Prospecção de genes com interesse biotecnológico

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

Objective CT-Based Quantification of Lung Sequelae in Treated Patients With Paracoccidioidomycosis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise da variabilidade genética e expressão de HPV em papilomatose de laringe

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

Funcionalização de celulose bacteriana com peptídeo RGD para reparação tecidual de pele

Pós-graduação em Química - IQ

Quantification of pulmonary inflammatory processes using chest radiography: tuberculosis as the motivating application

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

Influência das não linearidades geométricas em sistemas de suspensão com amortecimento assimétrico sob excitação harmônica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Consultório odontológico: uma AET utilizando-se da EWA

This work tells the first steps of a larger project, that has for objective to develop the ergonomic evaluation of clinics odontologics installed in the Basic Units of Health of the municipal districts from São Paulo of São José dos Campos and Bauru. It is looked for to the end of the work to have characterized them, making possible like this the analysis in the way as it happens the interface among the users, equipments and atmosphere. For so much some will be used methodologies consecrated in the international scenery. It is told the results obtained with the first developed analysis, as test equal calibration of the chosen methodologies, as well as determination of procedures and worn-out times, for planning of the process.

Análise computacional do fenômeno de transferência de calor em paredes divisórias do tipo dry wall

O presente trabalho visa a fornecer uma contribuição ao estudo dos perfis formados a frio sob altas temperaturas, em conseqüência da deflagração de um incêndio. Especificamente, abordam–se assuntos inerentes ao fenômeno da transferência de calor em paredes do tipo steel frame – dry wall com ou sem isolamento térmico na cavidade. Para tanto, propõem–se modelos computacionais capazes de fornecer, com certa precisão, o valor de temperatura em qualquer ponto do sistema estudado. Dessa forma, é possível, então, traçar configurações de distribuição de temperatura (uniforme ou não–uniforme) na seção transversal dos montantes que constituem o painel, fornecendo subsídios para análise de estabilidade e pós–flambagem dos elementos estruturais em questão. As simulações numéricas de transferência de calor são efetuadas com auxílio dos programas computacionais ABAQUS e SAFIR, ambos baseados no método dos elementos finitos.

Structural Insights into Human Peroxisome Proliferator Activated Receptor Delta (PPAR-Delta) Selective Ligand Binding

Peroxisome proliferator activated receptors (PPARs delta, alpha and gamma) are closely related transcription factors that exert distinct effects on fatty acid and glucose metabolism, cardiac disease, inflammatory response and other processes. Several groups developed PPAR subtype specific modulators to trigger desirable effects of particular PPARs without harmful side effects associated with activation of other subtypes. Presently, however, many compounds that bind to one of the PPARs cross-react with others and rational strategies to obtain highly selective PPAR modulators are far from clear. GW0742 is a synthetic ligand that binds PPAR delta more than 300-fold more tightly than PPAR alpha or PPAR gamma but the structural basis of PPAR delta: GW0742 interactions and reasons for strong selectivity are not clear. Here we report the crystal structure of the PPAR delta:GW0742 complex. Comparisons of the PPAR delta:GW0742 complex with published structures of PPARs in complex with alpha and gamma selective agonists and pan agonists suggests that two residues (Val312 and Ile328) in the buried hormone binding pocket play special roles in PPAR delta selective binding and experimental and computational analysis of effects of mutations in these residues confirms this and suggests that bulky substituents that line the PPAR alpha and gamma ligand binding pockets as structural barriers for GW0742 binding. This analysis suggests general strategies for selective PPAR delta ligand design.

Short steel and concrete columns under high temperatures

The growing demand for knowledge about the effect of high temperatures on structures has stimulated increasing research worldwide. This article presents experimental results for short composite steel and concrete columns subjected to high temperatures in ovens with or without an axial compression load, numerically analyzes the temperature distribution in these columns after 30 and 60 minutes and compares them with experimental results. The models consist of concrete-filled tubes of three different thicknesses and two different diameters, and the concrete fill has conventional properties that remained constant for all of the models. The stress-strain behavior of the composite columns was altered after exposure to high temperatures relative to the same columns at room temperature, which was most evident in the 60-minute tests due to the higher temperatures reached. The computational analysis adopted temperature rise curves that were obtained experimentally.

