This work introduces two unconventional applications for sequence alignment algorithms outside the domain of bioinformatics: handwriting recognition and speech recognition. In each application we treated data samples, such as the path of a and written pen stroke, as a protein sequence and use the FastA sequence alignment tool to classify unknown data samples, such as a written character. That is, we handle the handwriting and speech recognition problems like the protein annotation problem: given a sequence of unknown function, we annotate the sequence via sequence alignment. This approach achieves classification rates of 99.65% and 93.84% for the handwriting and speech recognition respectively. In addition, we provide a framework for applying sequence alignment to a variety of other non–traditional problems. / Singapore-MIT Alliance (SMA)

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Food webs are structured by intricate nodes of species interactions which govern the flow of organic matter in natural systems. Despite being long recognized as a key component in ecology, estimation of food web functioning is still challenging due to the difficulty in accurately measuring species interactions within a food web. Novel tracing methods that estimate species diet uptake and trophic position are therefore needed for assessing food web dynamics. The focus of this thesis is the use of compound specific nitrogen and carbon stable isotopes and molecular techniques for assessing predator-prey interactions and energy flow in natural aquatic ecosystems, with a particular focus on the species links between phytoplankton and zooplankton. The use of δ15N amino acid values to predict organism trophic position are evaluated through a meta-analysis of available literature which included measurements from 359 marine species (article I). Through a controlled feeding study isotope incorporation in aquatic organisms, across both plant-animal and animal-animal species linkages is further assessed (article II). These studies showed that δ15N amino acid values are useful tools for categorizing animal trophic position. Organism feeding ecology influenced nitrogen trophic discrimination (difference in isotope ratio between consumer and diet), with higher discrimination in herbivores compared to omnivores and carnivores (article I). Nitrogen isotope trophic discrimination also varied among feeding treatments in the laboratory study (article II). The combined findings from articles I &amp; II suggest that researchers should consider using group specific nitrogen trophic discrimination values to improve accuracy in species trophic position predictions.  Another key finding in the controlled laboratory study (article II) was consistently low carbon isotope discrimination in essential amino acids across all species linkages, confirming that these compounds are reliable dietary tracers. The δ13C ratios of essential amino acids were applied to study seasonal dynamics in zooplankton resource use in the Baltic Sea (article III). Data from this study indicated that zooplankton assimilate variable resources throughout the growing season. Molecular diet analysis (article IV) showed that marine copepod and cladoceran species ingested both autotrophic and heterotrophic resources. Evidence from both articles III &amp; IV also revealed that zooplankton feed on a relatively broad range of diet items but not opportunistically on all available food sources. Mesozooplankton feeding patterns suggested that energy and nutritional flows were channelled through an omnivorous zooplankton food web including microzooplankton prey items. Overall the results of this thesis highlight that stable isotope ratios in specific compounds and molecular techniques are useful tracing approaches that improve our understanding of food web functioning. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript.</p><p> </p>

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Made available in DSpace on 2014-06-11T19:30:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-07-03Bitstream added on 2014-06-13T20:00:51Z : No. of bitstreams: 1 portella_cg_dr_jabo.pdf: 619272 bytes, checksum: 967fa2a2ecd78204650d28b2592f3a8e (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Universidade Estadual Paulista (UNESP) / Macrobrachium amazonicum e Macrobrachium rosenbergii são espécies de camarão de água doce de grande importância econômica e como fontes de alimento de alto valor nutritivo. Existem poucas informações a respeito da composição química do camarão de água doce produzido no Brasil. O objetivo deste trabalho foi avaliar a composição química das duas espécies e determinar o perfil de aminoácidos de M. amazonicum. Exemplares provenientes de cultivo foram lavados e limpos (retirada cefalotórax e exoesqueleto) para a determinação dos teores de umidade, proteína, cinzas, lipídeos e aminoácidos totais. Os teores de umidade foram 76,55 e 78,39g/100g, cinzas de 1,34 e 1,31g/100g, proteína de 21,49 e 18,48g/100g e lipídeo de 1,48 e 1,17g/100g, para M. amazonicum e M. rosenbergii, respectivamente. O conteúdo total de M. amazonicum foi 20,60g/100g. Os aminoácidos mais representativos foram ácidos glutâmico e aspártico, arginina, alanina e glicina. Estes dados podem ser utilizados futuramente como informação nutricional aos consumidores e para análises em estudos de nutrição e no processamento. / Species of freshwater prawn Macrobrachium amazonicum and Macrobrachium rosenbergii are species of freshwater prawn of great importance and that may be utilized as source of high nutritional value food. There are few data about the chemical composition of freshwater prawns produced in Brazil. The aim of this study was evaluate the chemical composition of both species and determinate the amino acids profile of M. amazonicum and M. rosenbergii. Samples from culture were washed and have peeled tails. They were determined moisture, protein, ash, lipid and total amino acids contents. The values of moisture were 76.55 and 78.39g/100g, ash 1.34 and 1.31g/100g, protein 21.49 and 18.48g/100g and lipid 1.48 and 1.17g/100g to M. amazonicum and M. rosenbergii, respectively. The total amino acid content of M. amazonicum were 20.60g/100g. The most abundant amino acids were glutamic and aspartic acids, arginine, alanine, and glycine. These data may use as nutritional information for consumers and for future analysis on nutrition and processing.