Unlike the autosomes, the Y chromosome in humans and other primates has few protein coding genes, with only a few dozen single-copy genes and several tandem duplicated gene families, called the "ampliconic" genes. The interaction of many biological and evolutionary factors is responsible for this structural heterogeneity among different parts of the genome. We sequenced and assayed the copy numbers of Y-linked, single-copy genes and ampliconic genes in a group of closely related macaque monkeys, then fit models of gene family evolution to this data along with whole genome data from human, chimpanzee, and rhesus macaque. Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys, (ii) indicate that ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome, and that (iii) Y-linked singleton and autosomal gene families evolved faster in great apes than they do in other Old World higher Primates. These findings highlight the evolutionary eccentricity of duplicated genes on the Y chromosome and suggest an important role for natural selection and gene conversion in the evolution of Y-linked gene duplicates. / Thesis / Master of Science (MSc)

Atualmente a procura por produtos sustentáveis têm-se mostrado cada vez mais frequente e promissora. Em espécies de importância comercial, procura-se obter a maior produtividade possível dentro de um curto espaço de tempo aliado à preservação do meio ambiente. Dentro disso, a transformação genética de plantas se mostra uma alternativa atrativa para a geração de variedades de cana-de-açúcar que gerem produtos de maneira mais eficaz. O sucesso da transformação genética está diretamente associada a cultura de tecidos de plantas que precisa ser adequada a cada genótipo e situação de cultivo, sendo a luminosidade um dos principais fatores para a produção de plantas vigorosas. Outro fator importante é a seleção das plantas transgênicas, que precisam ser submetidas a uma quantidade de agente seletivo suficiente para identificar as plantas modificadas geneticamente. Em cana-de-açúcar, a identificação de plantas transgênicas por PCR e a definição do número de cópias é um procedimento de difícil execução e muito oneroso. Isto se dá pois no processo transformação via biolística, a inserção de genes é aleatória, produzindo plantas com variados números de cópias. Em consideração a estes fatores envolvidos na eficiência de obtenção de plantas transgênicas de cana-de-açúcar, os objetivos deste trabalho foram o aperfeiçoamento do protocolo de cultura de tecidos, transformação genética da variedade SP803280 com os genes xth, AtDdm1, como também, definir genes de referência para a quantificação do número de cópias dos genes xth e AtDdm1 inseridos na variedade SP803280 e do gene neo na RB835089, análise de ploidia e tamanho de genoma dos eventos transgênicos comparado com as plantas controle. No estudo a respeito da melhor qualidade de luz durante o cultivo in vitro na fase de regeneração de plantas, tem-se que a luz branca e a junção das luzes LED e branca se mostraram melhores para regeneração e desenvolvimento das plantas enquanto que para plântulas, as luzes LED e branca separadamente foram mais efetivas no crescimento. Para a seleção das plantas uma concentração de geneticina entre 40 e 50 mgL-1 é recomendada. As taxas de sucesso nas transformações genéticas para o gene xth variaram entre 2,5 a 18,3% dependendo do experimento e para AtDdm1 foi de 2,2% em um bombardeamento.Não houveram alterações de ploidia e tamanho do genoma nos transgênicos das duas variedades em relação à planta selvagem. Os genes p4h e prr foram identificados como os melhores para a quantificação relativa de genes inseridos por PCR em tempo real na variedade SP803280 enquanto que para a RB835089 aprt e prr se mostraram mais eficazes. A análise do número de cópias inseridas em eventos transgênicos por PCR em tempo real foi possível através das duas metodologias de cálculo testados por este trabalho, com resultados que concordam com uma tendência nesta determinação de maneira simples e rápida. / Currently the demand for sustainable products has been shown to be frequent and promising. In species of commercial importance, there is an effort to obtain the highest possible productivity in a short time, along with the environment preservation. In this context, genetic transformation of plants appears as an attractive alternative for the development of sugarcane varieties able to generate products in a more effective way. The genetic transformation success is directly associated to plant tissue culture that requires specific condition for each genotype and cultivation process, in which, luminosity is one of the main factors that determines the production of vigorous plants. Another important factor is the selection of transgenic plants, that occur by exposing plants to a sufficient amount of selective agent in order to identify only genetic modified plants. In sugarcane, identification of transgenic plants by PCR and the definition of copy numbers is a difficult procedure to implement and usually is very costly. It is because in the process of genetic transformation by biolistic, the insertion of genes occurs randomly and also produce plants with varied copy numbers. In consideration of these factors directly involved in the efficiency to obtain sugarcane transgenic plants the objectives of this study were the improvement of a tissue culture protocol, the genetic transformation of the variety SP803280 with xth and AtDdm1 genes. Also, the studies include the definition of reference genes for determining the number of copies inserted of xth and AtDdm1 genes into the variety SP803280 and neo gene in RB835089, ploidy analysis and genome size of the transgenic events compared to control plants. In the study related to the best light quality for in vitro plant regeneration, white light and the combination of LED and white lights proved to be better for plants regeneration and development while for seedlings, LED and white light separately were more effective for growth. In order to obtain selection of transgenic plants, geneticin concentration between 40 and 50 mg L-1 is recommended. Success rates in xth genetic transformation ranged from 2.5 to 18.3% depending on the experiment, and for AtDdm1 was only 2.2% in just one biolistic bombardment. There were no changes in ploidy and genome size in transgenic events related to their wild type plant. The genes p4h and prr were defined to be the best for determining the copy number of transgenic events by real time PCR in SP803280 variety, while for RB835089, the genes aprt and prr were the most effective. The analysis of the number of inserted copies was possible using the two calculation methodologies tested by this work, with results that agree with a tendency in a simple and fast quantification methodology.

