514 resultados para Genoma do cloroplasto


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Dengue virus is an important patogen that causes Dengue desease in all world, and belongs to Flavivirus gender. The virus consists of enveloped RNA with a single strand positive sense, 11Kb genome. The RNA is translated into a polyprotein precursor, wich is cleaved into 3 structural proteins (C, prM e E) and 7 non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B e NS5). The NS3 is a multifunctional protein, that besides to promote the polyprotein precursor cleavage, also have NTPase, helicase and RTPase activity. The NS3 needs a hydrophilic segment of 40 residues from the transmembrane NS2B protein (who acts like cofator) to realize this functions. Actually, there's no vacines available on the market, and the treatment are just symptomatic. The tetrapeptide inhibitor Bz-Nle-Lys-Arg-Arg-H (Ki de 5,8-7,0 M) was showed as a potent inhibitor μ for NS3prot in Dengue virus. That is a inteligent alternative to treat the dengue desease. The present work aimed analyse the interactions of the ligand bounded to the activity site to provid a clear and depth vision of that interaction. For this purpouse, it was conducted an in silico study, by using quantum mechanical calculations based on Density Functional Theory (DFT), with Generalized Gradient approximation (GGA) to describe the effects of exchange and correlation. The interaction energy of each amino acid belonging to the binding site to the ligand was calculated the using the method of molecular fragmentation with conjugated caps (MFCC). Besides energy, we calculated the distances, types of molecular interactions and atomic groups involved. The theoretical models used were satisfactory and show a more accurate description when the dielectric constant = 20 ε and 80 was used. The results demonstrate that the interaction energy of the system reached convergence at 13.5 A. Within a radius of 13,5A the most important residues were identified. Met49, Met84 and Asp81 perform interactions of hydrogen with the ligant. The Asp79 and Asp75 residues present high energy of attraction. Arg54, Arg85 and Lys 131 perform hydrogen interactions with the ligand, however, appear in BIRD graph having high repulsion energy with the inhibitor. The data also emphasizes the importance of residue Tyr161 and the involvement of the catalytic triad composed by Asp75, His51 and Ser135

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The microorganisms have a vast genetic diversity and they are present throughout the biosphere, however, only about 1% of the species can be cultivated by traditional cultivation techniques. Within this diversity there is a huge pool genetic and biological being explored. The metagenomics has enabled direct access to microbial genome derived from environmental samples using independent methods of cultivation. The methodology enables to obtain functional information about the proteins, as well as identify potential products with biotechnological interest and new industrially exploitable biological resources, such as new solutions to environmental impacts. Oil-contaminated areas are characterized by a large accumulation of hydrocarbons and surfactants may be used for bioremediation. Thus, the metagenomic approach was used in this study in order to select genes involved in the degradation and hydrocarbon emulsification. In a previous work, the environmental DNA (eDNA) was extracted from soil samples collected from two different areas (Caatinga and Saline River) of Rio Grande do Norte (Brazil), the metagenomic libraries were constructed and functionally analyzed. The clone able to degrade the oil was evaluated for the ability to synthesize biosurfactants. The sequence analysis revealed an ORF with 897 bp, 298 amino acids and a protein with around 34 kDa. The search for homology in GenBank revealed sequence similarity with a hypothetical protein of representatives Halobacteriaceae family, who were recently shown as strains producing biosurfactants. The presence of the inserted coding sequence and the acquired phenotype was confirmed. Primers were designed and the ORF amplified by PCR. The ORF was subcloned into pETDuet-1 expression vector for subsequent purification of the protein of interest containing a histidine tail. The tests performed to confirm the biosurfactant activity and the ability of hydrocarbon degradation showed positive results. The immunodetection test (western blot) using the monoclonal AntiHis® confirmed the presence of the environmental protein. This study was the first to report a possible protein with biosurfactant activity obtained from a metagenomic approach

