The Centromere is a vital chromosomal structure that ensures faithful segregation of replicated chromosomes to their respective daughter cells. With such an important structure, one would expect the underlying centromeric DNA sequence would be highly conserved across all species. It turns out that the underlying centromeric DNA sequences between species ranging from the yeast, fly, mouse to humans are in fact highly diverged suggesting a DNA sequence independent or an epigenetic mechanism of centromere formation. / Neocentromeres are centromeres that form de-novo at genomic locations that are devoid of highly repetitive a-satellite DNA sequences of which normal centromeres are usually comprised from. To date, the 10q25 neocentromere is the most well-characterised, fully functional human centromere that has been used previously to characterise the extent of a number of centromeric protein binding domains and characterise the properties of the underlying DNA sequence. Along with other factors, the existence of neocentromeres has given rise to a hypothesis where centromeres are defined by epigenetic or DNA sequence independent mechanisms. / The putative 10q25 neocentromere domain was recently redefined by high resolution mapping of Centromeric protein A (CENP-A) binding through a chromatin immunoprecipitation and array (CIA) analysis. The underlying DNA sequence was investigated to determine and confirm that the formation of the 10q25 neocentromere was through an epigenetic mechanism. Through a high-density restriction fragment length polymorphism (RFLP) analysis using overlapping PCR amplified DNA derived from genomic DNA representing the 10q25 region before and after neocentromere activation. No sequence polymorphisms, large insertions or deletions were detected and confirmed the epigenetic hypothesis of centromere formation. / DNA methylation is one of many epigenetic factors that are important for cellular differentiation, gene regulation and genomic imprinting. As the mechanisms and functions of DNA methylation have been well characterised, its role at the 10q25 neocentromere was investigated to try and identify the candidate epigenetic mechanism involved in the formation of centromeres. DNA methylation across the neocentromere was assessed using sodium bisulfite PCR and sequencing of selected CpG islands located across the 10q25 neocentromere. Overall, the methylation level of the selected CpG islands demonstrated no difference in DNA methylation before and after neocentromere activation. However, significant hypomethylation upon neocentromere formation was detected close to the protein-binding domain boundaries mapped previously suggesting that this may have a role in demarcating protein binding domains at the neocentromere. / Further analysis of DNA methylation investigated non-CpG island methylation at sites defined as CpG islets and CpG orphans. Interestingly, the DNA methylation level measured at selected CpG islets and CpG orphans across the 10q25 neocentromere were not completely hypermethylated as previously thought, but demonstrated variable methylation that became fully hypermethylated upon neocentromere activation in most sites investigated. These results suggested that a role for DNA methylation existed at the 10q25 neocentromere and that it occurred at sites devoid of CpG islands. / This study has found that DNA methylation at non-CpG island sites was variable contrary to popular belief and, was linked with neocentromere formation through the observation of increased DNA methylation at the 10q25 neocentromere. Inhibition of DNA methylation demonstrated increased neocentromere instability and a decrease in methylation of these CpG islets and CpG orphans confirming the importance of DNA methylation at neocentromeres. This study has characterised a new class of sequences that are involved in the maintenance of chromatin structure through DNA methylation at the 10q25 neocentromere.

