Дисертації з теми "3105 Genetics"

Bibliography: leaves 116-130.
Hereditary macular degeneration describes a group of conditions causing macular pathology. Stargardt disease (STGD) is the most common inherited juvenile macular dystrophy characterised by severed reduction of central visual acuity and normal peripheral vision. The ABCA4 (adenosine triphosphate binding cassette transporter) gene is the only gene implicated in the autosomal recessive (ar) form of the STGD phenotype, while one genetic locus and one gene have been shown to be causative of the autosomal dominant form.

Type 2 diabetes and metabolic syndrome are the metabolic disorders which constitute a major public health problem in both developed and developing countries. Various studies have suggested the genetic susceptibility to the disorders. The main aim of the thesis was to investigate the putative association of single nucleotide polymorphisms with Type 2 diabetes (T2D), metabolic syndrome (MetS) and the major components of metabolic syndrome. This study used meta‐analysis, polymerase chain reaction (PCR) based restriction fragment length polymorphism (RFLP) and Sanger sequencing methods to analyse the results. The single nucleotide polymorphism rs57829442 of peroxisome proliferator‐activated receptor‐γ coactivator‐1 (PPARGC1A) gene and its relation to risk of type 2 diabetes has been studied in the United Kingdom population. A meta‐analysis of genetic variant rs8192678 (Gly482Ser) of peroxisome proliferator‐activated receptor‐γ coactivator‐1 (PPARGC1A) gene and its association with the components of metabolic syndrome has been studied. An association of the genetic variants rs8192678 (Gly482Ser) of the PPARGC1A gene, rs7903146 of Transcription Factor 7 Like 2 (TCF7L2) gene, rs9939609 of Fat mass and obesity‐associated (FTO) gene and rs1801282 (Pro12Ala) of peroxisome proliferator‐activated receptor gamma (PPARG) gene with the metabolic syndrome and its components has been studied in the Nepalese population. The results showed that variant rs57829442 of PPARGC1A is not associated with T2D in the United Kingdom population. Further investigation with increased sample size is warranted. In the meta‐analysis, the variant rs8192678 (Gly482Ser) of PPARGC1A gene was found to be significantly associated with body mass index (BMI) in Asian populations under dominant genetic model, total cholesterol (TC) in non‐Asian population under recessive genetic model and with fasting plasma glucose (FPG) under a recessive model in overall and non‐Asian populations. No significant association of the variants rs8192678 (Gly482Ser), rs7903146, rs9939609 and rs1801282 (Pro12 Ala) was found associated with MetS under dominant, recessive, co‐dominant and additive models in the Nepalese population. However, the genotypes (AG and AA) of rs8192678 (Gly482Ser) had a statistically significant protective effect on systolic blood pressure. The genotypes with the risk allele of rs9930609 of FTO gene was significantly associated with weight, waist circumference and diastolic blood pressure under dominant genetic model and with BMI under both dominant and recessive genetic models in the Nepalese population. To the best of our knowledge, this is the first study to report the findings in the Nepalese population.

The debate regarding the contribution of adult stem/progenitor cells during normal growth and beta-cell regeneration is far from being resolved. Therefore, we addressed in two distinct situations the origin of new beta-cells. We exploited a Cre/loxP lineage tracing system to efficiently label beta-cells in double transgenic mice (Z/AP; RIPCreERTAM) to address the origin of new beta-cell during the beta-cell mass expansion in response to one and two pregnancies. Similarly, we examined origin of new beta-cell after diabetic recovery in triple transgenic mouse (Z/AP; RIPCreERTAM; pIns-c-MycERTAM). Finally we evaluated the functionality of regenerated beta-cells after diabetic recovery in the single pIns-c-MycERTAM mouse model by microfluorimetry, in collaboration with Dr P. Squires. We showed that the beta-cell functionality in the pIns-c-MycERTAM line was abnormal. Second, we showed that the human placental alkaline phosphatase label (HPAP) in the double and triple transgenic mice was 1) specific to beta-cells, 2) irreversible and heritable and 3) tamoxifen dose-dependant. Third, the analysis of the proportion of beta-cells labelled for HPAP in one pregnancy, showed that the HPAP labelling index of the non-pregnant animals (0.44±0.05) was greater that in the pregnant group (0.33±0.06),(paired two-tailed t-test, P-value 0.021), indicating a dilution of the label in pregnant animal pancreata. Furthermore the combined results of the mean HPAP labelling index in non-pregnant animals (0.44±0.12) and pregnant animals (0.33±0.09) in one and two pregnancies reinforced our results above by indicating that the difference between the two groups was considered extremely significant (paired, two-sided student t-test, P-value 0.0007). Likewise, we showed that two to three months after the tamoxifen pulse, beta-cells do not fully lose differentiation or transdifferentiate into other lineages of either endocrine or exocrine compartment. In conclusion, we demonstrated for the first time that non-beta-cell progenitors contribute significantly to the increase of the beta-cell mass in response to pregnancy in combination with pre-existing beta-cell self-duplication.

Includes abstract.
Includes bibliographical references (leaves 118-133).
The polyglutamine disorders are a subgroup of inherited neurodegenerative disorders with a common mutation which confers toxicity via a polyglutamine tract in the protein leading ultimately to various forms of neurodegeneration. One of these disorders, spinocerebellar ataxia 7 (SCA7) exists at a higher frequency in South Africa, than elsewhere in the world, and a founder effect has been demonstrated in South Africa, such that every patient tested thus far is linked to a common ancestor. The manipulation of RNA interference (RNAi) has been used with increasing success to selectively knockdown the expression of disease-causing genes at the RNA level. Thus, the possibility of applying this method to SCA7 in South Africa was considered. However, the wild-type allele of ataxin-7 is likely to be necessary for cellular function therefore a form of allele-specific silencing is required, such as a SNP linked to the mutation.

Includes abstract.
Includes bibliographical references.
Spinocerebellar ataxia type 7 (SCA7) is a dominantly-inherited neurodegenerative disease, resulting from a CAG trinucleotide repeat expansion in the ataxin-7 gene. The Ataxin-7 protein is known to play a role in transcriptional regulation through association with cellular histone acetylation complexes, and several studies have highlighted the role of transcriptional dysregulation, caused by the presence of mutant Ataxin-7, in the neuronal dysfunction that precedes the onset of disease symptoms.This study aimed to establish patient-derived cell models of SCA7, for use in the investigation of pathogenesis (with particular reference to transcriptional alterations), and in the evaluation of previously-developed therapies for the disease.The high prevalence of SCA7 in the South African population, as a result of a founder effect, makes this disease particularly amenable to allele-specific RNA interference (RNAi)-based therapy. Thus, this study also evaluated the feasibility of these cell models as a vehicle to test previously-developed RNAi therapeutics, using the alteration of expression of key transcripts as a phenotypic marker. SCA7 patient and control dermal fibroblasts were reprogrammed to pluripotency by retroviral transduction. The resultant induced pluripotent stem cell (iPSC) lines were characterised with respect to endogenous markers of pluripotency, differentiation capacity and transgene silencing. These cells were then subjected to neuronal differentiation, the success of which was confirmed by the expression of early neuronal markers.

Includes abstract.
Includes bibliographical references.
Host genetic variation is an important determinant of HIV infection, disease progression and HIV-associated neurocognitive deficits. However, there is no sufficient knowledge on the role of genetic variants especially among African populations. This study is focused on investigating variation in HIV/AIDS restriction genes; CCR2, CX3CR1, SDF1, RANTES, APOBEC3G and MBL2 and their possible role in HIV infection and neurocognitive function among children born to HIV infected mothers, recruited in Harare, Zimbabwe. A total of 116 children comprising of 73 perinatally exposed to HIV (34 who were born infected and 39 who were uninfected) and 43 unexposed controls were recruited in 2011(at ages 7-9 years) from a cohort of mother-baby pairs that has been followed up since 2002. The demographic characteristics of the recruited children were captured from their medical records. A McCarthy Scale of Children‟s Abilities (MSCA) was administered to determine each child‟s neurocognitive status. Genotyping for allelic variants was done using PCR-RFLP, SNaPshot® and Sanger DNA sequencing. Statistical analysis was carried out to determine association between genotypes, HIV status and neurocognitive function. The observation of different genetic variants or combinations of genotypes between the HIV-exposed and infected group and that of the HIV-exposed but uninfected group may be a pointer to critical pathways in differential HIV susceptibility. Exposure and infection with HIV is controlled by a multitude of genes/processes, thus, SNPs are unlikely to show statistically significant effects individually and may be more useful in a multifactorial model, as observed from comparisons of genotype combinations and haplotypes. The role of host genetic variation on neurocognitive function remains disputed but our observations suggest innate immune factors such as MBL2 may have a pronounced effect. Therefore, it may be possible to genotype for a suite of genes and use them as markers of either HIV susceptibility or neuro-developmental patterns.

Non-coding small RNAs (sRNAs) regulate various cellular processes in bacteria. They bind to a chaperone protein Hfq for stability and regulate gene expression by base-pairing with target mRNAs. Although the importance of sRNAs in bacteria has been well established, the mode of origination of novel sRNA genes is still elusive, mainly because the rapid rate of evolution of sRNAs obscures their original sources. To overcome this impediment, we identified a recently formed sRNA (EcsR2) in E. coli, and show that it evolved from a degraded bacteriophage gene. Our analyses also revealed that young sRNAs such as EcsR2 are expressed at low levels and evolve at a rapid rate in comparison to older sRNAs, thereby uncovering a novel process that potentially facilitates newly emerging (and probably mildly deleterious) sRNAs to persist in bacterial genomes. We also show that even though EcsR2 is slightly deleterious to E. coli, it could bind to Hfq and mRNAs to regulate the expression of several genes. Interestingly, while EcsR2 expression is induced by glucose, the expression of its putative targets are regulated by the transcription factor CRP in response to glucose, indicating that EcsR2 has been incorporated into the carbon regulatory network in E. coli. Collectively, this work provides evidence for the emergence, evolution and functions of a novel "young" sRNA in bacteria.

