Com o avanço no desenvolvimento industrial sustentável estão sendo exploradas novas aplicações de uso dos subprodutos agroindustriais. O bagaço de uva obtido a partir da vinificação ou produção de sucos mantém importantes quantidades de polifenóis em suas cascas, sementes e engaço após o processamento, úteis para proteção da pele contra os raios ultravioleta. Neste contexto, o objetivo do nosso estudo foi caracterizar quimicamente o extrato do bagaço de uva Cabernet Sauvignon e avaliar a sua segurança e eficácia clínica em fotoprotetor tópico. Nesta dissertação, o extrato hidroetanólico (70% v/v) do bagaço de uva total, incluindo cascas, sementes e engaços de Vitis vinifera L., foi obtido por percolação seguido de liofilização. Os ensaios divididos em duas etapas: i) In vitro: determinação dos fenólicos totais (FT) usando Folin-Ciocalteu e expresso em equivalentes de ácido gálico (GAE); flavonoides por meio da reação com tricloreto de alumínio e expresso em quercetina; atividade antioxidante do extrato e das formulações através da desativação de radicais livres de DPPH• expressa em equivalentes de Trolox (TE); identificação dos principais compostos fenólicos do extrato bruto por espectrometria de massa (HPLC/ESI-MS/MS); desenvolvimento de nove formulações usando o delineamento experimental; medição dos valores de transmitância das formulações referentes ao fator de proteção solar (FPS), fotoestabilidade e fator de proteção UVA (FP-UVA) através do equipamento Labsphere UV-2000S® e ii) Em seres humanos, apenas duas formulações foram avaliadas clinicamente, C sem extrato e com filtros UVA e UVB: butilmetoxidibenzoilmetano, etil-hexilmetoxicinamato e etil-hexildimetil PABA (11,5% p/p) e D com extrato (bagaço de uva 10% p/p) e filtros UV. Inicialmente, a segurança dermatológica, irritabilidade e sensibilização; fototoxicidade e fotossensibilização foram avaliadas pelo Teste de Contato Repetitivo em Humanos (HRIPT). Posteriormente, a eficácia fotoprotetora clínica foi testada na pele de dez voluntários. O teor de FT encontrado no extrato de bagaço de uva foi de 141,11 ± 3,38 mg GAE.g-1 e de flavonoides 3,01 ± 0,14 mg QE.g-1. A eficácia antioxidante das soluções metanólicas com extrato e fotoprotetor na concentração de 1 mg.mL-1 em peso seco em pH 5 e 7 foram aproximadamente: 707 µmol TE.g-1 e 520 µmol TE.g-1, respectivamente. Isto significa uma queda em torno de 26,45% da capacidade antioxidante do extrato quando incorporado à formulação. Foram identificadas por espectrometria de massa dezenove substâncias fenólicas, entre elas dímeros e trímeros de procianidinas, di-hidroflavonol, flavonóis e antocianidinas. Os resultados demonstraram efeito sinérgico entre os filtros UV e extrato vegetal no FPS e efeito antagônico com a variação do tempo de irradiação sobre as respostas do FPS, atividade antioxidante, comprimento de onda crítico, proteção UVA, proteção UVB e razão UVA/UVB. A melhor combinação eficiência-resposta foi detectada na formulação D com um aumento do FPS in vitro em cerca de 210%. Os testes de segurança não induziram qualquer reação adversa. A eficácia fotoprotetora clínica de D foi 21% (10,20 - 12,30) superior em relação à formulação C, demonstrando maior eficiência na proteção UVA. Sendo assim, C e D foram consideradas seguras para uso tópico e D estatisticamente superior tanto na proteção UVA quanto UVB comparado à amostra só associada de