Bioinformatic methods in applied genomic research

Here I will focus on three main topics that best address and include the projects I have been working in during my three year PhD period that I have spent in different research laboratories addressing both computationally and practically important problems all related to modern molecular genomics. The first topic is the use of livestock species (pigs) as a model of obesity, a complex human dysfunction. My efforts here concern the detection and annotation of Single Nucleotide Polymorphisms. I developed a pipeline for mining human and porcine sequences. Starting from a set of human genes related with obesity the platform returns a list of annotated porcine SNPs extracted from a new set of potential obesity-genes. 565 of these SNPs were analyzed on an Illumina chip to test the involvement in obesity on a population composed by more than 500 pigs. Results will be discussed. All the computational analysis and experiments were done in collaboration with the Biocomputing group and Dr.Luca Fontanesi, respectively, under the direction of prof. Rita Casadio at the Bologna University, Italy. The second topic concerns developing a methodology, based on Factor Analysis, to simultaneously mine information from different levels of biological organization. With specific test cases we develop models of the complexity of the mRNA-miRNA molecular interaction in brain tumors measured indirectly by microarray and quantitative PCR. This work was done under the supervision of Prof. Christine Nardini, at the “CAS-MPG Partner Institute for Computational Biology” of Shangai, China (co-founded by the Max Planck Society and the Chinese Academy of Sciences jointly) The third topic concerns the development of a new method to overcome the variety of PCR technologies routinely adopted to characterize unknown flanking DNA regions of a viral integration locus of the human genome after clinical gene therapy. This new method is entirely based on next generation sequencing and it reduces the time required to detect insertion sites, decreasing the complexity of the procedure. This work was done in collaboration with the group of Dr. Manfred Schmidt at the Nationales Centrum für Tumorerkrankungen (Heidelberg, Germany) supervised by Dr. Annette Deichmann and Dr. Ali Nowrouzi. Furthermore I add as an Appendix the description of a R package for gene network reconstruction that I helped to develop for scientific usage (http://www.bioconductor.org/help/bioc-views/release/bioc/html/BUS.html).

Bestimmung der Analysierstärke des A4-Compton-Rückstreupolarimeters zur Messung der longitudinalen Spinpolarisation des MAMI-Elektronenstrahls

Das A4-Experiment bestimmt den Beitrag der Strangequarks zu den elektromagnetischen Formfaktoren des Nukleons durch Messung der Paritätsverletzung in der elastischen Elektron-Nukleon-Streuung. Diese Messungen werden mit dem spinpolarisierten Elektronenstrahl des Mainzer Mikrotrons (MAMI) bei Strahlenergien zwischen 315 und 1508 MeV ndurchgeführt. Die Bestimmung des Strahlpolarisationsgrades ist für die Analyse der Daten unerläßlich, um die physikalische Asymmetrie aus der gemessenen paritätsverletzenden Asymmetrie extrahieren zu können. Aus diesem Grund wird von der A4-Kollaboration ein neuartiges Compton-Laserrückstreupolarimeter entwickelt, das eine zerstörungsfreie Messung der Strahlpolarisation, parallel zum laufenden Paritätsexperiment erlaubt. Um den zuverlässigen Dauerbetrieb des Polarimeters zu ermöglichen, wurde das Polarimeter im Rahmen dieser Arbeit weiterentwickelt. Das Datenerfassungssystem für Photonen- und Elektronendetektor wurde neu aufgebaut und im Hinblick auf die Verarbeitung hoher Raten optimiert. Zum Nachweis der rückgestreuten Photonen wurde ein neuartiger Detektor (LYSO) in Betrieb genommen. Darüber hinaus wurden GEANT4-Simulationen der Detektoren durchgeführt und eine Analyseumgebung für die Extraktion von Comptonasymmetrien aus den Rückstreudaten entwickelt. Das Analyseverfahren nutzt die Möglichkeit, die rückgestreuten Photonen durch koinzidente Detektion der gestreuten Elektronen energiemarkiert nachzuweisen (Tagging). Durch die von der Energiemarkierung eingeführte differentielle Energieskala wird somit eine präzise Bestimmung der Analysierstärke möglich. In der vorliegenden Arbeit wurde die Analysierstärke des Polarimeters bestimmt, so daß nun das Produkt von Elektronen- und Laserstrahlpolarisation bei einem Strahlstrom von 20 muA, parallel zum laufenden Paritätsexperiment, mit einer statistischen Genauigkeit von 1% in 24 Stunden bei 855 MeV bzw. <1% in 12 Stunden bei 1508 MeV gemessen werden kann. In Kombination mit der Bestimmung der Laserpolarisation in einer parallelen Arbeit (Y. Imai) auf 1% kann die statistische Unsicherheit der Strahlpolarisation im A4-Experiment von zuvor 5% auf nun 1,5% bei 1508MeV verringert werden. Für die Daten zur Messung der paritätsverletzenden Elektronenstreuung bei einem Viererimpulsübertrag von $Q^2=0,6 (GeV/c)^2$ beträgt die Rohasymmetrie beim derzeitigen Stand der Analyse $A_{PV}^{Roh} = ( -20,0 pm 0,9_{stat} ) cdot 10^{-6}$. Für eine Strahlpolarisation von 80% erhält man einen Gesamtfehler von $1,68 cdot 10^{-6}$ für $Delta P_e/P_e = 5 %$. Als Ergebnis dieser Arbeit wird sich dieser Fehler durch Analyse der Daten des Compton-Laserrückstreupolarimeters um 29% auf $1,19 cdot 10^{-6}$ ($Delta P_e/P_e = 1,5 %$) verringern lassen.

