Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Comments on ‘‘Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions

Applied Mathematical Modelling, Vol.33

Structure to function studies in UDP-glucose dehydrogenases and nitroreductases

The thesis is divided into two parts corresponding to structural studies on two different proteins. The first part concerns the study of two UDP-glucose dehydrogenases (UGDs) from Sphingomonas elodea ATCC 31461 and Burkholderia cepacia IST 408, both involved in exopolysaccharide production. Their relevance arises because some of these bacterial exopolysaccharides are valuable as established biotechnological products, the former case, whilst others are highly problematic, when used by pathogens in biofilm formation over biological surfaces, as the latter case, namely in the human lungs. The goal of these studies is to increase our knowledge regarding UGDs structural properties, which can potentiate either the design of activity enhancers to respond to the increased demand of useful biofilms, or the design of inhibitors of biofilm production, in order to fight invading pathogens present in several infections. The thesis reports the production and crystallisation of both proteins, the determination of initial phases by single-wavelength anomalous dispersion (SAD) in S. elodea crystals using a seleno-methionine isoform, and phasing of B. cepacia crystals by molecular replacement (MR) using the S. elodea model, as well as the refinement, structural analysis and comparison between the several UGDs structures available during this work.(...)

Functional domains of Bacillus subtilis transcription factor AraR and identification of aminoacids important for nucleoprotein complex assembly and effector-binding.

Journal of Bacteriology (Apr 2006) 3024-3036

Aplicação do Método SFA (Safety Function Analisys) a um. Posto de Transformação de Energia Eléctrica da Renova

Riscos Industriais e Emergentes, 2009 pp. 827-844

Avaliação do débito máximo da tosse (peak cough flow) na doença pulmonar obstrutiva crónica

