The endangered species Brycon orbignyanus: genetic analysis and definition of priority areas for conservation

Currently, biodiversity is threatened by several factors often associated with human population growth and the extension of areas occupied by human activity. In particular, freshwater fish fauna is affected by overfishing, deforestation, water pollution, introduction of exotic species and habitat fragmentation promoted by hydroelectric dams, among other environmental impact factors. Several action plans to preserve ichthyofauna biodiversity have been adopted; however, these plans frequently cover only a small number of species, and decisions are often made without strong scientific support. This study aimed to evaluate the genetic aspects of wild groups of Brycon orbignyanus, an endangered fish species, using microsatellites and D-loop regions to identify the genetic structure of the samples and to establish priority areas for conservation based on the genetic patterns of this species. The results indicated that the samples showed levels of genetic variability compatible with others studies with Neotropical fishes. However, the results obtained in the analysis of molecular variance (AMOVA) for microsatellites (F (ST) = 0.258) and D-loop (F (ST) = 0.234) and the interpopulation fixation index revealed that B. orbignyanus was structured in different subpopulations in the La Plata River basin; the areas with better environmental conditions also showed subgroups with higher rates of genetic variability. Future conservation actions addressing these sites should consider two different management units: the complex formed by the Ivinhema River, Upper Parana, Camargo Port and Ilha Grande groups; and the complex formed by the Verde River and Sucuriu River groups.

The definition of potential infiltration areas in Guaratingueta watershed, Paraiba do Sul Basin, Southeastern Brazil: an integrated approach using physical and land-use elements

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

The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

Framework for analysis and representation of external systems for online reactive-optimisation studies

The paper proposes a framework for the analysis and representation of external systems for online optimisation studies. The basis for this framework is the equivalent OPF (EOPF), an optimisation model obtained by partitioning of the OPF model. The EOPF is mathematically redefined in the paper to accommodate the concept of a buffer zone. The resulting model is more useful for online optimisation, since external information obtained through intercontrol-centre exchange contracts can be used to improve internal control calculation. Numerical results obtained with original studies involving the boundary-matching procedure have provided a conceptual basis for the definition of a buffer zone for optimisation studies with the EOPF. In the proposed framework, the accuracy of the external representation in optimisation studies is evaluated by comparing the controls obtained by an EOPF procedure with those obtained by the reference-optimisation procedure defined in this paper. The framework is then used to evaluate the accuracy of equivalent optimisation studies involving the IEEE 118-bus test system and the Brazilian South Southeast 810-bus system. The results show that the incorporation of a buffer zone improves the external system representation for all optimisation studies performed.

Non-destructive evaluation tool for monitoring and detection of structural damage by using neural network.

This work studies the capability of generalization of Neural Network using vibration based measurement data aiming at operating condition and health monitoring of mechanical systems. The procedure uses the backpropagation algorithm to classify the input patters of a system with different stiffness ratios. It has been investigated a large set of input data, containing various stiffness ratios as well as a reduced set containing only the extreme ones in order to study generalizing capability of the network. This allows to definition of Neural Networks capable to use a reduced set of data during the training phase. Once it is successfully trained, it could identify intermediate failure condition. Several conditions and intensities of damages have been studied by using numerical data. The Neural Network demonstrated a good capacity of generalization for all case. Finally, the proposal was tested with experimental data.

Definition of a diagnostic routine in individuals with inconclusive serology for chagas disease

Despite the existence of highly sensitive tests, inconclusive serological results are frequent in chronic chagasic infection. This study aimed to define a diagnostic conduct for 30 individuals with inconclusive serology (G3) for chagasic infection assisted at the Outpatient Unit for Infectious and Parasitic Diseases of the Botucatu School of Medicine. Twenty-one individuals with negative serology (G1) and 33 with positive serology (G2) were also studied. Serological methods ELISA, HAI, IFI and immunoblotting TESA-cruzi were used for G1, G2 and G3, and parasitological methods xenodiagnosis, hemoculture and PCR-LIT were used for G2 and G3 individuals. ELISA, HAI and IFI were performed in 5 different blood samples in G2 and G3. TESA-cruzi was carried out only once in G1, G2 and G3 and, since it is the most sensitive, it was utilized as standard. In G3, positivity for ELISA reached 86% in the fifth blood sample; the ELISA+HAI+IFI combination showed a maximum of 44.8% in the second sample; and TESA-cruzi, 76% in one single sample. Xenodiagnosis positivity was 9.4%; hemoculture showed 15.2%; and PCR-LIT exhibited 22% positivity in G2. Nevertheless, in G3, positivity percentage was 3.4% for xenodiagnosis, 6.7% for PCR-LIT, and no positive result was found for hemoculture. In G3, PCR-LIT resolved one case which was still inconclusive according to serology tests. In order to define inconclusive diagnoses, the results suggest the combined use of ELISA+HAI+IFI in 2 blood samples, decreasing the occurrence of false positive/negative results. If results remain inconclusive, the performance of TESA-cruzi and PCR-LIT, if necessary, is recommended.

