Diss. Stockholm : Karol. inst., 2001.

Diss. (sammanfattning) Stockholm : Karol. inst., 2001. / Härtill 5 uppsatser.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves [118]-129).

Polifosfato inorgânico (PPi) é um polímero linear formado por diversas moléculas de ortofosfato (Pi) unidas por ligações fosfoanidridas de alta energia. Bactérias da espécie Pseudomonas aeruginosa acumulam grandes quantidades de PPi. Moléculas de Pi são captadas do meio através de dois sistemas de transporte. O principal deles é o sistema Pst, que possui alta afinidade por seu substrato. Pst é codificado por um operon de mesmo nome, formado por cinco genes. Os quatro primeiro genes codificam para as proteínas envolvidas no transporte de Pi, sendo que o último gene do operon, phoU, codifica para uma proteína cuja exata função é desconhecida. Com o objetivo de elucidar o papel deste gene e avaliar a sua relação com o acúmulo de PPi, foi construída uma mutação phoU na cepa PA14 de P. aeruginosa. O mutante não só apresentou uma maior capacidade de acumular PPi mas também se mostrou mais sensível a estresses ambientais e a antibióticos. Os resultados obtidos indicam que o gene phoU possui uma função regulatória sobre o acúmulo de PPi. O mutante phoU também apresentou níveis mais altos da molécula de alarme guanosina tetrafosfato (ppGpp). Foi proposto um modelo que explica a relação entre o gene phoU, o acúmulo de polifosfato e ppGpp. O mutante phoU foi também cultivado em cultura contínua em um quimiostato limitado em Pi por 13 dias. Diversos ensaios fenotípicos foram realizados com bactérias isoladas do quimiostato. Estes apresentaram algumas características fisiológicas distintas da cepa ancestral. / Inorganic polyphosphate (PPi) is a linear polymer composed of several molecules of orthophosphate (Pi) linked by energy-rich phosphoanhydride bonds. Bacteria of the species Pseudomonas aeruginosa accumulate large amounts of PPi. Pi molecules are captured via two trasport systems. The main one is the Pst system, which has high affinity for its substrate. Pst is encoded by an operon of the same name, consisting of five gene. The first four genes encode proteins involved in the transport of Pi and the last gene of the operon, phoU, encodes a protein whose exact function is unknown. To elucidate the role of phoU and its relation to PPi accumulation, a phoU mutant was constructed in strain PA14 of P. aeruginosa. The mutant accumulated high levels of PPi but was more sensitive to environmental stresses and antibiotics. The results indicate that phoU plays a regulatory role in the accumulation of PPi. The phoU mutant also displays high levels of the alarmone guanosine tetraphosphate (ppGpp). A model that explains the relation between phoU, ppGpp and polyphosphate accumulation is proposed. The phoU mutant was grown under steady-state conditions in a chemostat limited Pi for 13 days. Phenotypic assays performed with the bacteria isolated from the chemostat showed they acquired some distinct physiological characteristics.