Includes abstract.
Includes bibliographical references (p. 197-215).
The primary aim of this thesis was to identify candidate genes that may be associated with ACL ruptures, and then use a genetic association approach following a case-control study design to identify specific sequence variants (single nucleotide polymorphisms, SNPs) within these candidate genes which may predispose individuals to ACL ruptures. Candidate genes (COL1A1, COL5A1 and COL12A1) were selected based on the biological function of their encoded proteins (type I, type V and type XII collagen respectively) within the basic structural and functional unit of ligaments, namely the collagen microfibril.

Includes bibliographical references (leaves 94-103).
The aims of the present study were to determine the level of genetic knowledge of parents with a child with cystic fibrosis; to determine the impact of the birth of a child with cystic fibrosis upon subsequent reproductive choices and to investigate family communication about genetic risk. A qualitative approach was selected as it aims to understand, attempts to make sense of and provides descriptions that portray the richness and complexity of ordinary events from the perspective of the participants.

The helix-loop-helix (HLH) family of transcription regulatory proteins are fundamental regulators in the processes of cell proliferation and differentiation, cell lineage determination, myogenesis, neurogenesis, and sex determination in a wide range of multicellular organisms. A gene encoding a novel class II HLH protein has recently been identified from a human B-cell eDNA library using a yeast two-hybrid screen. The predicted human ABF -1 polypeptide sequence was used to search the Caenorhabditis elegans genome database for a C. elegans ABF-1 homolog. This bHLH protein, called C. elegans ABF -1 (CeABF -1 ), has a bHLH domain that shares 72% amino acid similarity with its human ABF-1 relative. The expression of the CeABF-1 mRNA has been detected in larval stages L2, L3, L4, and adult, however the mRNA is most highly expressed at the L3 and L4 stages. CeABF -1 protein is capable of heterodimerizing with the human E2A gene product, E4 7. Like human ABF -1, CeABF -1 expression in the presence of the E4 7 protein results in a reduction in E2A mediated gene activation. It has therefore been concluded that CeABF -1 , like human ABF -1 , also acts as a transcriptional repressor. Because C. elegans shares many conserved genes with higher eukaryotic organisms it has become a model organism for in depth genetic studies. It has therefore become increasingly desirable to investigate the possibility of alternative protein-protein interactions that can potentially occur within C. elegans, so it was necessary to construct a C. elegans eDNA library along with the appropriate bait vector expressing the CeABF- 1 protein. The titer ofthe primary library was calculated to be 9.7 x I06 clones, 10-fold greater than minimum titer requirement of I x I 06 clones for a good representational library. Sequencing of the CeABF -I insert confirmed successful construction of a mutation-free bait construct suitable for use in yeast two-hybrid screening. Yeast-two hybrid analysis revealed two new interactors, one of which was identified as an aldose reductase homolog, while the other remains uncharacterized.

The aim was to develop new methods for measuring texture of Atlantic salmon (Salmo salar L.) fillets and investigate the genetic basis of flesh quality traits. Firstly, a new tensile strength method was developed to quantify the force required to tear a standardized block of salmon muscle with the aim of identifying those samples more prone to factory downgrading as a result of gaping. The repeatability, sensitivity and predictability of the new technique was evaluated against other common instrumental texture measurement methods. Data from the new method were shown to have the strongest correlations with gaping severity r=-0.514, P<0.001) and the highest level of repeatability of data when analysing cold-smoked samples. The Warner Bratzler shear method gave the most repeatable data from fresh samples and had the highest correlations between fresh and smoked product from the same fish (r=0.811, P<0.001). It is therefore recommended that the new method be adopted for measuring gaping potential and the Warner Bratzler method become the standard for firmness assessment. Genes associated with post mortem softening in mammals were characterised in Atlantic salmon. A previously unknown ancient paralogue of calpastatin (here named CAST2) was identified. Evidence was provided for the existence of highly homologous recent paralogues of CAST2 and CTSD1. Evidence for the ancestral history of these paralogues was provided by phylogenetic analysis. Recent gene duplicates of 6 further genes were identified. In all cases, homology between recent paralogues was greater than 94%. Analysis of synonymous vs non-synonymous nucleotide substitution between the observed paralogue pairs shows a significant purifying selection in most cases. The CTSD1 gene shows significant purifying selection in a pairwise analysis between 12 teleost species (all cases P<0.0001) but a similar analysis of CTSD2 revealed no significant occurrence of purifying selection. The present study provides further support for the idea of asymmetrical selective pressure on paralogues. Genetic markers were developed that can distinguish individuals with above average fillet yield and texture. A database of firmness, tensile strength and fillet yield was made from 254 individuals from 5 batches of farmed salmon and these fish were genotyped at 7 novel SNP loci. Individuals with the combined favourable genotype at CAPN1a and MYOD1b were associated with an average increase in fillet yield of 2.7% above batch average. A combined genotype of CAPN1a, MYOD1b and MYF5 was significantly associated with an average increase in tensile strength of 9.8% above batch average (P=0.015). In both cases individuals with the combined favourable genotype occurred with a frequency of c. 6% across all batches. The favourable genotypes had no unfavourable effects on other traits. Highly polymorphic microsatellite loci were used to perform tests of assignment, which revealed an overall correct assignment rate of 92.7% to batch of origin and a minimum reference sample number of 25 was empirically determined. A phylogenetic analysis supported the results of the assignment tests. Given that 7 microsatellites is a relatively small number for a study of this nature, these results suggest that reliable assignment of unknown fish to the true batch of origin is potentially rapid and cost effective. Overall, the thesis presents molecular markers for broodstock selection, new genes of relevance to flesh quality, a new method of texture analysis and a proposal for an escapee traceability project.

Escherichia coli O157:H7 is an enteric pathogen that can cause severe gastrointestinal disease, sometimes leading to hospitalization and death. These bacteria have a variety of virulence factors that can be encoded for on pathogenicity islands (PAIs). The goal of this study was to characterize specific E. coli O157:H7 PAI deletion mutants using three methods: Phentotype Microarrays (PM), growth curves and survival curves were used to elucidate possible roles for the PAIs. Results from the PM study suggest that PAIs have a role in carbon substrate utilization; i.e., four of the O-island (OI) deletion mutants (OI-87, 98, 102 and 172) and an S-Loop (SL-72) deletion mutant exhibited differences in substrate utilization (gains and losses in utilization) compared to parental O157:H7 strains EDL933 (OI) and Sakai (SL), respectively. All of the mutants with the exception of the OI-135 mutant exhibited differences in level of substrate utilization for substrates shown to have important roles in the bacterium. Cell growth results showed that three OI deletion mutants (OI-55, 87 and 102) and the SL (SL-72) mutant exhibited a difference in rate of growth compared to the parental strains. Cell viability results showed that seven of the OI deletion mutants (OI-51, 55, 98, 108, 135, 172 and 176) exhibited different rates of decline in cell number when transferred to sterile water compared to the parental strain. The results show that removal of PAIs from E. coli O157:H7 can affect carbon utilization, growth and survival demonstrating the importance of PAIs in the ecology of these bacteria.
xx, 208 leaves : ill. (some col.) ; 29 cm

During protein synthesis, elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to the A-site of mRNA-programmed ribosomes in a GTP-dependent manner. To enable future studies on the functional and structural requirement of EF-Tu’s function, a Cysteine-free variant of EF-Tu was constructed suitable for subsequent labelling of the protein and use in kinetic studies. Here, the kinetic properties of three Cysteine-less EF-Tu variants are reported, demonstrating that only the variant with the Alanine substitution in position 81 retains wild-type activity with respect to the interaction with guanine nucleotides, aa-tRNA and the ribosome. To explore a possible tRNA independent pathway for the GTPase activation signal, three residues in domain II of EF-Tu (Arginine 279, Glycine 280, Arginine 283) were mutated; the activity of EF-Tu variants were analyzed. Results suggest that these residues are indeed required for efficient ribosome-dependent stimulation of the GTPase activity of EF-Tu.
x, 85 leaves : ill. (some col.) ; 29 cm

Mannheimia haemolytica is the principal bacterial agent associated with bovine respiratory disease (BRD). It has a significant economic impact on the beef feedlot industry. The current methods for BRD prevention and treatment have various problems and limitations, especially with reports of increased antimicrobial resistance in M. haemolytica. Bacteriophage therapy presents a novel method to mitigate M. haemolytica. This study aimed to isolate strictly lytic M. haemolytica-specific bacteriophages from bovine nasopharyngeal swabs and feedlot trough water. This was accompanied by an extensive characterization of temperate bacteriophages induced from representative strains of a M. haemolytica collection. Phage morphology, host specificity, genomic diversity, and comparative genomics were determined. Even though temperate bacteriophages are not ideal candidates for phage therapy, they can be engineered or modified to serve this function. Genome sequences of selected temperate bacteriophages also provide a foundation for future studies on the biology of these microorganisms.
viii, 107 leaves : ill. ; 29 cm

Estimation of Distribution Algorithm (EDA) is a branch of evolutionary computation that learn a probabilistic model of good solutions. Probabilistic models are used to represent relationships between solution variables which may give useful, human-understandable insights into real-world problems. Also, developing an effective PM has been shown to significantly reduce function evaluations needed to reach good solutions. This is also useful for real-world problems because their representations are often complex needing more computation to arrive at good solutions. In particular, many real-world problems are naturally represented as permutations and have expensive evaluation functions. EDAs can, however, be computationally expensive when models are too complex. There has therefore been much recent work on developing suitable EDAs for permutation representation. EDAs can now produce state-of-the-art performance on some permutation benchmark problems. However, models are still complex and computationally expensive making them hard to apply to real-world problems. This study investigates some limitations of EDAs in solving permutation and scheduling problems. The focus of this thesis is on addressing redundancies in the Random Key representation, preserving diversity in EDA, simplifying the complexity attributed to the use of multiple local improvement procedures and transferring knowledge from solving a benchmark project scheduling problem to a similar real-world problem. In this thesis, we achieve state-of-the-art performance on the Permutation Flowshop Scheduling Problem benchmarks as well as significantly reducing both the computational effort required to build the probabilistic model and the number of function evaluations. We also achieve competitive results on project scheduling benchmarks. Methods adapted for solving a real-world project scheduling problem presents significant improvements.