Atualmente a procura por produtos sustentáveis têm-se mostrado cada vez mais frequente e promissora. Em espécies de importância comercial, procura-se obter a maior produtividade possível dentro de um curto espaço de tempo aliado à preservação do meio ambiente. Dentro disso, a transformação genética de plantas se mostra uma alternativa atrativa para a geração de variedades de cana-de-açúcar que gerem produtos de maneira mais eficaz. O sucesso da transformação genética está diretamente associada a cultura de tecidos de plantas que precisa ser adequada a cada genótipo e situação de cultivo, sendo a luminosidade um dos principais fatores para a produção de plantas vigorosas. Outro fator importante é a seleção das plantas transgênicas, que precisam ser submetidas a uma quantidade de agente seletivo suficiente para identificar as plantas modificadas geneticamente. Em cana-de-açúcar, a identificação de plantas transgênicas por PCR e a definição do número de cópias é um procedimento de difícil execução e muito oneroso. Isto se dá pois no processo transformação via biolística, a inserção de genes é aleatória, produzindo plantas com variados números de cópias. Em consideração a estes fatores envolvidos na eficiência de obtenção de plantas transgênicas de cana-de-açúcar, os objetivos deste trabalho foram o aperfeiçoamento do protocolo de cultura de tecidos, transformação genética da variedade SP803280 com os genes xth, AtDdm1, como também, definir genes de referência para a quantificação do número de cópias dos genes xth e AtDdm1 inseridos na variedade SP803280 e do gene neo na RB835089, análise de ploidia e tamanho de genoma dos eventos transgênicos comparado com as plantas controle. No estudo a respeito da melhor qualidade de luz durante o cultivo in vitro na fase de regeneração de plantas, tem-se que a luz branca e a junção das luzes LED e branca se mostraram melhores para regeneração e desenvolvimento das plantas enquanto que para plântulas, as luzes LED e branca separadamente foram mais efetivas no crescimento. Para a seleção das plantas uma concentração de geneticina entre 40 e 50 mgL-1 é recomendada. As taxas de sucesso nas transformações genéticas para o gene xth variaram entre 2,5 a 18,3% dependendo do experimento e para AtDdm1 foi de 2,2% em um bombardeamento.Não houveram alterações de ploidia e tamanho do genoma nos transgênicos das duas variedades em relação à planta selvagem. Os genes p4h e prr foram identificados como os melhores para a quantificação relativa de genes inseridos por PCR em tempo real na variedade SP803280 enquanto que para a RB835089 aprt e prr se mostraram mais eficazes. A análise do número de cópias inseridas em eventos transgênicos por PCR em tempo real foi possível através das duas metodologias de cálculo testados por este trabalho, com resultados que concordam com uma tendência nesta determinação de maneira simples e rápida. / Currently the demand for sustainable products has been shown to be frequent and promising. In species of commercial importance, there is an effort to obtain the highest possible productivity in a short time, along with the environment preservation. In this context, genetic transformation of plants appears as an attractive alternative for the development of sugarcane varieties able to generate products in a more effective way. The genetic transformation success is directly associated to plant tissue culture that requires specific condition for each genotype and cultivation process, in which, luminosity is one of the main factors that determines the production of vigorous plants. Another important factor is the selection of transgenic plants, that occur by exposing plants to a sufficient amount of selective agent in order to identify only genetic modified plants. In sugarcane, identification of transgenic plants by PCR and the definition of copy numbers is a difficult procedure to implement and usually is very costly. It is because in the process of genetic transformation by biolistic, the insertion of genes occurs randomly and also produce plants with varied copy numbers. In consideration of these factors directly involved in the efficiency to obtain sugarcane transgenic plants the objectives of this study were the improvement of a tissue culture protocol, the genetic transformation of the variety SP803280 with xth and AtDdm1 genes. Also, the studies include the definition of reference genes for determining the number of copies inserted of xth and AtDdm1 genes into the variety SP803280 and neo gene in RB835089, ploidy analysis and genome size of the transgenic events compared to control plants. In the study related to the best light quality for in vitro plant regeneration, white light and the combination of LED and white lights proved to be better for plants regeneration and development while for seedlings, LED and white light separately were more effective for growth. In order to obtain selection of transgenic plants, geneticin concentration between 40 and 50 mg L-1 is recommended. Success rates in xth genetic transformation ranged from 2.5 to 18.3% depending on the experiment, and for AtDdm1 was only 2.2% in just one biolistic bombardment. There were no changes in ploidy and genome size in transgenic events related to their wild type plant. The genes p4h and prr were defined to be the best for determining the copy number of transgenic events by real time PCR in SP803280 variety, while for RB835089, the genes aprt and prr were the most effective. The analysis of the number of inserted copies was possible using the two calculation methodologies tested by this work, with results that agree with a tendency in a simple and fast quantification methodology.