The Centromere is a vital chromosomal structure that ensures faithful segregation of replicated chromosomes to their respective daughter cells. With such an important structure, one would expect the underlying centromeric DNA sequence would be highly conserved across all species. It turns out that the underlying centromeric DNA sequences between species ranging from the yeast, fly, mouse to humans are in fact highly diverged suggesting a DNA sequence independent or an epigenetic mechanism of centromere formation. / Neocentromeres are centromeres that form de-novo at genomic locations that are devoid of highly repetitive a-satellite DNA sequences of which normal centromeres are usually comprised from. To date, the 10q25 neocentromere is the most well-characterised, fully functional human centromere that has been used previously to characterise the extent of a number of centromeric protein binding domains and characterise the properties of the underlying DNA sequence. Along with other factors, the existence of neocentromeres has given rise to a hypothesis where centromeres are defined by epigenetic or DNA sequence independent mechanisms. / The putative 10q25 neocentromere domain was recently redefined by high resolution mapping of Centromeric protein A (CENP-A) binding through a chromatin immunoprecipitation and array (CIA) analysis. The underlying DNA sequence was investigated to determine and confirm that the formation of the 10q25 neocentromere was through an epigenetic mechanism. Through a high-density restriction fragment length polymorphism (RFLP) analysis using overlapping PCR amplified DNA derived from genomic DNA representing the 10q25 region before and after neocentromere activation. No sequence polymorphisms, large insertions or deletions were detected and confirmed the epigenetic hypothesis of centromere formation. / DNA methylation is one of many epigenetic factors that are important for cellular differentiation, gene regulation and genomic imprinting. As the mechanisms and functions of DNA methylation have been well characterised, its role at the 10q25 neocentromere was investigated to try and identify the candidate epigenetic mechanism involved in the formation of centromeres. DNA methylation across the neocentromere was assessed using sodium bisulfite PCR and sequencing of selected CpG islands located across the 10q25 neocentromere. Overall, the methylation level of the selected CpG islands demonstrated no difference in DNA methylation before and after neocentromere activation. However, significant hypomethylation upon neocentromere formation was detected close to the protein-binding domain boundaries mapped previously suggesting that this may have a role in demarcating protein binding domains at the neocentromere. / Further analysis of DNA methylation investigated non-CpG island methylation at sites defined as CpG islets and CpG orphans. Interestingly, the DNA methylation level measured at selected CpG islets and CpG orphans across the 10q25 neocentromere were not completely hypermethylated as previously thought, but demonstrated variable methylation that became fully hypermethylated upon neocentromere activation in most sites investigated. These results suggested that a role for DNA methylation existed at the 10q25 neocentromere and that it occurred at sites devoid of CpG islands. / This study has found that DNA methylation at non-CpG island sites was variable contrary to popular belief and, was linked with neocentromere formation through the observation of increased DNA methylation at the 10q25 neocentromere. Inhibition of DNA methylation demonstrated increased neocentromere instability and a decrease in methylation of these CpG islets and CpG orphans confirming the importance of DNA methylation at neocentromeres. This study has characterised a new class of sequences that are involved in the maintenance of chromatin structure through DNA methylation at the 10q25 neocentromere.

Alzheimer's disease (AD) is a neurodegenerative condition affecting millions of individuals worldwide and is a major source of mortality in elderly populations. While it is well established that there is a strong genetic basis for the disease, the epigenetic mechanism underlying the disease is largely unknown. The main purpose of this thesis is to understand the alteration of epigenetic modifications associated with the disease and its progression. In particular, we examine how alterations in the cytosine methylation and cytosine hydroxymethylation, two epigenetic modifications that are critically important for the development and function of the brain, are associated with advancing stages of Alzheimer's disease. Eight progressive AD brain samples were examined for changes in DNA methylation and hydroxymethylation by both dot blot analysis and a new oxidative bisulfite (OXBS) deep sequencing technology. The initial results of dot blot analysis reveal a statistically significant decrease in 5hmC associated with intermediate stage AD among the samples. This data suggests that the alterations in epigenetic modifications is likely associated with the pathophysiology of Alzheimer's disease, not only shedding new light on our understanding of the epigenetics of the disease, but also providing the basis for our future investigation on the exact cause and effect relationships of these epigenetic changes and their respective stages in Alzheimer's.