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This thesis deals with the issues of genetic heritage and traditional knowledge associated: potential for transformation and creation of new products and technologies in the Amazon. With advances in biotechnology, traditional knowledge associated with genetic resources have become important inputs for bioinformational innovation. Provisional Measure No. 2,186-16 of August 23, 2001 regulates the procedures for access to the components of the genetic heritage with scientific research, technological development and bioprospecting. It remains unquestionable the importance of traditional knowledge associated with genetic resources conferred on the biotech industry, particularly pharmaceuticals, and agricultural chemicals. This research aims to analyze the utilization of traditional knowledge associated with genetic possibilities for transformation and the creation of new products and technologies in the Amazon. We discuss the legal protection of traditional knowledge associated with genetic resources analyzing guarantee sovereignty and ownership of the states and their peoples over natural resources as the common heritage of humanity, asking about the subjectivity of people and traditional knowledge related to the consent and authorization. In the methodological approach adopted , we defend the access to genetic resources and traditional knowledge associated with the creation of products and processes with the objective of regional development on a sustainable and equitable sharing of the results obtained with its use. The present investigation was characterized from the point of view of its nature as literature and empirical , developed primarily from a qualitative approach. In this sense , critical reason was adopted as a broader methodological approach , not limited to dogmatisms and pure and simple analysis of positive laws , however , we sought to climb, in critical relational subsidies , a new perspective of overcoming legal treatment in relation to traditional knowledge associated with genetic resources as a support in the sovereignty and security of the property of the State and its peoples over natural resources and their genetic heritage . It analyzes access to traditional knowledge and genetic resources as a new mode of appropriation of nature and natural resources and the equitable sharing of benefits. In its final part , the research seeks to demonstrate the need to seek a balance between economic use of components of biological diversity in the form and pace that does not cause genetic decreased while maintaining the potential to meet the aspirations of the present and future generations . The compatibility of conservation of the immense potential of the natural resources of the Amazon with the consolidation of a sustainable development policy is urgent. The benefits produced by research provide directions for finding alternatives and strategies to democratize access to genetic resources and traditional knowledge and facilitate construction of guiding principles for the construction of consistent and relevant public policies for the development and sustainability of Amazon. The study also concludes that the wealth of genetic resources in Brazil, especially in the Amazon region, can be used in a sustainable manner, however, is essential scientific and technological infrastructure able to harness its potential benefits for people and the populations of the Amazon to the promotion of regional development.
A presente tese analisa o Patrimônio Genético e Conhecimentos Tradicionais Associados: possibilidades de transformação e criação de novos produtos e tecnologias na Amazônia. Com os avanços nos domínios da biotecnologia os conhecimentos tradicionais associados ao patrimônio genético se tornaram importantes inputs bioinformacionais para a inovação. A Medida Provisória nº 2.186-162001 regula as formas de acesso a componentes do patrimônio genético para fins de pesquisa científica, desenvolvimento tecnológico e bioprospecção. Resta incontroverso a importância que os conhecimentos tradicionais associados ao patrimônio genético conferem para a indústria da biotecnologia, principalmente de produtos farmacêuticos, químicos e agrícolas. O escopo da pesquisa é análise do uso dos conhecimentos tradicionais associados ao patrimônio genético em possibilidades de transformação e criação de novos produtos e tecnologias na Amazônia. Discute-se a proteção jurídica dos conhecimentos tradicionais associados ao patrimônio genético analisando a soberania e garantia da titularidade dos Estados e seus povos sobre recursos naturais, inquirindo sobre a subjetividade dos povos e conhecimentos tradicionais relacionados com o consentimento e autorização. Na linha metodológica adotada, defende-se o acesso ao patrimônio genético e aos conhecimentos tradicionais a ele associados para a criação de produtos e processos com o objetivo do desenvolvimento regional de forma sustentável e a justa partilha dos resultados obtidos com o seu uso. A presente pesquisa foi caracterizada quanto ao ponto de vista da sua natureza, como bibliográfica e empírica, desenvolvida predominantemente, a partir de uma abordagem qualitativa. Nesse sentido, adotou-se a razão crítica como linha metodológica mais ampla não limitada aos confins dos dogmatismos e das análises puras e simples das legislações positivadas, no entanto, buscou-se, na análise crítica relacional subsídios para dimensionar uma nova perspectiva de superação do tratamento jurídico em relação aos conhecimentos tradicionais associados ao patrimônio genético, com fulcro na soberania e garantia da titularidade dos Estados e seus povos sobre recursos naturais e patrimônio genético. Desse modo, analisou-se o acesso aos conhecimentos tradicionais e ao patrimônio genético como novo modo de apropriação da natureza e dos recursos naturais e a justa repartição de benefícios. Na sua parte final, a pesquisa procurou demonstrar a necessidade de se buscar o equilíbrio entre a utilização econômica de componentes da diversidade biológica de modo e ritmo tais que não levem à diminuição do patrimônio genético, mantendo potencial para atender as aspirações das gerações presentes e futuras. A conciliação entre a conservação do imenso potencial de recursos naturais da Amazônia com a consolidação de uma política de desenvolvimento sustentável se faz urgente. Os subsídios produzidos pela pesquisa fornecem indicativos para a busca de alternativas e estratégias que democratizam o acesso ao patrimônio genético e aos conhecimentos tradicionais e proporcionaram a construção de princípios norteadores para a construção de políticas públicas coerentes e competentes para o desenvolvimento com sustentabilidade na Amazônia. A Investigação também conclui que a grande riqueza dos recursos genéticos do Brasil, e especialmente da região Amazônica, poderá ser utilizada de forma sustentável, para tanto é imprescindível infraestrutura científico-tecnológica capaz de aproveitar seus potenciais benefícios em favor dos povos e populações da Amazônia com a promoção do desenvolvimento regional.

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In recent years, the evolution of health expenditures and specifically drugs, has worried governments. Among the various specialties, oncology is among those dealing with the greatest difficulties in the management of drug therapy. It is known that patients treated with various drugs have variability of response and susceptibility to drug toxicity. In present work, we study the role of Multiple Drug Resistance gene (MDR1) polymorphisms C1236T and C3435T frequencies and response to treatment with imatinib mesylate in 96 patients with chronic myeloid leukemia (CML). A total of 96 patients with CML were treated according to the Brazilian National Cancer Institute (INCA) guidelines and the blood samples were collected for genotyping. Genomic DNA was extracted and C1236T and C3435T polymorphisms genotyping was performed by the polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP), which detects a variation in length of a DNA fragment generated (370pb and 340pb) by a specific endonuclease in a specific site of the genome (HaeIII and MboI). Of the 96 CML samples, 31 samples were homozygous (CC), 13 homozygous (TT) and 52 heterozygous (CT) for exon 12 (1236). For the exon 26 (3435), 35 were homozygous (CC), 12 homozygous (TT) and 49 heterozygotes (CT). All frequencies for both polymorphisms were in Hardy-Weinberg equilibrium (p = 0.229 and q = 0.414). We found percentage association between polymorphisms and their distribution in different populations, and the response to treatment both cytogenetic and molecular difference was not statistically significant (p <0.05) when compared to age and sex presented response by patients and also no statistical difference (p <0,050). We conclude that the observed allele frequency for exons 1236 were 59.4% for C and 40.6% for T and the frequencies for the exon 3435 were 62.0% for C and 38.0% for T. That the relationship between the frequencies of polymorphisms of MDR1 in populations of different geographic locations, can provide tools that help in choosing a more appropriate and effective treatment of CML.
Neste estudo, o papel dos polimorfismos C1236T e C3435T do gene de Resistência a Múltiplas Drogas (MDR1) foram investigados em relação à frequência e a resposta ao tratamento com imatinibe em pacientes com leucemia mielóide crônica (LMC). Um total de 96 pacientes com LMC foram tratados de acordo com as diretrizes do Instituto Nacional do Câncer (INCA) e amostras de sangue foram coletadas para genotipagem do gene MDR (Resistência à Multiplas Drogas). O DNA genômico foi extraído e a genotipagem dos polimorfismos C1236T e C3435T foi realizada por meio da reação em cadeia da polimerase com fragmentos de restrição (PCR-RFLP), que detectou uma variação no comprimento de um fragmento de DNA gerado (370pb e 340pb) por uma endonuclease específica em um sítio específico do genoma (HaeIII e Mbol). Analisando as 96 amostras de pacientes para o polimorfismo no éxon 12 (1236) com LMC, 31 amostras apresentaram homozigose (CC), 13 homozigose (TT) e 52 heterozigose (CT). Para o estudo do polimorfismo no éxon 26 (3435), 35 foram homozigotas (CC), 12 homozigotas (TT) e 49 heterozigotas (CT). Todas as frequências para ambos os polimorfismos apresentaram-se em equilíbrio de Hardy-Weinberg (p = 0,229 e q = 0,414). Foi encontrada associação do percentual dos polimorfismos estudados em relação à distribuição dos mesmos em grupos de diferentes localizações geográficas, e sobre a resposta ao tratamento tanto citogenética e molecular, não houve diferença estatísticamente significante (p<0,05), quando foi comparado à idade e ao gênero apresentados pelos pacientes e a resposta também não houve diferença estatística (p<0,05). Conclui-se que as frequências alélicas observadas para o éxon 1236 foram de 59,4% para C e 40,6% para T e as frequências para o éxon 3435 foram de 62,0% para C e 38,0% para T e que a relação entre as frequências de polimorfismos de MDR1 nas populações de diferentes localizações geográficas, pode fornecer ferramentas que auxiliem na escolha de um tratamento mais adequado e eficaz da LMC.

