Introdução: Com o melhor controle das causas ambientais, as doenças genéticas e as malformações congênitas cada vez mais ganham destaque como fatores morbidade e mortalidade, assim como cada vez mais se reconhece a importância da base genética para as doenças comuns. Desta forma, é necessário desenvolver estratégias de prevenção e controle destas condições, assim como acesso aos cuidados de saúde para pessoas com ou em risco de desenvolver uma doença genética. A integração da genética na Atenção Primária à Saúde (APS) parece ser uma alternativa para se desenvolver ações de prevenção e controle, assim como facilitar o acesso da comunidade aos cuidados de saúde com base no conhecimento sobre a genética. Para tanto, é necessário que os profissionais da APS tenham um conhecimento básico sobre genética, as principais condições, as formas de manejo e prevenção. Objetivo: Avaliar se a aplicação de um programa educativo de genética médica direcionado às equipes de APS pode contribuir para integrar conceitos e atitudes relacionados à identificação, ao manejo e à prevenção de malformações congênitas e doenças genéticas. Métodos: O programa foi planejado por profissionais do Serviço de Genética Médica do Hospital de Clínicas de Porto Alegre e aplicado em três Unidades Básicas de Saúde (UBS) do Serviço de Saúde Comunitária do Grupo Hospitalar Conceição. O programa foi constituído por encontros realizados nas próprias UBS com ênfase nos seguintes temas: conceitos básicos em genética, avaliação genética de famílias, teratógenos e prevenção de defeitos congênitos, genética da deficiência intelectual, erros inatos do metabolismo e triagem neonatal, oncogenética, genética das doenças crônicas comuns e aconselhamento genético e préconcepcional. Foi desenvolvido material de apoio para os participantes e material educativo para a comunidade. O programa foi avaliado através de pré e pós-teste, bem como um questionário de auto-avaliação aplicado aos profissionais da APS sobre o conhecimento e confiança em prover cuidados com bases genéticas aos pacientes e famílias. Além disso, foi aplicado um questionário sobre a relevância do programa para a prática clínica e a utilização dos recursos apresentados ou disponibilizados durante o programa. Resultados: Quarenta e três profissionais participaram do programa. Em duas das três UBS encontramos um aumento estatisticamente significativo no número de acertos do pós-teste quando comparado ao préteste. Durante o programa foram desenvolvidos materiais educativos para a comunidade (folders) e para os profissionais (Manual de Genética Médica para a Atenção Primária à Saúde). A maioria dos profissionais relatou um maior conhecimento e confiança após o programa, referiu que o programa influenciou a sua prática clínica e informou utilizar os recursos de informação apresentados e o material educativo elaborado durante o programa. Conclusão: O programa proporcionou uma aproximação da genética médica com a APS, fazendo com que os profissionais atentem para a genética como determinante de doenças na comunidade. Entretanto percebeu-se a necessidade de estratégias de educação continuada e suporte contínuo à APS, com o intuito de fortalecer a integração das duas especialidades, colocando-se em prática a genética comunitária. / Introduction: Genetic disease and birth defects are increasingly gaining prominence as factors morbidity and mortality, as well as it is increasingly recognized the importance of the genetic basis for common diseases. So, it is necessary to develop strategies for the prevention and control of these conditions, as well for the access to health care for people with or at risk of developing a genetic disease. On this way, it is necessary to develop strategies for prevention and control of these conditions, as well as to provide access to health care for people with or at risk of developing a genetic disease. The integration of Medical Genetics and Primary Health Care (PHC) seems to be an alternative to develop actions of prevention and control, and to facilitate community access to health care based on knowledge about genetics. Therefore, it is necessary that primary care professionals have a basic knowledge about genetics, the main conditions, management measures and prevention of genetics conditions. Aim: To evaluate if the application of an educational program in Medical Genetics directed to PHC teams can help to integrate concepts and attitudes related to the identification, management and prevention of congenital malformations and genetic diseases. Method: The program was designed by health professional of the Medical Genetics Service/Hospital de Clínicas de Porto Alegre and applied to three Basic Health Unitis (BHU) of Community Health Service/Grupo Hospitalar Conceição. The program consisted of meetings that took place at the BHU, which emphasis on the following topics: basic concepts in genetics; genetic evaluation of families; teratogenic agents and prevention of birth defects; genetics of mental retardation; inborn errors of metabolism and neonatal screening; cancer genetics; genetics of common chronic diseases; and genetic and preconception counseling. It was developed support materials for participants and educational material for the community. The program was evaluated through pre and post-test, as well through self-assessment questionnaire applied to the PHC professionals based on the knowledge and confidence in providing care with genetic basis to patients and families. In addition, a questionnaire was applied about the relevance of the program for clinical practice and use of the resources presented or made available during the program. Results: Forty three professionals participated in the program. In two of the three BHU it was found a statistically significant increase in the number of hits from the post-test compared to pre-test. Most professionals reported increased knowledge and confidence after the program, said that the program influenced their clinical practice and informed that the information resources and educational material presented during the program were useful. Conclusions: The program provided an approximation between Genetic Medicine and PHC, so that professionals pay attention to the genetic determinants of disease in the community. However it was realized the need for strategies for continuing education and ongoing support to the APS, with the aim of strengthening the integration of the two specialties, bringing to practice the community genetics.

