Evolução molecular Darwiniana nas proteínas relacionadas à patogênese (PRs) em plantas

Um total de 201 seqüências de DNA, de 50 espécies pertencentes a 32 gêneros e 12 famílias, foi investigado através do método da máxima verossimilhança para identificar, nas proteínas respectivas, possíveis códons nos quais estivesse ocorrendo seleção positiva. Foram considerados 15 tipos de proteínas relacionadas à patogênese (PR1-PR15), quanto a 14 modelos diferentes de seleção. Tanto quanto se possa avaliar, não há qualquer estudo disponível na literatura que tenha examinado de maneira homogênea tal número de seqüências de forma tão abrangente.

A família Pso2/Snm1 e suas possíveis funções na reparação de DNA e na manutenção genômica dos cromossomos

O genoma das células eucarióticas é um dos principais alvos para danos induzidos por inúmeros fatores ambientes, sejam estes de origem biótica ou abiótica. Considerando a complexidade da molécula de DNA, não é supreendente que existam diferentes tipos de lesões com os mais variados graus de severidade. Dentre todas as lesões que podem ser induzidas no DNA, as pontes intercadeias (ICLs) estão entre as mais graves. Se não forem reparadas, a presença de apenas um ICL pode ser letal para a célula. Além disso, as lesões do tipo ICLs são quimicamente heterogêneas, podendo modificar a estrutura do DNA de forma permanente ou temporária. Os mecanismos relacionados à reparação de ICLs ainda são pouco conhecidos em eucariotos. Apesar de várias proteínas terem sido descritas como essenciais ao processo, não há um modelo único que explique esta reparação. Contudo, dentre as diferentes proteínas que participam na reparação de ICLs, destacam-se as nucleases Pso2/Snm1. A forma de atuação das proteínas Pso2/Snm1 não é conhecida, mas inúmeros dados obtidos com mutantes de Saccharomyces cerevisiae e, recentemente, com células de mamífero, mostram que a ausência de Pso2p/Snm1p bloqueia a restituição do DNA de alta massa molecular. Por outro lado, tem sido mostrado que o Pso2p/Snm1p provavelmente atua na manutenção da cromatina, mas de uma forma ainda não completamente esclarecida. Uma das proteínas pertencentes à família Pso2p/Snm1p, Ártemis, possui um papel importante no desenvolvimento do sistema imunológico adaptativo de metazoários e parece ser essencial para outros processos relacionados ao metabolismo de DNA eucariótico. Desta maneira, este trabalho teve como objetivo principal o estudo da família Pso2p/Snm1p por meio da análise filogenética e de seqüências, comparando-a com proteínas homólogas já descritas em outros organismos. Além disso, esta comparação XVII permitiu estabelecer uma correlação funcional entre as proteínas em termos de reparação de DNA e manutenção da cromatina eucariótica. As análises de filogenia e de seqüências claramente demonstraram que as proteínas Pso2/Snm1 podem ser agrupadas em quatro grupos principais ao invés de três, ao contrário do que se conhecia previamente. Três destes grupos, por sua vez, são formados por subgrupos específicos, que possivelmente atuam de forma diferenciada na reparação de DNA, na manutenção da cromatina e na geração de diversidade biológica. Por outro lado, os estudos das seqüências Pso2/Snm1, baseados principalmente na técnica de análises de agrupamentos hidrofóbicos (HCA), revelaram um alto grau de similaridade de estruturas primárias e secundárias entre os diferentes grupos, um indicativo da importância estrutural para a função destas proteínas no metabolismo de DNA. A técnica de HCA permitiu mapear regiões conservadas (CRs) em todas as seqüências estudadas, compondo o chamado domínio Pso2p/Snm1p. Em alguns casos, o domínio Pso2p/Snm1p encontra-se fusionado a outros domínios catalíticos. Neste caso, destaca-se o estudo de uma nova família de DNA ligases dependentes de ATP que são exclusivas de plantas. Esta nova família, denominada de Lig6p, parece ter funções importantes no metabolismo do DNA de plantas, sendo esta a primeira DNA ligase eucariótica com função nucleásica identificada. Usando os dados obtidos neste trabalho em conjunto com os resultados de outros autores, é sugerido um possível modo de atuação das proteínas Pso2p/Snm1p na reparação de danos do tipo ICL, na manutenção da cromatina e na geração de diversidade biológica.