filtros. Logo, o bagaço de uva é um promissor ingrediente sustentável multifuncional útil para o uso em protetor solar. / With the advance in sustainable industrial development, new applications of agro-industrial by-products are being explored. Grape pomace obtained from winemaking or juice production keeps important amounts of polyphenols in their skins, seeds and stalks after processing that are useful for protection of skin against ultraviolet rays. In this context, the objective of our study was to chemically characterize Cabernet Sauvignon pomace extract and to evaluate its safety and clinical efficacy in topical photoprotector. The hydroethanolic extract (70% v/v) of the Vitis vinifera L. whole grape pomace, including seeds, skins and stalks, was obtained by percolation after lyophilization. The tests were divided into two stages: i) In vitro: total phenols (TF) using Folin-Ciocalteu and expressed in Gallic Acid Equivalent (GAE); flavonoids by reaction with aluminum trichloride and expressed as quercetin; antioxidant activity of the extract and formulations by inhibition by DPPH• expressed as Trolox equivalents (TE); identification of the main phenolic compounds of the crude extract by mass spectrometry (HPLC/ESI-MS/MS); development of nine formulations using experimental design and evaluated the SPF, photostability and UVA protection factor (UVA-PF) through the Labsphere UV-2000S® equipment; ii) In humans, only two formulations were clinically evaluated, C without extract and with UVA and UVB filters: butilmetoxidibenzoilmetano, etil-hexilmetoxicinamato and etil-hexildimetil PABA (11.5% w/w) and D with extract (10% w/w grape pomace) and filters UV. Initially, the dermatological safety, irritability and sensitization; phototoxicity and photosensitization were evaluated by the Human Repeat Insult Patch Test (HRIPT). After, the clinical photoprotective efficacy was tested on the skin of ten volunteers. The FT content found in the dried extract was 141.11 ± 3.38 mg GAE.g-1 and flavonoids 3.01 ± 0.14 mg QE.g-1. The antioxidant potential of the methanolic solutions with extracts and photoprotectors at the concentration of 1 mg.ml-1 in dry weight and at pH 5 and 7 were around: 707 µmol TE.g-1 and 520 µmol TE.g-1, respectively. This means a drop of about 26.45% of the antioxidant capacity of the extract when incorporated into the formulation. Mass spectrometry identified nineteen phenolic substances, among them procyanidins dimers and trimmers, di-hydroflavonol, flavonols and anthocyanin. The results showed a synergistic effect between the UV filters and the herbal extract in the SPF and the antagonistic effect with the variance of the irradiation time in the SPF responses, antioxidant activity, critical wavelength, UVA protection, UVB protection and UVA/UVB ratio. The best efficiency-response combination was detected in the D formulation with an in vitro SPF increase of about 210%. Safety tests did not induce any adverse reaction. The clinical efficiency of D photoprotection was 21% (10.20 - 12.30) higher than the C formulation, demonstrating high efficiency in UVA protection. Thus, C and D were considered safe for topical use and D statistically superior in both UVA and UVB protection to the only combined sample of filters. Therefore, grape pomace is a promising multifunctional sustainable ingredient qualified to be used in sunscreen industry.