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The Rachycentron canadum species, commonly known as beijupirá or cobia is the only representative of Rachycentridae family which has been increasingly used in marine fish farming, in intensive cultivation. As advantageous features it has easy adaptation, prolific behavior, early growth in captivity and high commercial value. Additionally, specie of Lutjanidae family (Lutjanus synagris, Lutjanus jocu, Lutjanus analis, Lutjanus alexandrei and Ocyurus chrysurus) represents an important fisheries resource in all areas of its occurrence. In Brazil, the commercial exploitation of Lutjanidae which begun in the 60's and 80's, already has showed a decline in catch volumes. This fact suggests that the snappers must have a conservative management. Despite the economic potential, little is known about the genetic and cytogenetic characteristics of these species, especially with respect to repetitive DNA analysis, which represents the major part of the eukaryotes genome, playing important evolutionary roles in the fish genome. Cytogenetic data is increasingly being used in population studies and biotechnological purposes in fishes. The cytogenetical analyzes were performed using classical methods such as Giemsa staining, C-banding and Ag-NORs, fluorochromes base-specific staining (DAPI and MM) and physical mapping of repetitive sequences among which, telomeric sequences, transposons (Tol2), retrotransposons (Rex1 and Rex3), repetitive DNA (microsatellites and Cot-1) and transcriptionally active regions of the 18S and 5S ribosomal genes and histone (H3 and H2BA) by in situ hybridization with fluorescent probes (FISH). The chromosomal patterns obtained contributed to the organization of repetitive sequences in the genome of the species, as well as karyotypical differentiation. Unusual patterns of histone sequences expansion depict the first occurrence in marine fishes. The obtained data provided subsides to the genetic knowledge of the important fisheries resource represented by the species here analyzed, seeking the marine pisciculture improvement.

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DNA repair systems play a critical role in protecting the human genome from damage caused by carcinogens present in the environment. Mutations in DNA repair genes may be responsible for tumor development and resistance of malignant cells to chemotherapeutic agents. The major pathway for oxidative DNA damage repair is the base excision repair pathway. The objective of this study was to investigate the immunoexpression of APE-1 and XRCC-1, which are proteins involved in DNA base excision repair and its association with clinical and histopathological parameters in oral tongue squamous cell carcinoma (OTSCC), in order to investigate a possible prognostic value for those proteins. The expression of APE-1 and XRCC-1 was evaluated semi-quantitatively by immunohistochemistry in 50 OTSCC cases. Clinical data was collected from patients’ medical charts and histopathological grading was performed for each case. Statistical analysis (Chi-square and Fisher’s exact tests; significance of 5%) was performed to determine the association between protein expressions and clinico-pathological characteristics. APE-1 was highly expressed in nucleus and cytoplasm in 56% of cases. XRCC-1 showed overexpression only in nucleus in 60% of cases. High expression of XRCC-1 was significantly associated to clinical stages I and II (P=0.02). Both proteins were not associated to other clinical parameters or histopathological grading. Our findings demonstrate that DNA base excision repair proteins APE-1 and XRCC-1 are upregulated in OTSCC, however, they are not related to clinical and histologic parameters, except for XRCC-1 association to better clinical staging. Our results indicate that the immunohistochemical expression of these proteins has no association with prognostic parameters in this tumor.

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DNA repair systems play a critical role in protecting the human genome from damage caused by carcinogens present in the environment. Mutations in DNA repair genes may be responsible for tumor development and resistance of malignant cells to chemotherapeutic agents. The major pathway for oxidative DNA damage repair is the base excision repair pathway. The objective of this study was to investigate the immunoexpression of APE-1 and XRCC-1, which are proteins involved in DNA base excision repair and its association with clinical and histopathological parameters in oral tongue squamous cell carcinoma (OTSCC), in order to investigate a possible prognostic value for those proteins. The expression of APE-1 and XRCC-1 was evaluated semi-quantitatively by immunohistochemistry in 50 OTSCC cases. Clinical data was collected from patients’ medical charts and histopathological grading was performed for each case. Statistical analysis (Chi-square and Fisher’s exact tests; significance of 5%) was performed to determine the association between protein expressions and clinico-pathological characteristics. APE-1 was highly expressed in nucleus and cytoplasm in 56% of cases. XRCC-1 showed overexpression only in nucleus in 60% of cases. High expression of XRCC-1 was significantly associated to clinical stages I and II (P=0.02). Both proteins were not associated to other clinical parameters or histopathological grading. Our findings demonstrate that DNA base excision repair proteins APE-1 and XRCC-1 are upregulated in OTSCC, however, they are not related to clinical and histologic parameters, except for XRCC-1 association to better clinical staging. Our results indicate that the immunohistochemical expression of these proteins has no association with prognostic parameters in this tumor.