Epigenetics are stable heritable traits that are not a result of the DNA sequence. Epigenetic modification of DNA cytosine plays a role in development and disease. The covalent bonding of a methyl group or a hydroxymethyl group to the 5-carbon of cytosine epigenetically modifies cytosine to 5-methylcytosine or 5-hydroxymethylcytosine. Upon PCR amplification, the bisulfite treatment of DNA converts unmethylated cytosine to thymine, while 5-methylcytosine, 5-hydroxymethylcytosine, and other bases remain unchanged. The resulting sequences can be mapped to a reference genome; however, this can be challenging due to sequencing technology complexity, low sequence complexity, and biases and errors introduced with bisulfite treatment. Once the short read is mapped, the identity of 5-methylcytosine or 5-hydroxymethylcytosine can be determined by comparing the mapped read to the aligned reference genome. Bisulfite DNA read mapping is characterized by mapping performance as low as 40%. This research improves bisulfite short read mapping quality. First, reads generated from the bisulfite hairpin PCR protocol are used to study mapping failure and solutions. A read may not map to the genome; it may map uniquely, or it may map to multiple locations. Sequence complexity correlates with these mapping categories. The hairpin protocol allows for a recovery, in some cases, of the original untreated read, and mapping this read with the regular read mapper Bowtie2 improved mapper performance by 10%. New bisulfite read mapping software called BisPin was created that calls BFAST (BLAT-like Fast Accurate Search Tool) for mapping. BisPin resolves ambiguously mapped reads with a rescoring strategy, which yields a statistically significant improvement. BFAST-Gap for Ion Torrent reads was developed, since Ion Torrent machines are less expensive than Illumina machines and since Ion Torrent reads are longer. There are few mappers for Ion Torrent data. BFAST-Gap uses homopolymer run length for contextual gap penalty functions, since homopolymer runs cause errors in Ion Torrent reads. In conjunction with BisPin, this software performed well on real and simulated bisulfite Ion Torrent data and Illumina data. InfoTrim, a read trimmer with an entropy term, was developed with competitive results. / Ph. D. / DNA, deoxyribonucleic acid, is a large molecule comprised of four molecular bases: adenine, cytosine, thymine, and guanine, and it determines heritable traits in living organisms. Sequencing DNA determines the sequential arrangement of bases. A read is a small sequence of DNA bases. Epigenetics are stable heritable traits that are not a result of the DNA sequence. Chemical groups called methyl and hydroxymethyl can be attached to cytosine. These groups are an epigenetic modification of cytosine, and they play a role in disease and development. The chemical bisulfite is used to discover these chemical groups. The bisulfite sequencing of DNA is a process where bisulfite is introduced to DNA, and then the DNA is sequenced. Bisulfite treatment converts cytosines without the methyl and hydroxymethyl chemical groups into thymine. Software is then used to align and match the resulting DNA strands to a large reference DNA strand called a reference genome to distinguish between cytosines that have these chemical groups. This process is called mapping or alignment, and its performance can be as low as 40% for bisulfite data. This research improves this performance. The hairpin protocol is a known bisulfite sequencing method that sequences two opposing DNA strands, where the original untreated strand can sometimes be recovered. Mapping the recovered strands improved performance by 10%. Using hairpin data, sequence complexity, a measure of DNA sequence randomness, correlated with mapping performance. BisPin mapping software was created that implements the hairpin recovery approach. BisPin rescores DNA strands that map to multiple locations on the reference genome, and it supports multiple sequencing technologies. BFAST-Gap, a modified mapping program callable by BisPin, uses a context sensitive function to better align Ion Torrent reads, which tend to have errors in regions of repeated bases. BFAST-Gap was developed, since Ion Torrent sequencing machines are less expensive than Illumina machines and since Ion Torrent reads tend to be longer and have more information. The read trimmer InfoTrim was developed to trim the lengths of short DNA sequences to improve the quality of alignments. These programs were validated on real and simulated DNA data and performed well.