Introdução: Com o melhor controle das causas ambientais, as doenças genéticas e as malformações congênitas cada vez mais ganham destaque como fatores morbidade e mortalidade, assim como cada vez mais se reconhece a importância da base genética para as doenças comuns. Desta forma, é necessário desenvolver estratégias de prevenção e controle destas condições, assim como acesso aos cuidados de saúde para pessoas com ou em risco de desenvolver uma doença genética. A integração da genética na Atenção Primária à Saúde (APS) parece ser uma alternativa para se desenvolver ações de prevenção e controle, assim como facilitar o acesso da comunidade aos cuidados de saúde com base no conhecimento sobre a genética. Para tanto, é necessário que os profissionais da APS tenham um conhecimento básico sobre genética, as principais condições, as formas de manejo e prevenção. Objetivo: Avaliar se a aplicação de um programa educativo de genética médica direcionado às equipes de APS pode contribuir para integrar conceitos e atitudes relacionados à identificação, ao manejo e à prevenção de malformações congênitas e doenças genéticas. Métodos: O programa foi planejado por profissionais do Serviço de Genética Médica do Hospital de Clínicas de Porto Alegre e aplicado em três Unidades Básicas de Saúde (UBS) do Serviço de Saúde Comunitária do Grupo Hospitalar Conceição. O programa foi constituído por encontros realizados nas próprias UBS com ênfase nos seguintes temas: conceitos básicos em genética, avaliação genética de famílias, teratógenos e prevenção de defeitos congênitos, genética da deficiência intelectual, erros inatos do metabolismo e triagem neonatal, oncogenética, genética das doenças crônicas comuns e aconselhamento genético e préconcepcional. Foi desenvolvido material de apoio para os participantes e material educativo para a comunidade. O programa foi avaliado através de pré e pós-teste, bem como um questionário de auto-avaliação aplicado aos profissionais da APS sobre o conhecimento e confiança em prover cuidados com bases genéticas aos pacientes e famílias. Além disso, foi aplicado um questionário sobre a relevância do programa para a prática clínica e a utilização dos recursos apresentados ou disponibilizados durante o programa. Resultados: Quarenta e três profissionais participaram do programa. Em duas das três UBS encontramos um aumento estatisticamente significativo no número de acertos do pós-teste quando comparado ao préteste. Durante o programa foram desenvolvidos materiais educativos para a comunidade (folders) e para os profissionais (Manual de Genética Médica para a Atenção Primária à Saúde). A maioria dos profissionais relatou um maior conhecimento e confiança após o programa, referiu que o programa influenciou a sua prática clínica e informou utilizar os recursos de informação apresentados e o material educativo elaborado durante o programa. Conclusão: O programa proporcionou uma aproximação da genética médica com a APS, fazendo com que os profissionais atentem para a genética como determinante de doenças na comunidade. Entretanto percebeu-se a necessidade de estratégias de educação continuada e suporte contínuo à APS, com o intuito de fortalecer a integração das duas especialidades, colocando-se em prática a genética comunitária. / Introduction: Genetic disease and birth defects are increasingly gaining prominence as factors morbidity and mortality, as well as it is increasingly recognized the importance of the genetic basis for common diseases. So, it is necessary to develop strategies for the prevention and control of these conditions, as well for the access to health care for people with or at risk of developing a genetic disease. On this way, it is necessary to develop strategies for prevention and control of these conditions, as well as to provide access to health care for people with or at risk of developing a genetic disease. The integration of Medical Genetics and Primary Health Care (PHC) seems to be an alternative to develop actions of prevention and control, and to facilitate community access to health care based on knowledge about genetics. Therefore, it is necessary that primary care professionals have a basic knowledge about genetics, the main conditions, management measures and prevention of genetics conditions. Aim: To evaluate if the application of an educational program in Medical Genetics directed to PHC teams can help to integrate concepts and attitudes related to the identification, management and prevention of congenital malformations and genetic diseases. Method: The program was designed by health professional of the Medical Genetics Service/Hospital de Clínicas de Porto Alegre and applied to three Basic Health Unitis (BHU) of Community Health Service/Grupo Hospitalar Conceição. The program consisted of meetings that took place at the BHU, which emphasis on the following topics: basic concepts in genetics; genetic evaluation of families; teratogenic agents and prevention