Diss. (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2005. / Härtill 4 uppsatser.

Thesis (Ph. D.)--University of Hong Kong, 2007. / Title proper from title frame. Also available in printed format.

Thesis (Ph. D.)--Duke University, 2007. / Includes bibliographical references.

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Vita. Bibliography: 163-187.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (p. 155-162).

A família gênica Forkhead P {FOXP) tem sido alvo de muitos estudos envolvendo evolução do cérebro e comportamento animal. Destacam-se particularmente as investigações com o gene FOXP2, que indicam que mudanças neste gene estariam associadas com a evolução da vocalização em algumas espécies de mamíferos, incluindo o Homo sapiens. Recentemente, estudos de desordem intrínseca de proteínas (IDPs) tem ganhado ênfase no contexto evolut ivo, visto que uma correlação posit iva entre regiões de desordem e altas taxas evolutivas tem sido observada. Através de um conjunto de abordagens que inclui predizer o conteúdo de desordem e os motivos lineares de interação, bem como as taxas evolutivas, buscamos desvendar a historia evolutiva dos genes da subfamília FOXP. Concentramos nossas análises sobre regiões desordenadas das proteínas FOXPl, FOXP2, FOXP3 e FOXP4 encontradas em 77 espécies de tetrápodes. Tais regiões proteicas são normalmente negligenciadas em estudos dessa natureza, pois se localizam fora de seus tra dicionais domínios conservados, normalmente associados à função principal da proteína. Sít ios apontados estando sob seleção positiva e relaxamento da restrição seletiva mostraram-se hotspots importantes para mudanças que podem impactar na capacidade de interação das proteínas. Encontramos que os maiores valores de w são mais prevalentes em regiões desordenadas que em ordenadas. Ainda, alto e similar valor de desordem (70%) foi encontrado nas 77 proteínas ortólogas de FOXPl , FOXP2, e FOXP4, indicando a manutenção de um "padrão geral" sobre um longo tempo evolutivo. Portanto, a variabilidade tanto de aminoácidos quanto de motivos lineares dentro das regiões de desordem foi marcante. A proteína FOXP3 apresentou menor nível de desordem (30%), mas signif icante sinal de seleção positiva em alguns sítios. Composição idênt ica de resíduo de aminoácido e/ou motivos lineares em espécies filogeneticamente distantes, indica clara convergência molecular, provavelmente associada a pressões seletivas similares. Sucessivamente, nossos achados mostraram uma clara diferença na composição de motivos lineares entre mamíferos e não mamíferos, dando suporte para a importância dos estudos de evolução da interatividade proteica para as compreensões de características taxa-específicas. / Forkhead Family P (FOXP) has been target of many studies about brain and behavior evo lution among species. FOXP2 receives special attention in academic society, due associations with vocalízation evolution in mammals, including Homo sapiens. Recently, intrinsically disorder proteins studies have gained emphasis in the evolutionary context, as positive correlation between disorder regions and higher evolutionary rate has been observed. Through a set of approaches, including disorder and linear motif predictions, as well as estimate evolutionary rates, we aimed to unveil the evolutionary history of FOXP subfamily genes. We focused our ana lysis over disordered regions of FOXPl, FOXP2, FOXP3 and FOXP4 proteins retrieved in 77 tetrapods. Such protein regions are usually neglected in studies of this nature, for being localized out of the traditional conserved domains, usua lly associated with the main function of the protein. Sites indicated as under relaxation of selective constrains or positive selection have shown to be important hotspots for changes that can impact in protein interaction capability. Higher w va lues are prevalent in disordered regions than in ordered ones. Still, high and similar disorder proportion (~70%) was found among 77 orthologues proteins of FOXPl, FOXP2 and FOXP4, indicating general pattern of disorder maintenance, along tetrapod's evolutionary tree. However, amino acid and linear motifs variability within disordered regions was observed. FOXP3 protein presented lower disorder leveis (~30%), when compared with other paralogues, but signal of positive selection was observed in some sites. ldentical composition of amino acid residues and/or linear motifs is, probably, associated with similar selective pressure. Successively, ou r results showed clear differences in linear motif composition between mammals and non-mammals, supporting the importance of evolutionary studies on protein interaction for the understanding of taxa-specifics characteristics.

