974 resultados para CDNA MICROARRAY


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354 p. (Bibliogr. 271-303) - Correo electrónico de la autora: andrea.guridi@gmail.com

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A rapid detection and identification of pathogens is important for minimizing transfer and spread of disease. A label-free and multiplex biosensor based on imaging ellipsometry (BIE) had been developed for the detection of phage M13KO7. The surface of silicon wafer is modified with aldehyde, and proteins can be patterned homogeneously and simultaneously on the surface of silicon wafer in an array format by a microfluidic system. Avidin is immobilized on the surface for biotin-anti-M13 immobilization by means of interaction between avidin and biotin, which will serve as ligand against phage M13KO7. Phages M13KO7 are specifically captured by the ligand when phage M13KO7 solution passes over the surface, resulting in a significant increase of mass surface concentration of the anti-M13 binding phage M13KO7 layer, which could be detected by imaging ellipsometry with a sensitivity of 10(9) pfu/ml. Moreover, atomic force microscopy is also used to confirm the fact that phage M13KO7 has been directly captured by ligands on the surface. It indicates that BIE is competent for direct detection of phage M13KO7 and has potential in the field of virus detection. (C) 2008 Elsevier B.V. All rights reserved.

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Micro-fabrication technology has substantial potential for identifying molecular markers expressed on the surfaces of tissue cells and viruses. It has been found in several conceptual prototypes that cells with such markers are able to be captured by their antibodies immobilized on microchannel substrates and unbound cells are flushed out by a driven flow. The feasibility and reliability of such a microfluidic-based assay, however, remains to be further tested. In the current work, we developed a microfluidic-based system consisting of a microfluidic chip, an image grabbing unit, data acquisition and analysis software, as well as a supporting base. Specific binding of CD59-expressed or BSA-coupled human red blood cells (RBCs) to anti-CD59 or anti-BSA antibody-immobilized chip surfaces was quantified by capture efficiency and by the fraction of bound cells. Impacts of respective flow rate, cell concentration, antibody concentration and site density were tested systematically. The measured data indicated that the assay was robust. The robustness was further confirmed by capture efficiencies measured from an independent ELISA-based cell binding assay. These results demonstrated that the system developed provided a new platform to effectively quantify cellular surface markers effectively, which promoted the potential applications in both biological studies and clinical diagnoses.

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The Drosophila compound eye has provided a genetic approach to understanding the specification of cell fates during differentiation. The eye is made up of some 750 repeated units or ommatidia, arranged in a lattice. The cellular composition of each ommatidium is identical. The arrangement of the lattice and the specification of cell fates in each ommatidium are thought to occur in development through cellular interactions with the local environment. Many mutations have been studied that disrupt the proper patterning and cell fating in the eye. The eyes absent (eya) mutation, the subject of this thesis, was chosen because of its eyeless phenotype. In eya mutants, eye progenitor cells undergo programmed cell death before the onset of patterning has occurred. The molecular genetic analysis of the gene is presented.

The eye arises from the larval eye-antennal imaginal disc. During the third larval instar, a wave of differentiation progresses across the disc, marked by a furrow. Anterior to the furrow, proliferating cells are found in apparent disarray. Posterior to the furrow, clusters of differentiating cells can be discerned, that correspond to the ommatidia of the adult eye. Analysis of an allelic series of eya mutants in comparison to wild type revealed the presence of a selection point: a wave of programmed cell death that normally precedes the furrow. In eya mutants, an excessive number of eye progenitor cells die at this selection point, suggesting the eya gene influences the distribution of cells between fates of death and differentiation.

In addition to its role in the eye, the eya gene has an embryonic function. The eye function is autonomous to the eye progenitor cells. Molecular maps of the eye and embryonic phenotypes are different. Therefore, the function of eya in the eye can be treated independently of the embryonic function. Cloning of the gene reveals two cDNA's that are identical except for the use of an alternatively-spliced 5' exon. The predicted protein products differ only at the N-termini. Sequence analysis shows these two proteins to be the first of their kind to be isolated. Trangenic studies using the two cDNA's show that either gene product is able to rescue the eye phenotype of eya mutants.