Resumo Objectivos: Avaliação da Tosse em doentes com Doença Pulmonar Obstrutiva Crónica (DPOC). Identificar e determinar a relação dos factores preditivos que contribuem para a deterioração da capacidade de tosse nestes indivíduos. Tipo de estudo: Estudo observacional descritivo de natureza transversal. Definição dos casos: Os critérios de diagnóstico da DPOC são o quadro clínico e o Gold standard para diagnóstico da DPOC – a espirometria. População-alvo: Todos os utentes com patologia primária de DPOC diagnosticada que se desloquem ao serviço de função respiratória do Hospital de Viseu, para realizar provas. Método de Amostragem: Foi utilizada uma amostra aleatória constituída por todos os indivíduos, que cumpriram os critérios de inclusão, conscientes e colaborantes, que aceitaram participar neste estudo. Dimensão da amostra: Uma amostra de 55 indivíduos que se deslocaram ao serviço de função respiratória, entre Janeiro e Junho de 2009, para realizar provas de função respiratória. Condução do estudo: Os utentes que aceitaram participar neste estudo foram sujeitos a um questionário de dados clínicos e realizaram 5 testes: índice de massa corporal (IMC), estudo funcional respiratório e gasometria arterial, avaliação da força dos músculos respiratórios (PImax e PEmax) e avaliação do débito máximo da tosse (Peak Cough Flow). Análise estatística: Foram obtidos dados caracterizadores da amostra em estudo, sendo posteriormente correlacionado o valor de débito máximo da tosse (Peak Cough Flow) com os resultados obtidos para as avaliações do IMC, estudo funcional respiratório, PImax e PEmax, gasometria, avaliação da capacidade de Tosse e número de internamentos no último ano por agudização da DPOC. Tendo sido encontrados os valores de correlação entre o Peak Cough Flow e os restantes parâmetros. Resultados: Após análise dos resultados, foram obtidos os valores de Peak Cough Flow para a população com DPOC e verificou-se valores diminuídos em comparação com os valores normais da população, tendo-se verificado maiores valores de PCF em indivíduos do sexo masculino, em comparação aos valores do sexo feminino. Foi analisada a relação entre o PCF e a idade, peso, altura e IMC, não tendo sido encontrada relação, dado que a tosse não apresenta uma variação segundo os valores antropométricos, tal como a relação com os valores espirométricos. Quanto aos parâmetros funcionais respiratórios foram analisadas as relações com o PCF. Verificou-se relações significativas entre o PCF e o FEV1, a FVC, o PEF, apresentando uma relação positiva, onde maiores valores destes parâmetros estão correlacionados com maiores picos de tosse. Quanto a RAW e RV, o PCF apresenta uma relação negativa, onde uma maior resistência da via aérea ou doentes mais hiperinsuflados leva a menores valores de PCF. Por outro lado não foi encontrada relação entre o PCF e a FRC e o TLC. Quanto à força dos músculos respiratórios, verificou-se relação significativa com o PImax e a PEmax em que a fraqueza ao nível dos músculos respiratórios contribuem para um menor valor de PCF. Relativamente aos valores da gasometria arterial, verificou-se relação entre o PCF e a PaO2 de forma positiva, em que doentes hipoxémicos apresentam menores valores de tosse, e a PaCO2, de forma negativa, em que os doentes hipercápnicos apresentam menores valores de PCF tendo sido verificada relação entre o PCF e o pH e sO2. Quanto à relação entre o número de internamentos por agudização da DPOC no último ano e o PCF verificou-se uma relação significativa, onde um menor valor de PCF contribui para uma maior taxa de internamento por agudização da DPOC. Conclusão: Este conjunto de conclusões corrobora a hipótese inicialmente formulada, de que o Peak Cough Flow se encontra diminuído nos indivíduos com Doença Pulmonar Obstrutiva Crónica onde a variação do PCF se encontra directamente relacionada com os parâmetros funcionais respiratórios, com a força dos músculos respiratórios e com os valores de gasometria arterial. ABSTRACT: Aims: Cough evaluation in Chronic Obstructive Pulmonary Disease (COPD) patients. Identify and determine the relation of the predictive factors that contribute to the cough capacity degradation in this type of patients. Type of study: Descriptive observational study of transversal nature. Case definition: The COPD diagnosis criteria are the clinical presentation and the gold standard to the COPD diagnosis- the Spirometry. Target Population: Every patients, with primary pathology of COPD diagnosed, who went to the respiratory function service of Viseu hospital to perform tests. Sampling Method: It was used a random sample constituted by all the, conscious and cooperating individuals, who complied with the inclusion criteria and who accepted to make part of this study. Sample size: A sample of 55 individuals that went to the respiratory function service between January and June 2009 to perform respiratory function tests. Study: The patients who accepted to make part of this study were submitted to a clinical data questionary and performed 5 tests: body mass index (BMI), respiratory functional study, arterial blood gas level, evaluation of respiratory muscles strength (maximal inspiratory pressure (MIP) and maximum expiratory pressure (MEP)), and Peak Cough Flow evaluation. Statistic Analysis: Were obtained characterizing data of the sample in study, and later correlated the value of the Peak Cough Flow with the results from the evaluation of the body mass index (BMI), the respiratory functional study the MIP and MEP, the arterial blood gas level and also with the ability to cough evaluation and the number of hospitalizations in the last year for COPD exacerbations. The values of correlation between the Peak Cough Flow and the other parameters were found. Results: After analyzing the results, were obtained the values of Peak Cough Flow for the population with COPD. There were decreased values compared with the population normal values, having been found higher values of PCF in males compared to female values. It was analyzed the relation between the PCF and the age, weight, height and BMI but no relation was found on account of the fact that the cough does not show a variation according to anthropometric parameters, such as the relation with spirometric values. As for the respiratory functional parameters were analyzed relations with the PCF. There were significant relations between the PCF and FEV1, the FVC, the PEF, presenting a positive relation, where higher values of these parameters are correlated with higher incidence of cough. Concerning the RAW and RV, the PCF has a negative relation, in which a higher airway resistance or in more hyperinflated patients, leads to lower values of PCF. On the other hand no correlation was found between the PCF and the FRC and TLC. Regarding the respiratory muscle strength, there was a significant relation with the MIP and MEP, in which the weakness at the level of respiratory muscles contribute to a lower value of PCF. For values of arterial blood gas level, there was no relation between the PCF and PaO2, in a positive way, in which patients with hypoxemia present lower values of cough, and PaCO2, in a negative way in which hypercapnic patients had lower values of PCF, having being founded a relation between the PCF and the pH and sO2. As for the relation between the number of hospitalizations for COPD exacerbation in the last year and the PCF was found a significant relation, in which a smaller value of PCF contributes to a higher rate of hospitalization for COPD exacerbation. Conclusion: This set of findings supports the hypothesis first formulated that Peak Cough Flow is decreased in individuals with Chronic Obstructive Pulmonary Disease, in which the variation of the PCF is directly related to the respiratory function parameters, the strength of respiratory muscles and the values of arterial blood gases.