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DNA repair systems, genes and proteins are essential for genome integrity maintenance, avoiding serious diseases such as cancer. Deregulation in the expression of those proteins has been associated with both the risk of development and evolution of various human cancers, including oral squamous cell carcinoma. The purpose of this study was to analyze the immunoreactivity of the DNA repair proteins XRCC1, THIIF and XPF in oral tongue squamous cell carcinoma (OTSCC) and to investigate its association with clinical and histopathological parameters, outcome and 5-year survival rate. Seventy-four cases of OTSCC were analyzed semi-quantitatively through immunohistochemistry. We observed that DNA repair proteins were highly expressed in parenchymal cells; however, we only observed a significant association between XRCC1 high expression and better clinical staging (p=0,02). Cox regression showed that tumor size (p<0,01), lymph node involvement (p=0,04), tumor stage (p=0,02) and depth of invasion> 4mm (p=0,05) were prognostic factors. The results of this experiment suggest that XRCC1, TFIIH and XPF participate in the tumorigenic process, however, their immunoexpression may not be used as an independent prognostic indicator for OTSCC.

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DNA repair systems, genes and proteins are essential for genome integrity maintenance, avoiding serious diseases such as cancer. Deregulation in the expression of those proteins has been associated with both the risk of development and evolution of various human cancers, including oral squamous cell carcinoma. The purpose of this study was to analyze the immunoreactivity of the DNA repair proteins XRCC1, THIIF and XPF in oral tongue squamous cell carcinoma (OTSCC) and to investigate its association with clinical and histopathological parameters, outcome and 5-year survival rate. Seventy-four cases of OTSCC were analyzed semi-quantitatively through immunohistochemistry. We observed that DNA repair proteins were highly expressed in parenchymal cells; however, we only observed a significant association between XRCC1 high expression and better clinical staging (p=0,02). Cox regression showed that tumor size (p<0,01), lymph node involvement (p=0,04), tumor stage (p=0,02) and depth of invasion> 4mm (p=0,05) were prognostic factors. The results of this experiment suggest that XRCC1, TFIIH and XPF participate in the tumorigenic process, however, their immunoexpression may not be used as an independent prognostic indicator for OTSCC.

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Leishmania infantum is the main etiologic agent of visceral leishmaniasis in the New World. The pattern of distribution of leishmaniasis has changed substantially and has presented an emerging profile within the periphery of the Large Urban Centers. Leishmania infection can compromise skin, mucosa and viscera. Only 10% of the individuals infected develop the disease and 90% of human infection is asymptomatic. The main factors involved in the development of the disease are the host immune response, the vector’s species and the parasite’s genetic content. The sequencing of Leishmania isolated seeks to increase the understanding of the symptoms of individuals. The aim of this study was to evaluate the genetic diversity of circulating Leishmania strains among humans, and symptomatic and asymptomatic, and dogs from endemic areas of Rio Grande do Norte State and analyze sandflies from endemic areas for cutaneous and visceral disease. The genetic variability was evaluated by the use of markers hsp70 , ITS1 and a whole genome sequencing was also carried out. The amplified hsp70 and ITS1 of samples were analyzed and assembled using a Phred / Phrap package. The dendograms were constructed using the same methodology, but adding 500 bootstraps, followed by inferences on the relationships between Leishmania variants. The sequences of the 20 Brazilian isolates were mapped to the reference genome L. infantum JPCM5, using the Bowtie2 program and the identification of 36 contigs. The information of the valid SNPs were used in the PCA. SNPs were visualized by Geneious 7.1 and IGV. The genome annotations were transferred to their respective chromosomes and displayed on Geneious. The matching sequences of all chromosomes were aligned using Mauve. The phylogenetic trees were calculated according to maximum likelihood and JTT models. Sandflies were analyzed by PCR for the identification of Leishmania infection, a blood meal source and GAPDH sand fly. As a result, hsp70 and ITS1 were not capable of identifying genetic variability among human isolates from symptomatic and asymptomatic, and dogs. The complete sequencing of the 20 Brazilian isolates revealed a strong similarity between the circulating Leishmania strains in Rio Grande do Norte. The isolates collected in the city of Natal from humans and canines remained grouped in all analyzes, suggesting that there is genotypic and geographic proximity among the isolates. The isolated samples in the 1990s had a higher genotypic diversity when compared to freshly isolated samples. All isolates presented 36 chromosomes with variable ploidy among them, no correlation was found between the number of amastina genes copies, gp63, A2 and SSG with such clinic forms. In general, we did not find correlation between symptomatic and asymptomatic clinical forms and the gene content of the Brazilian isolates of Leishmania. 34,28% of the sandflies collected in the upper west region were L. longipalpis and the main sources of blood meal were humans, dogs and chickens.

