Yes / The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and “M. avium subsp. hominissuis”), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections.

A presente dissertação pretende analisar a terminologia da Economia Internacional, mais especificamente, estudar sua constituição morfológica e a presença de relações sinonímicas. Para tanto, além de um embasamento teórico inicial referente à Terminologia, aos processos de formação de palavras e às relações sinonímicas, foi necessária a elaboração de um corpus de análise, formado por termos coletados de livros utilizados na disciplina de Economia Internacional da FEA-USP. Em seguida, realizou-se a análise dos processos de formação morfológica das unidades terminológicas coletadas. Conforme foi possível perceber, num domínio especializado, o falante utiliza os mesmos recursos oferecidos pelo sistema para nomear a realidade. Entretanto, alguns processos, como a formação sintagmática, destacam-se pela produtividade. De fato, este estudo demonstra que o processo de formação sintagmática é extremamente fecundo na terminologia da Economia Internacional. Ademais, observou-se também a presença de relações sinonímicas entre os termos e verificamos que esta é bastante recorrente e expressiva. Com isso, comprova-se a existência da sinonímia no léxico especializado, o que era negado pelos adeptos da Terminologia tradicional. Com base na análise dos dados e nas reflexões teóricas apontadas, é possível demonstrar que as palavras de âmbito especializado funcionam como as demais palavras do léxico da língua. / The present dissertation aims to analyze the terminology of International Economics, more precisely, to study its morphological constitution as well as the presence of synonymous relationships. In order to do so, besides an initial theoretical grounding relating to Terminology, to the word formation processes and to the synonymous relationships, it was necessary the elaboration of a corpus of analysis, which was composed of terms collected from books used in the subject of International Economics at FEA-USP. Subsequently, an analysis of the morphological formation processes of the collected terminological units was carried out. As it has been possible to notice, in a specialized domain, the speaker uses the same resources as in the general language to name the reality. Nevertheless, some processes, such as the syntagmatic formation, stand out because of their productivity. Indeed, this study shows that the process of syntagmatic formation is extremely prolific in the terminology of International Economics. Furthermore, the presence of synonymous relationships was also observed and we have confirmed that synonymy is remarkably common and expressive in terminology, which was denied by the former adepts of traditional Terminology. Finally, based on the analysis of the data and on the theoretical reflections, it has been possible to demonstrate that the terms of specialty areas work in the same way as the other words of the lexicon of a given language.

A presente dissertação pretende analisar a terminologia da Economia Internacional, mais especificamente, estudar sua constituição morfológica e a presença de relações sinonímicas. Para tanto, além de um embasamento teórico inicial referente à Terminologia, aos processos de formação de palavras e às relações sinonímicas, foi necessária a elaboração de um corpus de análise, formado por termos coletados de livros utilizados na disciplina de Economia Internacional da FEA-USP. Em seguida, realizou-se a análise dos processos de formação morfológica das unidades terminológicas coletadas. Conforme foi possível perceber, num domínio especializado, o falante utiliza os mesmos recursos oferecidos pelo sistema para nomear a realidade. Entretanto, alguns processos, como a formação sintagmática, destacam-se pela produtividade. De fato, este estudo demonstra que o processo de formação sintagmática é extremamente fecundo na terminologia da Economia Internacional. Ademais, observou-se também a presença de relações sinonímicas entre os termos e verificamos que esta é bastante recorrente e expressiva. Com isso, comprova-se a existência da sinonímia no léxico especializado, o que era negado pelos adeptos da Terminologia tradicional. Com base na análise dos dados e nas reflexões teóricas apontadas, é possível demonstrar que as palavras de âmbito especializado funcionam como as demais palavras do léxico da língua. / The present dissertation aims to analyze the terminology of International Economics, more precisely, to study its morphological constitution as well as the presence of synonymous relationships. In order to do so, besides an initial theoretical grounding relating to Terminology, to the word formation processes and to the synonymous relationships, it was necessary the elaboration of a corpus of analysis, which was composed of terms collected from books used in the subject of International Economics at FEA-USP. Subsequently, an analysis of the morphological formation processes of the collected terminological units was carried out. As it has been possible to notice, in a specialized domain, the speaker uses the same resources as in the general language to name the reality. Nevertheless, some processes, such as the syntagmatic formation, stand out because of their productivity. Indeed, this study shows that the process of syntagmatic formation is extremely prolific in the terminology of International Economics. Furthermore, the presence of synonymous relationships was also observed and we have confirmed that synonymy is remarkably common and expressive in terminology, which was denied by the former adepts of traditional Terminology. Finally, based on the analysis of the data and on the theoretical reflections, it has been possible to demonstrate that the terms of specialty areas work in the same way as the other words of the lexicon of a given language.