A família gênica Forkhead P {FOXP) tem sido alvo de muitos estudos envolvendo evolução do cérebro e comportamento animal. Destacam-se particularmente as investigações com o gene FOXP2, que indicam que mudanças neste gene estariam associadas com a evolução da vocalização em algumas espécies de mamíferos, incluindo o Homo sapiens. Recentemente, estudos de desordem intrínseca de proteínas (IDPs) tem ganhado ênfase no contexto evolut ivo, visto que uma correlação posit iva entre regiões de desordem e altas taxas evolutivas tem sido observada. Através de um conjunto de abordagens que inclui predizer o conteúdo de desordem e os motivos lineares de interação, bem como as taxas evolutivas, buscamos desvendar a historia evolutiva dos genes da subfamília FOXP. Concentramos nossas análises sobre regiões desordenadas das proteínas FOXPl, FOXP2, FOXP3 e FOXP4 encontradas em 77 espécies de tetrápodes. Tais regiões proteicas são normalmente negligenciadas em estudos dessa natureza, pois se localizam fora de seus tra dicionais domínios conservados, normalmente associados à função principal da proteína. Sít ios apontados estando sob seleção positiva e relaxamento da restrição seletiva mostraram-se hotspots importantes para mudanças que podem impactar na capacidade de interação das proteínas. Encontramos que os maiores valores de w são mais prevalentes em regiões desordenadas que em ordenadas. Ainda, alto e similar valor de desordem (70%) foi encontrado nas 77 proteínas ortólogas de FOXPl , FOXP2, e FOXP4, indicando a manutenção de um "padrão geral" sobre um longo tempo evolutivo. Portanto, a variabilidade tanto de aminoácidos quanto de motivos lineares dentro das regiões de desordem foi marcante. A proteína FOXP3 apresentou menor nível de desordem (30%), mas signif icante sinal de seleção positiva em alguns sítios. Composição idênt ica de resíduo de aminoácido e/ou motivos lineares em espécies filogeneticamente distantes, indica clara convergência molecular, provavelmente associada a pressões seletivas similares. Sucessivamente, nossos achados mostraram uma clara diferença na composição de motivos lineares entre mamíferos e não mamíferos, dando suporte para a importância dos estudos de evolução da interatividade proteica para as compreensões de características taxa-específicas. / Forkhead Family P (FOXP) has been target of many studies about brain and behavior evo lution among species. FOXP2 receives special attention in academic society, due associations with vocalízation evolution in mammals, including Homo sapiens. Recently, intrinsically disorder proteins studies have gained emphasis in the evolutionary context, as positive correlation between disorder regions and higher evolutionary rate has been observed. Through a set of approaches, including disorder and linear motif predictions, as well as estimate evolutionary rates, we aimed to unveil the evolutionary history of FOXP subfamily genes. We focused our ana lysis over disordered regions of FOXPl, FOXP2, FOXP3 and FOXP4 proteins retrieved in 77 tetrapods. Such protein regions are usually neglected in studies of this nature, for being localized out of the traditional conserved domains, usua lly associated with the main function of the protein. Sites indicated as under relaxation of selective constrains or positive selection have shown to be important hotspots for changes that can impact in protein interaction capability. Higher w va lues are prevalent in disordered regions than in ordered ones. Still, high and similar disorder proportion (~70%) was found among 77 orthologues proteins of FOXPl, FOXP2 and FOXP4, indicating general pattern of disorder maintenance, along tetrapod's evolutionary tree. However, amino acid and linear motifs variability within disordered regions was observed. FOXP3 protein presented lower disorder leveis (~30%), when compared with other paralogues, but signal of positive selection was observed in some sites. ldentical composition of amino acid residues and/or linear motifs is, probably, associated with similar selective pressure. Successively, ou r results showed clear differences in linear motif composition between mammals and non-mammals, supporting the importance of evolutionary studies on protein interaction for the understanding of taxa-specifics characteristics.