Das mitochondriale Genom der Pflanze weist mit einer heterogenen Population linearer, häufig auch verzweigten und zusätzlichen kleineren, zirkulären Molekülen eine komplexe Struktur auf. Um Einblicke in die mitochondrialen Genkopienzahl und deren Regulation sowohl unter normalen als auch unter Stressbedingungen zu erhalten, wurde die Kopienzahl pro Zelle vier repräsentativer Gene mittels qRT-PCR und Durchflusszytometrie ermittelt. Die Bestimmung der mitochondrialen Genkopienzahl in unterschiedlichen Spezies sowie in Organen der Modellpflanze Arabidopsis thaliana zeigte, dass die Kopienzahl mitochondrialer Gene sich nicht nur in den unterschiedlichen Spezies, sondern auch zwischen den unterschiedlichen Organen unterschied, wobei die höchsten Werte in der Wurzelspitze erreicht wurden. In Arabidopsis Keimlingen, welche zur Unterdrückung der plastidären Translation auf Spectinomycin-haltigem Medium angezogen wurden, wurde im Vergleich zu Kontrollpflanzen ein dreifacher Anstieg der Genkopienzahl festgestellt. Dieser Effekt erwies sich als spezifisch für Blatt- bzw. Kotyledonengewebe und warr unabhängig vom Licht. Mutanten mit Defekten in der Respiration zeigten ebenfalls erhöhte Genkopienzahlen, die durch Anzucht der Pflanzen auf Spectinomycin noch erhöht werden konnten. Dieses Ergebnis legt ein komplexes, regulatorisches Netzwerk nahe, in welchem sowohl Respiration als auch Photosynthese die Aufrechterhaltung einer stabilen Genkopienzahl innerhalb der Pflanzenzelle beeinflussen. Die Untersuchungen einer Spectinomycin-behandelter mt-GFP Arabidopsis Pflanzenlinie mittels CLSM zeigten einen Stillstand der Motilität der Mitochondrien in den epidermalen Zellen der weißen Kotyledonen, obwohl eine TEM Analyse eine normale, interne Morphologie ergab. Weitere Untersuchungen führten zu der Schlussfolgerung, dass es auch hier die Stärke der plastidären Beeinträchtigung, welche zu einem gelb-weißen Phänotyp führt, für den Arrest der Mobilität verantwortlich ist. / The plant mitochondrial genome has a complex structure. It exists in the form of a heterogeneous population of linear, often branched molecules with smaller than genome-size circular molecules being present in low abundance. In order to study the mitochondrial genome abundance and its regulation in plants under both standard and stress conditions, we determined the gene copy number of four representative mitochondrial genes using quantitative real-time PCR and flow-cytometry. Determination of mitochondrial gene copy number in different plant species and in organs of the model plant Arabidopsis thaliana showed that the copy number of the four investigated genes varied between species and also between different organs, having the highest values in the root tips. The growth of Arabidopsis seedlings on MS medium containing spectinomycin (a plastid translation inhibitor) led to a three-fold increase in the copy number in white versus green seedlings, an effect that is leaf/cotyledon specific and light-independent. Respiration deficient mutants also showed an increase in the gene copy number, this effect being further amplified when the mutants were grown on spectinomycin. The data suggest a complex regulatory network in which both photosynthesis and respiration influence the maintenance of a stable mitochondrial gene copy number within plant cells. CLSM investigations of a spectinomycin-treated mt-GFP line showed that in epidermal cells of white cotyledons most of the mitochondria are not motile with TEM analysis presenting normal internal morphology. Further investigations led to the conclusion that the threshold level of chloroplast impairment that leads to a motility arrest is represented by the appearance of a yellow-white cotyledon phenotype. These results point to a new regulatory mechanism of mitochondrial dynamics that is directly influenced by impaired chloroplast development under standard growth conditions.