Introdução: A cesárea vem aumentando progressivamente no Brasil e no mundo. Dentre os fatores associados a esse evento, destaca-se a cesárea prévia. Embora a maioria dos partos realizados em mulheres com história de cesárea seja cirúrgico, autores tem demonstrado altos índices de partos vaginais após cesárea - PVAC com baixa incidência de complicações. Diante do alarmante crescimento das taxas de cesárea, o presente estudo objetiva identificar a proporção e o perfil das mães com história de repetição de cesárea - RC no Estado de São Paulo, em 2012. Métodos: Os dados provenientes do Sistema de Informações Sobre Nascidos Vivos foram vinculados aos do Cadastro Nacional de Estabelecimentos de Saúde. Os resultados a respeito das características das mães com história de RC foram analisados segundo características da gestação, do recém-nascido RN e segundo tipo do hospital do parto. Os dados foram descritos na forma de medidas de proporção (frequências), com diferenças entre variáveis de interesse verificadas pelos testes de proporção e de médias (nível de significância de 5 por cento ). Resultados: Foram estudados 273.329 nascidos vivos de mães com pelo menos um filho anterior. Destes, 43 por cento nasceram por RC e 7,4 por cento por PVAC. As mães que realizaram CR são mais velhas e mais escolarizadas e os RNs nascidos desse grupo apresentaram menor proporção de baixo peso ao nascer. O início do pré-natal no primeiro trimestre e a realização de 7 ou mais consultas de pré-natal foi mais frequente no grupo CR. Termo precoce foi a classificação mais frequente para idade gestacional dos que nasceram por CR. Em contrapartida, os RNs por parto vaginal apresentaram maiores proporções de termo tardio do que aqueles por repetição de cesárea. A RC foi mais frequente nos hospitais sem vínculo com o Sistema Único de Saúde - SUS (44,1 por cento ). Dentre esses, a maioria (54,3 por cento ) teve idade gestacional classificada como termo precoce. Somente o grupo SUS alcança uma melhor proporção de termo pleno (46,5 por cento ), contudo esse grupo tem a frequência mais elevada de termos tardios (10,9 por cento ). Conclusão: As altas taxas de cesárea de repetição, principalmente no setor privado, evidenciam a necessidade de melhoras no modelo de atenção ao parto no Estado de São Paulo. / Background: Cesarean section has been progressively increasing in Brazil and worldwide. Among the factors associated with this event stands out a prior cesarean delivery. Although most deliveries in women with a prior cesarean delivery is surgical, authors have demonstrated high levels of vaginal births after cesarean - VBAC with low incidence of complications. Given the alarming increase in cesarean rates, this study aims to identify the proportion and profile of mothers with repeat cesarean delivery - RCD in the State of São Paulo, in 2012. Methods: Data from Live Births Information Systems were linked to the National Health Establishments Registration. The results about the characteristics of mothers with RCD were analyzed according to characteristics of pregnancy, newborn and type of maternity hospital. Data were presented in the form of proportion measures (frequencies), with differences between variables of interest verified by the proportion and average tests (5 per cent significance level). Results: 273 329 live births of mothers with at least one previous child were studied. 43 per cent of these were born by RCD and 7.4 per cent by PVAC. Mothers who underwent RCD are older and more highly educated and newborn infants in this group had a lower incidence of low birth weight. The beginning of prenatal care in the first trimester and the realization of 7 or more prenatal visits was more frequent in the RCD group. Early term was the most frequent rating for gestational age born by RCD. In contrast, newborns by vaginal delivery had greater proportions of late term than those by repeat cesarean. The RCD was more common in hospitals not affiliated with the Unified Health System - UHS (44.1 per cent ). In these, the majority (54.3 per cent ) of newborn had gestational age of early term. Only the UHS group achieves a better proportion of full term (46.5 per cent ), however, this group has the highest frequency of late terms (10.9 per cent ). Conclusion: The high repeat cesarean rates, especially in the private sector, highlight the need for improvements in childbirth care model in São Paulo.