Defective protein folding and function in metabolic disorders: studies on the mitochondrial flavoenzyme ETF

Dissertation presented to obtain the PhD degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

Constructing the National Canon in Ireland and Macedonia: The Function of Folklore in the Plays The Countess Cathleen and The Land of Heart’s Desire by William Butler Yeats, and Proud Flesh and The Black Hole by Goran Stefanovski and Their Role in Strengthening National Identity

Erasmus Mundus Masters “Crossways in European Humanities” June 2011

Cavin 1 and cavin 2 roles on adipocyte cell function

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Microglial clearance function: dependence on phenotypes

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Molecular modulation of brain development and function: lessons from “old” and “new”

Dissertation presented to obtain the Ph.D degree in Biology

Ankylosing spondylitis: genomic and functional characterization of candidate genes and their repercussion in clinical practice

RESUMO: Introdução: A espondilite anquilosante (EA) é uma doença inflamatória crónica caracterizada pela inflamação das articulações sacroilíacas e da coluna. A anquilose progressiva motiva uma deterioração gradual da função física e da qualidade de vida. O diagnóstico e o tratamento precoces podem contribuir para um melhor prognóstico. Neste contexto, a identificação de biomarcadores, assume-se como sendo muito útil para a prática clínica e representa hoje um grande desafio para a comunidade científica. Objetivos: Este estudo teve como objetivos: 1 - caracterizar a EA em Portugal; 2 - investigar possíveis associações entre genes, MHC e não-MHC, com a suscetibilidade e as características fenotípicas da EA; 3 - identificar genes candidatos associados a EA através da tecnologia de microarray. Material e Métodos: Foram recrutados doentes com EA, de acordo com os critérios modificados de Nova Iorque, nas consultas de Reumatologia dos diferentes hospitais participantes. Colecionaram-se dados demográficos, clínicos e radiológicos e colhidas amostras de sangue periférico. Selecionaram-se de forma aleatória, doentes HLA-B27 positivos, os quais foram tipados em termos de HLA classe I e II por PCR-rSSOP. Os haplótipos HLA estendidos foram estimados pelo algoritmo Expectation Maximization com recurso ao software Arlequin v3.11. As variantes alélicas dos genes IL23R, ERAP1 e ANKH foram estudadas através de ensaios de discriminação alélica TaqMan. A análise de associação foi realizada utilizando testes da Cochrane-Armitage e de regressão linear, tal como implementado pelo PLINK, para variáveis qualitativas e quantitativas, respetivamente. O estudo de expressão génica foi realizado por Illumina HT-12 Whole-Genome Expression BeadChips. Os genes candidatos foram validados usando qPCR-based TaqMan Low Density Arrays (TLDAs). Resultados: Foram incluídos 369 doentes (62,3% do sexo masculino, com idade média de 45,4 ± 13,2 anos, duração média da doença de 11,4 ± 10,5 anos). No momento da avaliação, 49,9% tinham doença axial, 2,4% periférica, 40,9% mista e 7,1% entesopática. A uveíte anterior aguda (33,6%) foi a manifestação extra-articular mais comum. Foram positivos para o HLA-B27, 80,3% dos doentes. Os haplótipo A*02/B*27/Cw*02/DRB1*01/DQB1*05 parece conferir suscetibilidade para a EA, e o A*02/B*27/Cw*01/DRB1*08/DQB1*04 parece conferir proteção em termos de atividade, repercussão funcional e radiológica da doença. Três variantes (2 para IL23R e 1 para ERAP1) mostraram significativa associação com a doença, confirmando a associação destes genes com a EA na população Portuguesa. O mesmo não se verificou com as variantes estudadas do ANKH. Não se verificou associação entre as variantes génicas não-MHC e as manifestações clínicas