Are affects important for the definition of depression?

Many of the nosological features, subtypes, biochemical, neurophysiological mechanisms, and therapeutic proposals are controversial in depression. Methods: We review theories and discuss affects and mood as criteria For depression or mania diagnosis. Results: Our work was to show that mood and affections are poorly conceived. Conclusions: Mood and affection do not serve as a basis for the diagnosis of depression or mania.

The use of biodiversity as source of new chemical entities against defined molecular targets for treatment of malaria, tuberculosis, and T-cell mediated diseases: a review

The modern approach to the development of new chemical entities against complex diseases, especially the neglected endemic diseases such as tuberculosis and malaria, is based on the use of defined molecular targets. Among the advantages, this approach allows (i) the search and identification of lead compounds with defined molecular mechanisms against a defined target (e.g. enzymes from defined pathways), (ii) the analysis of a great number of compounds with a favorable cost/benefit ratio, (iii) the development even in the initial stages of compounds with selective toxicity (the fundamental principle of chemotherapy), (iv) the evaluation of plant extracts as well as of pure substances. The current use of such technology, unfortunately, is concentrated in developed countries, especially in the big pharma. This fact contributes in a significant way to hamper the development of innovative new compounds to treat neglected diseases. The large biodiversity within the territory of Brazil puts the country in a strategic position to develop the rational and sustained exploration of new metabolites of therapeutic value. The extension of the country covers a wide range of climates, soil types, and altitudes, providing a unique set of selective pressures for the adaptation of plant life in these scenarios. Chemical diversity is also driven by these forces, in an attempt to best fit the plant communities to the particular abiotic stresses, fauna, and microbes that co-exist with them. Certain areas of vegetation (Amazonian Forest, Atlantic Forest, Araucaria Forest, Cerrado-Brazilian Savanna, and Caatinga) are rich in species and types of environments to be used to search for natural compounds active against tuberculosis, malaria, and chronic-degenerative diseases. The present review describes some strategies to search for natural compounds, whose choice can be based on ethnobotanical and chemotaxonomical studies, and screen for their ability to bind to immobilized drug targets and to inhibit their activities. Molecular cloning, gene knockout, protein expression and purification, N-terminal sequencing, and mass spectrometry are the methods of choice to provide homogeneous drug targets for immobilization by optimized chemical reactions. Plant extract preparations, fractionation of promising plant extracts, propagation protocols and definition of in planta studies to maximize product yield of plant species producing active compounds have to be performed to provide a continuing supply of bioactive materials. Chemical characterization of natural compounds, determination of mode of action by kinetics and other spectroscopic methods (MS, X-ray, NMR), as well as in vitro and in vivo biological assays, chemical derivatization, and structure-activity relationships have to be carried out to provide a thorough knowledge on which to base the search for natural compounds or their derivatives with biological activity.

The Pediatric Rheumatology International Trials Organization American-College-of-Rheumatology provisional criteria for the evaluation of response to therapy in juvenile systemic lupus erythematosus: Prospective validation of the definition of improvement