Interactions of G-quadruplex binders and Topoisomerase I inhibitors in cancer cells

Top1-DNA cleavage complexes (Top1ccs) trigger an accumulation of antisense RNAPII transcripts specifically at active divergent CpG-island promoters in a replication independent and Top1 dependent manner, leading to transcription-dependent genome instability and altered transcription regulation. Using different cancer cell lines of colon and osteo origins, we show that they display different sensitivity to CPT and G4 binder that is independent from Top1 level. To look at the interactions between Top1 and G4, we show that co-treatment with G4 binders potentiate the cell cytotoxicity of CPT regardless of the treatment sequences. Potentiation is indicated by a reduced inhibition concentration (IC50) with a more profound cytotoxicity in CPT-resistant cell lines, HCT15 and U2OS, hence, indicating an interaction between Top1inhibitor and G4 binders. Moreover, computational analysis confirmed the present of G4 motifs in genes with CPT-induced antisense transcription. G4 motifs are present mostly 5000 bp upstream from transcription start site and notably lower in genes. Comparisons between genes with no antisense transcription and genes with antisense transcription show that G4 motifs in this region are notably lower in the genes with antisense transcripts. Since CPT increases negative supercoils at promoters of intermediate activity, the formation of G4 is also increased in CPT-treated cells. Suprisingly, formation of G4 is regulated in parallel to the transient stabilization of R-loops, indicating a role in response to CPT-induced stress. G4 formation is highly elevated in Pyridostatin treated cells, which previous study shows increased formation of γH2Ax foci. This effect is also seen in the CPT-resistant cell lines, HCT15, indicating that the formation is a general event in response to CPT. We also show that R-loop formation is greatly increased in Pyridostatin treated cells. In order to study the role of R-loops and G4 structures in Top1cc-dependant repair pathway, we inhibited tyrosyl-phosphodiestrase 1 (TDP-1) using a TDP-1 inhibitor.

Learning Spike-Based Population Codes by Reward and Population Feedback

We investigate a recently proposed model for decision learning in a population of spiking neurons where synaptic plasticity is modulated by a population signal in addition to reward feedback. For the basic model, binary population decision making based on spike/no-spike coding, a detailed computational analysis is given about how learning performance depends on population size and task complexity. Next, we extend the basic model to n-ary decision making and show that it can also be used in conjunction with other population codes such as rate or even latency coding.

Implementation of monotonic higher order upwind scheme in KIVA 4

KIVA is a FORTRAN code developed by Los Alamos national lab to simulate complete engine cycle. KIVA is a flow solver code which is used to perform calculation of properties in a fluid flow field. It involves using various numerical schemes and methods to solve the Navier-Stokes equation. This project involves improving the accuracy of one such scheme by upgrading it to a higher order scheme. The numerical scheme to be modified is used in the critical final stage calculation called as rezoning phase. The primitive objective of this project is to implement a higher order numerical scheme, to validate and verify that the new scheme is better than the existing scheme. The latest version of the KIVA family (KIVA 4) is used for implementing the higher order scheme to support handling the unstructured mesh. The code is validated using the traditional shock tube problem and the results are verified to be more accurate than the existing schemes in reference with the analytical result. The convection test is performed to compare the computational accuracy on convective transfer; it is found that the new scheme has less numerical diffusion compared to the existing schemes. A four valve pentroof engine, an example case of KIVA package is used as application to ensure the stability of the scheme in practical application. The results are compared for the temperature profile. In spite of all the positive results, the numerical scheme implemented has a downside of consuming more CPU time for the computational analysis. The detailed comparison is provided. However, in an overview, the implementation of the higher order scheme in the latest code KIVA 4 is verified to be successful and it gives better results than the existing scheme which satisfies the objective of this project.