Estudo do genoma do vírus causador da mionecrose infecciosa em camarões e desenvolvimento de métodos para detecção de diferentes variantes

Shrimp farming is one of the activities that contribute most to the growth of global aquaculture. However, this business has undergone significant economic losses due to the onset of viral diseases such as Infectious Myonecrosis (IMN). The IMN is already widespread throughout Northeastern Brazil and affects other countries such as Indonesia, Thailand and China. The main symptom of disease is myonecrosis, which consists of necrosis of striated muscles of the abdomen and cephalothorax of shrimp. The IMN is caused by infectious myonecrosis virus (IMNV), a non-enveloped virus which has protrusions along its capsid. The viral genome consists of a single molecule of double-stranded RNA and has two Open Reading Frames (ORFs). The ORF1 encodes the major capsid protein (MCP) and a potential RNA binding protein (RBP). ORF2 encodes a probable RNA-dependent RNA polymerase (RdRp) and classifies IMNV in Totiviridae family. Thus, the objective of this research was study the IMNV complete genome and encoded proteins in order to develop a system differentiate virus isolates based on polymorphisms presence. The phylogenetic relationship among some totivirus was investigated and showed a new group to IMNV within Totiviridae family. Two new genomes were sequenced, analyzed and compared to two other genomes already deposited in GenBank. The new genomes were more similar to each other than those already described. Conserved and variable regions of the genome were identified through similarity graphs and alignments using the four IMNV sequences. This analyze allowed mapping of polymorphic sites and revealed that the most variable region of the genome is in the first half of ORF1, which coincides with the regions that possibly encode the viral protrusion, while the most stable regions of the genome were found in conserved domains of proteins that interact with RNA. Moreover, secondary structures were predicted for all proteins using various softwares and protein structural models were calculated using threading and ab initio modeling approaches. From these analyses was possible to observe that the IMNV proteins have motifs and shapes similar to proteins of other totiviruses and new possible protein functions have been proposed. The genome and proteins study was essential for development of a PCR-based detection system able to discriminate the four IMNV isolates based on the presence of polymorphic sites

Surface-enhanced raman scattering: metal nanostructures coated with langmuir-blodgett films

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

Portable smart films for ultrasensitive detection and chemical analysis using SERS and SERRS

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

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Synthesis, Infrared Spectroscopy and Crystal Structure Determination of a New Decavanadate

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Phase separation suppression in InGaN epitaxial layers due to biaxial strain

Phase separation suppression due to external biaxial strain is observed in InxGa1-xN alloy layers by Raman scattering spectroscopy. The effect is taking place in thin epitaxial layers pseudomorphically grown by molecular-beam epitaxy on unstrained GaN(001) buffers. Ab initio calculations carried out for the alloy free energy predict and Raman measurements confirm that biaxial strain suppress the formation of phase-separated In-rich quantum dots in the InxGa1-xN layers. Since quantum dots are effective radiative recombination centers in InGaN, we conclude that strain quenches an important channel of light emission in optoelectronic devices based on pseudobinary group-III nitride semiconductors. (C) 2002 American Institute of Physics.

Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Structure control of poly(p-phenylene vinylene) in layer-by-layer films by deposition on a charged poly(o-methoxyaniline) cushion

In this paper, we demonstrate that the intrinsic electric field created by a poly(o-methoxyaniline) (POMA) cushion layer hinders the changes in molecular conformation of poly(p-phenylenevinylene) (PPV) in layer-by-layer with dodecylbenzene sulfonic acid (DBS). This was modeled with density functional theory (DFT) calculations where an energy barrier hampered molecular movements of PPV segments when they were subjected to an electric field comparable to that caused by a charged POMA layer. With restricted changes in molecular conformation, the PPV film exhibited Franck-Condon transitions and the photoexcitation spectra resembled the absorption spectra, in contrast to PPV/DBS films deposited directly on glass, with no POMA cushion. Other effects from the POMA cushion were the reduced number of structural defects, confirmed with Raman spectroscopy, and an enhanced PPV emission at high temperatures (300 K) in comparison with the films on bare glass. The positive effects from the POMA cushion may be exploited for enhanced opto-electronic devices, especially as the intrinsic electric field may assist in separating photoexcited electron-hole pairs in photovoltaic devices. © 2013 American Institute of Physics.

Estudo das propriedades de fotogeração e transporte de portadores de cargas em dispositivos optoeletrônicos orgânicos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modelo cinético estocástico para a transcrição considerando colisões entre as moléculas de RNA polimerase

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo do coeficiente de difusão no enovelamento de proteína

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Aplicação de métodos teóricos na investigação da transferência auto-consistente de elétrons em nano-retificador orgânico

Neste trabalho apresentamos um estudo teórico da estrutura eletrônica de uma molécula do tipo Doador-dinitrobenzene e um grupo Aceitador-dihydrophenazine (D-A) com pontes poliênicas variando de π = 0 à π = 10. Trata-se de um sistema promissor para o desenvolvimento de retificadores moleculares, que sob dopagem química podem vir a adquirir propriedades elétricas de material condutor. E ainda, sob ação de campo elétrico externo apresenta comportamento equivalente ao de dispositivos usuais, mas com inúmeras vantagens como, por exemplo, tamanho extremamente reduzido e intensa resposta ótica em regime não-linear. Para estudar esse sistema, fizemos otimizações de geometria sistematicamente, levando em conta cálculos de ZINDO/S-CIS (Zerner´s Intermediate Neglect of Differential Orbital/Spectroscopic – Configuration Interaction Single) que utilizam 220 configurações em média. Observamos uma transferência eletrônica calculada por métodos derivados de Hartree-Fock. Nossos resultados mostram uma delocalização bem definida dos Orbitais Moleculares de Fronteira (OMFs) HOMO[LUMO] nos grupos D[A] para molécula com ponte poliênica relativamente grande. Para estruturas com ponte poliênica relativamente pequena o contrário é observado, e uma uniformidade dos OMFs nos terminais DA é verificada. O que indicaria que somente as estruturas com ponte poliênica relativamente grande seriam promissoras pra criação de dispositivos, tendo LUMO como canal de condução. Um estudo detalhado do rearranjo de carga molecular para a mesma estrutura, sob a ação de um campo elétrico externo mostrou que o transporte de carga no grupo D[A] independe do tamanho da ponte poliênica. A voltagem aplicada é intensa o bastante para criar um potencial de saturação para este sistema com grupos DA muito próximos (evidenciando uma região de saturação e uma região de operação para sistemas com pontes pequenas), normalmente presente e sistemas com ponte molecular relativamente grande e nos dispositivos semicondutores macroscópicos. Acreditamos que o OMF LUMO desempenha um papel importante no que diz respeito ao transporte de carga em estruturas relativamente grandes, seguido de falhas em estruturas moleculares onde o grupo D está muito próximo do A. Nossos resultados mostram que temos um retificador molecular que pode trabalhar corretamente como um retificador macroscópico.

Detection of trace levels of atrazine using surface-enhanced Raman scattering and information visualization

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

Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

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

Non-centrosymmetric crystals of new N-benzylideneaniline derivatives as potential materials for non-linear optics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)