<p>Kratki uzastopni ponovci predstavljaju klasu mikrosatelitskih segmenata DNK, rasprostranjenih &scaron;irom genoma čoveka. Građeni su od uzastopno ponavljajućih sekvenci dužine 2-6 parova nukleotida. Zahvaljujući različitom broju ponavljanja repetitivne jedinice, većina mikrosatelitskih markera pokazuje visok stepen polimorfizma dužine, koji je moguće ispitati primenom tehnike lančane reakcije polimeraze. Pored utvrđivanja spornih srodničkih odnosa, analiza X hromozom mikrosatelitskih markera može se uspe&scaron;no koristiti i u oblastima kriminalistike, humane identifikacije, populaciono-genetičkim i demografskim istraživanjima i dr. Cilj istraživanja je izrada populacione studije, iz koje će se izračunati broj i frekvencija alela, struktura i frekvencija haplotipova, utvrditi vrednosti relevantnih statističkih parametara, oceniti mogućnost primene analize X-STR markera u slučajevima iz oblasti medicinske kriminalistike, humane identifikacije i ve&scaron;tačenja spornih srodničkih odnosa u populaciji Vojvodine. Istraživanjem je obuhvaćeno 200 odraslih, međusobno nesrodnih osoba. Izolacija DNK materijala iz krvnih mrlja vr&scaron;ena je Chelex metodom, a amplifikacija dobijenih uzoraka DNK metodom PCR, uz kori&scaron;ćenje komercijalnog Mentype&reg; Argus X-12 PCR Amplification Kit &ndash; a. Razdvajanje i detekcija dobijenih fragmenata izvr&scaron;eno je kapilarnom elektroforezom GeneScan i Genotyper programom. Statististička obrada rezultata izvr&scaron;ena je pomoću Arlequin i GENEPOP programa. Za vizuelizaciju interpopulacionih genetičkih odnosa, upotrebljen je program POPTREE2 i koordinatna analiza (Principal Coordinate Analysis - PCoA). Dobijeni rezultati ukazuju da se analiza ispitivanih X-STR markera može uspe&scaron;no primeniti u slučajevima iz oblasti medicinske kriminalistike, humane identifikacije i ve&scaron;tačenja spornih srodničkih odnosa u populaciji Vojvodine, kao i da mogu poslužiti kao osnova za dalja istraživanja u&nbsp; populacionogenetičkim, antropolo&scaron;kim, demografskim i drugim oblastima.</p> / <p>Short tandem repeats (STR) represent a class of microsatellites, widely spread throughout the human genome, consisting of tandemly repeated sequences of 2-6 bp. Related to variation in the number of repeat unit displayed, most of microsatellites show a high degree of length polymorphism, investigated by the PCR techniques. The aim of this research is to create a population study, which will be used to calculate allele and haplotype frequencies, determine the value of relevant statistical parameters and assess the possibility of applying X-STR markers analysis in the fields of forensics, human identification and kinship testing. The study included 200 unrelated adults. DNA isolation was performed by Chelex method and DNA amplification by PCR, using commercial Mentype Argus X-12 PCR Amplification Kit. Separation and detection of fragments was obtained by capillary electrophoresis using Gene Scanand Genotyper program. Statistical analysis of the result was performed using Arlequin and GENEPOP program. For visualization of inter population genetic distances POPTREE2 program and coordinate analysis (PCoA) was used. The results show that the analysis of X-STR markers can be successfully applied in the field of forensics, human identification and kinship testing in the population of Vojvodina, as well as to serve as a basis for further research in population genetic, anthropological, demographic and other scientific areas.</p>

