form and mycelium cells obtained from in vitro cultures (https://dna.biomol.unb.br/Pb/) and of those, 1172 ESTs (23.75% of the described sequences) represented transcripts overexpressed during the infection process. Comparative analysis identified 1750 ESTs (35.47% of the total), comprising 649 UniGene sequences representing novel transcripts of P. brasiliensis, not previously described for this isolate or for other isolates in public databases. KEGG pathway mapping showed that the novel and overexpressed transcripts represented standard metabolic pathways, including glycolysis, amino acid biosynthesis, lipid and sterol metabolism. The unique and divergent representation of transcripts in the cDNA library of yeast cells recovered from infected mice suggests differential gene expression in response to the host milieu.

AN ULTRASTRUCTURAL-STUDY ON THE ENDOCRINE PANCREAS OF CAIMAN-LATIROSTRIS, WITH SPECIAL REFERENCE TO PANCREATIC MOTILIN CELLS

Pancreatic endocrine cells of Caiman latirostris were investigated by electron microscopy using conventional and immunocytochemical methods. Ultrastructurally, four types of endocrine cells were classified according to the morphology of their secretory granules. Three types of endocrine cells were identified as either glucagon, insulin or somatostatin cells by the presence of such characteristic granules well established in mammals. The remaining endocrine cell type could not be classified by its ultrastructural features alone.Immunocytochemical observations confirmed the ultrastructural classification of glucagon, insulin and somatostatin cells. In addition, endocrine cells immunoreactive for either pancreatic polypeptide (PP) or motilin were identified. Morphometric analysis of PP- and motilin-immunoreactive granules demonstrated that they were the most polymorphous and smallest granules among the pancreatic endocrine cell granules. Although both PP and motilin granules closely resemble each other, motilin granules were smaller in size and more spherical in shape than PP granules.

Leukocyte and thrombocyte reference values for channel catfish (Ictalurus punctatus Raf), with an assessment of morphologic, cytochemical, and ultrastructural features

Background: Hematology tests are useful to evaluate physiologic disturbances in fish and can provide important information for the diagnosis and prognosis of disease. Objectives: the primary purpose of this study was to define reference intervals for thrombocytes and leukocytes in healthy channel catfish (Ictalurus punctactus). In addition, the morphologic, cytochernical, and ultrastructural features of blood cells were assessed. Methods: Blood samples (0.5 mL were collected into EDTA from 40 clinically healthy catfish on a commercial fish farm in Jaboticabal, Brazil. Thrombocyte, total WBC, and differential WBC counts were determined and reference intervals were calculated as the 25-95th percentiles of data. Thrombocyte and leukocyte morphology was assessed in blood smears stained with May Griinwald-Giemsa-Wright and ultrastructurally by transmission electron microscopy. Cytochemical staining patterns were described using periodic acid-Schiff (PAS), peroxidase, nonspecific esterase, alkaline phosphatase, and toluidine blue. Results: Reference intervals were as follows: thrombocytes 58,802-99,569/mu L; total WBCs 27,460-41,523/mu L; lymphocytes 5380-11,581/mu L; monocytes 2949-7459/mu L; neutrophils 12,529-22,748/mu L, and basophils 736-2003/mu L. Neutrophils were positive for peroxidase and PAS; monocytes were positive for nonspecific esterase; and basophils were positive with toluidine blue. Conclusion: the morphologic and staining features of neutrophils and monocytes of channel catfish are similar to those of mammals, and the presence of basophils in this species was verified. These reference intervals and morphologic findings provide a foundation for future investigations on the functions and alterations of blood cells in channel catfish.

CLINICAL BIOCHEMICAL DETERMINATIONS IN THE MANGALARGA-PAULISTA HORSE - REFERENCE VALUES

Biochemical values are widely related with environmental agents, sex and age, and are used in disease diagnosis. Numerous reports have been published on the biochemical parameters of different breeds of horses. However, there is a paucity of information concerning Cu-Zn superoxide dismutase (SOD), ceruloplasmin, copper and zinc determinations in the serum. Blood samples from a total of 60 horses of the Mangalarga-Paulista breed, representing three age groups (0 to 4 months old, 6 to 18 months old and adult) were examined. Male horses have a higher mean value of SOD, ceruloplasmin and copper than do females. No significant sex-related difference was observed in serum zinc content of weaned and adult horses. SOD activity was significantly higher in adult animals. Since SOD has a protective effect against superoxide free radical toxicity and possesses anti-inflammatory activity, it is reasonable to assume that the increased activity of this enzyme may be due to an adaptation mechanism which protects the adult animal against oxygen toxicity.