<p>In this thesis, genetic methods for individual identification and sex determination of wolverines from non-invasive samples were developed and applied in genetic monitoring of Scandinavian wolverine populations. Paternity and mating system of wolverines were studied by combining genetic analysis with telemetry data. Moreover, the possibility to obtain DNA from claws left on tanned carnivore hides was investigated.</p><p>Non-invasive genetic sampling was effective in revealing important population parameters. For the subpopulation in southern Norway, a population size of approximately 90 individuals, an equal sex ratio and similar levels of genetic diversity as in the main Scandinavian population were revealed. Genetic erosion in this small population has likely been counteracted by immigration of individuals from the main population since its re-establishment around 1970.</p><p>During the 1990s, two areas in east-central Sweden were colonised by wolverines. In a survey comprising 400 non-invasive samples collected during five winters, a total of 22 wolverines were detected. Genetic data suggest that inbreeding has occurred in both areas and that the two populations were founded by as few as 2-4 individuals. These findings suggest that gene flow from the main population is crucial for their survival even in a short time perspective. The detection of occasional stray individuals from the main population shows that this is indeed feasible. </p><p>Paternity analysis of 145 wolverine offspring in northern Sweden and southern Norway confirmed a polygamous mating system in wolverines. Breeding pair formation was generally consistent with the territories held by males and females, i.e. breeding pairs had overlapping territories. In the majority of litters, siblings were assigned the same father, thus indicating that multiple paternity is rare. </p><p>Tanning is a common form of preservation of mammalian specimens that normally precludes genetic analysis. Nevertheless, I demonstrate the possibility to successfully extract and amplify DNA from claws left on tanned carnivore hides.</p>

In this thesis, genetic methods for individual identification and sex determination of wolverines from non-invasive samples were developed and applied in genetic monitoring of Scandinavian wolverine populations. Paternity and mating system of wolverines were studied by combining genetic analysis with telemetry data. Moreover, the possibility to obtain DNA from claws left on tanned carnivore hides was investigated. Non-invasive genetic sampling was effective in revealing important population parameters. For the subpopulation in southern Norway, a population size of approximately 90 individuals, an equal sex ratio and similar levels of genetic diversity as in the main Scandinavian population were revealed. Genetic erosion in this small population has likely been counteracted by immigration of individuals from the main population since its re-establishment around 1970. During the 1990s, two areas in east-central Sweden were colonised by wolverines. In a survey comprising 400 non-invasive samples collected during five winters, a total of 22 wolverines were detected. Genetic data suggest that inbreeding has occurred in both areas and that the two populations were founded by as few as 2-4 individuals. These findings suggest that gene flow from the main population is crucial for their survival even in a short time perspective. The detection of occasional stray individuals from the main population shows that this is indeed feasible. Paternity analysis of 145 wolverine offspring in northern Sweden and southern Norway confirmed a polygamous mating system in wolverines. Breeding pair formation was generally consistent with the territories held by males and females, i.e. breeding pairs had overlapping territories. In the majority of litters, siblings were assigned the same father, thus indicating that multiple paternity is rare. Tanning is a common form of preservation of mammalian specimens that normally precludes genetic analysis. Nevertheless, I demonstrate the possibility to successfully extract and amplify DNA from claws left on tanned carnivore hides.

Polifosfato inorgânico (PPi) é um polímero linear formado por diversas moléculas de ortofosfato (Pi) unidas por ligações fosfoanidridas de alta energia. Bactérias da espécie Pseudomonas aeruginosa acumulam grandes quantidades de PPi. Moléculas de Pi são captadas do meio através de dois sistemas de transporte. O principal deles é o sistema Pst, que possui alta afinidade por seu substrato. Pst é codificado por um operon de mesmo nome, formado por cinco genes. Os quatro primeiro genes codificam para as proteínas envolvidas no transporte de Pi, sendo que o último gene do operon, phoU, codifica para uma proteína cuja exata função é desconhecida. Com o objetivo de elucidar o papel deste gene e avaliar a sua relação com o acúmulo de PPi, foi construída uma mutação phoU na cepa PA14 de P. aeruginosa. O mutante não só apresentou uma maior capacidade de acumular PPi mas também se mostrou mais sensível a estresses ambientais e a antibióticos. Os resultados obtidos indicam que o gene phoU possui uma função regulatória sobre o acúmulo de PPi. O mutante phoU também apresentou níveis mais altos da molécula de alarme guanosina tetrafosfato (ppGpp). Foi proposto um modelo que explica a relação entre o gene phoU, o acúmulo de polifosfato e ppGpp. O mutante phoU foi também cultivado em cultura contínua em um quimiostato limitado em Pi por 13 dias. Diversos ensaios fenotípicos foram realizados com bactérias isoladas do quimiostato. Estes apresentaram algumas características fisiológicas distintas da cepa ancestral. / Inorganic polyphosphate (PPi) is a linear polymer composed of several molecules of orthophosphate (Pi) linked by energy-rich phosphoanhydride bonds. Bacteria of the species Pseudomonas aeruginosa accumulate large amounts of PPi. Pi molecules are captured via two trasport systems. The main one is the Pst system, which has high affinity for its substrate. Pst is encoded by an operon of the same name, consisting of five gene. The first four genes encode proteins involved in the transport of Pi and the last gene of the operon, phoU, encodes a protein whose exact function is unknown. To elucidate the role of phoU and its relation to PPi accumulation, a phoU mutant was constructed in strain PA14 of P. aeruginosa. The mutant accumulated high levels of PPi but was more sensitive to environmental stresses and antibiotics. The results indicate that phoU plays a regulatory role in the accumulation of PPi. The phoU mutant also displays high levels of the alarmone guanosine tetraphosphate (ppGpp). A model that explains the relation between phoU, ppGpp and polyphosphate accumulation is proposed. The phoU mutant was grown under steady-state conditions in a chemostat limited Pi for 13 days. Phenotypic assays performed with the bacteria isolated from the chemostat showed they acquired some distinct physiological characteristics.