Com o avanço no desenvolvimento industrial sustentável estão sendo exploradas novas aplicações de uso dos subprodutos agroindustriais. O bagaço de uva obtido a partir da vinificação ou produção de sucos mantém importantes quantidades de polifenóis em suas cascas, sementes e engaço após o processamento, úteis para proteção da pele contra os raios ultravioleta. Neste contexto, o objetivo do nosso estudo foi caracterizar quimicamente o extrato do bagaço de uva Cabernet Sauvignon e avaliar a sua segurança e eficácia clínica em fotoprotetor tópico. Nesta dissertação, o extrato hidroetanólico (70% v/v) do bagaço de uva total, incluindo cascas, sementes e engaços de Vitis vinifera L., foi obtido por percolação seguido de liofilização. Os ensaios divididos em duas etapas: i) In vitro: determinação dos fenólicos totais (FT) usando Folin-Ciocalteu e expresso em equivalentes de ácido gálico (GAE); flavonoides por meio da reação com tricloreto de alumínio e expresso em quercetina; atividade antioxidante do extrato e das formulações através da desativação de radicais livres de DPPH&#8226; expressa em equivalentes de Trolox (TE); identificação dos principais compostos fenólicos do extrato bruto por espectrometria de massa (HPLC/ESI-MS/MS); desenvolvimento de nove formulações usando o delineamento experimental; medição dos valores de transmitância das formulações referentes ao fator de proteção solar (FPS), fotoestabilidade e fator de proteção UVA (FP-UVA) através do equipamento Labsphere UV-2000S® e ii) Em seres humanos, apenas duas formulações foram avaliadas clinicamente, C sem extrato e com filtros UVA e UVB: butilmetoxidibenzoilmetano, etil-hexilmetoxicinamato e etil-hexildimetil PABA (11,5% p/p) e D com extrato (bagaço de uva 10% p/p) e filtros UV. Inicialmente, a segurança dermatológica, irritabilidade e sensibilização; fototoxicidade e fotossensibilização foram avaliadas pelo Teste de Contato Repetitivo em Humanos (HRIPT). Posteriormente, a eficácia fotoprotetora clínica foi testada na pele de dez voluntários. O teor de FT encontrado no extrato de bagaço de uva foi de 141,11 ± 3,38 mg GAE.g-1 e de flavonoides 3,01 ± 0,14 mg QE.g-1. A eficácia antioxidante das soluções metanólicas com extrato e fotoprotetor na concentração de 1 mg.mL-1 em peso seco em pH 5 e 7 foram aproximadamente: 707 &#181;mol TE.g-1 e 520 &#181;mol TE.g-1, respectivamente. Isto significa uma queda em torno de 26,45% da capacidade antioxidante do extrato quando incorporado à formulação. Foram identificadas por espectrometria de massa dezenove substâncias fenólicas, entre elas dímeros e trímeros de procianidinas, di-hidroflavonol, flavonóis e antocianidinas. Os resultados demonstraram efeito sinérgico entre os filtros UV e extrato vegetal no FPS e efeito antagônico com a variação do tempo de irradiação sobre as respostas do FPS, atividade antioxidante, comprimento de onda crítico, proteção UVA, proteção UVB e razão UVA/UVB. A melhor combinação eficiência-resposta foi detectada na formulação D com um aumento do FPS in vitro em cerca de 210%. Os testes de segurança não induziram qualquer reação adversa. A eficácia fotoprotetora clínica de D foi 21% (10,20 - 12,30) superior em relação à formulação C, demonstrando maior eficiência na proteção UVA. Sendo assim, C e D foram consideradas seguras para uso tópico e D estatisticamente superior tanto na proteção UVA quanto UVB comparado à amostra só associada de filtros. Logo, o bagaço de uva é um promissor ingrediente sustentável multifuncional útil para o uso em protetor solar. / With the advance in sustainable industrial development, new applications of agro-industrial by-products are being explored. Grape pomace obtained from winemaking or juice production keeps important amounts of polyphenols in their skins, seeds and stalks after processing that are useful for protection of skin against ultraviolet rays. In this context, the objective of our study was to chemically characterize Cabernet Sauvignon pomace extract and to evaluate its safety and clinical efficacy in topical photoprotector. The hydroethanolic extract (70% v/v) of the Vitis vinifera L. whole grape pomace, including seeds, skins and stalks, was obtained by percolation after lyophilization. The tests were divided into two stages: i) In vitro: total phenols (TF) using Folin-Ciocalteu and expressed in Gallic Acid Equivalent (GAE); flavonoids by reaction with aluminum trichloride and expressed as quercetin; antioxidant activity of the extract and formulations by inhibition by DPPH&#8226; expressed as Trolox equivalents (TE); identification of the main phenolic compounds of the crude extract by mass spectrometry (HPLC/ESI-MS/MS); development of