The aim of this thesis is to evaluate the usage of synonyms in teaching Russian language at high schools. The theoretical part of this thesis outlines the issues of synonyms and synonymous series from the linguistic (paradigmatic relations, semantics, stylistic) and linguodidactic point of view. The theoretical part also includes the issue of vocabulary from the didactic point of view. Furthermore, in the practical part, the diversity of synonyms used in curriculum of Russian language teaching are evaluated as well as the methods of demonstration and practising of such curriculum. In the final part of this thesis my own concepts for working with synonyms in teaching Russian language at high schools are suggested. KEYWORDS: synonyms, synonymous series, foreign languages, vocabulary, Russian language teaching

High-throughput genomics projects have resulted in a rapid accumulation of protein sequences. Therefore, computational methods that can predict protein functions and functional sites efficiently and accurately are in high demand. In addition, prediction methods utilizing only sequence information are of particular interest because for most proteins, 3-dimensional structures are not available. However, there are several key challenges in developing methods for predicting protein function and functional sites. These challenges include the following: the construction of representative datasets to train and evaluate the method, the collection of features related to the protein functions, the selection of the most useful features, and the integration of selected features into suitable computational models. In this proposed study, we tackle these challenges by developing procedures for benchmark dataset construction and protein feature extraction, implementing efficient feature selection strategies, and developing effective machine learning algorithms for protein function and functional site predictions. We investigate these challenges in three bioinformatics tasks: the discovery of transmembrane beta-barrel (TMB) proteins in gram-negative bacterial proteomes, the identification of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs), and the identification of helix-turn-helix (HTH) motifs from protein sequence.

O grande grupo heterogêneo de neuropatias periféricas hereditárias estão entre os casos mais comuns de perda sensitiva e fraqueza muscular em crianças e adolescentes. Pelo menos 84 genes estão envolvidos com neuropatias sensitivo-motoras hereditárias (NSMH), sendo suas formas de herança mais comuns as autossômico-dominantes desmielinizante e axonal e as neuropatias ligadas ao cromossomo X, e as mais raras as autossômicorecessivas desmielinizante e axonal e as formas ainda não classificadas. O gene HINT1, possuinte de 3 exons e localizado no cromossomo 5, codifica a proteína Histidine triad nucleotide binding protein 1, uma variante transcricional (mRNA) regulatória que hidroliza substratos. Recentemente mutações em HINT1 foram também relacionadas à neuropatias axonais com neuromiotonia (ARCMT2-NM), e portanto à CMT. O objetivo deste trabalho foi realizar o screening mutacional do gene HINT1 em uma amostra da população brasileira com quadro clínico de CMT recessivo (CMT2-AR), e foram encontradas 1 mutação silenciosa já previamente descrita, 1 polimorfismo exônico e 1 polimorfismo intrônico, também já conhecidos. Concluiu-se que mutações no gene HINT1 não são portanto responsáveis pela CMT-AR nesta amostra da população brasileira. / The large heterogeneous group of inherited peripheral neuropathies are among the most common causes of sensory loss and muscle weakness in children and adolescents. At least 84 genes are involved in inherited sensorymotor neuropathies (NSMH), being the demyelinating and axonal autosomaldominant and the X-linked neuropathies their most common forms of inheritance, and the demyelinating and axonal autosomal-recessive and not yet classified forms the most rare ones. The HINT1 gene, with 3 exons and located on chromosome 5, encodes the protein Histidine triad nucleotide binding protein 1, a regulatory transcriptional variant (mRNA) that hydrolyzes substrates. Recently, mutations in HINT1 were also related to axonal neuropathy with neuromyotonia (ARCMT2-NM), and therefore to CMT. The objective of this study was the mutational screening of the HINT1 gene in a sample of the Brazilian population with clinical recessive CMT (CMT2-AR), and 1 silent mutation previously described, 1 intronic polymorphism and 1 exonic polymorphism, both also known, were founded. It was then concluded that mutations in the HINT1 gene are not responsible for CMT2-AR in this particular sample of the Brazilian population.