Análise do efeito de polimorfismos não-sinônimos em genes de reparo de DNA da via BER na resposta inflamatória da meningite

In vitro and in animal models, APE1, OGG1, and PARP-1 have been proposed as being involved with inflammatory response. In this work, we have investigated if the SNPs APE1 Asn148Glu, OGG1 Ser326Cys, and PARP-1 Val762Ala are associated to meningitis and also developed a system to enable the functional analysis of polymorphic proteins. Patients with bacterial meningitis (BM), aseptic meningitis (AM) and controls (non-infected) genotypes were investigated by PIRA-PCR or PCR-RFLP. DNA damages were detected in genomic DNA by Fpg treatment. IgG and IgA were measured from plasma and the cytokines and chemokines were measured from cerebrospinal fluid samples using Bio-Plex assays. The levels of NF-κB and c-Jun were measured in CSF by dot blot assays. A significant (P<0.05) increase in the frequency of APE1 148Glu allele in BM and AM patients was observed. A significant increase in the genotypes Asn/Asn in control group and Asn/Glu in BM group was also found. For the SNP OGG1 Ser326Cys, the genotype Cys/Cys was more frequent (P<0.05) in BM group. The frequency of PARP-1 Val/Val genotype was higher in control group (P<0.05). The occurrence of combined SNPs increased significantly in BM patients, indicating that these SNPs may be associated to the disease. Increasing in sensitive sites to Fpg was observed in carriers of APE1 148Glu allele or OGG1 326Cys allele, suggesting that SNPs affect DNA repair activity. Alterations in IgG production were observed in the presence of SNPs APE1Asn148Glu, OGG1Ser326Cys or PARP-1Val762Ala. Reductions in the levels ofIL-6, IL-1Ra, MCP-1/CCL2and IL-8/CXCL8 were observed in the presence of APE1148Glu allele in BM patients, however no differences were observed in the levels of NF-κB and c-Jun considering genotypes and analyzed groups. Using APE1 as model, a system to enable the analysis of cellular effects and functional characterization of polymorphic proteins was developed using strategies of cloning APE1 cDNA in pIRES2-EGFP vector, cellular transfection of the construction obtained, siRNA for endogenous APE1 and cellular cultures genotyping. In conclusion, we obtained evidences of an effect of SNPs in DNA repair genes on the regulation of immune response. This is a pioneering work in the field that shows association of BER variant enzymes with an infectious disease in human patients, suggesting that the SNPs analyzed may affect immune response and damage by oxidative stress level during brain infection. Considering these data, new approaches of functional characterization must be developed to better analysis and interactions of polymorphic proteins in response to this context

Modelagem molecular na caracterização eletrônica de oligopeptídeos e na descrição quântica da interação fármaco-receptor

In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicosídico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced.

Interação competitiva do zinco e ferro após administração oral e venosa de zinco em crianças eutróficas

The aim of this study was to assess the acute and chronic effects of zinc in serum iron profile of children aged 6-9 years in relation to nutritional status and dietary intake. The study participants were 11 children regardless of sex, aged 6-9 years. They were selected from three public schools of the city of Natal, Brazil. Body mass index was used to assess nutritional status. In order to determine the patterns of childhood growth and ideal weight we used the standards of the World Health Organization. The dietary intake assessment was based on information from a three-day prospective food survey. The variables were energy intake, protein, lipids, carbohydrates, fiber, calcium, iron and zinc. All children underwent an intravenous administration of zinc (IVAZn) before and after oral administration of zinc (OAZn) (5 mg Zn / day) for three months. We measured serum iron, hematocrit, hemoglobin and total protein, before and after the use of oral zinc. The analysis of hematocrit, hemoglobin and total protein was performed using standard methods of clinical laboratory. Zinc levels and serum iron were measured by atomic absorption spectrophotometry. The project was evaluated and approved by the Ethics in Research Committee of Federal University of Rio Grande do Norte. Results: All children had normal weight. The consumption of energy, fat, fiber, calcium and iron were below recommended levels. However, the levels of protein and carbohydrates were high. Protein and zinc increased significantly after OAZn. Carbohydrate and protein were elevated in the blood. After OAZn, both protein and zinc increased, being statistically significant. Conclusion: The potential inhibitory effect of physiological or pharmacological doses of zinc on the profile of serum iron was observed in children with healthy weight and aged between 6 and 9 years. This negative effect of zinc did not affect the levels of hematocrit or hemoglobin, and therefore did not cause anemia. This was a multidisciplinary study, involving researchers from medicine, nutrition and pharmacy. This met the requirements of multidisciplinarity of the Post Graduate Program in Health Sciences of Federal University of Rio Grande do Norte.