nine formulations using experimental design and evaluated the SPF, photostability and UVA protection factor (UVA-PF) through the Labsphere UV-2000S® equipment; ii) In humans, only two formulations were clinically evaluated, C without extract and with UVA and UVB filters: butilmetoxidibenzoilmetano, etil-hexilmetoxicinamato and etil-hexildimetil PABA (11.5% w/w) and D with extract (10% w/w grape pomace) and filters UV. Initially, the dermatological safety, irritability and sensitization; phototoxicity and photosensitization were evaluated by the Human Repeat Insult Patch Test (HRIPT). After, the clinical photoprotective efficacy was tested on the skin of ten volunteers. The FT content found in the dried extract was 141.11 ± 3.38 mg GAE.g-1 and flavonoids 3.01 ± 0.14 mg QE.g-1. The antioxidant potential of the methanolic solutions with extracts and photoprotectors at the concentration of 1 mg.ml-1 in dry weight and at pH 5 and 7 were around: 707 &#181;mol TE.g-1 and 520 &#181;mol TE.g-1, respectively. This means a drop of about 26.45% of the antioxidant capacity of the extract when incorporated into the formulation. Mass spectrometry identified nineteen phenolic substances, among them procyanidins dimers and trimmers, di-hydroflavonol, flavonols and anthocyanin. The results showed a synergistic effect between the UV filters and the herbal extract in the SPF and the antagonistic effect with the variance of the irradiation time in the SPF responses, antioxidant activity, critical wavelength, UVA protection, UVB protection and UVA/UVB ratio. The best efficiency-response combination was detected in the D formulation with an in vitro SPF increase of about 210%. Safety tests did not induce any adverse reaction. The clinical efficiency of D photoprotection was 21% (10.20 - 12.30) higher than the C formulation, demonstrating high efficiency in UVA protection. Thus, C and D were considered safe for topical use and D statistically superior in both UVA and UVB protection to the only combined sample of filters. Therefore, grape pomace is a promising multifunctional sustainable ingredient qualified to be used in sunscreen industry.

Esta tese é estruturada em dois capítulos. O primeiro capítulo explora os retrotransposons com LTR (LTR-RT) em cana-de-açúcar e grande parte de seus resultados foram publicados no artigo \'\'Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns\'\'. Nossos resultados mostraram que as diferentes famílias de LTR-RT em cana-de-açúcar possuem estruturas e regulação distintas. O segundo capítulo desta tese visa responder a perguntas que surgiram durante a primeira metade deste trabalho, mas ao invés de focar no genoma de uma planta optamos por trabalhar com linhagem Del de LTR-RT em dez genomas de angiospermas sequenciados. Os resultados desta parte do trabalho foram submetidos para publicação no artigo intitulado \'\'Virus-like attachment sites and plastic CpG islands: landmarks of diversity in plant Del retrotransposons\'\'. Os resultados mostraram que a LTR é uma região dinâmica e importante para a evolução dos LTR-RTs. Nós especulamos que mudanças nas LTR atuem como gatilhos para a diversificação dos LTR-RTs. / This doctoral thesis is structured in two chapters. In the first chapter we explore the LTRretrotransposons (LTR-RT) in sugarcane, these results were published in an article entitled \'\'Analysis of plant LTR-etrotransposons at the fine-scale family level reveals individual molecular patterns\'\'. In this paper we show that different sugarcane LTR-RT families have distinct structure and are differentially regulated. In the second chapter we try to find answers to questions that came up in the first half of this work, but instead of focusing in one plant genome we chose to work with the Del lineage of LTR-RT in tem angiosperm sequenced genomes. These results are submitted to publication as an article entitled \'\'Virus-like attachment sites and plastic CpG islands: landmarks of diversity in plant Del retrotransposons\'\'. Our results indicate that the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.