Made available in DSpace on 2015-04-11T13:38:47Z (GMT). No. of bitstreams: 1 Janaina de Araujo Evangelista.pdf: 5258011 bytes, checksum: f25739b96a1b2d123d21c1753b3204e8 (MD5) Previous issue date: 2011-05-06 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / subtropical regions of the planet. In North America, Plasmodium vivax is responsible for the most part of the infections. In 2011, 250,498 cases of malaria fever were studied; 80% of these cases were caused by Plasmodium vivax. The purpose of this study was to investigate the diversity generation of the gene MSP1 from Plasmodium vivax through the analisys of a specific mutation in the region from the block 2 genetic precombination events. In order to identify the existing mutations in multiclonal infections and generation of diversity in PvMSP1 a series of experiments were done, respectively, the extraction of genomic DNA of the parasite, PCR (polymerase chain reaction) using specific primers for the block 2, ligation of the fragment to cloning vector (top), processing using Escherichia coli competent cells, selection of colonies belonging to the same sample, DNA sequencing and analysis of synonymous and nonsynonymous mutations as their location in the prediction of B and T cell epitopes (not synonymous). The calculation of genetic distance between recombinant clones of the same sample by the MEGA 4.0 program confirmed the multiclonality of samples. The alignment of amino acid sequences showed the presence of genetic recombination events using DNASP program. DNA sequences obtained showed another interesting result: several synonymous and non-synonymous mutations in a relatively small stretch of DNA. Genetic diversity showed most mutations are not synonymous, and that most of them were located in regions referred to as B and T cell epitopes by BcPred and ProPred. So, as expected, the genetic diversity based on synonymous mutations and not synonymous possible sustains the phenomenon of escape on the immunity of the host. The characterization of these polymorphisms may contribute to immunological studies aiming at the development of a vaccine against malaria on stages caused by p. vivax. / A malária é um problema da saúde pública amplamente distribuída nas regiões tropicais e subtropicais do globo. No continente americano, o Plasmodium vivax é responsável por maior parte das infecções. No ano de 2011, 250.498 casos de malária foram observados no estado do Amazonas; 80% destes casos foram causados por Plasmodium vivax. O objetivo desse trabalho foi Investigar a geração de diversidade do gene MSP1 de Plasmodium vivax através da análise de mutações pontuais na região do bloco 2, eventos de precombinação genética. Para identificar as mutações existentes nas infecções multiclonais e geração de diversidade em PvMSP1 realizou-se uma série de experimentos, respectivamente, a extração de DNA genômico do parasita, PCR (Reação da Polimerase em Cadeia) utilizando primers específicos para o bloco 2, ligação do fragmento ao vetor de clonagem ( TOPO), transformação utilizando células de E.coli competentes , seleção de colônias pertencentes a uma mesma amostra, seqüenciamento de DNA e análise das mutações não sinônimas e sinônimas quanto sua localização em regiões de predição de epítopos de células B e T (não sinônimas). O cálculo da distância genética entre clones recombinantes de uma mesma amostra pelo programa MEGA 4.0 confirmou a multiclonalidade das amostras. O alinhamento das sequências de aminoácidos mostrou a presenção de eventos de recombinação genética utilizando o programa DNASP. As sequências de DNA obtidas demonstrou outro resultado interessante: várias mutações sinônimas e não sinônimas num trecho relativamente pequeno de DNA. A diversidade genética mostrou mais mutações não sinônimas, sendo que maior parte delas estavam localizadas em regiões previstas como epítopos das células B e T pelo programa BcPred e ProPred. Assim, como esperado, a diversidade genética baseado nas mutações sinônimas e não sinônimas sustenta o fenômeno de escape sobre a imunidade do hospedeiro. A caracterização desses polimorfismos poderá contribuir para estudos imunológicos visando o desenvolvimento de uma vacina contra os estágios eritrocitários da malária causada por P.vivax.

The study of bacterial evolution is fundamental for addressing current problems of antibiotic resistance and emerging infectious diseases and lays a solid foundation for successful and rational design in biotechnology and synthetic biology. The main aim of this thesis is to test evolutionary hypotheses, largely based on theoretical considerations and sequence analysis, by designing scenarios in a laboratory setting to obtain experimental data. Paper I examines how genomic GC-content can be reduced following a change in mutation rate and spectrum. Transcription-related biases in mutation location were found, but no replicative bias was detected. Paper II explores the distribution of fitness effects of random substitutions in two ribosomal protein genes using a highly sensitive fitness assay. The substitutions had a weakly deleterious effect, with low frequencies of both neutral and inactivating mutations. The surprising finding that synonymous and non-synonymous substitutions have very similar distribution of fitness effects suggests that, at least for these genes, fitness constraints are present mainly on the level of mRNA instead of protein. Paper III examines selective barriers to inter-species gene transfer by constructing mutants with a native gene replaced by an orthologue from another species. Results suggest that the fitness costs of these gene replacements are large enough to provide a barrier to this kind of horizontal gene transfer in nature. The paper also examines possible compensatory mechanisms that can reduce the cost of the poorly functioning alien genes and found that gene amplification acts as a first step to improve the selective contribution after transfer. Paper IV investigates the fitness constraints on horizontal gene transfer by inserting DNA from other species into the Salmonella chromosome. Results suggest that insertion of foreign DNA often is neutral and the manuscript provides new experimental data for theoretical analysis of interspecies genome variation and horizontal gene transfer between species.