The eya gene exhibits interallelic complementation. This interaction is an example of an "allelic position effect": an interaction that depends on the relative position in the genome of the two alleles, which is thought to be mediated by chromosomal pairing. The interaction at eya is essentially identical to a phenomenon known as transvection, which is an allelic position effect that is sensitive to certain kinds of chromosomal rearrangements. A current model for the mechanism of transvection is the trans action of gene regulatory regions. The eya locus is particularly well suited for the study of transvection because the mutant phenotypes can be quantified by scoring the size of the eye.

The molecular genetic analysis of eya provides a system for uncovering mechanisms underlying differentiation, developmentally regulated programmed cell death, and gene regulation.

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The sea urchin embryonic skeleton, or spicule, is deposited by mesenchymal progeny of four precursor cells, the micromeres, which are determined to the skeletogenic pathway by a process known as cytoplasmic localization. A gene encoding one of the major products of the skeletogenic mesenchyme, a prominent 50 kD protein of the spicule matrix, has been characterized in detail. cDNA clones were first isolated by antibody screening of a phage expression library, followed by isolation of homologous genomic clones. The gene, known as SM50, is single copy in the sea urchin genome, is divided into two exons of 213 and 1682 bp, and is expressed only in skeletogenic cells. Transcripts are first detectable at the 120 cell stage, shortly after the segregation of the skeletogenic precursors from the rest of the embryo. The SM50 open reading frame begins within the first exon, is 450 amino acids in length, and contains a loosely repeated 13 amino acid motif rich in acidic residues which accounts for 45% of the protein and which is possibly involved in interaction with the mineral phase of the spicule.

The important cis-acting regions of the SM50 gene necessary for proper regulation of expression were identified by gene transfer experiments. A 562 bp promoter fragment, containing 438 bp of 5' promoter sequence and 124 bp of the SM50 first exon (including the SM50 initiation codon), was both necessary and sufficient to direct high levels of expression of the bacterial chloramphenicol acetyltransferase (CAT) reporter gene specifically in the skeletogenic cells. Removal of promoter sequences between positions -2200 and -438, and of transcribed regions downstream of +124 (including the SM50 intron), had no effect on the spatial or transcriptional activity of the transgenes.

Regulatory proteins that interact with the SM50 promoter were identified by the gel retardation assay, using bulk embryo mesenchyme blastula stage nuclear proteins. Five protein binding sites were identified and mapped to various degrees of resolution. Two sites are homologous, may be enhancer elements, and at least one is required for expression. Two additional sites are also present in the promoter of the aboral ectoderm specific cytoskeletal actin gene CyIIIa; one of these is a CCAA T element, the other a putative repressor element. The fifth site overlaps the binding site of the putative repressor and may function as a positive regulator by interfering with binding of the repressor. All of the proteins are detectable in nuclear extracts prepared from 64 cell stage embryos, a stage just before expression of SM50 is initiated, as well as from blastula and gastrula stage; the putative enhancer binding protein may be maternal as well.

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The genomes of many positive stranded RNA viruses and of all retroviruses are translated as large polyproteins which are proteolytically processed by cellular and viral proteases. Viral proteases are structurally related to two families of cellular proteases, the pepsin-like and trypsin-like proteases. This thesis describes the proteolytic processing of several nonstructural proteins of dengue 2 virus, a representative member of the Flaviviridae, and describes methods for transcribing full-length genomic RNA of dengue 2 virus. Chapter 1 describes the in vitro processing of the nonstructural proteins NS2A, NS2B and NS3. Chapter 2 describes a system that allows identification of residues within the protease that are directly or indirectly involved with substrate recognition. Chapter 3 describes methods to produce genome length dengue 2 RNA from cDNA templates.