Conhecer a relação entre a comunidade de pequenos mamíferos e os agroecossistemas associados aos olivais é fundamental para a conservação. Este estudo aborda esta temática relativamente aos olivais do NE de Portugal, avaliando os atributos da paisagem que determinam a ocorrência das espécies, e focando-se numa espécie protegida (Microtus cabrerae) e noutra considerada potencial praga agrícola (M. lusitanicus). Recorrendo a amostragem genética não-invasiva, estimou-se a probabilidade de ocupação das espécies relativamente às variáveis da paisagem. M.cabrerae ocorre sobretudo em mosaicos de usos do solo incluindo zonas agrícolas com elevada densidade de orlas, enquanto M.lusitanicus tem maior probabilidade de ocorrência em mosaicos com elevada densidade de pastagens. Globalmente, os resultados sugerem que a heterogeneidade dos agroecossistemas de olival do NE de Portugal estão associados a uma comunidade rica de pequenos mamíferos, com probabilidades de ocupação relativamente altas para espécies com problemas de conservação e relativamente baixas para espécies consideradas potenciais pragas; ABSTRACT: Factors driving the small mammal occupancy of olive groves in NE Portugal How small mammals associate to environmental characteristics in olive groves is an important conservation question. Here are provided first insights on this topic applied to NE Portugal olive groves, by assessing the landscape attributes that determine the occurrence of small mammals, focusing on one protected species (Microtus cabrerae) and one potential pest (M. lusitanicus). Species occupancy probabilities relative to landscape variables were estimated based on genetic non-invasive sampling. M. cabrerae was more likely to occur in land mosaics including high edge density of agricultural fields, while M. lusitanicus was more likely to occur in land mosaics with high density of pasture lands. Overall, the results suggest that the heterogeneous olive grove agroecosystems from NE Portugal allow for the occurrence of a species-rich small mammal community, including species of conservation concern at relatively high occupancy rates and potential pests at relatively low occupancy rates.

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Increasingly, learning in groups has become present in school environments. This fact is also part of the organizations, when considers learning in the workplace. Conscious of the importance of group learning at the workplace (CSCL@Work) emerges as an application area. In Computer Supported Collaborative Learning(CSCL), researchers have been struggling to maximize the performance of groups by techniques for forming groups. Is that why this study developed three (3) algorithmic approaches to formation of intraheterogeneous and inter-homogeneous groups, as well as a model proposed in this work in which integrates dichotomous functional characteristics and preferred roles. We made an algorithm that generates random groups, a Canonical Genetic Algorithm and Hybrid Genetic Algorithm. We obtained the input data of the algorithm by a survey conducted at the Court of the State of Goiás to identify dichotomous functional characteristics, and after we categorize these characteristics, based on the data found and the model proposed group formation. Starting at real data provided of employees whom participated in a course by Distance Education (EaD), we apply the model and we obtained the input data related to functional features. As regards the favorite roles, we assigned randomly values to the employees aforementioned, from a statistical statement made by Belbin into companies in the United Kingdom. Then, we executed the algorithms in three test cases, one considering the preferred papers and functional characteristics, while the other two separately considering each of these perspectives. Based on the results obtained, we found that the hybrid genetic algorithm outperforms the canonical genetic algorithm and random generator.
A aprendizagem em grupos tem se tornado realidade cada vez mais presente nos ambientes de ensino. Esta realidade também faz parte das organizações quando considera-se a aprendizagem no contexto do trabalho. Cientes da importância da aprendizagem em grupo no ambiente de trabalho, uma nova abordagem, denominada CSCL@Work, surge como uma aplicação da área Aprendizagem Colaborativa Apoiada pelo Computador, no inglês, Computer Supported Collaborative Learning (CSCL), no ambiente de trabalho. Em CSCL, pesquisadores tem se esforçado cada vez mais para maximizar o desempenho dos grupos através de técnicas para formação de grupos. Por isso neste trabalho desenvolvemos 3 (três) abordagens algorítmicas para formação de grupos intra-heterogêneos e inter-homogêneos, a partir de um modelo proposto nesta pesquisa, que integra características funcionais dicotômicas e papéis preferidos. Confeccionamos um algoritmo que gera grupos aleatoriamente, um algoritmo genético canônico e um algoritmo genético híbrido. Para obter os dados de entrada do algoritmo, realizamos uma pesquisa no Tribunal de Justiça do Estado de Goiás para identificar características funcionais dicotômicas, categorizamos estas características, com base nos dados encontrados e no modelo de formação de grupos proposto. A partir de dados reais fornecidos de funcionários que participaram de um curso por Educação a Distância (EaD), aplicamos o modelo e obtivemos os dados de entrada relativos às características funcionais. Quanto aos papéis preferidos, atribuímos os valores aleatoriamente aos funcionários mencionados, partindo de um levantamento estatístico feito por Belbin em empresas no Reino Unido. Em seguida, executamos os algoritmos em três casos de testes, um considerando as características funcionais e papéis preferidos, e os outros dois considerando separadamente cada uma destas perspectivas. A partir dos resultados obtidos, constatamos que o algoritmo genético híbrido obtém resultados superiores ao algoritmo genético canônico e método aleatório.

Este trabalho apresenta um processo racional para a seleção das dimensões e coeficientes de forma ótimos para um navio petroleiro usando a técnica dos algoritmos genéticos. É proposto um procedimento para balanceamento em função do peso e espaço disponível de carga, determinando sua viabilidade e permitindo balancear navios de peso ou de volume. A elaboração de um procedimento e sua implementação em um programa eficiente é muito importante no dimensionamento preliminar de um navio, assim, esta pesquisa é uma divulgação da técnica dos algoritmos genéticos como uma técnica robusta para o projeto preliminar do navio. Duas funções de mérito são usadas para avaliar cada projeto: custo e vazamento médio de óleo. Estes atributos são conflitantes entre si, isto é, um baixo custo corresponde a um alto vazamento e vice-versa. O vazamento médio de óleo é avaliado com a metodologia probabilística proposta pela INTERTANKO (INTERTANKO, 2002). A avaliação do vazamento médio, através de um adimensional, considera a possibilidade de ocorrência de eventos de encalhes e/ou colisão resultando, respectivamente, em dano ao fundo e ao costado. Para a estimativa do custo são utilizados dois modelos, apresentando-se uma comparação dos seus efeitos nos valores finais das dimensões principais. Além disso, para o procedimento de balanceamento, cinco modelos de peso do casco são testados e analisados os impactos na forma e distribuição da fronteira de Pareto. Um algoritmo genético é implementado para buscar os parâmetros de projeto ótimos e identificar a fronteira não-dominada de Pareto. O algoritmo é testado com quatro funções encontradas na literatura técnica. As funções de teste são convexas, não-convexa, descontínua e uma com quatro restrições funcionais. A implementação mostra resultados similares com os apresentados na literatura. Um navio Suezmax, um Aframax e um Panamax são usados como estudo de casos para comparar os resultados obtidos com o programa implementado. Um objetivo adicional deste trabalho é expor à comunidade naval a utilidade e efetividade dos algoritmos genéticos nos problemas de projeto multiobjetivo. O enfoque desta pesquisa está na metodologia implementada e na sua recomendação para o projeto preliminar de navios.
This paper shows the rational process of selecting the optimal dimensions and forms coefficients of tanker ships using the technique of genetic algorithm. It is proposed a procedure to balance designs in weight and useful space and assesses their feasibility so that weight and volume limited tankers can be balanced. The elaboration of a procedure and its implementation in an efficient program is so important in the preliminary dimension of a ship, so this paper is a divulgation of the genetic algorithm as robust technique for the preliminary ship design. Two objective attributes are used to evaluate each design: Total Cost and Mean Oil Outflow. This attributes are conflicting between them, that is, a low cost correspond a high outflow and vice versa. The Mean Oil Outflow is evaluated with the probabilistic methodology proposed by the INTERTANKO to IMO. The assessment of mean oil outflow, by a non dimensional parameter, supposes the event of grounding and/or collision resulting in bottom and side damage respectively. In estimating the cost two models are used performing a comparison of their effects on the final values of principal dimension. In addition, for the balance procedure, five hull weight models are tested and analyzed the impact on the form and distribution of Pareto frontier. A genetic algorithm is implemented to search the optimal design parameters and identify non-dominated frontier of Pareto. The algorithm is tested with four test functions found in the technical literature. The test functions selected are convex, non convex, discontinuing and one with four restrictions. The implementation shows similar results with those showed in others papers. A Suezmax, an Aframax, and a Panamax ships are used as case study in order to compare the gotten results by the implemented program. One additional goal of this work is to expose to naval community the usefulness and effectiveness of the genetic algorithm in the Multi-Objective design. The emphasis of this paper is on methodology of design implemented and is suggested for preliminary ship design.