A neoplasia endócrina múltipla tipo 1 (NEM1) é uma doença genética, de herança autossômica dominante, caracterizada pelo desenvolvimento de tumores endócrinos acometendo, principalmente, hipófise, paratireoide e pâncreas/duodeno endócrinos. É causada, principalmente, por mutação germinativa no gene supressor tumoral MEN1 (11q13). A tumorigênese segue o modelo de Knudson (1971). O diagnóstico genético de famílias com NEM1 reconhece os portadores assintomáticos de mutação MEN1, permite o diagnóstico e tratamento precoce de tumores, promove a redução da morbimortalidade relacionada à NEM1 e exclui familiares não portadores de mutação do rastreamento clínico periódico. O diagnóstico genético de NEM1 tem sido realizado por meio da técnica de sequenciamento Sanger. Entretanto, limitações desta técnica a tornam menos custo efetiva, devido a sua reduzida capacidade de geração de dados, que leva a necessidade de obtenção de produtos de PCR de até 700 pb para adequada leitura do sequenciamento. Além disto, condições específicas do gene MEN1, como a ausência de \"hot spots\" mutacionais, levam a necessidade de sequenciamento de toda sua extensão (7Kb) e contribuem para tornar esta técnica laboriosa e dispendiosa. A subdivisão do gene para sequenciamento Sanger pode ocultar informações, principalmente de regiões intrônicas, que podem ser importantes para o desenvolvimento da doença. Tais dificuldades impedem a incorporação do diagnóstico gênico de NEM1 na prática clínica. Desde 2005, estão disponíveis tecnologias denominadas NGS (Next- Generation Sequencing), que consistem em ferramentas para o sequenciamento genético com capacidade aumentada de geração de dados, tornando-as mais atrativas e de melhor custo-benefício. O NGS confere, ainda, maior velocidade ao processo de obtenção de dados e detém a capacidade de realizar a leitura completa do gene, incluindo regiões promotoras e intrônicas. Por isto, torna a leitura mais ampla e informativa, sem desconsiderar aspectos qualitativos. Dentre várias opções de NGS disponíveis, plataformas leves são consideradas mais adequadas para aplicação clínica, destacando-se as plataformas Ion PGM e Illumina MiSeq. Uma forte tendência tem sido mostrada de migração do sequenciamento Sanger para o NGS, incluindo a aplicação da mesma em diagnóstico genético de doenças complexas e de câncer hereditário. Entretanto, não há estudos prévios envolvendo NGS em NEM1. Diante disto, foi avaliado a qualidade desta técnica como método de diagnóstico genético em NEM1 em comparação ao sequenciamento Sanger. Objetivos: validação da técnica de NGS utilizando como parâmetro o sequenciamento Sanger; avaliação da sensibilidade, especificidade e relação custo-benefício do NGS. Para tal, foram analisados 76 casos-índices com diagnóstico clínico de NEM1 na plataforma Illumina MiSeq. As análises foram subdivididas em duas fases. O enriquecimento da região genômica do gene MEN1 foi realizado por meio de PCR longa. Com base nos dados obtidos foi possível aferir 96% de reprodutibilidade entre as diferentes fases do estudo e aproximadamente 99% de precisão para detecção de variantes. Exatidão, sensibilidade e especificidade resultaram em 100%. Não houve falsos-positivos ou negativos. A técnica de NGS também se mostrou mais custo-efetiva do que o sequenciamento Sanger. Este estudo permitiu validar e introduzir esta técnica como ferramenta de diagnóstico gênico de NEM1 para rastreamento genético de casos-índices / The multiple endocrine neoplasia type 1 (MEN1) is a genetic, autossomic and dominant disease and is correlated with the development of endocrine tumors affecting pituitary gland, parathyroid, endocrine pancreas or duodenum. It is mainly caused by a germinative mutation in tumor suppressor gene MEN1 (11q13). The tumorigenesis follow the Knudson\'s model (1971). Genetic diagnosis of families with MEN1 is essential to recognizes asymptomatic mutation carriers, and allows an earlier detection and treatment of tumors leading to a reduction of mortality and morbidity associated to MEN1. Furthermore, it can exclude family members that do not carry mutations from the periodical screening. The genetic diagnosis for MEN1 is held using