O grande grupo heterogêneo de neuropatias periféricas hereditárias estão entre os casos mais comuns de perda sensitiva e fraqueza muscular em crianças e adolescentes. Pelo menos 84 genes estão envolvidos com neuropatias sensitivo-motoras hereditárias (NSMH), sendo suas formas de herança mais comuns as autossômico-dominantes desmielinizante e axonal e as neuropatias ligadas ao cromossomo X, e as mais raras as autossômicorecessivas desmielinizante e axonal e as formas ainda não classificadas. O gene HINT1, possuinte de 3 exons e localizado no cromossomo 5, codifica a proteína Histidine triad nucleotide binding protein 1, uma variante transcricional (mRNA) regulatória que hidroliza substratos. Recentemente mutações em HINT1 foram também relacionadas à neuropatias axonais com neuromiotonia (ARCMT2-NM), e portanto à CMT. O objetivo deste trabalho foi realizar o screening mutacional do gene HINT1 em uma amostra da população brasileira com quadro clínico de CMT recessivo (CMT2-AR), e foram encontradas 1 mutação silenciosa já previamente descrita, 1 polimorfismo exônico e 1 polimorfismo intrônico, também já conhecidos. Concluiu-se que mutações no gene HINT1 não são portanto responsáveis pela CMT-AR nesta amostra da população brasileira. / The large heterogeneous group of inherited peripheral neuropathies are among the most common causes of sensory loss and muscle weakness in children and adolescents. At least 84 genes are involved in inherited sensorymotor neuropathies (NSMH), being the demyelinating and axonal autosomaldominant and the X-linked neuropathies their most common forms of inheritance, and the demyelinating and axonal autosomal-recessive and not yet classified forms the most rare ones. The HINT1 gene, with 3 exons and located on chromosome 5, encodes the protein Histidine triad nucleotide binding protein 1, a regulatory transcriptional variant (mRNA) that hydrolyzes substrates. Recently, mutations in HINT1 were also related to axonal neuropathy with neuromyotonia (ARCMT2-NM), and therefore to CMT. The objective of this study was the mutational screening of the HINT1 gene in a sample of the Brazilian population with clinical recessive CMT (CMT2-AR), and 1 silent mutation previously described, 1 intronic polymorphism and 1 exonic polymorphism, both also known, were founded. It was then concluded that mutations in the HINT1 gene are not responsible for CMT2-AR in this particular sample of the Brazilian population.

Many Chinese classifiers are nearly synonymic – they can be used with the same head nouns without changing the meaning of the sentence, in other words, such classifiers can be used interchangeably or almost interchangeably. This poses a challenge for Chinese language learners, especially those who lack such a grammatical category in their own native language. Another complication arises from the ambiguous English translations of many classifiers. In this paper we investigate the collocation behavior of near-synonymous Chinese classifiers, focusing on their semantic nuances and interchangeability. Analyzing 6 pairs of classifiers — 栋 and 幢, 匹 and 头, 批 and 派, 颗 and 粒, 辆 and 台, and 根 and 支— drawn from the HSK exam glossary, the dataset for this study encompasses 1200 samples (100 per each variable) and 416 distinct head nouns. Through a corpus-based approach we analyze collocation behavior of each classifier on its own and as a part of the pair. The results showcase that not all pairs exhibit complete interchangeability. The collocation behavior of 批 and 派 differ significantly, where 批 primarily quantifies batches with a 'first' connotation, while 派 is used more in artistic expressions. The interchangeability of 栋 and 幢 varies with context. 幢 emerges as the least fre¬¬quent morpheme in the corpus, emphasizing its specific contextual usage. While both are used in address lines, 栋 predominantly quantifies standalone buildings, whereas 幢 is more aligned with larger architectural complexes. The analysis of 匹 and 头 highlights their distinctiveness, with 匹 counting horses and wolves and 头 being more versatile with various animals. 颗 and 粒 appear partially interchangeable, particularly with 珠-related head nouns and items associated with plants, fruits, and trees. The research also underscores that 辆 is primarily linked to car-related nouns, while 台 is used more versatile as a classifier for machines and electronic devices, including computers, printers, phones, cameras. 根 and 支 only overlap in the head noun 笔, and their roles diverge, with 根 being a versatile classifier and 支 also appearing as part of medical terms.