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Leishmania infantum is the main etiologic agent of visceral leishmaniasis in the New World. The pattern of distribution of leishmaniasis has changed substantially and has presented an emerging profile within the periphery of the Large Urban Centers. Leishmania infection can compromise skin, mucosa and viscera. Only 10% of the individuals infected develop the disease and 90% of human infection is asymptomatic. The main factors involved in the development of the disease are the host immune response, the vector’s species and the parasite’s genetic content. The sequencing of Leishmania isolated seeks to increase the understanding of the symptoms of individuals. The aim of this study was to evaluate the genetic diversity of circulating Leishmania strains among humans, and symptomatic and asymptomatic, and dogs from endemic areas of Rio Grande do Norte State and analyze sandflies from endemic areas for cutaneous and visceral disease. The genetic variability was evaluated by the use of markers hsp70 , ITS1 and a whole genome sequencing was also carried out. The amplified hsp70 and ITS1 of samples were analyzed and assembled using a Phred / Phrap package. The dendograms were constructed using the same methodology, but adding 500 bootstraps, followed by inferences on the relationships between Leishmania variants. The sequences of the 20 Brazilian isolates were mapped to the reference genome L. infantum JPCM5, using the Bowtie2 program and the identification of 36 contigs. The information of the valid SNPs were used in the PCA. SNPs were visualized by Geneious 7.1 and IGV. The genome annotations were transferred to their respective chromosomes and displayed on Geneious. The matching sequences of all chromosomes were aligned using Mauve. The phylogenetic trees were calculated according to maximum likelihood and JTT models. Sandflies were analyzed by PCR for the identification of Leishmania infection, a blood meal source and GAPDH sand fly. As a result, hsp70 and ITS1 were not capable of identifying genetic variability among human isolates from symptomatic and asymptomatic, and dogs. The complete sequencing of the 20 Brazilian isolates revealed a strong similarity between the circulating Leishmania strains in Rio Grande do Norte. The isolates collected in the city of Natal from humans and canines remained grouped in all analyzes, suggesting that there is genotypic and geographic proximity among the isolates. The isolated samples in the 1990s had a higher genotypic diversity when compared to freshly isolated samples. All isolates presented 36 chromosomes with variable ploidy among them, no correlation was found between the number of amastina genes copies, gp63, A2 and SSG with such clinic forms. In general, we did not find correlation between symptomatic and asymptomatic clinical forms and the gene content of the Brazilian isolates of Leishmania. 34,28% of the sandflies collected in the upper west region were L. longipalpis and the main sources of blood meal were humans, dogs and chickens.

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Nella Tesi viene riportata l’analisi genetica di un campione di 128 famiglie con Disturbo dello Spettro Autistico, tramite il sistema di SNP array “PsychArray” (Illumina ), contenente oltre 500.000 sonde sull’intero genoma. Questi dati sono stati utilizzati per individuare Copy Number Variants (CNVs) rari e rilevanti da un punto di vista clinico. Sono stati quindi selezionati tre CNVs per un ulteriore approfondimento: due microdelezioni già descritte come patologiche (rispettivamente nella regione 1p36.32 e 22q13.33 comprendente il gene SHANK3) sono risultate essere “de novo”, mentre una terza microdelezione nel gene CTNNA3 è ereditata dalla madre. Tutti e tre i CNV sono stati validati tramite Real Time-PCR, definendone i confini. Per quanto riguarda la microdelezione in CTNNA3, poiché difetti di questo gene sono stati implicati nell’autismo con un meccanismo recessivo, è stata anche condotta un’analisi di sequenza di tutti gli esoni del gene negli individui della famiglia interessata, al fine di ricercare eventuali mutazioni puntiformi sull’allele non deleto. Questa analisi non ha individuato nessuna variante potenzialmente dannosa, pertanto il difetto in CTNNA3 non risulta essere la causa principale del fenotipo autistico in questa famiglia, anche se potrebbe avere un ruolo come fattore di suscettibilità.