Abstract Dupuytren’s disease is a Caucasian male-dominant disease that affects the palmar fascia. Incidence grows with age, but persons with strong diathesis seem to develop the disease at an earlier age than the majority of the diseased. Myofibroblasts are histopathologically the main cell type in DD tissue. Despite scientific research, the aetiology of the disease is still unrevealed. Only genetic susceptibility is generally accepted as predisposing to DD. Available treatment has thus far been unsatisfactory, because only symptoms can be cured to date.The disease recurs. With genetic susceptibility the recurrence rates are high (even up to 70%) and the time to recurrence is inevitably shorter. This behaviour is considered the aggressive type of DD. To be able to predict the behaviour of DD, whether it is an aggressive or conventional type, twenty-one Dupuytren samples were gathered and compared with five controls by means of immunohistochemical stainings. It was found that cellularity was better expresented in aggressive and recurred samples. Alfa-SMA and Ki-67 showed more activity in the aggressive tissue type of DD. Tenascin was vaguely expressed in aggressive-type samples. To compare the gene and protein expressions and to obtain a more profound understanding of the disease, a microarray technique was used. With a microarray it is possible to compare nucleotide pair hybridisations to resolve the genome of the tissues. In this study RT-PCR was used to examine mRNA levels to determine gene expression changes. Twelve DD palmar fascia samples were compared with three healthy control samples. Both myoglobin and ROR2, which we considered as the most valuable results, were found in the DD samples. ROR2 acts as a receptor or co-receptor for the Wnt system. The Wnt signalling pathway transfers signals from outside of the cell through cell surface receptors, and plays a significant role in proliferation processes such as in fibrotic conditions. To evaluate a possible chromosomal imbalance behind the aetiology of the disease, eighteen DD palmar fascia samples were compared with two reference samples. However, we were not able to detect any chromosomal imbalance in the DD samples. The method used was Oligonucleotide aCGH Agilent’s 60-mer oligonucleotide-based microarray according to the manufacturer’s instructions, which can reveal gains and losses of approximately 35 kilobases in the whole genome. The result does not exclude copy number changes entirely; a small presence of aberrant cells will not be detected if the change is less than 50%. In conclusion, we revealed elements in DD tissue that would enable us to predict the nature of the disease; whether the disease is aggressive with a stronger tendency to recur. Histological differences could be detected, and this can be used to benefit patients. As a new element, ROR2 was discovered in DD tissue.The genome-wide analysis with the 44K oligonucleotide-based array method revealed no changes of DNA number sequences. / Tiivistelmä Kämmenkalvon kuroumatauti eli Dupuytrenin kontraktuura on valkoihoisen miehen kämmenkalvon sairaus. Sairastumisen todennäköisyys lisääntyy ikääntymiseen liittyen, mutta vahva sukurasitus poikkeuksellisesti altistaa sairaudelle jo tavanomaista nuoremmalla iällä. Myofibroblastit ovat tärkein ja edustetuin solutyyppi Dupuytren kudoksessa. Huolimatta runsaasta tutkimustyöstä ei etiologiaa ole saatu vielä selvitettyä. Sukurasitus näyttää selkeästi altistavan taudille. Toistaiseksi kyetään hoitamaan ainoastaan sairauden aiheuttamat seuraukset, mutta ei perussyytä. Lisäksi tauti uusiutuu. Dupuytrenin sukurasitus lisää uusiutumista suurella todennäköisyydellä. Myös uusiutumisaika on tuolloin tavanomaista nopeampi, ja kyseessä katsotaan olevan ns.aggressiivisempi taudin muoto. Väitöskirjatyössäni pyrittiin löytämään mahdollisia tekijöitä, joiden perusteella voitaisiin ennustaan onko kyseessä aggressiivisempi vai tavanomainen taudin muoto. Tätä varten tutkittiin kaksikymmentä yksi Dupuytren kudosnäytettä ja viisi tervettä kämmenkalvon näytettä immunohistologisilla värjäyksillä, ja voitiin todeta, että soluisuus oli selkeästi koholla aggressiivisten ja taudin uusineiden potilaiden näytteissä. Tulos oli samanlainen myös alfa-SMA ja Ki-67 suhteen. Tenaskiiniä voitiin löytää edellisiä niukemmin aggressiivisista näytteistä. Dupuytrenin taudin luonteen lisäselvittelemiseksi geeni- ja proteiinitasolla tehtiin mikroarray, jossa emäsparien pariutumisen avulla selvitetään taudin genomia ja myös sitten tästä aiheutuvien proteiinien ilmentymistä. Kahtatoista Dupuytren potilaan kämmenkalvon kudosnäyttettä verrattiin kolmeen terveeseen verrokki kudosnäytteeseen ja voitiin todeta myoglobiinin ja ROR2:n