da EA. Foi identificado um perfil de expressão génica para a EA, tendo sido validados catorze genes - alguns têm um papel bem documentado em termos de inflamação, outros no metabolismo da cartilagem e do osso. Conclusões: Foi estabelecido um perfil demográfico e clínico dos doentes com EA em Portugal. A identificação de variantes génicas e de um perfil de expressão contribuem para uma melhor compreensão da sua fisiopatologia e podem ser úteis para estabelecer modelos com relevância em termos de diagnóstico, prognóstico e orientação terapêutica dos doentes. -----------ABSTRACT: Background: Ankylosing Spondylitis (AS) is a chronic inflammatory disorder characterized by inflammation in the spine and sacroiliac joints leading to progressive joint ankylosis and in progressive deterioration of physical function and quality of life. An early diagnosis and early therapy may contribute to a better prognosis. The identification of biomarkers would be helpful and represents a great challenge for the scientific community. Objectives: The present study had the following aims: 1- to characterize the pattern of AS in Portuguese patients; 2- to investigate MHC and non-MHC gene associations with susceptibility and phenotypic features of AS and; 3- to identify candidate genes associated with AS by means of whole-genome microarray. Material and Methods: AS was defined in accordance to the modified New York criteria and AS cases were recruited from hospital outcares patient clinics. Demographic and clinical data were recorded and blood samples collected. A random group of HLA-B27 positive patients and controls were selected and typed for HLA class I and II by PCR-rSSOP. The extended HLA haplotypes were estimated by Expectation Maximization Algorithm using Arlequin v3.11 software. Genotyping of IL23R, ERAP1 and ANKH allelic variants was carried out with TaqMan allelic discrimination assays. Association analysis was performed using the Cochrane-Armitage and linear regression tests as implemented in PLINK, for dichotomous and quantitative variables, respectively. Gene expression profile was carried out using Illumina HT-12 Whole-Genome Expression BeadChips and candidate genes were validated using qPCR-based TaqMan Low Density Arrays (TLDAs). Results: A total of 369 patients (62.3% male; mean age 45.4±13.2 years; mean disease duration 11.4±10.5 years), were included. Regarding clinical disease pattern, at the time of assessment, 49.9% had axial disease, 2.4% peripheral disease, 40.9% mixed disease and 7.1% isolated enthesopathic disease. Acute anterior uveitis (33.6%) was the most common extra-articular manifestation. 80.3% of AS patients were HLA-B27 positive. The haplotype A*02/B*27/Cw*02/DRB1*01/DQB1*05 seems to confer susceptibility to AS, whereas A*02/B*27/Cw*01/DRB1*08/DQB1*04 seems to provide protection in terms of disease activity, functional and radiological repercussion. Three markers (two for IL23R and one for ERAP1) showed significant single-locus disease associations. Association of these genes with AS in the Portuguese population was confirmed, whereas ANKH markers studied did not show an association with AS. No association was seen between non-MHC genes and clinical manifestations of AS. A gene expression signature for AS was established; among the fourteen validated genes, a number of them have a well-documented inflammatory role or in modulation of cartilage and bone metabolism. Conclusions: A demographic and clinical profile of patients with AS in Portugal was established. Identification of genetic variants of target genes as well as gene expression signatures could provide a better understanding of AS pathophysiology and could be useful to establish models with relevance in terms of susceptibility, prognosis, and potential therapeutic guidance.