of birth defects; genetics of mental retardation; inborn errors of metabolism and neonatal screening; cancer genetics; genetics of common chronic diseases; and genetic and preconception counseling. It was developed support materials for participants and educational material for the community. The program was evaluated through pre and post-test, as well through self-assessment questionnaire applied to the PHC professionals based on the knowledge and confidence in providing care with genetic basis to patients and families. In addition, a questionnaire was applied about the relevance of the program for clinical practice and use of the resources presented or made available during the program. Results: Forty three professionals participated in the program. In two of the three BHU it was found a statistically significant increase in the number of hits from the post-test compared to pre-test. Most professionals reported increased knowledge and confidence after the program, said that the program influenced their clinical practice and informed that the information resources and educational material presented during the program were useful. Conclusions: The program provided an approximation between Genetic Medicine and PHC, so that professionals pay attention to the genetic determinants of disease in the community. However it was realized the need for strategies for continuing education and ongoing support to the APS, with the aim of strengthening the integration of the two specialties, bringing to practice the community genetics.

Cette thèse part de la proposition d\'une rencontre possible entre psychanalyse et génétique médicale par le biais des soins offerts aux enfants porteurs de syndromes génétiques, notamment le syndrome de l\'X fragile. Nous avons trouvé dans les recherches en épigénétique une voie de rapprochement de ces différents champs du savoir. L\'idée selon laquelle l\'environnement est capable de modifier l\'expression des gènes représente la rupture d\'un certain déterminisme génétique autrefois accepté, et ouvre un espace où penser la singularité. Notre travail propose d\'élargir le concept d\'environnement, en y considérant la relation de l\'enfant avec l\'Autre, lieu du langage, comme opérateur de marques sur son corps : marques symboliques, constituées dès le tout début de la rencontre de l\'infans et de ceux qui s\'occupent de lui. C\'est justement dans cet espace d\'échange avec l\'Autre qu\'a lieu l\'émergence d\'un sujet. Nous avons opté pour les concepts de sujet et de transfert pour soutenir l\'articulation de la clinique psychanalytique et de la génétique médicale en ce qui concerne le traitement. Nous avons donc exposé trois cas cliniques issus de notre pratique, d\'enfants traversés par le diagnostic de l\'X fragile afin d\'illustrer de quelle manière les conceptions de sujet et de transfert se reflètent dans la clinique. Tenant compte que la psychothérapie est également prise comme objet d\'étude de l\'épigénétique, et qu\'elle est donc considérée comme un environnement capable de provoquer, voire de renverser des marques épigénétiques, l\'enjeu de notre travail repose sur la proposition suivante : et pourquoi pas la psychanalyse également ? La psychothérapie psychanalytique, ancrée sur le transfert, ne peut-elle pas, elle aussi, laisser des marques sur le petit patient / The current thesis assumes a possible encounter between psychoanalysis and medical genetics based on the treatment applied to children carrying genetic syndromes such as the Fragile X Syndrome. Epigenetic studies are a way to approximate different knowledge fields. The assumption that the environment is able to change gene expression strays from the genetic determinism we once believed and opens the way for us to reason about singularity. The proposition in the present study lies on expanding the concept of environment, by taking into consideration the relation between the child and the Other in the environment in question, as well as the place of language as the operator marking the childs body. These symbolic marks start emerging in the first encounter between the infans and caregivers. The subject emerges precisely 3 within an environment of exchanges that is set with the Other. The concepts of subject and transference were chosen to support the treatment articulation between psychoanalytic clinic and medical genetics. Thus, the present study reports three clinical cases followed by the authors, which involved children diagnosed with fragile X syndrome. These cases illustrate how the aforementioned concepts affect the clinical practice. Since psychotherapy has also been taken as the object of epigenetic studies, and as it is considered an environment able to cause, and even reverse, epigenetic marks, the current study relies on the following proposition: why not psychoanalysis as well? Can the psychoanalytic psychotherapy, anchored in the concept of transference, leave marks on the little patient too?