A energia é o maior contribuinte para os custos de operação de uma indústria, portanto, estudos para melhoria da eficiência dos sistemas que utilizam alguma fonte de energia são indispensáveis. O presente trabalho tem por objetivo a obtenção de configurações ótimas para satisfazer demandas de eletricidade e cargas térmicas de aquecimento e refrigeração a partir de uma fonte primaria de energia, avaliando o impacto dessas nos custos de produção de eletricidade, vapor e água gelada. Estes tipos de sistemas são conhecidos como sistemas de trigeração. A avaliação de desempenho dos sistemas de trigeração é conduzida através da aplicação da análise exergética e exergoeconômica das alternativas propostas para a determinação do rendimento exergético e custos em base exergética de produção de utilidades desse tipo de sistema. Após apresentar uma breve discussão sobre o uso eficiente e racional de energias primárias e mostrar um panorama da situação para a aplicação de sistemas de trigeração para satisfazer demandas energéticas na indústria e o setor terciário, são descritas diferentes tecnologias envolvidas neste tipo de sistemas e algumas configurações propostas por vários pesquisadores nos anos recentes. O trabalho mostra o impacto das tecnologias de trigeração nos custos em base exergética dos produtos: eletricidade, vapor para processo e água gelada. Sistemas de refrigeração por absorção de efeito simples, duplo efeito e o sistema híbrido de absorção/ejeto compressão são analisados, como parte do estudo dos sistemas de trigeração. Diversos sistemas de trigeração, incluindo o sistema tetra-combinado, são comparados satisfazendo demandas energéticas para três aplicações diferentes: indústria de laticínios, hospital e indústria de bebidas. As configurações em estudo são otimizadas usando o método de algoritmo genético. Os resultados mostram que o sistema de refrigeração híbrido de absorção/ejeto compressão é uma boa alternativa para a produção da água gelada porque o coeficiente de desempenho (COP) e a eficiência exergética são maiores do que no sistema de refrigeração por absorção de efeito simples. Observando o impacto na formação dos custos de conversão de energia para os sistemas de trigeração propostos, os sistemas que utilizam unidade de refrigeração por absorção de duplo efeito são os que apresentam menor impacto. O sistema tetra-combinado apresenta um menor impacto quanto comparado com o ciclo combinado com unidade de refrigeração por absorção de simples efeito. O consumo de combustível e a destruição de exergia dos diferentes sistemas são refletidos nos custos em base exergética dos diferentes produtos. A otimização com algoritmos genéticos mostrou ganhos importantes nos custos em base exergética dos produtos, mediante a maximização da eficiência exergética dos diferentes sistemas de trigeração. O método dos algoritmos genéticos mostra-se como um método robusto para a otimização de sistemas de conversão de energia, mesmo que exija um grande esforço computacional.
Energy is the largest contributor to operating costs of any industry; therefore, studies for improving systems efficiency that use some energy source are essential. This work aims to obtain optimal configurations in order to satisfy required demands for electricity and thermal loads for heating and cooling from a primary source of energy, evaluating the impact of the electricity, steam and chilled water production costs. These types of systems are known as trigeneration systems. The performance evaluation of trigeneration systems is carried out by the application of exergy and exergoeconomic analysis of the proposed alternatives in order to determine exergy efficiency and exergy based costs on production of this type of system utilities. After presenting a brief discussion about efficient and rational use of primary energies and an overview of situation for trigeneration systems application, various technologies involved in this type of systems and some configurations proposed by several authors are described. This research shows the impact of trigeneration technologies in exergy-based costs of products: electricity, steam process and chilled water. Absorption refrigeration systems of simple effect, double effect and the hybrid absorption/ejecto compression are analyzed, as part of the trigeneration systems study. Several trigeneration systems, including the tetra-combined system, are compared with each other, satisfying energetic demands for three different applications: a dairy industry, a hospital and a drinks industry. The configurations in study are optimized using the Genetic Algorithm method. The results show that the hybrid absorption/ejecto compression refrigeration system is a good alternative for chilled water production due to that the coefficient of performance (COP) and the exergetic efficiency are higher than simple effect absorption refrigeration system. Observing the impact in the formation of the energy conversion costs for trigeneration systems proposed, the systems that use a double effect absorption refrigeration system presents the less impact. When tetra-combined system is compared with the system using a simple effect absorption refrigeration system, the results show a reduction in the impact of costs formation. The fuel consumption and exergy destruction of the different systems is reflected in the exergy based costs of the different products. The optimization with genetic algorithms shown important profits in the exergy based costs of products, by means of the exergetic efficiency maximization of the different trigeneration systems. The genetic algorithm method is a robust method for energy conversion systems optimization, even that it demands a great computational effort.

O presente trabalho aborda o desenvolvimento de um modelo de síntese para o projeto conceitual de uma embarcação rápida do tipo trimarã, destinada ao transporte de passageiros. Tal modelo visa possibilitar o entendimento dos mecanismos que governam o projeto deste tipo de navio, através de analises comparativas (atributos de desempenho) entre diferentes soluções de projeto, em função dos parâmetros escolhidos para sua representação (variáveis de projeto). Foram desenvolvidos dois modelos de síntese, em programas comerciais distintos. Cada modelo gera a superfície do casco, a partir de series sistemáticas, e calcula a resistência ao avanço dividindo-a nas parcelas viscosa e de ondas. A parcela viscosa e calculada pela aproximação de placa plana e a parcela de ondas calculada pela teoria de navio no. São feitas, ainda, estimativas preliminares do fator de forma e da resistência adicional em ondas. O arranjo geral dos principais espaços e subsistemas foi parametrizado com base no arranjo de embarcações semelhantes e o conforto dos passageiros a bordo e calculado segundo padrões estabelecidos por sociedades classificadoras internacionais. As variáveis de projeto escolhidas foram o comprimento do casco central e razões entre as demais dimensões, de modo a permitir o calculo das dimensões principais de cada casco e o posicionamento relativo entre eles. Com isso, tem-se que, ao mudar o valor do comprimento, escala-se o casco mantendo-se todas as proporções. A vantagem buscada ao se utilizar esta abordagem e a extinção das restrições geométricas implícitas, pois estarão embutidas diretamente nas restrições explícitas que definem os limites de exploração de cada variável de projeto. Estes modelos foram integrados a procedimentos de otimização mono e multiobjetivo, com base em diferentes versões do algoritmo genético, e aplicados a um problema de projeto exemplo. As funções de mérito, ou funções objetivo, escolhidas para este problema foram a potencia requerida pela embarcação para navegar na velocidade de projeto e a disponibilidade operacional da embarcação, calculada a partir dos índices de conforto dos passageiros. Com isso, descobriu-se que os parâmetros com maior influencia na resistência ao avanço e no conforto dos passageiros são o comprimento do casco central e sua razão de comprimento por boca. O posicionamento relativo entre os cascos e extremamente importante para a resistência de ondas geradas pela embarcação, mas não e possível observar nenhuma grande tendência em relação a posições que privilegiam seja a resistência seja o comportamento, pois o posicionamento ótimo para cada objetivo depende tanto do número de Froude quanto das demais dimensões da embarcação.
The present work studies the development of a synthesis model for the conceptual design of a fast trimaran passenger vessel, in order to understand the mechanisms that govern the design of such a vessel through a comparative analysis (performance parameters) between different design solutions, as a function of the variables chosen to uniquely represent them (design variables). Two separate models were developed, using different commercial softwares. Each model generates the hull surface based on systematic hull series and calculates the ship\'s forward resistance as the sum of the viscous and wave components. The viscous component is estimated by at plate approximation, corrected by a form factor, and the wave component is calculated according to thin ship theory. A preliminary estimate of the ship\'s added resistance in waves is also made. The general layout of the main volumes and systems was parametrized following design trends of similar ships and passenger comfort on board was calculated using international classification societies standards. The design variables chosen were the length of the center hull, the ratios between the main dimensions of each hull as to allow for their calculation and two coeficients regarding the relative positioning of the center and side hulls. The advantage sought by adopting this approach is the elimination of implicit geometrical constraints, once they will be automatically included in the explicit constraints defining the exploration range of each design variable. These models were then coupled to mono and multi objective optimization procedures, based on different versions of the genetic algorithm, and applied to a case study.The objective functions taken for this problem were the required power to achieve the design speed and the operational availability, measured from passengers comfort thresholds. It was found that the parameters with the most influence on the forward resistance, and thus on required power, and on passengers comfort level are the center hull length and its length to breadth ratio. The relative positioning of the side hulls play an important role on the total wave resistance of the ship, although it was not possible to observe any clear trend concerning positions that would favor nor the ship forward resistance neither its seakeeping performance. This is due the fact that the optimum positions of the side hulls are also a function of the Froude number and the remaining design variables.

In the last few decades, augmentation of heat transfer has emerged as an important research topic. Although many promising heat transfer enhancement techniques have been proposed, such as the use of longitudinal vortex generators, few researches deal with thermal optimization. In the present work, it was conducted an optimization of delta winglet vortex generators position and angles in a fin-tube compact heat exchanger with two rows of tubes in staggered tube arrangement. Two approaches were evaluated: Response Surface Methodology (Neural Networking) and Direct Optimization. Finite-Volume based commercial software (Fluent) was used to analyze heat transfer, flow structure and pressure loss in the presence of longitudinal vortex generators (LVG). The delta winglet aspect ratio was 2 and the Reynolds numbers, based on fin pitch, were 250 and 1400. Four vortex generator parameters which impact heat exchanger performance were analyzed: LVG position in direction x-y, attack angle (θ) and roll angle (ᵩ). The present work is the first to study the influence of LVG roll angle on heat transfer enhancement. In total, eight independent LVG parameters were considered: (x₁y₁θ₁ᵩ₁) for the first tube and (x₂y₂θ₂ᵩ₂) for the second tube. Factor Analysis method (software ModeFrontier) was used to study of the influence of these LVG parameters in heat exchanger performance. The effect of each LVG parameter on heat transfer and pressure loss, expressed in terms of Colburn factor (j) and Friction factor (f), respectively, were evaluated. The optimized LVG configurations led to heat transfer enhancement rates that are much higher than reported in the literature. Direct Optimization reported better results than Response Surface Methodology for all objective functions. Important interactions were found between VG1 and VG2, which influenced the results of Colburn (j) and Friction (f) factors for each Reynolds number. Particularly, it was found that the asymmetry of the LVG, in which the VG2 parameters strongly depend on the VG1 parameters, plays a key role to enhance heat transfer. Moreover, for each Reynolds number and each objective function, there is an optimal LVG arrangement. If the objective is to mitigate pressure drop, VG1 may be suppressed because its main goal is increasing the heat transfer downstream. On the other hand, VG2 was relevant for both increase the heat transfer and decrease the pressure drop. Roll angle had a strong influence on Friction factor (f), especially for VG1 and low Reynolds number.
Por muitos anos, a intensificação da transferência de calor tem despontado como um importante tópico de pesquisa. Embora existam muitas técnicas eficazes de intensificação da transferência de calor, como o uso de geradores de vórtices, poucos trabalhos de pesquisa lidam com a otimização. Neste trabalho, foi realizada a otimização das posições e ângulos dos geradores de vórtice longitudinal (LVG) tipo meia asa delta, considerando um trocador de calor tubo-aleta compacto com duas linhas de tubos desalinhados. Duas abordagens foram empregadas: Método da Superfície de Resposta (Neural Networking) e Otimização Direta. Um software comercial (Fluent), baseado na metodologia de volumes finitos, foi empregado na análise numérica da transferência de calor, estruturas vorticais e perda de pressão no escoamento, na presença de LVG. A razão de aspecto dos geradores de vórtice foi 2 e o número de Reynolds, baseado na distância entre as aletas, foram de 250 e 1400. Foram analisados quatro parâmetros dos LVG, os quais impactam na performance do trocador de calor: a posição do LVG na direção x-y, o ângulo de ataque (θ) e o ângulo de rolamento (ᵩ). O ângulo de rolamento foi primeiramente estudado neste trabalho. No total, oito parâmetros independentes do LVG foram considerados: (x₁y₁θ₁ᵩ₁) para o primeiro tubo e (x₂y₂θ₂ᵩ₂) para o segundo tubo. O método da Análise Fatorial (software ModeFrontier) foi aplicado no estudo da influência destes parâmetros dos LVG na performance do trocador de calor. Também foi avaliado o efeito de cada um destes parâmetros na transferência de calor e perda de pressão do escoamento, expressos em termos do fator de Colburn (j) e do fator de Atrito (f), respectivamente. As configurações otimizadas dos LVG, conduziram à taxas de transferência de calor maiores do que aquelas reportadas pela literatura. A Otimização Direta mostrou resultados melhores do que através da metodologia de Superfície de Resposta para todas as funções objetivas avaliadas neste trabalho. Importantes interações foram identificadas entre VG1 e VG2, os quais influenciaram nos resultados dos fatores de Colburn (j) e Atrito (f) para cada número de Reynolds. Particularmente, foi identificado que a assimetria dos LVG desempenha um papel fundamental na intensificação da transferência de calor, onde os parâmetros de VG2 dependem fortemente dos parâmetros de VG1. Além disso, para cada número de Reynolds e para cada função objetivo, existe uma configuração ótima dos parâmetros do LVG. Se o objetivo é a redução da perda de pressão global, VG1 poderia ser suprimido da modelagem, pois a sua principal função é aumentar a transferência de calor ao longo da aleta. Por outro lado, VG2 foi relevante tanto para aumentar a transferência de calor quanto para diminuir a perda de pressão. O ângulo de rolamento teve grande influência sobre o resultado do fator de Atrito (f), especialmente para VG1 e para baixo número de Reynolds.