The nonstructural protein NS3 is structurally related to viral trypsinlike proteases from the alpha-, picorna-, poty-, and pestiviruses. The hypothesis that the flavivirus nonstructural protein NS3 is a viral proteinase that generates the termini of several nonstructural proteins was tested using an efficient in vitro expression system and antisera specific for the nonstructural proteins NS2B and NS3. A series of cDNA constructs was transcribed using T7 RNA polymerase and the RNA translated in reticulocyte lysates. Proteolytic processing occurred in vitro to generate NS2B and NS3. The amino termini of NS2B and NS3 produced in vitro were found to be the same as the termini of NS2B and NS3 isolated from infected cells. Deletion analysis of cDNA constructs localized the protease domain necessary and sufficient for correct cleavage to the first 184 amino acids of NS3. Kinetic analysis of processing events in vitro and experiments to examine the sensitivity of processing to dilution suggested that an intramolecular cleavage between NS2A and NS2B preceded an intramolecular cleavage between NS2B and NS3. The data from these expression experiments confirm that NS3 is the viral proteinase responsible for cleavage events generating the amino termini of NS2B and NS3 and presumably for cleavages generating the termini of NS4A and NS5 as well.

Biochemical and genetic experiments using viral proteinases have defined the sequence requirements for cleavage site recognition, but have not identified residues within proteinases that interact with substrates. A biochemical assay was developed that could identify residues which were important for substrate recognition. Chimeric proteases between yellow fever and dengue 2 were constructed that allowed mapping of regions involved in substrate recognition, and site directed mutagenesis was used to modulate processing efficiency.

Expression in vitro revealed that the dengue protease domain efficiently processes the yellow fever polyprotein between NS2A and NS2B and between NS2B and NS3, but that the reciprocal construct is inactive. The dengue protease processes yellow fever cleavage sites more efficiently than dengue cleavage sites, suggesting that suboptimal cleavage efficiency may be used to increase levels of processing intermediates in vivo. By mutagenizing the putative substrate binding pocket it was possible to change the substrate specificity of the yellow fever protease; changing a minimum of three amino acids in the yellow fever protease enabled it to recognize dengue cleavage sites. This system allows identification of residues which are directly or indirectly involved with enzyme-substrate interaction, does not require a crystal structure, and can define the substrate preferences of individual members of a viral proteinase family.

Full-length cDNA clones, from which infectious RNA can be transcribed, have been developed for a number of positive strand RNA viruses, including the flavivirus type virus, yellow fever. The technology necessary to transcribe genomic RNA of dengue 2 virus was developed in order to better understand the molecular biology of the dengue subgroup. A 5' structural region clone was engineered to transcribe authentic dengue RNA that contains an additional 1 or 2 residues at the 5' end. A 3' nonstructural region clone was engineered to allow production of run off transcripts, and to allow directional ligation with the 5' structural region clone. In vitro ligation and transcription produces full-length genomic RNA which is noninfectious when transfected into mammalian tissue culture cells. Alternative methods for constructing cDNA clones and recovering live dengue virus are discussed.

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Interleukin 2 (IL2) is the primary growth hormone used by mature T cells and this lymphokine plays an important role in the magnification of cell-mediated immune responses. Under normal circumstances its expression is limited to antigen-activated type 1 helper T cells (TH1) and the ability to transcribe this gene is often regarded as evidence for commitment to this developmental lineage. There is, however, abundant evidence than many non-TH1 T cells, under appropriate conditions, possess the ability to express this gene. Of paramount interest in the study of T-cell development is the mechanisms by which differentiating thymocytes are endowed with particular combinations of cell surface proteins and response repertoires. For example, why do most helper T cells express the CD4 differentiation antigen?

As a first step in understanding these developmental processes the gene encoding IL2 was isolated from a mouse genomic library by probing with a conspecific IL2 cDNA. The sequence of the 5' flanking region from + 1 to -2800 was determined and compared to the previously reported human sequence. Extensive identity exists between +1 and -580 (86%) and sites previously shown to be crucial for the proper expression of the human gene are well conserved in both sequence location in the mouse counterpart.

Transient expression assays were used to evaluate the contribution of various genomic sequences to high-level gene expression mediated by a cloned IL2 promoter fragment. Differing lengths of 5' flanking DNA, all terminating in the 5' untranslated region, were linked to a reporter gene, bacterial chloramphenicol acetyltransferase (CAT) and enzyme activity was measured after introduction into IL2-producing cell lines. No CAT was ever detected without stimulation of the recipient cells. A cloned promoter fragment containing only 321 bp of upstream DNA was expressed well in both Jurkat and EL4.El cells. Addition of intragenic or downstream DNA to these 5' IL2-CAT constructs showed that no obvious regulatory regions resided there. However, increasing the extent of 5' DNA from -321 to -2800 revealed several positive and negative regulatory elements. One negative region that was well characterized resided between -750 and -1000 and consisted almost exclusively of alternating purine and pyrimidines. There is no sequence resembling this in the human gene now, but there is evidence that there may have once been.