Sanger sequencing. However, limitations of this technique make it less cost-effective, mostly, the less capacity of data generation that leads to the need of PCR products up to 700 bp to obtain a suitable read. Moreover, specific conditions of the MEN1 gene contributes to make this process more laborious and expensive, like the need to read all gene sequence (7kb) to make a correct analysis due to the absence of \"hot spots\". This way, the need of \"fragmentation\" to allow the sequencing can hide important information to disease development, mostly in introns. These limitations preclude the clinical application of genetic diagnosis of MEN1. Since 2005, new technologies are available; they are called Next Generation Sequencing (NGS) and consist in a new tool that allow the same sequencing, but with a larger data generation capacity, making them more attractive and costeffective. The NGS also gives a higher speed to the process of data acquiring and allows the complete read of gene, including promoters and introns. Therefore, it makes the results more informative, not forgetting quality aspects. Among lot of options of NGS available, lighter platforms are recommended, for example, Ion PGM and Illumina MiSeq. A strong tendency has been shown in order to change the Sanger sequencing to NGS, including clinical application to genetic diagnosis of complex diseases and inherited cancer. However, there is not previous studies evaluating NGS to MEN1 genetic diagnosis. Thus, present study evaluated NGS as a genetic diagnosis method for MEN1, comparing with Sanger sequencing. This study aimed to validate the NGS method using as model the Sanger sequencing and evaluated sensibility, specificity and costeffectiveness of NGS. For this purpose, 76 index-cases with clinical MEN1 diagnosis were analyzed on Illumina MiSeq. Analyzes were divided in two phases. After analyzes, 96% of reproducibility and 99% of precision were calculated. Accuracy, sensibility and specificity were resulted in 100%. There were not falses negatives or positives. NGS showed more cost-effectiveness with lower costs. This study allowed validation of genetic screening of MEN1 indexcases applying NGS platform

A neoplasia endócrina múltipla tipo 1 (NEM1) é uma doença genética, de herança autossômica dominante, caracterizada pelo desenvolvimento de tumores endócrinos acometendo, principalmente, hipófise, paratireoide e pâncreas/duodeno endócrinos. É causada, principalmente, por mutação germinativa no gene supressor tumoral MEN1 (11q13). A tumorigênese segue o modelo de Knudson (1971). O diagnóstico genético de famílias com NEM1 reconhece os portadores assintomáticos de mutação MEN1, permite o diagnóstico e tratamento precoce de tumores, promove a redução da morbimortalidade relacionada à NEM1 e exclui familiares não portadores de mutação do rastreamento clínico periódico. O diagnóstico genético de NEM1 tem sido realizado por meio da técnica de sequenciamento Sanger. Entretanto, limitações desta técnica a tornam menos custo efetiva, devido a sua reduzida capacidade de geração de dados, que leva a necessidade de obtenção de produtos de PCR de até 700 pb para adequada leitura do sequenciamento. Além disto, condições específicas do gene MEN1, como a ausência de \"hot spots\" mutacionais, levam a necessidade de sequenciamento de toda sua extensão (7Kb) e contribuem para tornar esta técnica laboriosa e dispendiosa. A subdivisão do gene para sequenciamento Sanger pode ocultar informações, principalmente de regiões intrônicas, que podem ser importantes para o desenvolvimento da doença. Tais dificuldades impedem a incorporação do diagnóstico gênico de NEM1 na prática clínica. Desde 2005, estão disponíveis tecnologias denominadas NGS (Next- Generation Sequencing), que consistem em ferramentas para o sequenciamento genético com capacidade aumentada de geração de dados, tornando-as mais atrativas e de melhor custo-benefício. O NGS confere, ainda, maior velocidade ao processo de obtenção de dados e detém a capacidade de realizar a leitura completa do gene, incluindo regiões promotoras e intrônicas. Por isto, torna a leitura mais ampla e informativa, sem desconsiderar aspectos