Objective. To use the Pediatric Rheumatology International Trials Organization (PRINTO) core set of outcome measures to develop a validated definition of improvement for the evaluation of response to therapy in juvenile systemic lupus erythematosus (SLE).Methods. Thirty-seven experienced pediatric rheumatologists from 27 countries, each of whom had specific experience in the assessment of juvenile SLE patients, achieved consensus on 128 patient profiles as being clinically improved or not improved. Using the physicians' consensus ratings as the gold standard measure, the chi-square, sensitivity, specificity, false-positive and false-negative rates, area under the receiver operating characteristic curve, and kappa level of agreement for 597 candidate definitions of improvement were calculated. Only definitions with a kappa value greater than 0.7 were retained. The top definitions were selected based on the product of the content validity score multiplied by its kappa statistic.Results. The definition of improvement with the highest final score was at least 50% improvement from baseline in any 2 of the 5 core set measures, with no more than 1 of the remaining worsening by more than 30%.Conclusion. PRINTO proposes a valid and reproducible definition of improvement that reflects well the consensus rating of experienced clinicians and that incorporates clinically meaningful change in core set measures in a composite end point for the evaluation of global response to therapy in patients with juvenile SLE. The definition is now proposed for use in juvenile SLE clinical trials and may help physicians to decide whether a child with SLE responded adequately to therapy.

The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximate to23,500 genes, of which only approximate to1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.

Spatial variability of soil attributes and sugarcane yield in relation to topographic location

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

Sperm motility of Prochilodus lineatus in relation to dilution rate and temperature of the activating medium

The objective of this study was to assess the effects of an activating solution on the sperm motility duration (SMD) of 'curimbatá', Prochilodus lineatus through of the definition of qualitative and quantitative parameters of the semen pool used in the experiment; evaluation of the effects of different ratios of semen dilution corresponding to 1-:-1, 1-:-2, 1-:-20, 1-:-200, 1-:-2000, 1-:-20-000 and 1-:-100-000 semen:dilute solution on the SMD and, assessment of the effects of different temperatures of the activating solution (5, 10, 15, 20, 25, 30, 35, 40, 45 and 50°C) on the SMD. The results of SMD were directly proportional to the dilution (P<0.05), starting from the dilution of 1-:-2 (semen:water), with 23.04-s. Were used three replicates of the semen pool for each test. Two-year-old brookstock were maintained in ponds culture conditions. In November-December 2006, twelve mature males broodfish were selected (mean weight and length of 405.8±134.2-g and 25.6±3.1-cm, respectively). The males released that semen under slight pressure of the urogenital papilla were selected for the experiment. The SMD increased proportionally to the increase in dilution, until it reached a maximum of 28.83-s for the ratio 1-:-100-000 semen: dilute solution. The results of SMD in relation to the temperature of the activating solution exhibited a quadratic behavior (P<0.05) with a maximum theoretical performance in terms of sperm motility duration of 21.36-s at a temperature of 17.3°C. Thus, for the species considered, the increase in the dilution ratio proved favorable for the rise in motility duration until the maximum value studied of 1-:-100-000 semen:dilute solution. As for the temperature of the activating solution, the best results of SMD were obtained at the temperature of 17.3°C. At higher temperatures used in the experiment (25, 30, 35, 40, 45 and 50°C), a decrease in motility duration. © 2010 Blackwell Verlag, Berlin.

Cytogenetic evidence for de novo synthesis of rRNA and involvement of nucleolar material in the organization of cell structures during spermiogenesis of Chariesterus armatus (Heteroptera, Coreidae).

The nucleolar material of Chariesterus armatus was analyzed during spermiogenesis in cell preparations impregnated with silver nitrate. Nucleolar corpuscles were observed in spermatids at the beginning of the process, showing that this organoid is also maintained after meiosis. In addition, nucleoli were seen in the round spermatids connected to the X-chromosome (bearer of the nucleolar organizer in C. armatus), indicating de novo synthesis of nucleolar material. This differs from the reorganization of ribosomal granules, transported from meiotic spermatocytes to round spermatids, where they would support protein synthesis, which is reported for other species. We also observed connections of nucleolar corpuscles to the nuclear membrane regions where the tail and the acrosome will be formed, suggesting close involvement of the nucleolar material in the formation of these structures. In addition to the nucleolar bodies, we detected silver-positive structures, which will require new approaches to clarify their role. One of these structures, observed in the cytoplasm, appears to correspond to the chromatoid body, which has been found in several organisms, but is still poorly understood; another is a complex structure to which the tail appears to be connected. We conclude that C. armatus is an appropriate model for understanding not only the synthesis of rRNA in the spermiogenesis, but also the functional meaning of the close relationship of nucleolar material with other structures during this process.