selkeät pitoisuuden muutokset terveisiin näytteisiin verrattaessa. ROR2 toimii solujen välisten viestien välityksen reseptorina, eli siirtää signaalin solun ulkopuolelta sen sisäpuolelle solun pinnalla olevan kiinnittymiskohdan avulla. Sillä on selkeä merkitys ja tehtävä proliferatiivisissä tapahtumissa, kuten sidekudoksen lisääntymisessä. Mahdollisia kromosomin määrän muutoksia Dupuytren kudoksessa selviteltiin kahdeksantoista kudosnäytteen tutkimisella ja löydösten tulosta verrattiin sitten kahteen normaaliin verrokki kudosnäytteen tulokseen. Tutkimuksessa ei saatu selville kromosomien määrän muutosta, kun muutosten kokonaismäärä on vähäinen tai ainakin alle 50 % kokonaismäärää alhaisempi. Yhteenvetona voidaan todeta, että löytyi histologisia kudoselementtejä, joiden perusteella voidaan ennustaa, onko Dupuyrenin tauti aggressiivisempi ja todennäköisemmin uusiutuva luonteeltaan. ROR2 ei ole aikaisemmin yhdistetty Dupuytrenin kontraktuuraan. Dupuytren kudoksesta ei voitu 44K oligonukleotide mikroarray tekniikalla paljastaa geenimäärien muutoksia.

Cancer is a very complex genetic disease driven by combinations of mutated genes. This complexity strongly complicates the identification of driver genes and puts enormous challenges to reveal how they influence cancerogenesis, prognosis or therapy response. Thousands of molecular profiles of the major human types of cancer have been measured over the last years. Apart from well-studied frequently mutated genes, still only little is known about the role of rarely mutated genes in cancer or the interplay of mutated genes in individual cancers. Gene expression and mutation profiles can be measured routinely, but computational methods for the identification of driver candidates along with the prediction of their potential impacts on downstream targets and clinically relevant characteristics only rarely exist. Instead of only focusing on frequently mutated genes, each cancer patient should better be analyzed by using the full information in its cancer-specific molecular profiles to improve the understanding of cancerogenesis and to more precisely predict prognosis and therapy response of individual patients. This requires novel computational methods for the integrative analysis of molecular cancer data. A promising way to realize this is to consider cancer as a disease of cellular networks. Therefore, I have developed a novel network-based approach for the integrative analysis of molecular cancer data over the last years. This approach directly learns gene regulatory networks form gene expression and copy number data and further enables to quantify impacts of altered genes on clinically relevant downstream targets using network propagation. This habilitation thesis summarizes the results of seven of my publications. All publications have a focus on the integrative analysis of molecular cancer data with an overarching connection to the newly developed network-based approach. In the first three publications, networks were learned to identify major regulators that distinguish characteristic gene expression signatures with applications to astrocytomas, oligodendrogliomas, and acute myeloid leukemia. Next, the central publication of this habilitation thesis, which combines network inference with network propagation, is introduced. The great value of this approach is demonstrated by quantifying potential direct and indirect impacts of rare and frequent gene copy number alterations on patient survival. Further, the publication of the corresponding user-friendly R package regNet is introduced. Finally, two additional publications that also strongly highlight the value of the developed network-based approach are presented with the aims to predict cancer gene candidates within the region of the 1p/19q co-deletion of oligodendrogliomas and to determine driver candidates associated with radioresistance and relapse of prostate cancer. All seven publications are embedded into a brief introduction that motivates the scientific background and the major objectives of this thesis. The background is briefly going from the hallmarks of cancer over the complexity of cancer genomes down to the importance of networks in cancer. This includes a short introduction of the mathematical concepts that underlie the developed network inference and network propagation algorithms. Further, I briefly motivate and summarize my studies before the original publications are presented. The habilitation thesis is completed with a general discussion of the major results with a specific focus on the utilized network-based data analysis strategies. Major biologically and clinically relevant findings of each publication are also briefly summarized.