qualitativos. Dentre várias opções de NGS disponíveis, plataformas leves são consideradas mais adequadas para aplicação clínica, destacando-se as plataformas Ion PGM e Illumina MiSeq. Uma forte tendência tem sido mostrada de migração do sequenciamento Sanger para o NGS, incluindo a aplicação da mesma em diagnóstico genético de doenças complexas e de câncer hereditário. Entretanto, não há estudos prévios envolvendo NGS em NEM1. Diante disto, foi avaliado a qualidade desta técnica como método de diagnóstico genético em NEM1 em comparação ao sequenciamento Sanger. Objetivos: validação da técnica de NGS utilizando como parâmetro o sequenciamento Sanger; avaliação da sensibilidade, especificidade e relação custo-benefício do NGS. Para tal, foram analisados 76 casos-índices com diagnóstico clínico de NEM1 na plataforma Illumina MiSeq. As análises foram subdivididas em duas fases. O enriquecimento da região genômica do gene MEN1 foi realizado por meio de PCR longa. Com base nos dados obtidos foi possível aferir 96% de reprodutibilidade entre as diferentes fases do estudo e aproximadamente 99% de precisão para detecção de variantes. Exatidão, sensibilidade e especificidade resultaram em 100%. Não houve falsos-positivos ou negativos. A técnica de NGS também se mostrou mais custo-efetiva do que o sequenciamento Sanger. Este estudo permitiu validar e introduzir esta técnica como ferramenta de diagnóstico gênico de NEM1 para rastreamento genético de casos-índices / The multiple endocrine neoplasia type 1 (MEN1) is a genetic, autossomic and dominant disease and is correlated with the development of endocrine tumors affecting pituitary gland, parathyroid, endocrine pancreas or duodenum. It is mainly caused by a germinative mutation in tumor suppressor gene MEN1 (11q13). The tumorigenesis follow the Knudson\'s model (1971). Genetic diagnosis of families with MEN1 is essential to recognizes asymptomatic mutation carriers, and allows an earlier detection and treatment of tumors leading to a reduction of mortality and morbidity associated to MEN1. Furthermore, it can exclude family members that do not carry mutations from the periodical screening. The genetic diagnosis for MEN1 is held using Sanger sequencing. However, limitations of this technique make it less cost-effective, mostly, the less capacity of data generation that leads to the need of PCR products up to 700 bp to obtain a suitable read. Moreover, specific conditions of the MEN1 gene contributes to make this process more laborious and expensive, like the need to read all gene sequence (7kb) to make a correct analysis due to the absence of \"hot spots\". This way, the need of \"fragmentation\" to allow the sequencing can hide important information to disease development, mostly in introns. These limitations preclude the clinical application of genetic diagnosis of MEN1. Since 2005, new technologies are available; they are called Next Generation Sequencing (NGS) and consist in a new tool that allow the same sequencing, but with a larger data generation capacity, making them more attractive and costeffective. The NGS also gives a higher speed to the process of data acquiring and allows the complete read of gene, including promoters and introns. Therefore, it makes the results more informative, not forgetting quality aspects. Among lot of options of NGS available, lighter platforms are recommended, for example, Ion PGM and Illumina MiSeq. A strong tendency has been shown in order to change the Sanger sequencing to NGS, including clinical application to genetic diagnosis of complex diseases and inherited cancer. However, there is not previous studies evaluating NGS to MEN1 genetic diagnosis. Thus, present study evaluated NGS as a genetic diagnosis method for MEN1, comparing with Sanger sequencing. This study aimed to validate the NGS method using as model the Sanger sequencing and evaluated sensibility, specificity and costeffectiveness of NGS. For this purpose, 76 index-cases with clinical MEN1 diagnosis were analyzed on Illumina MiSeq. Analyzes were divided in two phases. After analyzes, 96% of reproducibility and 99% of precision were calculated. Accuracy, sensibility and specificity were resulted in 100%. There were not falses negatives or positives. NGS showed more cost-effectiveness with lower costs. This study allowed validation of genetic screening of MEN1 indexcases applying NGS platform