<p>Sexual assault is a significant problem facing the South African society. In this context, efficient but also affordable genotyping systems are needed for positive identification of criminals in incidences of sexual violence. The aim of this study was therefore to develop non-commercial Y-STR genotyping systems suitable for sexual assault cases in South Africa. Y-chromosome STR loci constituting the minimal haplotype are still the most widely used loci in investigating sexual assault cases despite the fact that DYS391 and DYS392 have shown low levels of polymorphism in Xhosa populations in Cape Town. The minimal haplotype was, therefore, further investigated in the Cape Muslim population. The Cape Muslim population generally exhibited high GD values among all the South African populations. These values were higher than 0.5 for most loci, and ranged from 0.447 for DYS391 to 0.957 for DYS385. The highest number of alleles in most loci was also recorded in this population. The overall assessment of the minimal haplotype has shown that this system is still a useful in investigating sexual assault case in many South African subpopulations. Therefore the exercise of internal validation of the minimal haplotype system was successfully carried out in the laboratory. iii The properties of additional novel and widely used STRs were also investigated in this study. Loci were successfully sequenced and allele nomenclature was assigned to them according to the ISFG guidelines.</p>

<p>Ankyrin repeats (ARs) are polypeptide motifs identified in thousands of proteins. Many AR proteins play a function as scaffolds in protein-protein interactions which may require specific mechanical properties. Also, a number of AR proteins have been proposed to mediate mechanotransduction in a variety of different functional settings. The folding and stability of a number of AR proteins have been studied in detail by chemical and temperature denaturation experiments, yet the mechanic of AR proteins remain largely unknown. In this dissertation, we have researched the mechanical properties of AR proteins by using protein engineering and a combination of atomic force microscopy (AFM)-based single-molecule force spectroscopy and steered molecular dynamics (SMD) simulations. Three kinds of AR proteins were investigated: NI6C (synthetic AR protein), D34 (of ankyrin-R) and gankyrin (oncoprotein). While the main focus of this research was to characterize the response of AR proteins to mechanical forces, our results extended beyond the protein nanomechanics to the understanding of protein folding mechanisms.</p> / Dissertation

In this study, strawberry fruit was taken as the studied model. An attempt was carried on trying to identify a unique DNA fingerprint in each of the selected different strawberry cultivars of Fragaria x ananassa Duch species available in Turkey. The basis of the study was to examine the fruit characteristics at the molecular level rather than at the morphological level. It is of great importance to differentiate and trace the origin of any variety by examining its DNA by using a very sophisticated molecular technique. In this case, DNA fingerprinting technique depending on the Simple Sequence Repeats (SSRs) markers which are also called Microsatellite markers were used. DNA fingerprinting technique reveals the specific DNA profile which is unique as a fingerprint for a fruit specimen and this DNA profile is the same and constant throughout different parts of the fruit as well as its developmental stages. In this thesis work, nine primers flanking the SSR markers already available in the online databases were designed hoping to detect SSRs that could differentiate among the five selected cultivars of strawberry.