Atividade antibacteriana das plantas copaifera duckei dwyer e pseudobombax marginatum e sua interação com a superfície celular bacteriana

A resistência microbiana a antimicrobianos tem favorecido a busca por substâncias bioativas provenientes de plantas usadas na medicina popular, com o intuito de se obter novos fármacos com atividade antimicrobiana. Neste estudo, foi proposta a investigação da atividade antibacteriana do óleo-resina de Copaifera duckei e de diferentes extratos da casca de Pseudobombax marginatum, e seus possíveis mecanismos de ação. O potencial inibitório antibacteriano foi avaliado utilizando-se os métodos de difusão e diluição em ágar, e a bioautografia. O mecanismo de ação foi analisado por microscopia eletrônica, no qual se observou alterações na ultraestrutura bacteriana, e por eletroforese em SDS-PAGE, que determinou ação sobre as proteínas das superfícies celulares. A análise química foi realizada pelas técnicas de Espectrometria de massas acoplada ao Cromatógrafo a gás- EM/CG (C. duckei) e Cromatografia Líquida de Alta Eficiência- CLAE (P. marginatum). Entre as bactérias estudadas, B. cereus foi a mais suscetível às plantas em estudo, com concentrações inibitórias mínimas (CIMs) correspondentes a 0,3125 mg/mL para o óleo-resina de copaíba, e 0,5 mg/mL para extrato hidroalcoólico (1:1) e 0,512 mg/mL para a fração butanólica da casca P. marginatum, nos quais pôde-se observar alterações na parede celular do B. cereus, com remoção da camada S, espessamento da parede celular e formação de diversos septos nos centros de divisão celular. A análise química por EM/CG mostrou compostos terpênicos no óleo-resina de C. duckei, tendo como composto majoritário o β-bisaboleno, e a análise por CLAE mostrou a presença de compostos derivados da catequina na casca do P. marginatum. Desta forma, as plantas em estudo mostram um potencial antibacteriano considerável, podendo contribuir tanto na terapia antimicrobiana como na área de alimentos, tendo como um de seus prováveis sítios de ação a parede celular bacteriana

Caracterização molecular e laboratorial da talassemia beta e da interação hemoglobina s/talassemia beta