O quelóide é um processo cicatricial, com freqüência aumentada em regiões com maior tensão na pele ou onde a pele é mais espessa, caracterizado por exceder-se além dos limites da lesão que o originou e pela tendência à recidiva após sua ressecção. Ambos os sexos são acometidos, com maior incidência entre a primeira e a terceira década de vida e em indivíduos de etnia negra. A relação familial é sugerida como herança autossômica dominante. O quelóide apresenta características moleculares distintas da pele normal envolvendo uma variedade de sinalizações ainda pouco compreendidas e um aumento da expressão de componentes da matriz extracelular, como o colágeno, os glicosaminoglicanos e os proteoglicanos. Este estudo analisou a expressão gênica dos proteoglicanos de superfície celular sindecam-2 e sindecam-4 e dos de matriz extracelular decorim e versicam no tecido derivado de quelóide de indivíduos não tratados em comparação com a pele clinicamente normal. Participaram desse estudo 10 indivíduos portadores de quelóides (grupo Q) e 10 indivíduos não portadores dessa cicatriz (grupo N). A expressão gênica dos proteoglicanos foi amplificada pela reação em cadeia da polimerase por transcrição reversa e analisada através de eletroforese em gel de agarose. Foi realizada a localização dos proteoglicanos nos tecidos através de reação imunohistoquímica com anticorpos para os sindecans-2 e 4. Os grupos foram comparados pelo teste t de Student. Os proteoglicanos de superfície celular mostraram-se aumentados no grupo Q (93% para o sindecam-2 e 152,5% para o sindecam-4) em comparação com o grupo N (P<0,01). Não foram observadas diferenças significativas para os proteoglicanos de matriz extracelular entre os dois grupos. A análise imunohistoquímica mostrou uma distribuição marcante dos sindecans-2 e 4 no componente epitelial, conectivo, vascular e nervoso de toda a casuística. Concluímos que o quelóide apresenta aumento significativo da expressão gênica de sindecam- 2 e sindecam-4, mas não apresenta aumento significativo da expressão gênica de decorim e versicam, em relação à pele normal. / Keloid is a cicatricial process, with frequency increased in regions with bigger tension in the skin or where the skin is thicker, characterized for exceeding beyond the limits of the injury that originated it and for the tendency to relapse after its ressection. Its occurs in both genders, with bigger incidence between the first and the third decade of life and in individuals of black ethnia. The familial relation is consistent with an autosomal dominant inheritance. The keloid presents distinct molecular characteristics of the normal skin involving a variety of still little understood signallings and an increase of the expression of components of the extracellular matrix, as the collagen, the glicosaminoglycans and the proteoglycans. This study analyzed the gene expression of the proteoglycans of cell surface syndecan-2 and syndecan-4 and the ones of extracellular matrix decorin and versican in the keloid tissue from not treated individuals in comparison with the normal skin. Tissue samples was obtained from 10 individuals with keloid (Q group) and 10 individuals with normal skin (N group). The gene expression of the proteoglycans was amplified by reverse transcription polymerase chain reaction and analyzed through agarose gel electrophoresis. The localization of the proteoglycans in the tissues was performed through immunohistochemical reaction using panels of antibodies for syndecans-2 and 4. The groups was compared by the Student?s t test. The proteoglycans of cell surface revealed increased in Q group (93% for sydecan-2 and 152,5% for syndecan-4) in comparison with N group (P<0,01). Significant differences for the proteoglycans of extracellular matrix between the two groups was not observed. The immunohistochemical analysis showed a major distribution of syndecans-2 and 4 in epithelial, connective, vascular and neural components in both groups. We conclude that keloid reveal significant increase of the gene expression of syndecan-2 and syndecan-4, but does not present significant increase of the gene expression of decorin and versican, in relation to the normal skin.