El empleo de herramientas genómicas ayudará a superar dos de los retos que todavía subsisten en el campo de la mejora molecular (i.e., vía transformación): la identificación de los genes que realmente controlan los caracteres de interés agronómico y la detección de señales de regulación que permitan modular la expresión de los transgenes a nivel espacial y temporal. Entre las vías para lograr tales objetivos, destaca la mutagénesis insercional por T-DNA, que en los últimos años se ha convertido en una herramienta básica para la identificación y etiquetado de genes, así como para el análisis de su función. En efecto, la disrupción de un gen endógeno o la integración del T-DNA en la vecindad del mismo pueden ocasionar la anulación o alteración de función, dando una valiosa información sobre el papel de un cierto gen en un carácter dado. Otra aplicación de la mutagénesis insercional por T-DNA estriba en la detección de elementos de regulación mediante el empleo de los denominados "sistemas trampa" (trapping) que permiten detectar secuencias reguladoras y asignar una función a partir de datos de expresión del delator que mimetiza la expresión del gen endógeno. El aspecto más relevante de estas aproximaciones es que, tras la identificación de un cierto gen, éste queda etiquetado por el T-DNA, lo que facilita su clonación. El principal objetivo de esta Tesis Doctoral ha sido la generación una colección de líneas de inserción por T-DNA en tomate y la identificación de mutantes afectados en caracteres relacionados con el desarrollo. En concreto, se han generado más de 1200 líneas T-DNA y se han obtenido sus descendencias TG2. La caracterización de estas líneas en TG1 ha conducido a la detección de 255 mutantes (de tipo dominante, semidominante o aditivo) afectados en caracteres vegetativos y/o reproductivos. Asimismo, se ha caracterizado una pequeña muestra de progenies TG2 (en concreto 37) lo que ha permitido la identificación de 6 mutantes recesivos.
Angarita Díaz, MDP. (2009). Generación de líneas T-DNA de tomate (Solanum Lycopersicon cv.p73) e identificación de mutantes de inserción [Tesis doctoral]. Editorial Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/14718
Palancia

Social anxiety disorder, also known as social phobia, is one of the most prevalent anxiety disorders, affecting 7-13% of subjects in the community at some time in their lives. Despite being eminently treatable, it remains largely under-recognised and, therefore, undertreated. The disorder is characterized by a fear of scrutiny by others, with sufferers experiencing excessive anxiety in social and performance situations. This excessive anxiety usually leads to avoidance behaviour that can severely affect normal daily living. With onset commonly occurring during childhood or adolescence, social anxiety disorder may disrupt normal patterns of development of social and personal relationships, often having a long-term impact on emotional stability in social or working life. If left untreated, the course of social anxiety disorder is frequently complicated with comorbid conditions, particularly major depression or substance abuse. This review assesses the size of the clinical problem by evaluating current and lifetime prevalence estimates, age of onset, risk factors and evolution of the clinical course; thereby providing the rationale for early recognition and prompt treatment.

Esta pesquisa visa a análise da contribuição de cinco variáveis de entrada e a otimização do desempenho termo-hidráulico de trocadores de calor com venezianas combinados com geradores de vórtices delta-winglets. O desempenho termohidráulico de duas geometrias distintas, aqui nomeadas por GEO1 e GEO2, foram avaliadas. Smoothing Spline ANOVA foi usado para avaliar a contribuição dos parâmetros de entrada na transferência de calor e perda de carga. Considerando aplicação automotiva, foram investigados números de Reynolds iguais a 120 e 240, baseados no diâmetro hidráulico. Os resultados indicaram que o ângulo de venezianas é o maior contribuidor para o aumento do fator de atrito para GEO1 e GEO2, para ambos os números de Reynolds. Para o número de Reynolds menor, o parâmetro mais importante em termos de transferência de calor foi o ângulo das venezianas para ambas as geometrias. Para o número de Reynolds maior, o ângulo de ataque dos geradores de vórtices posicionados na primeira fileira é o maior contribuidor para a tranfesferência de calor, no caso da geometria GEO1, enquanto que o ângulo de ataque dos geradores de vórtices na primeira fileira foi tão importante quanto os ângulos das venezianas para a geometria GEO2. Embora as geometrias analisadas possam ser consideradas como técnicas compostas de intensificação da transferência de calor, não foram observadas interações relevantes entre ângulo de venezianas e parâmetros dos geradores de vórtices. O processo de otimização usa NSGA-II (Non-Dominated Sorting Genetic Algorithm) combinado com redes neurais artificiais. Os resultados mostraram que a adição dos geradores de vórtices em GEO1 aumentaram a transferência de calor em 21% e 23% com aumentos na perda de carga iguais a 24,66% e 36,67% para o menor e maior números de Reynolds, respectivamente. Para GEO2, a transferência de calor aumentou 13% e 15% com aumento na perda de carga de 20,33% e 23,70%, para o menor e maior número de Reynolds, respectivamente. As soluções otimizadas para o fator de Colburn mostraram que a transferência de calor atrás da primeira e da segunda fileiras de geradores de vórtices tem a mesma ordem de magnitude para ambos os números de Reynolds. Os padrões de escoamento e as características de transferência de calor das soluções otimizadas apresentaram comportamentos vi particulares, diferentemente daqueles encontrados quando as duas técnicas de intensificação de transferência de calor são aplicadas separadamente.
This doctoral thesis focuses on screening analysis of five input parameters and heat transfer and pressure drop optimization of flat-tube multi-louvered fin heat exchangers combined with delta-winglet vortex generators. The thermal-hydraulic performance of two distinct geometries, GEO1 and GEO2, were evaluated. Smoothing Spline ANOVA was used to evaluate the contribution of the input parameters such as louver angle, angle of attack of the delta-winglet and streamwise position of the delta-winglet on heat transfer and pressure drop. Taking the automotive application into account, Reynolds numbers of 120 and 240, based on hydraulic diameter, were investigated. The results indicated that the louver angle is the main contributor to increase the Friction factor for GEO1 and GEO2 for both Reynolds numbers. For the lower Reynolds number, the most important heat transfer parameter was the louver angle for both geometries, while at the higher Reynolds number, the angles of attack of the first row of delta-winglets mostly contributed to GEO1, and the angle of attack of the first row of delta-winglets was as important as the louver angle for GEO2. Although those specific geometries can be considered a kind of compound enhancement technique, relevant interactions were not verified between louvers and delta-winglet vortex generators parameters. The surrogatebased optimization procedure uses NSGA-II method (Non-Dominated Sorting Genetic Algorithm) combined with artificial neural networks. The results showed that the addition of DWLs on GEO1 increased the heat transfer of 21.27% and 23.52% with associated pressure loss increasing of 24.66% and 36.67% for the lower and the higher Reynolds numbers, respectively. For GEO2, the heat transfer was increased 13.48% and 15.67% with an increase of the pressure drop of 20.33% and 23.70%, for the lower and the higher Reynolds numbers, respectively. The optimized solutions for the Colburn factor showed that heat transfer behind the second row of deltawinglets has the same order of magnitude of that behind the first row, for both Reynolds numbers. The flow patterns and heat transfer characteristics from optimized solutions presented some particular behavior, differently from the findings when those two heat transfer enhancement techniques are applied separately.

Although much research has focused on cognitive ability and the genetic and environmental factors that might influence it, this aspect of human nature is still far from being well understood. It has been well-established that certain factors such as age and education have significant impacts on performance on most cognitive tests, but the effects of variables such as cognitive pastimes and strategies used during testing have generally not been assessed. Additionally, no genetic variant has yet been unequivocally shown to influence the normal variation in cognitive ability of healthy individuals. Candidate gene studies of cognition have produced conflicting results that have not been replicable, and genome-wide association studies have not found common variants with large influences on this trait.

Here, we have recruited a large cohort of healthy volunteers (n=1,887) and administered a brief cognitive battery utilizing diverse, common, and well-known tests. In addition to providing standard demographic information, the subjects also filled out a questionnaire that was designed to assess novel factors such as whether they had seen the test before, in what cognitive pastimes they participated, and what strategies they had used during testing. Linear regression models were built to assess the effects of these variables on the test scores. I found that the addition of novel covariates to standard ones increased the percent of the variation in test score that was explained for all tests; for some tests, the increase was as high as 70%.

Next, I examined the effects of genetic variants on test scores. I first performed a genome-wide association study using the Illumina HumanHap 550 and 610 chips. These chips are designed to directly genotype or tag the vast majority of the common variants in the genome. Despite having 80% power to detect a common variant explaining at least 3-6% (depending on the test) of the variation in the trait, I did not find any genetic variants that were significantly associated after correction for multiple testing. This is in line with the general findings from GWA studies that single common variants have a limited impact on complex traits.