The aim of this thesis is the development and benchmarking of computational methods for the analysis of high-throughput data from tiling arrays and next-generation sequencing. Tiling arrays have been a mainstay of genome-wide transcriptomics, e.g., in the identification of functional elements in the human genome. Due to limitations of existing methods for the data analysis of this data, a novel statistical approach is presented that identifies expressed segments as significant differences from the background distribution and thus avoids dataset-specific parameters. This method detects differentially expressed segments in biological data with significantly lower false discovery rates and equivalent sensitivities compared to commonly used methods. In addition, it is also clearly superior in the recovery of exon-intron structures. Moreover, the search for local accumulations of expressed segments in tiling array data has led to the identification of very large expressed regions that may constitute a new class of macroRNAs. This thesis proceeds with next-generation sequencing for which various protocols have been devised to study genomic, transcriptomic, and epigenomic features. One of the first crucial steps in most NGS data analyses is the mapping of sequencing reads to a reference genome. This work introduces algorithmic methods to solve the mapping tasks for three major NGS protocols: DNA-seq, RNA-seq, and MethylC-seq. All methods have been thoroughly benchmarked and integrated into the segemehl mapping suite. First, mapping of DNA-seq data is facilitated by the core mapping algorithm of segemehl. Since the initial publication, it has been continuously updated and expanded. Here, extensive and reproducible benchmarks are presented that compare segemehl to state-of-the-art read aligners on various data sets. The results indicate that it is not only more sensitive in finding the optimal alignment with respect to the unit edit distance but also very specific compared to most commonly used alternative read mappers. These advantages are observable for both real and simulated reads, are largely independent of the read length and sequencing technology, but come at the cost of higher running time and memory consumption. Second, the split-read extension of segemehl, presented by Hoffmann, enables the mapping of RNA-seq data, a computationally more difficult form of the mapping task due to the occurrence of splicing. Here, the novel tool lack is presented, which aims to recover missed RNA-seq read alignments using de novo splice junction information. It performs very well in benchmarks and may thus be a beneficial extension to RNA-seq analysis pipelines. Third, a novel method is introduced that facilitates the mapping of bisulfite-treated sequencing data. This protocol is considered the gold standard in genome-wide studies of DNA methylation, one of the major epigenetic modifications in animals and plants. The treatment of DNA with sodium bisulfite selectively converts unmethylated cytosines to uracils, while methylated ones remain unchanged. The bisulfite extension developed here performs seed searches on a collapsed alphabet followed by bisulfite-sensitive dynamic programming alignments. Thus, it is insensitive to bisulfite-related mismatches and does not rely on post-processing, in contrast to other methods. In comparison to state-of-the-art tools, this method achieves significantly higher sensitivities and performs time-competitive in mapping millions of sequencing reads to vertebrate genomes. Remarkably, the increase in sensitivity does not come at the cost of decreased specificity and thus may finally result in a better performance in calling the methylation rate. Lastly, the potential of mapping strategies for de novo genome assemblies is demonstrated with the introduction of a new guided assembly procedure. It incorporates mapping as major component and uses the additional information (e.g., annotation) as guide. With this method, the complete mitochondrial genome of Eulimnogammarus verrucosus has been successfully assembled even though the sequencing library has been heavily dominated by nuclear DNA. In summary, this thesis introduces algorithmic methods that significantly improve the analysis of tiling array, DNA-seq, RNA-seq, and MethylC-seq data, and proposes standards for benchmarking NGS read aligners. Moreover, it presents a new guided assembly procedure that has been successfully applied in the de novo assembly of a crustacean mitogenome. / Diese Arbeit befasst sich mit der Entwicklung und dem Benchmarken von Verfahren zur Analyse von Daten aus Hochdurchsatz-Technologien, wie Tiling Arrays oder Hochdurchsatz-Sequenzierung. Tiling Arrays bildeten lange Zeit die Grundlage für die genomweite Untersuchung des Transkriptoms und kamen beispielsweise bei der Identifizierung funktioneller Elemente im menschlichen Genom zum Einsatz. In dieser Arbeit wird ein neues statistisches Verfahren zur Auswertung von Tiling Array-Daten vorgestellt. Darin werden Segmente als exprimiert klassifiziert, wenn sich deren Signale signifikant von der Hintergrundverteilung