No region, when deleted, could relax either the stringent induction-dependence on cell-type specificity displayed by this promoter. Reagents that modulated endogenous IL2 expression, such as cAMP, cyclosporin A, and IL1, affected expression of the 5' IL2-CAT constructs also. For a given reagent, expression from all expressible constructs was suppressed or enhanced to the same extent. This suggests that these modulators affect IL2 expression through perturbation of a central inductive signal rather than by summation of the effects of discrete, independently regulated, negative and positive transcription factors.

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[EN] This paper reports an innovative technique for reagents storage in microfluidic devices by means of a one-step UV-photoprintable ionogel-based microarray on non-modified polymeric substrates. Although the ionogel and the ink-jet printing technology are well published, this is the first study where both are used for long-term reagent storage in lab-on-a-chip devices. This technology for reagent storage is perfectly compatible with mass production fabrication processes since pre-treatment of the device substrate is not necessary and inkjet printing allows for an efficient reagent deposition process. The functionality of this microarray is demonstrated by testing the release of biotin-647 after being stored for 1 month at room temperature. Analysis of the fluorescence of the ionogel-based microarray that contains biotin-647 demonstrated that 90% of the biotin-647 present was released from the ionogel-based microarray after pumping PBS 0.1% Tween at 37 °C. Moreover, the activity of biotin-647 after being released from the ionogel-based microarray was investigated trough the binding capability of this biotin to a microcontact printed chip surface with avidin. These findings pave the way for a novel, one-step, cheap and mass production on-chip reagents storage method applicable to other reagents such as antibodies and proteins and enzymes.

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Autism and Alzheimer's disease (AD) are, respectively, neurodevelopmental and degenerative diseases with an increasing epidemiological burden. The AD-associated amyloid-beta precursor protein-alpha has been shown to be elevated in severe autism, leading to the 'anabolic hypothesis' of its etiology. Here we performed a focused microarray analysis of genes belonging to NOTCH and WNT signaling cascades, as well as genes related to AD and apoptosis pathways in cerebellar samples from autistic individuals, to provide further evidence for pathological relevance of these cascades for autism. By using the limma package from R and false discovery rate, we demonstrated that 31% (116 out of 374) of the genes belonging to these pathways displayed significant changes in expression (corrected P-values <0.05), with mitochondria- related genes being the most downregulated. We also found upregulation of GRIN1, the channel-forming subunit of NMDA glutamate receptors, and MAP3K1, known activator of the JNK and ERK pathways with anti-apoptotic effect. Expression of PSEN2 (presinilin 2) and APBB1 (or F65) were significantly lower when compared with control samples. Based on these results, we propose a model of NMDA glutamate receptor-mediated ERK activation of alpha-secretase activity and mitochondrial adaptation to apoptosis that may explain the early brain overgrowth and disruption of synaptic plasticity and connectome in autism. Finally, systems pharmacology analyses of the model that integrates all these genes together (NOWADA) highlighted magnesium (Mg2+) and rapamycin as most efficient drugs to target this network model in silico. Their potential therapeutic application, in the context of autism, is therefore discussed.