Because of the recent technological advances in next-generation sequencing and the apparently limited role of very common variants, many human geneticists are making a transition from genome-wide association study to whole-genome and whole-exome sequencing, which allow for the identification of rarer variants. Because these methods are currently costly, it is important to utilize study designs that have the best chance of finding causal variants in a small sample size. One such method is the extreme-trait design, where individuals from one or both ends of a trait distribution are sequenced and variants that are enriched in the group(s) are identified. Here, I have sequenced the exomes of 20 young individuals of European ethnicity: 10 that performed at the top of the distribution for the cognitive battery and 10 that performed at the bottom. I identified rare genetic variants that were enriched in one extreme group as compared to the other and performed follow-up genotyping of the best candidate variant that emerged from this analysis. Unfortunately, this variant was not found to be associated in a larger sample of individuals. This pilot study indicates that a larger sample size will be needed to identify variants enriched in cognition extremes.

Finally, I assessed the effect of topiramate, an antiepileptic drug that causes marked side effects in certain cognitive areas in certain individuals, on some of the healthy volunteers (n=158) by giving them a 100 mg dose and then administering the cognitive test two hours later. I compared their scores at this testing session to those at the previous session and calculated the overall level to which they were affected by topiramate. I found that the topiramate blood levels, which were highly dependent on weight and the time from dosing to testing, varied widely between individuals after this acute dose, and that this variation explained 35% of the variability in topiramate response. A genome-wide association study of the remaining variability in topiramate response did not identify a genome-wide significant association.

In sum, I studied the contributions of both environmental and genetic variables to cognitive ability and cognitive response to topiramate. I found that I could identify environmental variables explaining large proportions of the variation in these traits, but that I could not identify genetic variants that influenced the traits. My analysis of genetic variants was for the most part restricted to the very common ones found on genotyping chips, and this and other studies have generally found that single common genetic variants do not have large affects on complex traits. As we move forward into studies that involve the sequencing of whole exomes and genomes, genetic variants with large effects on these complex traits may finally be found.

Dissertation

Cryptococcus gattii has been actively emerging and adapting to the climates and environment in western North America, bringing with it life-threatening disease to humans and animals. Through systematic investigations of the dynamics of this pathogen in the United States, by studying outbreaks and individual cases, our studies have aimed to increase the understanding of the expansion, emergence, pathogenicity, molecular epidemiology, population structure, and speciation dynamics of this organism that had previously been largely restricted to tropical and sub-tropical climates of the world.

Molecular sequence typing has revealed that there are four distinct C. gattii molecular types (VGI-VGIV). A major focus of our efforts to examine this pathogen in the United States surrounds the unprecedented C. gattii outbreak that emerged in British Columbia, Canada in 1999 and has since expanded throughout the Pacific Northwest region of the United States (Chapters 2, 3). This outbreak has resulted in a large number of infections in both humans and animals, including a high percentage of otherwise healthy individuals. The outbreak isolates are primarily molecular type VGIIa (the major genotype), VGIIb (the minor genotype), or VGIIc, a novel genotype that emerged in Oregon in approximately 2005.

The North American Pacific Northwest harbors one of the highest incidences of C. gattii infections. In an expansion of molecular epidemiology and population analysis of both MLST and VNTR markers, we show that the VGIIc group is clonal and hypothesize it arose recently. The VGIIa/c outbreak lineages are sexually fertile and studies support ongoing recombination in the global VGII population. This illustrates two hallmarks of emerging outbreaks: high clonality and the emergence of novel genotypes via recombination. In macrophage and murine infections, the novel VGIIc genotype and VGIIa/major isolates from the United States are highly virulent compared to similar non-outbreak VGIIa/major-related isolates. Molecular analysis distinguishes clonal expansion of the VGIIa/major outbreak genotype from related but distinguishable less-virulent genotypes isolated from other geographic regions. Our evidence documents emerging hypervirulent genotypes in the United States that may expand further and provides insight into the possible molecular and geographic origins of the outbreak.

While the outbreak is a significant public health concern, an overlooked but considerable disease burden attributable to C. gattii among HIV/AIDS patients in Southern California has also occurred (chapter 4). In our studies, we examined the molecular epidemiology, population structure, and virulence attributes of C. gattii isolates collected from a cohort of HIV/AIDS patients in Los Angeles County, California. We show that these isolates consist almost exclusively of VGIII molecular type (>93%), in contrast to the vast majority of VGII molecular type isolates found in the outbreak region. Based on molecular phylogenetic analysis, the global VGIII population structure can be divided into two groups, VGIIIa and VGIIIb. We show that isolates from the Californian patients are virulent in murine and macrophage models of infection, with VGIIIa significantly more virulent than VGIIIb. Several VGIII isolates are highly fertile and able to produce large numbers of spores that may serve as infectious propagules. Based on molecular analysis, the a and α VGIII MAT locus alleles are largely syntenic with limited rearrangements compared to the known VGI (a/α) and VGII (α) MAT loci, but each has unique characteristics including a distinct deletion flanking the 5' VGIII MAT a alleles. Fingerprinting analyses of the MAT locus shows that the α allele is more heterogeneous than the aallele. Our studies indicate that C. gattii VGIII is endemic in Southern California, with other isolates originating from the neighboring regions of Mexico, and in some rarer cases from Oregon and Washington state. Given that >1,000,000 cases of cryptococcal infection and >620,000 attributable mortalities occur annually in the context of the global AIDS pandemic, our findings suggest a significant burden of C. gattii infection in AIDS patients may be unrecognized, with potential prognostic and therapeutic implications. These results signify the need to classify pathogenic Cryptococcus cases and highlight possible host differences among the C. gattii molecular types, influencing infection of immunocompetent (VGI/VGII) vs. immunocompromised (VGIII/VGIV) hosts.

In 2007, the first confirmed case of Cryptococcus gattii was reported in the state of North Carolina, USA (chapter 5). An otherwise healthy HIV- male patient presented with a large upper thigh cryptococcoma in February, which was surgically removed and the patient was started on long-term high-dose fluconazole treatment. In May of 2007, the patient presented to the emergency room with seizures. Magnetic resonance imaging revealed two large CNS lesions found to be cryptococcomas based on brain biopsy. Prior chest CT imaging had revealed small lung nodules indicating that C. gattii spores or desiccated yeast were likely inhaled into the lungs and dissemination occurred to both the leg and CNS. The patient's travel history included a visit throughout the San Francisco, California region in September-October of 2006, consistent with acquisition during this time period. Cultures from both the leg and brain biopsies were subjected to analysis. Both isolates were C. gattii, VGI molecular type. Based on molecular studies and virulence in a heterologous host model, the leg and brain isolates are identical, but the two differed in mating fertility. Two clinical isolates, one from a transplant recipient in San Francisco and the other from Australia, were identical to the North Carolina isolate at all markers tested. Closely related isolates that differ at only one or a few noncoding markers are present in the Australian environment. Our findings support a model in which C. gattii VGI was transferred from Australia to California, possibly though an association with its common host plant E. camaldulensis, and the patient was exposed in San Francisco and returned to present with disease in North Carolina.

To elucidate the speciation dynamics between molecular types VGII and VGIII and what influence nuclear and mitochondrial genomes have on intracellular proliferation and hyoervirulence, we conducted a comprehensive analysis of progeny sets between these molecular types, including progeny sets of VGIIa x VGIIIα and VGIIα x VGIIIa crosses (chapter 6). Our analysis reveals that spore viability is exceedingly low, supporting that these are distinct species. We also found that the mitochondrial genome of virulent strains may be necessary but not fully sufficient to confer virulence characteristics. These studies show that each molecular type is likely a distinct species, which was further supported by high levels of diploid or aneuploid progeny, and also shed light into the possible control that both the mitochondrial and nuclear genomes may play in hypervirulence of C. gattii outbreak genotypes. Future analyses of both the regions regulating the virulence and also the generation of progeny sets between other species will further address the roles of both speciation and virulence evolution in C. gattii.

Overall, the studies documented in this dissertation have increased the understanding of molecular epidemiology, population structures, fertility, phenotypic characteristics, virulence characterizations, and speciation of this expanding and emerging fungal pathogen in the United States. This dissertation adds a foundation to the studies of C. gattii in the United States and enables future research to be conducted in several critical areas to better understand and ultimately influence surveillance, prognosis, and treatment of patients and animals in future years.