Orientador: Vera Lucia Gil da Silva Lopes / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-20T04:54:42Z (GMT). No. of bitstreams: 1 Vieira_TarsisAntonioPaiva_D.pdf: 3309313 bytes, checksum: 6d4805118bd5c929446b40064e1263b2 (MD5) Previous issue date: 2012 / Resumo: A aplicação de modernos conhecimentos sobre causa, efeito e métodos diagnósticos de doenças genéticas para cuidados de saúde é bastante complexa, especialmente no Brasil onde o sistema de saúde é predominantemente público. A síndrome de deleção 22q11.2 (S. Del 22q11.2) é a condição geneticamente determinada mais comum em indivíduos com anomalias palatais, com prevalência de 1/4.000 nascimentos. Considerando esta prevalência, as características do sistema de saúde e da atenção em genética no Brasil, o principal objetivo deste estudo foi realizar estudo multicêntrico para diagnóstico da S. Del 22q11.2 como modelo para otimização de estratégias diagnósticas em genética médica. Para isso, verificou-se a disponibilidade do diagnóstico laboratorial da S. Del 22q11.2 em 11 serviços de genética de diferentes regiões do país, e este foi centralizado nos Laboratórios de Citogenética Humana e Genética Molecular da FCM/UNICAMP por 30 meses. Foram estudados 100 pacientes (48M:52F) e as técnicas utilizadas foram FISH (Fluorescence in situ Hibridization) e MLPA (Multiplex Ligation-dependent Probe Amplification). Disponibilidade anterior e temporária do diagnóstico laboratorial de deleção em 22q11, vinculada a projetos de pesquisa, foi informada por sete instituições, sendo detectada desigualdade regional. Microdeleção em 22q11 foi identificada em 35% dos pacientes e aberrações cromossômicas não envolvendo a região 22q11 foram detectadas em três casos, obtendo-se conclusão diagnóstica em 38% dos casos. Encontrou-se diferença estatisticamente significativa para alguns sinais clínicos apresentados entre os pacientes com e sem deleção. As técnicas de FISH e MLPA mostraram 100% de sensibilidade e especificidade. Considerando a infraestrutura necessária e a adaptação da técnica de FISH, que permitiu reduzir a quantidade de sonda utilizada, esta foi eficaz, mais econômica e mais rápida em comparação a MLPA. A investigação centralizada mostrou-se vantajosa. Aponta-se o modelo estabelecido como uma estratégia importante e factível para o Brasil. Os resultados deste estudo propiciaram reflexões que culminaram em sugestões para o incremento desta abordagem para esta e outras condições geneticamente determinadas em nosso país / Abstract: The introduction of new technologies of molecular diagnosis for health care has been a challenge in the last years, especially in Brazil, where the majority of the population is served by the public health system. The 22q11.1 deletion syndrome is the most common syndrome that has palatal anomalies as a major feature, with a prevalence of 1/4000 births. Considering this prevalence, the Brazilian health system characteristics and the current situation of medical and clinical genetic services in the country, the main aim of this study was to conduct a multicenter study for 22q11.2 deletion diagnosis as a model for the optimization of diagnostic strategies in medical genetics. We investigated the access to laboratorial diagnosis of 22q11.2 deletion at 11 genetic services and centralized this diagnosis for 100 patients with palatal abnormalities and suspicion of 22q11.2 deletion syndrome, referred from these centers during 30 months, at the Cytogenetics and Molecular biology laboratories of the FCM/UNICAMP. To detect 22q11 deletions FISH (Fluorescence in situ Hibridization) and MLPA (Multiplex Ligation-dependent Probe Amplification) techniques were used. Previous and temporary availability for the diagnosis of 22q11 deletion, associated with research projects, was informed by seven centers, with remarkable geographic disparities. We detected 22q11 deletion in 35% of the patients, and chromosome abnormalities not related to 22q11 region in three patients; thus we reached diagnostic conclusion in 38% of the cases. There was significant difference between some clinical signs found in patients with or without 22q11 deletion. There was 100% of sensibility and specificity for both MLPA and FISH techniques. Considering the required infrastructure and the modifications in the FISH (allowing to reduce probe quantity), this technique was efficient, more economical and faster than MLPA. Centralizing the laboratorial diagnosis was considered advantageous, pointing to this model as an important and feasible strategy for genetic diagnosis in Brazil. These results allowed to suggestions for the improvement of laboratorial diagnosis of this and other genetic conditions in our country / Doutorado / Ciencias Biomedicas / Doutor em Ciências Médicas