unterscheiden. Dadurch werden keine auf den Datensatz abgestimmten Parameterwerte benötigt. Die hier vorgestellte Methode erkennt differentiell exprimierte Segmente in biologischen Daten bei gleicher Sensitivität mit geringerer Falsch-Positiv-Rate im Vergleich zu den derzeit hauptsächlich eingesetzten Verfahren. Zudem ist die Methode bei der Erkennung von Exon-Intron Grenzen präziser. Die Suche nach Anhäufungen exprimierter Segmente hat darüber hinaus zur Entdeckung von sehr langen Regionen geführt, welche möglicherweise eine neue Klasse von macroRNAs darstellen. Nach dem Exkurs zu Tiling Arrays konzentriert sich diese Arbeit nun auf die Hochdurchsatz-Sequenzierung, für die bereits verschiedene Sequenzierungsprotokolle zur Untersuchungen des Genoms, Transkriptoms und Epigenoms etabliert sind. Einer der ersten und entscheidenden Schritte in der Analyse von Sequenzierungsdaten stellt in den meisten Fällen das Mappen dar, bei dem kurze Sequenzen (Reads) auf ein großes Referenzgenom aligniert werden. Die vorliegende Arbeit stellt algorithmische Methoden vor, welche das Mapping-Problem für drei wichtige Sequenzierungsprotokolle (DNA-Seq, RNA-Seq und MethylC-Seq) lösen. Alle Methoden wurden ausführlichen Benchmarks unterzogen und sind in der segemehl-Suite integriert. Als Erstes wird hier der Kern-Algorithmus von segemehl vorgestellt, welcher das Mappen von DNA-Sequenzierungsdaten ermöglicht. Seit der ersten Veröffentlichung wurde dieser kontinuierlich optimiert und erweitert. In dieser Arbeit werden umfangreiche und auf Reproduzierbarkeit bedachte Benchmarks präsentiert, in denen segemehl auf zahlreichen Datensätzen mit bekannten Mapping-Programmen verglichen wird. Die Ergebnisse zeigen, dass segemehl nicht nur sensitiver im Auffinden von optimalen Alignments bezüglich der Editierdistanz sondern auch sehr spezifisch im Vergleich zu anderen Methoden ist. Diese Vorteile sind in realen und simulierten Daten unabhängig von der Sequenzierungstechnologie oder der Länge der Reads erkennbar, gehen aber zu Lasten einer längeren Laufzeit und eines höheren Speicherverbrauchs. Als Zweites wird das Mappen von RNA-Sequenzierungsdaten untersucht, welches bereits von der Split-Read-Erweiterung von segemehl unterstützt wird. Aufgrund von Spleißen ist diese Form des Mapping-Problems rechnerisch aufwendiger. In dieser Arbeit wird das neue Programm lack vorgestellt, welches darauf abzielt, fehlende Read-Alignments mit Hilfe von de novo Spleiß-Information zu finden. Es erzielt hervorragende Ergebnisse und stellt somit eine sinnvolle Ergänzung zu Analyse-Pipelines für RNA-Sequenzierungsdaten dar. Als Drittes wird eine neue Methode zum Mappen von Bisulfit-behandelte Sequenzierungsdaten vorgestellt. Dieses Protokoll gilt als Goldstandard in der genomweiten Untersuchung der DNA-Methylierung, einer der wichtigsten epigenetischen Modifikationen in Tieren und Pflanzen. Dabei wird die DNA vor der Sequenzierung mit Natriumbisulfit behandelt, welches selektiv nicht methylierte Cytosine zu Uracilen konvertiert, während Methylcytosine davon unberührt bleiben. Die hier vorgestellte Bisulfit-Erweiterung führt die Seed-Suche auf einem reduziertem Alphabet durch und verifiziert die erhaltenen Treffer mit einem auf dynamischer Programmierung basierenden Bisulfit-sensitiven Alignment-Algorithmus. Das verwendete Verfahren ist somit unempfindlich gegenüber Bisulfit-Konvertierungen und erfordert im Gegensatz zu anderen Verfahren keine weitere Nachverarbeitung. Im Vergleich zu aktuell eingesetzten Programmen ist die Methode sensitiver und benötigt eine vergleichbare Laufzeit beim Mappen von Millionen von Reads auf große Genome. Bemerkenswerterweise wird die erhöhte Sensitivität bei gleichbleibend guter Spezifizität erreicht. Dadurch könnte diese Methode somit auch bessere Ergebnisse bei der präzisen Bestimmung der Methylierungsraten erreichen. Schließlich wird noch das Potential von Mapping-Strategien für Assemblierungen mit der Einführung eines neuen, Kristallisation-genanntes Verfahren zur unterstützten Assemblierung aufgezeigt. Es enthält Mapping als Hauptbestandteil und nutzt Zusatzinformation (z.B. Annotationen) als Unterstützung. Dieses Verfahren ermöglichte die erfolgreiche Assemblierung des kompletten mitochondrialen Genoms von Eulimnogammarus verrucosus trotz einer vorwiegend aus nukleärer DNA bestehenden genomischen Bibliothek. Zusammenfassend stellt diese Arbeit algorithmische Methoden vor, welche die Analysen von Tiling Array, DNA-Seq, RNA-Seq und MethylC-Seq Daten signifikant verbessern. Es werden zudem Standards für den Vergleich von Programmen zum Mappen von Daten der Hochdurchsatz-Sequenzierung vorgeschlagen. Darüber hinaus wird ein neues Verfahren zur unterstützten Genom-Assemblierung vorgestellt, welches erfolgreich bei der de novo-Assemblierung eines mitochondrialen Krustentier-Genoms eingesetzt wurde.