Safety function analysis in an industrial production process

Dissertação para obtenção do Grau de Mestre em Engenharia e Gestão Industrial

Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductase

Dissertation presented to obtain the Ph.D degree in Biochemistry

Comparison of different techniques for mouse transgenesis

RESUMO: O uso de ratinhos transgénicos em neurociências aumentou consideravelmente nos últimos anos devido ao crescente interesse em compreender o cérebro e a necessidade de solucionar situações clínicas do foro neurológico e psiquiátrico. Para esse efeito, diferentes métodos de produção de animais transgénicos têm sido testados. O objectivo desta tese foi comparar métodos de integração aleatória de um transgene no genoma de ratinhos em termos de eficiência, estabilidade da integração do transgene, número de animais e de horas de trabalho necessárias para cada método. Assim, foi comparado o método mais utilizado - microinjecção pronuclear (PNMI) - com duas outras técnicas cujo desempenho foi considerado promissor – a transferência génica através dos testículos por electroporação e transfecção por lentivírus in vivo. As três técnicas foram realizadas usando um gene repórter sob o controlo de um promotor constitutivo, e depois reproduzidas usando um gene de interesse de modo a permitir obtenção de um animal capaz de ser usado em experimentação laboratorial. O transgene de interesse utilizado codifica uma proteína de fusão correspondendo a uma variante da rodopsina (channelrhodopsin) fundida à proteína enhanced yellow fluorescente protein ((EYFP) resultando num produto designado ChR2-EYFP. Este animal transgénico apresentaria expressão deste canal iónico apenas em células dopaminergicas, o que, com manipulação optogenética, tornaria possivel a activação especifica deste grupo de neurónios e, simultaneamente, a observação do impacto desta manipulação no comportamento num animal em livre movimento. Estas ferramentas são importantes na investigação básica em neurociências pois ajudam a esclarecer o papel de grupos específicos de neurónios e compreender doenças como a doença de Parkinson ou a esquizofrenia onde a função de certos tipos de neurónios de encontra alterada. Quando comparados os três métodos realizados verifica-se que usando um gene repórter PMNI resulta em 31,3% de, a de animais transgénicos obtidos, a electroporação de testículos em 0% e a injecção de lentivírus em 0%. Quando usado o gene de interesse, os resultados obtidos são, respectivamente, 18,8%, 63,9% e 0%.--------------ABSTRACT: The use of transgenic mice is increasing in all fields of research, particularly in neuroscience, due to the widespread need of animal models to solve neurological and psychiatric medical conditions. Different methodologies have been tested in the last decades in order to produce such transgenic animals. The ultimate goal of this thesis is to compare different methods of random integration of a transgene in the genome of mice in terms of efficiency, stability of the transgene integration, number of animals required and the labour intensity of each technique. We compared the most used method – pronuclear microinjection (PNMI) – with two other promising techniques – Testis Mediated Gene Transfer (TMGT) by electroporation and in vivo lentiviral transfection. The three techniques were performed using a reporter gene – green fluorescent protein (GFP), whose transcription was driven by the constitutive cytomegalovirus (CMV) promoter. These three techniques were later reproduced using the tyrosine hydroxylase promoter (TH) and the neuronal manipulator, channelrhodopsin-2 fused to the enhanced yellow fluorescent reporter protein (ChR2-EYFP). The transgenic animal we sough to produce would express the light driven channel only in dopaminergic cells, making possible to specifically activate this group of neurons, while simultaneously observe the behaviour in a freely moving animal. This is a very important tool in basic neuroscience research since it helps to clarify the role of specific groups of neurons, map circuits in the brain, and consequently understand neurological diseases such as Parkinson’s disease or schizophrenia, where the function of certain types of neurons is affected. When comparing the three methods, it was verified that using a reporter gene PNMI resulted in 31.3% of transgenic mice obtained, testis electroporation in 0% and lentiviral injection in 0%. When using the gene of interest, the results obtained were, respectively, 18.8%, 63.9% and 0%.