Beta thalassemia arises as a consequence of the reduction (β+, β++, βsilent) or absence (β0) of beta globin chain synthesis and results from a number of mechanisms that lead to genetic defects. The inheritance of beta thalassemia is characterized by the existence of heterozygous individuals, compound heterozygotes, homozygotes and those with coinheritance of beta thalassemia allele and other thalassemias and/or hemoglobin variants. The aim of this study was to perform molecular and laboratory characterization of beta thalassemia in heterozygous and homozygous individuals and in those with coinheritance of S beta thalassemia. A total of 48 individuals were included (35 heterozygotes, 4 homozygotes and 9 S beta thalessemia carriers) referred to the Integrated Laboratory of Clinical Analyses of the Federal University of Rio Grande do Norte (UFRN) and the Hematology Ambulatory Facility of the Dalton Barbosa Cunha Hemocenter (Hemonorte Natal, Brazil). Peripheral blood samples form each patient underwent the following laboratory examinations: erythrogram, hemoglobin electrophoresis at alkaline pH, measurements of Hb A2, Fetal Hb and serum ferritin. DNA was extracted using the illustra blood genomicPrep Mini Spin Kit and molecular characterization was performed by the PCR/RFLP technique, which involves digestion with specific restriction enzymes for IVS-1 nt 1 (G®A), IVS-1 nt 6 (T®C) and codon 39 (CAG®TAG) mutations. Of the 35 heterozygotes, 37.1% showed IVS-1 nt 6 mutation, 42.9% IVS-1 nt 1 and 20% were carriers of other mutations not identified by the technique used. The four homozygous patients presented with the IVS-1 nt 6 mutation, while 66.7% of the individuals with S beta thalassemia had the IVS-1 nt 1 mutation. Codon 39 was not detected in any of the patients investigated. Of the thallasemic alleles found, 40.4% were IVS- 1 nt 1, 40.4% IVS-1 nt 6 and 19.2% were not identified. Laboratory data showed that the heterozygotes exhibited microcytosis and hypochromia, evidenced by MCV ranging from 57 to 75fL and MCH from 15.9 to 23.6 pg. Hemoglobin A2 varied between 3.7 and 7.2%. The homogygotes also showed reduced MCV and MCH and elevated HbA2.. Comparison of laboratory data between heterozygous individuals with IVS-1 nt 1 and IVS-1 nt 6 mutations showed that heterozygotes for the IVS1-1 mutation had significantly lower mean MCV and MCH (p = 0.023 and 0.007, respectively) and significantly higher hemoglobin A2 (p < 0.001) when compared to heterozygotes for the IVS-1 nt 6 mutation. PCR/RFLP was useful in identifying the presence or absence of IVS-1 nt 6, IVS-1 nt 1 and codon 39 mutations in most of the patients investigated here. This is the first study conducted in the state of Rio Grande do Norte, Brazil aimed at identifying beta thalassemia mutations and represents an important contribution to the knowledge regarding the molecular profile of beta thalassemia in our country

Análise do perfil de expressão dos genes da cana-de-açúcar envolvidos na interação com Leifsonia xyli subsp: xyli

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

Análise comparativa da imunoexpressão das proteínas hmlh1 e hmsh2 em carcinomas epidermóides de lábio inferior e queilites actínicas com graus variados de displasia

Lip squamous cell carcinoma (SCC) may develop from a premalignant condition, actinic cheilitis (AC) in 95% of the cases. Both premalignant and neoplastic lip diseases are caused mainly by chronic exposure to the ultraviolet component of solar radiation, especially UVB. This exposure causes disruption of the cell cycle and damage to DNA repair systems, like mismatch repair, altering proteins repair as hMLH1 and hMSH2. This research aimed to investigate the immunohistochemical expression of hMLH1 and hMSH2 proteins in lower lip SCCs and ACs, providing additional information about carcinogenesis of the lower lip. The sample consisted 40 cases of ACs and 40 cases of lower lip SCCs. Histological sections of 3 μm were submitted to immunoperoxidase method, for immunohistochemical analysis of lesions were counted in 1000 cells (positive and negative), data were evaluated both in absolute numbers and percentage of immunostained cells, the latter by assigning scores. Associations of the variables and comparative analysis of biomarker expression were performed by Fisher s exact and Pearson s chi-square, "t" student, one-way ANOVA, Mann- Whitney e Kruskal-Wallis tests. The level of significance was 5%. It was found that, in lower lip SCC, the mean of the proteins was higher in female patients (hMLH1= 369,80 + 223,98; hMHS2 = 534,80 + 343,62), less than 50 years old (hMLH1 = 285,50 + 190,65; hMHS2 = 540,00 + 274,79) and classified as low-grade malignancy (hMLH1 = 264,59 + 179,21; hMHS2 = 519,32 + 302,58), in these data only to sex, for hMLH1 protein, was statistically significant (p=0.034). Comparing the different lesions, we observed that for both hMLH1 and hMSH2 protein, the average of positive epithelial cells decreased as the lesion was graded at later stages. The ACs classified without dysplasia or mild dysplasia had the highest average of immunostained cells (hMLH1 = 721.23 + 88.116; hMHS2 = 781.50 + 156.93). The ACs classified as moderate or severe dysplasia had intermediate values (hMLH1 = 532,86 + 197,72; hMHS2 = 611,14 + 172,48) and SSCs of the lower lip had the lowest averages (hMLH1 = 255,03 + 199,47; hMHS2 = 518,38 + 265,68). There was a statistically significant difference between groups (p<0.001). In conclusion, our data support the hypothesis that changes in immunoexpression of these proteins is related to the process of carcinogenesis of the lower lip