The unconventional myosin IC has previously been suggested to be a haploinsufficient tumour suppressor. The mechanism for this action has hitherto been unknown, however, and hence we decided to attempt to elucidate the genes involved. The first study involved knock-down of MYO1C using siRNA technology followed by whole transcriptiome microarray analysis performed on samples taken at different time points post transfection. This revealed a cornucopia of differential expressions compared to the negative control, among them we found an early up-regulation of the PI3K/AKT pathway and the pathway for prostate cancer. Among the down regulated pathways we found endometrial-, colorectal cancer and small cell lung cancer as well as the cell cycle pathway which was a little counter intuitive to the hypothesis that MYO1C suppresses cancer. For the next study six different genes (CCND1, CCND2, CDKN2B, CDKN2C, MYC, RBL1) important for the transitions into S-phase of the cell cycle were therefore chosen for validation using qPCR. These six genes and MYO1C were analysed on both the original time series and a new biological replicate as well as a well stratified set of endometrial carcinoma samples. We were able to verify the significant down-regulation of CCND2 in both time series indicating that this is caused by the depletion of MYO1C. In the tumour samples we saw a negative correlation between the expression of MYO1C and FIGO grade corroborating results previously found by our group when looking at protein expression.

The recent advances in molecular and computational biology have made possible the study of complicated transcriptional regulatory networks that control a wide range of biological processes and phenotypic traits. In this thesis, several approaches were combined including next generation sequencing, gene expression profiling, chromatin and RNA immunoprecipitation, bioinformatics and genome editing methods in order to characterize the biological significance of the ZBED6 and ZC3H11A genes. A mutation in the binding site of ZBED6, located in an intron of IGF2, disrupts the binding and leads to 3-fold upregulation of IGF2 mRNA in pig muscle tissues. The first part of the thesis presents a detailed functional characterization of ZBED6. Transient silencing of ZBED6 expression in mouse myoblasts led to increased Igf2 expression (~2-fold). ChIP-seq analysis of ZBED6 and histone modifications showed that ZBED6 preferentially binds active promoters and modulates their transcriptional activities (paper I). In the follow-up studies using CRISPR/Cas9 we showed that either the deletion of ZBED6 or its binding site in Igf2 (Igf2ΔGGCT) led to more than 30-fold up-regulation of Igf2 expression in myoblasts. Differentiation of these genetically engineered cells resulted in hypertrophic myotubes. Transcriptome analysis revealed ~30% overlap between the differentially expressed genes in Zbed6-/- and Igf2ΔGGCT myotubes, with significant enrichment of muscle-specific genes. ZBED6-overexpression in myoblasts led to cell cycle arrest, reduced cell viability, reduced mitochondrial activities and impaired the differentiation of myoblasts (paper II). Further studies on cancer cells showed that ZBED6 influences the growth of colorectal cancer cells with dramatic changes in the transcription of hundreds of cancer-related genes (paper III). The phenotypic characterization of Zbed6-/- and Igf2pA/mG mouse models showed that the ZBED6-Igf2 axis has a major effect on regulating muscle growth and the growth of internal organs. Transcriptome analysis demonstrated a massive up-regulation of Igf2 expression (~30-fold) in adult tissues, but not in fetal tissues, of transgenic mice (paper IV). In the second part of the thesis we investigated the cellular function of Zc3h11a, the gene harboring ZBED6 in one of its first introns. The function of the ZC3H11A protein is so far poorly characterized. We show that ZC3H11A is a novel stress-induced protein that is required for efficient mRNA export from the nucleus. The inactivation of ZC3H11A inhibited the growth of multiple viruses including HIV, influenza, HSV and adenoviruses (paper V).