Αντικείμενο της παρούσας διδακτορικής διατριβής είναι η μελέτη και η σχεδίαση αποδοτικών αλγορίθμων για τη διαχείριση και ανάλυση ακολουθιών βιολογικών δεδομένων. Οι αλγόριθμοι που θα περιγράψουμε εφαρμόζονται σε προβλήματα Βιοπληροφορικής, όπως η αναγνώριση γνωστών ή άγνωστων μοτίβων του DNA και RNA, που εμπλέκονται σε ποικίλες βιολογικές διεργασίες καθώς και η ανακάλυψη περιοδικοτήτων. Ειδικότερα οι αλγόριθμοι που θα παρουσιάσουμε χρησιμοποιούνται για την ανάλυση Βιολογικών Ακολουθιών με “αδιάφορους χαρακτήρες” και Βιολογικών Ακολουθιών με Βάρη. Οι Βιολογικές Ακολουθίες με “αδιάφορους χαρακτήρες” αναπαριστούν συνήθως οικογένειες πρωτεϊνών ενώ οι Βιολογικές Ακολουθίες με βάρη αναπαριστούν συναρμολογούμένες ακολουθίες γονιδιωμάτων που έχουν πρόσφατα αλληλουχηθεί. Στις Βιολογικές Ακολουθίες με αδιάφορους χαρακτήρες παρουσιάζουμε δυο αποδοτικούς αλγορίθμους γραμμικού χρόνου για τον υπολογισμό της περιόδου και τον υπολογισμό του καλύμματος. Ο δεύτερος αλγόριθμος εφαρμόζεται και σε κυκλικά (circular DNAs). Στις Βιολογικές Ακολουθίες με βάρη παρουσιάζουμε δυο αλγορίθμους για τον υπολογισμό των βασικών περιοδικοτήτων: της περιόδου και του καλύμματος ενώ επιλύουμε και το πρόβλημα της εύρεσης προτύπου. Η ανάγκη για αποδοτική διαχείριση βιολογικών ακολουθιών με βάρη μας ώθησε να εισάγουμε μια νέα αποδοτική δομή η οποία επιλύει αποδοτικά τα 2 προηγούμενα προβλήματα. Η δομή αυτή ονομάζεται Δέντρο Επιθεμάτων με Βάρη. Χρησιμοποιώντας το Δέντρο Επιθεμάτων με Βάρη επιλύουμε διάφορες παραλλαγές του προβλήματος εξαγωγής μοτίβων από Βιολογικές Ακολουθίες με Βάρη. Τέλος αποφασίσαμε να μελετήσουμε τη χρήση των Γενετικών Αλγορίθμων και του Εξελικτικού Προγραμματισμού στην ανάλυση ακολουθιών βιολογικών δεδομένων. Αποτέλεσμα αυτής της μελέτης είναι η περιγραφή ενός γενετικού αλγορίθμου που υπολογίζει τις επαναλήψεις σε μια βιολογική ακολουθία. / The object of this doctoral thesis is the study and the design of efficient algorithms for the analysis of sequences of biological data. The algorithms that we describe have application on Bioinformatics problems, such as the recognition of known or unknown patterns in DNA and RNA that are involved in various biological activities, as well as the discovery of periodicities. More specifically the algorithms that we present are used for the analysis of Biological Sequences with “don't care characters”' and Weighted Biological Sequences. Biological Sequences with “don't care characters”, usually represent protein families while Weighted Biological Sequences represent assembled sequences of genomes that they have been recently sequenced. In Biological Sequences with “don't care characters”' we present two efficient algorithms of linear time for the computation of the period and the cover. The second algorithm is also applied in circular DNAs . In Weighted Biological Sequences we present two algorithms for the computation of basic periodicities: the period and the cover, while we also solve the problem of pattern matching. The need for efficient management of biological sequences with weights prompted us to introduce a new efficient data structure which solves efficiently the two precedents problems. This structure is named Weighted Suffix Tree. Using the Weighted Suffix Tree we solve various instances of the motif discovery problem in Biological Weighted Sequences. Finally we decided to study the use of Genetic Algorithms and Evolutionary Programming in the analysis of biological sequences. The result of this study is the description of a genetic algorithm that computes the repetitions in a biological sequence.

<p>Sexual assault is a significant problem facing the South African society. In this context, efficient but also affordable genotyping systems are needed for positive identification of criminals in incidences of sexual violence. The aim of this study was therefore to develop non-commercial Y-STR genotyping systems suitable for sexual assault cases in South Africa. Y-chromosome STR loci constituting the minimal haplotype are still the most widely used loci in investigating sexual assault cases despite the fact that DYS391 and DYS392 have shown low levels of polymorphism in Xhosa populations in Cape Town. The minimal haplotype was, therefore, further investigated in the Cape Muslim population. The Cape Muslim population generally exhibited high GD values among all the South African populations. These values were higher than 0.5 for most loci, and ranged from 0.447 for DYS391 to 0.957 for DYS385. The highest number of alleles in most loci was also recorded in this population. The overall assessment of the minimal haplotype has shown that this system is still a useful in investigating sexual assault case in many South African subpopulations. Therefore the exercise of internal validation of the minimal haplotype system was successfully carried out in the laboratory. iii The properties of additional novel and widely used STRs were also investigated in this study. Loci were successfully sequenced and allele nomenclature was assigned to them according to the ISFG guidelines.</p>