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The non-standard decoding of the CUG codon in Candida cylindracea raises a number of questions about the evolutionary process of this organism and other species Candida clade for which the codon is ambiguous. In order to find some answers we studied the transcriptome of C. cylindracea, comparing its behavior with that of Saccharomyces cerevisiae (standard decoder) and Candida albicans (ambiguous decoder). The transcriptome characterization was performed using RNA-seq. This approach has several advantages over microarrays and its application is booming. TopHat and Cufflinks were the software used to build the protocol that allowed for gene quantification. About 95% of the reads were mapped on the genome. 3693 genes were analyzed, of which 1338 had a non-standard start codon (TTG/CTG) and the percentage of expressed genes was 99.4%. Most genes have intermediate levels of expression, some have little or no expression and a minority is highly expressed. The distribution profile of the CUG between the three species is different, but it can be significantly associated to gene expression levels: genes with fewer CUGs are the most highly expressed. However, CUG content is not related to the conservation level: more and less conserved genes have, on average, an equal number of CUGs. The most conserved genes are the most expressed. The lipase genes corroborate the results obtained for most genes of C. cylindracea since they are very rich in CUGs and nothing conserved. The reduced amount of CUG codons that was observed in highly expressed genes may be due, possibly, to an insufficient number of tRNA genes to cope with more CUGs without compromising translational efficiency. From the enrichment analysis, it was confirmed that the most conserved genes are associated with basic functions such as translation, pathogenesis and metabolism. From this set, genes with more or less CUGs seem to have different functions. The key issues on the evolutionary phenomenon remain unclear. However, the results are consistent with previous observations and shows a variety of conclusions that in future analyzes should be taken into consideration, since it was the first time that such a study was conducted.

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Induction of resistance is defined as the activation of a state of resistance against diseases which is induced systemically in plants by the use of biotic or abiotic agents without any modification of the plant genome, occurring non-specific way, by activating genes coding for various plant defense responses. Chitosan is a polymer derived from the deacetylation of chitin, which is found in large quantities in crustacean shell, and studied with the potential to control plant pathogens, both by its direct fungistatic action, as the ability to induce protection of plants, indicating the presence of molecules of elicitoras characteristics. Three experiments with objective of evaluating the potential of chitosan in the seedling resistance induction were developed, beet (Beta vulgaris) seeds, cucumber (Cucumis sativus) seeds and tomato (Solanum lycopersicum) seeds, and the control of Fusarium sp., Rhizoctonia solani K¨uhn e Pythium sp. in vitro conditions. The experimental design was completely randomized, with four replications. Beet seeds, tomato and cucumber were submerged in chitosan solution for 20 minutes, in concentrations of 0.25, 0.5, 1 and 2% in the control and distilled water. Seeds were sown in trays containing Plantmax Florestalr substrate sterilized and inoculated with Fusarium sp., Rhizoctonia solani K¨unh and Pythium sp., respectively for the three cultures. The experiment was conducted for 14 days in growth chamber with controlled temperature (25 C 2 C), light (12 hour photoperiod) and humidity (70% 10%). The evaluations were seed emergency, seedling damping-off, seedling length, fresh weight and activity of the enzymes phenylalanine amˆonia-liase (PAL), chitinase and b-1,3-glucanase. It was also rated the mycelial growth of Fusarium sp., Pythium sp. and R. solani on P.D.A. (Potato-Dextrose and Agar) culture medium containing chitosan at the same concentrations evaluated in seeds. For beet growing, seed treatment with chitosan presented higher emergence and the length of the seedlings, and reduced the percentage of tipping. Treatment with chitosan activated the systemic acquired resistance with expression of chitinase and b-1,3-glucanase enzymes. For the tomato crop in chitosan concentration of 0.25% favored the emergency of seedlings, reduced the incidence of tipping and activated the PAL enzymes, chitinase and b-1,3-glucanase. In cucumber on the concentration of up 0.5% favored seedlings emergence and reduces the incidence of tipping. Chitosan activated the PAL enzymes and b-1,3-glucanase. Chitosan also presented fungistatic action on the initial growth of Pythium sp. and R. solani in vitro conditions, however, such action did not prevail until the end of the experiment. To Fusarium sp. the concentration of chitosan resulted in the reduction of mycelial growth in vitro.