Master of Science / Department of Grain Science and Industry / X. Susan Sun / Soybean protein modified with sodium bisulfite behaves like latex adhesives, with adhesive strength comparable to formaldehyde-based adhesives. β-conglycinin and glycinin are two major protein components of the adhesive system. The objective of this research was to investigate the effect of sodium bisulfite on the physicochemical, morphological, and adhesion properties of glycinin and β-conglycinin in order to better understand the function of glycinin and β-conglycinin in the formation of the soy latex adhesive. Sodium bisulfite broke the disulfide bonds that linked acidic and basic polypeptides of glycinin, and the reducing effect was enhanced with increasing sodium bisulfite concentration. Although cleavage of disulfide bonds was expected to destabilize proteins, the thermal stability of glycinin increased as the sodium bisulfite concentration increased. Sodium bisulfite modified glycinin had higher surface hydrophobicity, which facilitated hydrophobic interations between molecules and aggregation of glycinin. The balance between hydrophobic interactions and electrostatic forces makes glycinin form unique chain-like structures. Adhesive performance of glycinin dropped significantly at lower sodium bisulfite concentration and then increased as sodium bisulfite concentration increased up to 24 g/L. Excess sodium bisulfite was detrimental to adhesive strength and water resistance. High-molecular-weight aggregates were observed in unmodified β-conglycinin, but these aggregates were dissociated by sodium bisulfite treatment. Similar to glycinin, the thermal stability of β-conglycinin was improved by the modification. However, the denaturation enthalpy of β-conglycinin decreased significantly at high level of sodium bisulfite (36 g/L). The turbidity at pH 4.8 also dropped extensively at the concentration of 36 g/L. The contact angle of β-conglycinin reached its minimum at 6 g/L sodium bisulfite on cherry wood and 24 g/L on glass. Morphology study proved that sodium bisulfite modification made the β-conglycinin solution more dispersed. At pH 9.5, water resistance of β-conglycinin was improved to a small extent by 6 g/L sodium bisulfite. At pH 4.8, adhesive performance was enhanced by 3 g/L and 6 g/L sodium bisulfite. High level of sodium bisulfite at 36 g/L reduced the adhesive performance of β-conglycinin drastically.

The sulfite pulping process is today practised in only a small number of pulp mills around the globe and the number of sulfite mills that use sodium as the base (cation) is less than five. However, due to the increasing interest in the wood based biorefinery concept, the benefits of sulfite pulping and especially the sodium based variety, has recently gained a lot of interest. It was therefore considered to be of high importance to further study the sodium based sulfite process to investigate if its benefits could be better utilized in the future in the production of dissolving pulps. Of specific interest was to investigate how the pulping conditions in the initial part of the cook (≥ 60 % pulp yield) should be performed in the best way. Thus, this thesis is focused on the initial phase of single stage sodium bisulfite cooking of either 100 % spruce or 100 % pine wood chips. The cooking experiments were carried out with either a lab prepared or a mill prepared cooking acid and the temperature and cooking time were varied. Activation energies for different wood components were investigated as well as side reactions concerning the formation of thiosulfate and sulfate. / Single stage sodium bisulfite cooking was carried out on either spruce or pine wood chips to investigate the influence of several process parameters in the initial phase of such a cook i.e. between 100 % and 60 % pulp yield. The cooking experiments were carried out with either a lab prepared or a mill prepared cooking acid and the temperature and time in the initial stage were varied. The influence of dissolved organics and inorganics components in the cooking liquor on the final pulp properties and side reactions were investigated. The impact of temperature and time on the pulp components were analyzed with respect to carbohydrates, lignin, extractives and thiosulfate. Kinetic equations were developed and the activation energies for delignification and carbohydrate dissolution were calculated using the Arrhenius equation. It was found that if using a mill prepared cooking acid, this had a beneficial effect with respect to side reactions, better extractives removal and higher pH stability during the cook, compared to a corresponding cook with a lab prepared cooking acid. Cooking with mill prepared and lab prepared cooking acids showed the same behaviour with respect to delignification and carbohydrate degradation, but the lab acid experiments resulted in a higher thiosulfate formation during the cook. The cellulose yield was not affected at all during the initial phase of the sulfite cook verifying earlier results by other researchers. The temperature had an influence on both the delignification rate and the rate of hemicelluloses removal.  