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A partir da década de 60, com a utilização do transplante renal em larga escala como terapia substitutiva para pacientes com falência do órgão, surgiu a preocupação quanto ao desenvolvimento do processo de rejeição do enxerto. Tal intercorrência, em geral, cursa com sinais e sintomas clínicos apenas quando o evento está bem estabelecido, ou mesmo quando lesões irreversíveis já se instalaram. Assim, é fundamental um acompanhamento rigoroso, visando detectar os casos subclínicos. O presente trabalho, a fim de fornecer novas ferramentas que auxiliem o diagnóstico precoce de rejeição do enxerto, avaliou a expressão imuno-histoquímica dos anticorpos CD3, CD5, CD20, CD68, CD25, FoxP3 e C4d em biópsias renais realizadas entre os anos de 2007 e 2009 em pacientes transplantados acompanhados pelo Serviço de Nefrologia do Hospital Universitário Pedro Ernesto, UERJ - RJ, correlacionando os resultados obtidos com o diagnóstico histológico. Para tal, as biópsias foram reavaliadas por três médicos patologistas que as classificaram, segundo Critérios de Banff 2007, quanto à presença ou não de rejeição do enxerto e seu tipo, aguda ou crônica. A partir de então, os blocos de parafina foram processados pela técnica Tissue Microarray for all (Pires, ARC. e cols.) e submetidos à imuno-histoquímica. A positividade dos marcadores foi avaliada e graduada e os resultados encontrados foram correlacionados, em um primeiro momento, com a presença ou ausência de rejeição. Posteriormente, os casos com diagnóstico histológico de rejeição tiveram seu perfil imuno-histoquímico analisado em função da positividade para C4d, marcador definidor de rejeição humoral. Neste momento, buscou-se averiguar se os anticorpos estudados seriam úteis em detectar, neste grupo, rejeição humoral e celular. Após a análise estatística, realizada pelo Teste Exato de Fisher, pode-se, então, concluir que o comportamento do marcador CD3 é capaz de inferir a presença de rejeição e que os anticorpos CD5 e CD25 permitem sugerir rejeição celular e humoral, respectivamente. Foi observado também que casos sem diagnóstico histológico de rejeição podem apresentar marcação para C4d em mais de 10% de seus capilares peritubulares.

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O câncer de próstata é o tumor não cutâneo mais comum entre homens e responsável pela segunda maior mortalidade entre os tumores neste sexo. Diferentes métodos são utilizados com o objetivo de determinar o prognóstico do paciente portador de câncer de próstata, contudo existe grande heterogeneidade quando estes são usados individualmente. A leptina é um hormônio peptídico envolvido na regulação da ingestão alimentar, do metabolismo, do gasto energético, além de função neuroendócrina. Este hormônio parece estar envolvido na patogênese de alguns tipos de tumores, inclusive os adenocarcinomas de próstata. Até o presente não se tem certeza se a leptina e seu receptor possam ser utilizados como fatores prognósticos no cancer de próstata. O objetivo do trabalho foi correlacionar os perfis de imunomarcação da leptina e seu receptor em adenocarcinomas de próstata com diferentes fatores prognósticos e comparar as análises de imunomarcação da leptina e seu receptor em adenocarcinomas de próstata por métodos semiquantitativos e quantitativos (morfometria). Foram analisadas 532 peças cirúrgicas de prostatectomias radicais por câncer prostático. A partir destas amostras, após estudo histopatológico, foi montado um arranjo de matriz tecidual, contendo fragmentos de áreas tumorais e não tumorais (peritumorais) destas amostras. Estas foram imunomarcadas com anticorpos antileptina e antirreceptor de leptina. Análises subjetivas (feitas por dois observadores) e objetivas (através da contagem de pontos) foram realizadas em cada uma das imunomarcações. Estes resultados foram comparados e correlacionados com os seguintes fatores prognósticos: invasão perineural, embolização neoplásica vascular, comprometimento bilateral da próstata, invasão das vesículas seminais, comprometimento de margem vesical, de margem uretral e de margem cirúrgica de ressecção. Houve diferença significativa entre as análises subjetivas dos dois observadores e, portanto, estas não foram utilizadas para as demais comparações. Em relação às análises objetivas, foi verificado que a expressão do receptor de leptina estava diminuída nos tumores com comprometimento de margem cirúrgica, de margem uretral e de vesículas seminais. Ainda foi observado correlação entre a expressão desse receptor e o somátório dos fatores prognósticos analisados. Para as demais análises não foi verificada diferença significativa. Métodos semiquantitativos podem ter grande variação e devem ser preteridos em relação a métodos quantitativos para as análises realizadas neste estudo. Nem a leptina nem o seu receptor apresentaram alterações de sua expressão em amostras neoplásicas de próstata quando comparado àquelas não neoplásicas. O receptor de leptina apresentou uma diminuição da sua expressão em tumores com margem cirúrgica comprometida, margem uretral comprometida e com vesículas seminais comprometidas. Houve correlação negativa entre o percentual de área imunomarcada com o anticorpo antirreceptor de leptina e o somatório dos fatores prognósticos analisados.