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Com o presente trabalho pretende-se discutir a importância do DNA na resolução de casos de investigação forense. O Homem, desde os tempos mais remotos tem revelado interesse na confirmação da identidade dos seus semelhantes, pelo desenvolvimento e prática de diversas técnicas de identificação. A partir de uma revisão da literatura, fez-se o estudo dos métodos de identificação humana, sendo este mais aprofundado no que diz respeito ao DNA. Frequentemente são encontrados corpos em que a única peça disponível para o processo de identificação é o dente. As peças dentárias são as estruturas mais resistentes e estáveis do corpo humano, mantendo as suas características e propriedades por longos períodos de tempo pós-morte. A análise do DNA contribui de forma muito importante para os processos de reconhecimento humano, principalmente em casos em que outros métodos de identificação falham devido a decomposição, fragmentação, incineração ou inexistência de dados comparativos ante-morte. Para a obtenção de um perfil genético é necessário executar as seguintes etapas: extração do DNA, sua quantificação e amplificação seguida de análise de determinadas regiões do genoma. Nos dias de hoje, muitos casos de identificação necessitam de uma abordagem multidisciplinar, isto porque em algumas situações existe falta de material padrão ou, por outro lado, pode haver mais do que uma evidência a ser examinada.

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O transplante de medula óssea (TMO) é um procedimento terapêutico importante em casos relacionados à pacientes com leucemia ou linfoma. Em decorrência desse processo, uma reação conhecida como doença enxerto-versus-hospedeiro (GVHD) pode ocorrer em pacientes susceptíveis como conseqüência da presença de células imunocompetentes do doador. Entretanto, não existe um modelo para descrever completamente as ações relacionadas ao mecanismo imunológico da GVHD desde a fase que inicializa a doença até a fase efetora. O Objetivo geral deste estudo é a investigação da resposta imunológica considerando-se o sistema HLA (antígenos leucocitários humano) em pacientes que desenvolveram a GVHD em decorrência do TMO. O National Cancer Institute (NCI) – Pathway interaction Database e Reactome foram usados como bases de dados com o objetivo de se estudar a expressão de genes e vias relacionados às Classes I e II do sistema HLA (antígenos leucocitários humano). O estudo considerou a mudança de expressão de genes relacionados às 17 vias do sistema imunológico com potencialidade para se expressar em pacientes que desenvolveram a GVHD associada à TMO. Dados referentes aos transcriptomas foram obtidos utilizando-se a plataforma GPL570 Affymetrix Genoma Humano U133 Plus. A atividade relativa foi usada para determinar as alterações das vias em amostras de GVHD em relação ao controle. As análises foram realizadas utilizando-se o software Via Complex e Bioconductor. Observou-se aumento significativo da expressão de genes ralacionados às vias do sistema imune adaptativo, antígenos associados às Classe I e II do HLA, fosforilação de CD3 e CD247, sinalização dos receptores de células T em CD4+ nativas e ativação de NF-kapa β nas células B. Também observou-se alterações significativas na mudança de expressão dos genes associados às vias relacionadas à super família de moléculas B7:CD28\CTLA-4 quando comparadas ao controle. Isso pode indicar a necessidade de geração de um segundo sinal co-estimulador em GVHD, acionado pelas moléculas dessa super família. O aumento da expressão do gene CD69 nas amostras experimentais caracteriza a ativação celular e, portanto, a sinalização de estímulos em GVHD. Os achados obtidos neste estudo contribuem para melhor elucidar o mecanismo imunopatogênico associado à GVHD. P