Evolution is the single cohesive logical framework in which all biological processes may exist simultaneously. Incremental changes in phenotype over imperceptibly large timescales have given rise to the enormous diversity of life we witness on earth both presently and through the natural record. The basic unit of evolution is mutation, and by perturbing biological processes, mutations may alter the fitness of an individual. However, the fitness effect of a mutation is difficult to infer from historical record, and complex to obtain experimentally in an efficient and accurate manner. We have recently developed a high throughput method to iteratively mutagenize regions of essential genes in yeast and subsequently analyze individual mutant fitness termed Exceedingly Methodical and Parallel Investigation of Randomized Individual Codons (EMPIRIC). Utilizing this technique as exemplified in Chapters II and III, it is possible to determine the fitness effects of all possible point mutations in parallel through growth competition followed by a high throughput sequencing readout. We have employed this technique to determine the distribution of fitness effects in a nine amino acid region of the Hsp90 gene of S. cerevisiae under elevated temperature, and found the bimodal distribution of fitness effects to be remarkably consistent with near-neutral theory. Comparing the measured fitness effects of mutants to the natural record, phylogenetic alignments appear to be a poor predictor of experimental fitness. In Chapter IV, to further interrogate the properties of this region, library competition under conditions of elevated temperature and salinity were performed to study the potential of protein adaptation. Strikingly, whereas both optimal and elevated temperatures produced no statistically significant beneficial mutations, under conditions of elevated salinity, adaptive mutations appear with fitness advantages up to 8% greater than wild type. Of particular interest, mutations conferring fitness benefits under conditions of elevated salinity almost always experience a fitness defect in other experimental conditions, indicating these mutations are environmentally specialized. Applying the experimental fitness measurements to long standing theoretical predictions of adaptation, our results are remarkably consistent with Fisher’s Geometric Model of protein evolution. Epistasis between mutations can have profound effects on evolutionary trajectories. Although the importance of epistasis has been realized since the early 1900s, the interdependence of mutations is difficult to study in vivo due to the stochastic and constant nature of background mutations. In Chapter V, utilizing the EMPIRIC methodology allows us to study the distribution of fitness effects in the context of mutant genetic backgrounds with minimal influence from unintended background mutations. By analyzing intragenic epistatic interactions, we uncovered a complex interplay between solvent shielded structural residues and solvent exposed hydrophobic surface in the amino acid 582-590 region of Hsp90. Additionally, negative epistasis appears to be negatively correlated with mutational promiscuity while additive interactions are positively correlated, indicating potential avenues for proteins to navigate fitness ‘valleys’. In summary, the work presented in this dissertation is focused on applying experimental context to the theory-rich field of evolutionary biology. The development and implementation of a novel methodology for the rapid and accurate assessment of organismal fitness has allowed us to address some of the most basic processes of evolution including adaptation and protein expression level. Through the work presented here and by investigators across the world, the application of experimental data to evolutionary theory has the potential to improve drug design and human health in general, as well as allow for predictive medicine in the coming era of personalized medicine.