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Systemic lupus erythematosus is a chronic autoimmune disease with multifactorial ethiopathogenesis. The complement system is involved in both the early and late stages of disease development and organ damage. To better understand autoantibody mediated complement consumption we examined ex vivo immune complex formation on autoantigen arrays. We recruited patients with SLE (n = 211), with other systemic autoimmune diseases (n = 65) and non-autoimmune control subjects (n = 149). Standard clinical and laboratory data were collected and serum complement levels were determined. The genotype of SNP rs1143679 in the ITGAM gene was also determined. Ex vivo formation of immune complexes, with respect to IgM, IgG, complement C4 and C3 binding, was examined using a functional immunoassay on autoantigen microarray comprising nucleic acids, proteins and lipids. Complement consumption of nucleic acids increased upon binding of IgM and IgG even when serum complement levels were decreased due to consumption in SLE patients. A negative correlation between serum complement levels and ex vivo complement deposition on nucleic acid autoantigens is demonstrated. On the contrary, complement deposition on tested protein and lipid autoantigens showed positive correlation with C4 levels. Genetic analysis revealed that the non-synonymous variant rs1143679 in complement receptor type 3 is associated with an increased production of anti-dsDNA IgG antibodies. Notwithstanding, homozygous carriers of the previously reported susceptible allele (AA) had lower levels of dsDNA specific IgM among SLE patients. Both the non-synonymous variant rs1143679 and the high ratio of nucleic acid specific IgG/IgM were associated with multiple organ involvement. In summary, secondary complement deficiency in SLE does not impair opsonization of nucleic-acid-containing autoantigens but does affect other antigens and potentially other complement dependent processes. Dysfunction of the receptor recognizing complement opsonized immune complexes promotes the development of class-switched autoantibodies targeting nucleic acids.

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Na medicina regenerativa há uma crescente utilização de lasers de baixa intensidade em protocolos terapêuticos para tratamento de doenças em tecidos moles e no tecido ósseo. Lasers emitem feixes de luz com características específicas, nas quais o comprimento de onda, a frequência, potência e modo de missão são propriedades determinantes para as respostas fotofísica, fotoquímica e fotobiológica. Entretanto, sugere-se que lasers de baixa potência induzem a produção de radicais livres, que podem reagir com biomoléculas importantes, como o DNA. Essas reações podem causar lesões e induzir mecanismos de reparo do DNA para preservar a integridade do código genético e homeostase celular. Portanto, o objetivo deste trabalho foi avaliar lesões no DNA de células do sangue periférico de ratos Wistar e a expressão dos genes ERCC1 e ERCC2 em tecidos biológicos expostos a lasers de baixa intensidade em comprimentos de onda, fluências, potências e modos de emissão utilizados em protocolos terapêuticos. Para tal, amostras de sangue periférico foram expostas ao laser vermelho (660 nm) e infravermelho (808 nm) em diferentes fluências, potências e modos de emissão, e a indução de lesões no DNA foi avaliada através do ensaio cometa. Em outros experimentos, lesões no DNA foram analisadas através do ensaio cometa modificado, utilizando as enzimas de reparo: formamidopirimidina DNA glicosilase (FPG) e endonuclease III. Pele e músculo de ratos Wistar foram expostos aos lasers e amostras desses tecidos foram retiradas para extração de RNA, síntese de cDNA e avaliação da expressão dos genes por PCR quantitativo em tempo real. Os dados obtidos neste estudo sugeriram que a exposição aos lasers induz lesões no DNA dependendo da fluência, potência e modo de emissão, e que essas lesões são alvos da FPG e endonuclease III. A expressão relativa do RNAm de ERCC1 e de ERCC2 foi alterada nos tecidos expostos dependendo do comprimento de onda e fluência utilizada. Os resultados obtidos neste estudo sugerem que danos oxidativos no DNA poderiam ser considerados para segurança do paciente e eficácia terapêutica, bem como alterações na expressão dos genes de reparo do DNA participariam dos efeitos de bioestimulação que justificam as aplicações terapêutica de lasers de baixa potência.