Dissertation

Exercise training provides health benefits to the general population, but there is considerable variability in the individual response to similar training. Some people have limited improvements following exercise (“low responders”), while others seem to improve considerably (“high responders”). To date, most exercise studies that have claimed to identify “low” or “high” responders assumed that if the participants were to repeat the same exercise training, they would show a similar response. However, within- subject variability has not been tested, which might lead to inaccurate classification of exercise responses at the individual level and the waste of precious research resources. Exposing individuals to a repeated or longer training intervention can assist in identifying the magnitude of responses to exercise training with better accuracy. Recent evidence also suggests that the response to exercise training may be influenced by epigenetic signatures. Epigenetics is a reversible process that affects how genes are expressed in cells, and it carries the memory of past cellular and environmental events. To date, no study has tested whether individual response is influenced by epigenetic marks. Thus, the overarching aim of this thesis is to identify the physiological, molecular, and epigenetic marks of exercise responses. Twenty young, healthy men from the Gene SMART (Skeletal Muscle Adaptive Response to Training) study completed a repeated and a longer exercise training intervention to measure within-subject variability and to obtain individual progress curves (See Figure 3.1 for study design). Participants underwent a four-week control period followed by four weeks of High-Intensity Interval Training (HIIT), had a washout period of > 1 year, and underwent another four weeks of HIIT followed by an additional 8 weeks of HIIT. The HIIT program was adjusted to individual fitness levels that were re-assessed every four weeks during the intervention to ensure improvements. Participants’ peak power output (Wpeak), lactate threshold (LT), and maximal oxygen uptake (VO2max) were assessed in duplicates at each time point. We used five known statistical methods to investigate changes in fitness and mixed models to estimate individual response. Muscle biopsies were collected at each time point to measure mitochondrial markers (i.e. mitochondrial respiration, citrate synthase, cytochrome C oxidase, succinate dehydrogenase, mitochondrial copy number, fibre typing, and myosin heavy chains PCRs), as well as genome-wide DNA methylation profiles in skeletal muscle using the Illumina HumanMethylation EPIC array. In Chapter 3, we show that at the group level, all physiological measures increased in a dose-response manner following HIIT (p<0.05). We found no changes in mitochondrial function and content or fibre type distributions. Baseline citrate synthase (CS) was associated with HIIT-induced changes in cytochrome-c oxidase (COX) and vice-versa (p < 0.05). At the individual level, we successfully identified trainability in physiological measurements using the repeated testing approach but failed to do so using the repeated intervention approach. We did not identify consistent individual response at the molecular level (mitochondrial function and content and fibre type distribution) using either approach, as measurements were highly variable within participants. We then investigated the reliability of the mitochondrial respiration technique (Chapter 4) by measuring the Technical Error of measurement (TEM) and the coefficient of variation (CV) for each mitochondrial complex. While the correlation between the two chambers was good for all complexes (R > 0.7 p < 0.001), the TEM was large (7.9 to 27 pmol·s-1·mg-1), and the CV was > 15% for all complexes. We performed statistical simulations to determine the sample size that would be required to detect a range of effect sizes at 80% power. We found that duplicate measurements on 75 participants are required to detect a 6% change in mitochondrial respiration after an intervention. Finally, Chapter 5 and 6 focus on the DNA methylation measures at the group and individual level respectively. For the first time at the group level, we have investigated DNA methylation patterns that are associated with fitness by combining three measurements of performance into a comprehensive z-score (Chapter 5). We found 12,107 DMPs that were associated with baseline fitness (z-score) (FDR < 0.005), 18.2% of which were hypomethylated and 81.8% hypermethylated with higher fitness levels. We identified 1,268 DMRs for baseline fitness, 15.3% of which hypomethylated and 85.7% hypermethylated. Hyper-DMRs were robustly over-represented in genic enhancers and flanking active TSS, and highly depleted in strong and weak candidate enhancers. Hypo and Hyper-DMRs had a moderate association with bivalent enhancers and promoters. Both hyper and hypo-DMRs presented a moderate representation in regions actively repressed by PolyComb proteins. Finally, significant DMRs were enriched for 26 GO terms, and these pathways were related to muscle system processes, actin cytoskeleton organization and regulation of actin filament and cytoskeleton processes. Next, we investigated the effects of exercise on the methylome, and surprisingly we observed an inverse pattern of DNA methylation profile after exercise. In summary, we found 568 DMPs that significantly changed after the 4 weeks (FDR < 0.005), and out of those only 1.4% were hypermethylated and 98.6% were hypomethylated. We identified 17 DMRs associated with changes in DNA methylation in response of 4 weeks of HIIT, and 100% of DMRs were hypomethylated. Lastly, we intersected DMPs that were significant for both baseline fitness z-score and after 4 weeks of HIIT. Five DMPs were significant, and they appeared to have inverse patterns for baseline z-score (more hypermethylation) and 4 weeks of HIIT (more hypomethylation). When we transitioned to the individual level study in Chapter 6, neither of our approaches (i.e. repeated intervention and repeated testing) yielded many significant results: only one DMP was significant (cg11260483, p-value: 3.22000e-10, adj.p-value: 0.00022) after the repeated intervention, and no DMPs significant after the repeated testing approach. The challenging experimental design of this thesis provided high resolution, longitudinal physiological and molecular profiles in skeletal muscle following repeated exercise training and testing. It yielded novel insights into the phenomenon of trainability in humans; young, healthy men displayed individual responses to HIIT at the physiological level, but not at the molecular level. This thesis also issued methodological considerations for protocols aimed at measuring individual response (Chapter 3). In particular, the high within-subject variability we observed led us to conclude that many repeated testings on the same individual at regular intervals during the training program, along with a moderate-to-large sample size, were necessary to estimate inter-individual variability in response to training. The mitochondrial respiration technique showed high technical variability (Chapter 4), making the measurement unreliable in our study with only n = 20 men and only two duplicates per individual. The typical sample sizes used in exercise training studies (n < 20) are likely insufficient to capture exercise-induced changes in mitochondrial respiration at the group level, let alone the individual level. Lastly, we observed a clear DNA methylation profile association with fitness levels (Chapter 5). However, when an exercise intervention was applied, we noticed a change in DNA methylation patterns that were inverse to those observed at baseline for the fitter participants. Such observations left us wondering on potential reasons to why this occurs. Thus, future research should also integrate the methylome with transcriptome and proteome to elucidate the mechanisms underlying adaptations to exercise training.

Many biological processes are effectively modeled as networks, but a frequent assumption is that these networks do not change during data collection. However, that assumption does not hold for many phenomena, such as neural growth during learning or changes in genetic regulation during cell differentiation. Approaches are needed that explicitly model networks as they change in time and that characterize the nature of those changes.

In this work, we develop a new class of graphical models in which the conditional dependence structure of the underlying data-generation process is permitted to change over time. We first present the model, explain how to derive it from Bayesian networks, and develop an efficient MCMC sampling algorithm that easily generalizes under varying levels of uncertainty about the data generation process. We then characterize the nature of evolving networks in several biological datasets.

We initially focus on learning how neural information flow networks change in songbirds with implanted electrodes. We characterize how they change in response to different sound stimuli and during the process of habituation. We continue to explore the neurobiology of songbirds by identifying changes in neural information flow in another habituation experiment using fMRI data. Finally, we briefly examine evolving genetic regulatory networks involved in Drosophila muscle differentiation during development.

We conclude by suggesting new experimental directions and statistical extensions to the model for predicting novel neural flow results.

Dissertation

Memory monitoring, or the ability to accurately assess one’s memory retrieval success, is known to be declined for older adults. The behavioral decline has been well explored, and is specific to tasks of source monitoring; tasks involving item memory monitoring do not show age-related deficits. This study attempts to further characterize the decline by exploring neuroanatomical contributions to the decline, and genetic influences that may explain performance variability in older adults. Older adults were genotyped for the serotonin transporter (5-HTTLPR) gene, and those that are carriers of the low-expressing allele demonstrate the expected age-related decline of source monitoring performance when compared to younger adults. Interestingly, older adults who lack this allele did not display any decline in performance when compared to younger adults. Neuroanatomical correlates of task performance indicate that prefrontal regions in the inferior and lateral cortices support accurate source memory monitoring, likely through their role in the proper selection of memory cues and inhibition of irrelevant information. This relationship suggests that age-related atrophy occurring in these structures could be responsible for the performance deficits on source memory monitoring tasks. There was no direct relationship seen between genotype for the 5-HTTLPR gene and cortical volumes, however diffusion tensor imaging shows that older adults who carry this allele have altered connections between the medial temporal lobe, responsible for memory retrieval, and prefrontal cortex, which monitors the retrieval process. Through stronger connections of critical networks, older adults who lack the 5-HTTLPR short allele may be able to compensate for the age-related atrophy seen in the prefrontal cortex. Functional results further indicate that the older adult non-carriers recruit inferior and lateral frontal regions to a greater extent than the older adult carriers during accurate memory monitoring. These results begin to suggest a neuroprotective mechanism for the 5-HTTLPR genotype, wherein some older adults may be able to postpone the expected decline of memory monitoring by retaining the ability to recruit essential inferior frontal structures through more organized white matter pathways.
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Indiana University-Purdue University Indianapolis (IUPUI)
Murine double minute (Mdm2) is a highly modified and multi-faceted protein that is overexpressed in numerous human malignancies. It engages in many cellular activities and is essential for development since deletion of mdm2 is lethal in early stages of embryonic development. The most studied function of Mdm2 is as a negative regulator of the tumor suppressor protein p53. Mdm2 achieves this regulation by binding to p53 and inhibiting p53 transcriptional activity. Mdm2 also functions as an E3 ubiquitin ligase that signals p53 for destruction by the proteasome. Interestingly recent evidence has shown that Mdm2 can also function as an E3 neddylating enzyme that can conjugate the ubiquitin-like molecule, nedd8, to p53. This modification results in inhibition of p53 activity, while maintaining p53 protein levels. While the signaling events that regulate Mdm2 E3 ubiquitin ligase activity have been extensively studied, what activates the neddylating activity of Mdm2 has remained elusive. My investigations have centered on understanding whether tyrosine kinase signaling could activate the neddylating activity of Mdm2. I have shown that c-Src, a non-receptor protein tyrosine kinase that is involved in a variety of cellular processes, phosphorylates Mdm2 on tyrosines 281 and 302. This phosphorylation event increases the half-life and neddylating activity of Mdm2 resulting in a neddylation dependent reduction of p53 transcriptional activity. Mdm2 also has many p53-independent cellular functions that are beginning to be linked to its role as an oncogene. There is an emerging role for Mdm2 in tumor metastasis. Metastasis is a process involving tumor cells migrating from a primary site to a distal site and is a major cause of morbidity and mortality in cancer patients. To date, the involvement of Mdm2 in breast cancer metastasis has only been correlative, with no in vivo model to definitively define a role for Mdm2. Here I have shown in vivo that Mdm2 enhances breast to lung metastasis through the up regulation of multiple angiogenic factors, including HIF-1 alpha and VEGF. Taken together my data provide novel insights into important p53-dependent and independent functions of Mdm2 that represent potential new avenues for therapeutic intervention.

Democratic and accountable policing is one of the hallmarks of democracy. In a healthy democracy, a police service exists to protect and support the rights of its community by successfully listening to those who are laying complaints and resolving to assist them by bringing the perpetrators to the grinding wheels of justice. Encouraging and ensuring that police officials utilise the most modern means of investigation such as the DNA technology, provides the necessary balance to the exercise of professional discretion and heightened conviction rate by the police officials. The utilisation of biological evidence in investigation of rape cases is such a modern intervention – a way of providing insulation against internal and external interference with the proper and successful investigation of rape cases.
Forensic Investigation
M. Tech. (Forensic Investigation)