The spun-out silk fiber consists of two fibroin filaments that are cemented together by sericin coating. The serine-rich sericins, which make 20-30% of the cocoon silk proteins in Bombyx mori, are dissolved in hot water during silk fiber reeling from the cocoon. The sericin extract is usually discarded. Only small amounts are currently used in cosmetics and lately also as replacement of bovine serum products in the cell culture media. The use in culture media is hindered by poor standardization of the extracts. To overcome this problem, we attempted preparation of several recombinant proteins based on partial sequences of one out of the three sericin genes of Bombyx mori, sericin 3. Translation product of the Ser3 gene is extremely serine-rich with a relatively high representation of the aspartate, asparagin, glutamate, and glutamine. Using specific primers we have prepared a cDNAs of 267, 279, 525, 672, and 528 bp, respectively, derived from the Ser3 gene. The cDNAs were cloned and expressed as fusion proteins with hexahistidine in Escherichia coli. The proteins were purified by affinity chromatography and analyzed by acrylamide electrophoresis. Ser3 gene contain repetitive motifs rich in serine and including some charged amino acids.

Dans ce document, nous étudions l’évitabilité de différentes formes de répétitions dans les mots. En particulier 3 des 6 chapitres sont dédiés aux répétitions abéliennes en lien notamment avec deux questions d’Erdős de 1957 et 1961. Nous commençons par montrer qu’il existe un algorithme décidant, sous certaines conditions, si un mot morphique évite des puissances abéliennes. Cet algorithme élargit la classe sur laquelle les précédents algorithmes pouvaient décider. Une généralisation de cet algorithme nous permet de montrer que les longs carrés abéliens sont évitables sur l’alphabet ternaire et que les carrés additifs sont évitables sur Z2 . Le premier résultat répond à une question ouverte de Mäkelä datant de 2003 alors que le deuxième rappelle la question ouverte de 1994 concernant l’évitabilité des carrés additifs sur Z.Une autre généralisation de notre algorithme permet d’étudier l’évitabilité des motifs au sens abélien. Nous montrons que les motifs binaires de longueur supérieure à 14 sont évitables sur l’alphabet binaire, améliorant la précédente borne de 118.Nous donnons des conditions suffisantes pour qu’un morphisme soit sans longues puissances nème k-abéliennes. Ce résultat nous permet de calculer, pour tout k ≥ 3, le nombre minimum de carrés k-abéliens qu’un mot binaire infini doit contenir en facteur. Il permet aussi de montrer que les longs carrés 2-abéliens sont évitables sur l’alphabet binaire et qu’il existe un mot ternaire qui ne contient qu’un seul carré 2-abélien en tant que facteur.Enfin, nous proposons une classification complète des formules binaires en fonction de la taille d’alphabet qu’il faut pour les éviter et du taux de croissance (exponentiel ou polynomial) du langage les évitant. / In this document, we study the avoidability of different kind of repetitions in words. We firstshow that under some conditions one can decide whether a morphic word avoids abelian n-thpowers. This algorithm can decide over a wider class of morphism than the previousalgorithms. We generalize this algorithm and use it to show that long abelian squares areavoidable over the ternary alphabet and that additive squares are avoidable over Z2 . The firstresult answers a weak version of a question formulated by Mäkelä in 2003 and the second oneis related to an open question from 1994 about the avoidability of additive squares over Z.Another generalization of this algorithm can be used to study avoidability of patterns in theabelian sense. In particular, we show that binary patterns of length more than 14 areavoidable over the binary alphabet in the abelian sense. This improves considerably theprevious bound of 118.We give sufficient conditions for a morphism to be long k-abelian n-th power-free. This resultallows us to compute for every k ≥ 3 the number of different k-abelian squares that a binaryword must contain. We prove that long 2-abelian squares are avoidable over the binaryalphabet and that over the ternary alphabet there exists a word that contains only one 2-abelian square.We also give a complete classification of binary formulas based on the size of the smallestalphabet over which they are avoidable and on the growth (exponential or polynomial) of theassociated language.