Infectious diseases are the top leading cause of death worldwide. Identifying essential genes, genes indispensable for survival, has been proven indispensable in defining new therapeutic targets against pathogens, major elements of the minimal set genome to be harnessed in synthetic biology, and determinants of evolutionary relationships of phylogenetically distant species. Thus, essentiality studies promise valuable revenues that can decipher much of biological complexities. Taking advantage of the available microbial sequences and the essentiality studies conducted in various microbial models, we proposed a framework for the prediction of essential genes based on our experimentally verified knowledge of the pathways involved in three essential xiv functions: genetic information processing, cell wall biosynthesis, and energy metabolism. We investigated physiological pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG) database and developed a bioinformatics approach to predict essential genes in 13 different microbial species. Our in silico findings matched to a high degree the experimental data derived from essentiality studies conducted on the same microbial models, providing insights about the microbial lifestyles, including energy resources, cell wall structure, and ecological preferences, but not virulence tools and mechanisms. Furthermore, we believe that essential genes have survived the evolutionary purifying selection due to their evolved capacity to re-wire genetic and protein networks in response to any emerging stress. In this sense, an environmental specificity (stress) provides a dominant determinant of an essential gene set. The new challenge was understanding the contribution of the essential genome in S. sanguinis to the coping mechanisms to different clinically relevant stress factors, namely temperature elevation (43oC) and sub-inhibitory concentration of ampicillin, an abundantly prescribed antibiotic for prophylaxis and treatment against S. sanguinis. The current project investigated the transcriptomic and proteomic profiles of essential genes and proteins, using RNA-seq and mass spectrometry respectively, under the impact of the two stressors separately, to elucidate the essential genome and proteome dynamics on a temporal basis and define “pathogenesis signatures” as potential therapeutic targets. We believe that the current findings will help characterize a bacterial model for studying the dynamics of essential genes and assist in designing evidence-based guidelines for drug prescription in clinical practice.

Sudden Infant Death (SIDS) has been associated with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency, an inborn error of fatty acid oxidation. Blood and tissue samples from a large cohort of SIDS victims were analyzed for the presence of dodecanoic acid (C₁₂) by gas chromatography. A subgroup of these cases had a significantly higher blood concentration than age-matched controls, suggesting MCAD deficiency. An animal study using Sprague-Dawley rats was done to mimic the effects of MCAD deficiency. Significantly increased blood concentrations of dodecanoic acid were observed. Decreased values in heart and liver were puzzling findings. The data indicate that dodecanoic acid is a blood marker for MCAD deficiency.

In the realm of biomedical technology, both accuracy and consistency are crucial to the development and deployment of these tools. While accuracy is easy to measure, consistency metrics are not so simple to measure, especially in the scope of biomedicine where prediction consistency can be difficult to achieve. Typically, biomedical datasets contain a significantly larger amount of features compared to the amount of samples, which goes against ordinary data mining practices. As a result, predictive models may fail to find valid pathways for prediction during training on such datasets. This concept is known as underspecification. Underspecification has been more accepted as a concept in recent years, with a handful of recent works exploring underspecification in different applications and a handful of past works experiencing underspecification prior to its declaration. However, underspecification is still under-addressed, to the point where some academics might even claim that it is not a significant problem. With this in mind, this thesis aims to identify and minimize underspecification of deep learning cancer subtype predictors. To address these goals, this work details the development of Predicting Underspecification Monitoring Pipeline (PUMP), a software tool to provide methodology for data analysis, stress testing, and model evaluation. In this context, the hope is that PUMP can be applied to deep learning training such that any user can ensure that their models are able to generalize to new data as best as possible.