Estudo da detecção do DNA do papiloma vírus humano (HPV) e da expressão imuno-histoquímica de proteína do ciclo celular no carcinoma epidermóide oral

Oral squamous cell carcinoma (OSCC) is the most common malignancy in oral cavity and human papillomavirus (HPV) may have an important role in its development. The aim of this experiment was to investigate the HPV DNA and viral types in 90 cases of OSCC. Moreover, a comparative analysis between the cases of OSSC with and without HPV DNA was performed by using cell cycle markers p21 and pRb in order to detect a possible correlation of these proteins and HPV infection. DNA was extracted from paraffin embedded tissue and amplified by PCR (polymerase chain reaction) with primers PCO3+ e PCO4+ for a fragment of human β-globin gene. After this procedure, PCR for HPV DNA detection was realized using a pair of generic primers GP5+ e GP6+. Immunohistochemical study was performed by streptoavidin-biotin technique and antibodies against p21 and pRb proteins were employed. Eighty-eight cases were positive for human β-globin gene and HPV DNA was found in 26 (29.5%) of then. It could not be detected significant correlation between HPV and age, sex and anatomical sites of the lesion. The most prevalent viral type was HPV 18 (80.8%). Regarding the immunohistochemical analysis, it was detected significant association between HPV presence and pRb immunoexpression (p=0,044), nevertheless, the same was not observed in relation to p21 protein (p =0,416). It can be concluded that the low detection of HPV DNA in OSCC by the present experiment suggests a possible role of the virus in the development and progression in just a subset of this disease

Síntese, caracterização e estudos de interação de um análogo da antitoxina CcdA empregando fluorescência no estado estacionário

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

Compensatory lung growth: protein, DNA and RNA lung contents in undernourished trilobectomized rats

OBJETIVO: demonstrar se ocorre crescimento pulmonar compensatório (CPC) representado pelos conteúdos de proteínas, DNA e RNA no rato adulto jovem, subnutrido, submetido à trilobectomia pulmonar. MÉTODOS: Utilizamos 137 ratos Wistar, machos, distribuídos por sorteio, em 9 grupos, submetidos a três tratamentos (controle, toracotomia, trilobectomia), sacrificados em três momentos (7, 30 e 90 dias). Na trilobectomia foram extirpados os lobos médio, acessório e caudal direitos. Variáveis estudadas: conteúdos pulmonares de proteínas, DNA e RNA. RESULTADOS: No lobo cranial e pulmão esquerdo o conteúdo protéico foi maior nos trilobectomizados. Ocorreu CPC insuficiente para suprir a perda desta variável, sendo menor nos pulmões dos trilobectomizados. O incremento nos conteúdos de DNA do lobo cranial e pulmão esquerdo dos trilobectomizados foram suficientes para compensar a perda desta variável, resultando num conteúdo de DNA dos pulmões semelhante aos controle. O conteúdo de RNA, nos trilobectomizados, foi maior no lobo cranial e pulmão esquerdo, com maior eficiência no primeiro, insuficiente para que se aproximassem aos obtidos nos demais grupos, ficando menores. CONCLUSÃO: Nos trilobectomizados ocorreu CPC, provavelmente com hiperplasia celular e pouca hipertrofia, devido a grande compensação do DNA e pequena do RNA. Esta foi a grande diferença quando comparamos este resultado ao obtido com animais nutridos, que apresentavam hipertrofia pronunciada.

Estudo físico-químico de nanopartículas de DNA com derivado de quitosana contendo grupos fosforilcolina

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

Estudo por simulação computacional da interação entre polianfóteros fracos e macroíons cilíndricos

Pós-graduação em Biofísica Molecular - IBILCE

Desenvolvimento de uma base de dados para fatores de transcrição de seres humanos e suas redes de interação: Human Transcriptional Regulation Interaction Database (HTRIDB 2.0)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)