The corresponding activation energies were found to increase in the following order; cellulose, xylan, glucomannan and lignin. / <p>Artikel 1: "The Initial Phase of Sodium Bisulfite Pulping of Spruce: Part 1" ingick i avhandlingen som manuskript. Nu publicerad.</p>

Os programas de melhoramento de figueira (Ficus carica L.) por métodos convencionais tais como cruzamentos dirigidos, para a obtenção de novos cultivares, são inviáveis em muitos países, como no Brasil, principalmente pela pequena variabilidade genética encontrada, e pela dificuldade de obtenção de plantas originadas pela fusão de gametas, uma vez que a vespa Blastophaga psenes, responsável pela polinização natural, não existe no país. Desse modo, o melhoramento genético, com o uso de mutagênicos, se torna uma linha de pesquisa importante para a melhoria da cultura, sendo necessário reunir informações sobre essa espécie, principalmente, em relação à sua variabilidade genética, para que projetos de propagação e manejo adequados sejam realizados. Diante do exposto, o objetivo do presente trabalho foi verificar a existência de variabilidade epigenética devido à metilação do DNA em seleções irradiadas de figueiras, entre si e quando comparadas ao principal cultivar comercial, Roxo-de-Valinhos, utilizando as técnicas de MSAP e ELISA, e posterior sequenciamento do DNA, tratado com bissulfito de sódio, para detecção do posicionamento das regiões polimórficas, analisado por ferramentas de bioinformática. Amostras do DNA genômico foram duplamente digeridas com a enzima HpaII (sensível à metilação) ou com o seu isoesquizomero MspI (não sensível à metilação), juntamente com a enzima EcoRI. Foram testadas 14 combinações de primers e obteve-se 87.9%, 10.1% e 2.0%, respectivamente, de regiões não metiladas CCGG, regiões metiladas CmCGG e regiões hemimetiladas hmCCGG, de um total de 553 produtos de amplificação, demostrando que a técnica MSAP é eficiente para detecção de sítios diferencialmente metilados no material genômico estudado, evidenciando sua divergência epigenética. Com o sequenciamento do DNA isolado desses sítios diferencialmente metilados, foi possível verificar diferentes padrões de metilação nos mesmos pelo sequenciamento dos DNAs tratados com bissulfito de sódio, em regiões codificadoras de genes regulatórios do desenvolvimento e amadurecimento dos frutos, além de terem sido encontrados no DNA mitocondrial dos tratamentos, o qual regula o fornecimento de energia em forma de ATP para as plantas, estando intimamente relacionado com o desenvolvimento das mesmas, justificando os diferentes fenótipos encontrados, tanto nos frutos, quanto no crescimento das plantas que sofreram estresse devido à exposição à radiação gama. Pela técnica de imunoquímica (ELISA), utilizando anticorpos anti 5-mC, foram observadas diferenças significativas pelo teste de Tukey, a 95 % de confiabilidade, no conteúdo global de metilação dos DNAs dos tratamentos, indicando que este fator abiótico foi responsável pelas alterações no epigenoma das plantas. Como o material utilizado como controle se encontrou também metilado, uma possível desmetilação dos materiais genômicos pode ser a responsável pela variação fenotípica entre os tratamentos. Diante disso, o estudo futuro da expressão gênica entre os tratamentos torna-se uma estratégia de extrema importância para o entendimento dos complexos sistemas regulatórios, levando à identificação de genes de interesse agronômico para a cultura da figueira, possibilitando a sua manipulação subsequente e propagação de cultivares melhorados para fins comerciais. / The fig tree (Ficus carica L.) breeding programs by conventional methods such as directed crosses, in order to obtain new cultivars, are unworkable in many countries, as in Brazil, mainly by small genetic variability found, and by the difficulty for obtaining plants originated from the fusion of gametes, since the wasp Blastophaga psenes, responsible for natural pollination, doesn`t exist in the country. In this way, the genetic breeding, with the use of mutagenic, becomes an important research line for the improvement of culture, being necessary to gather information about this species, mainly in relation to its genetic variability, for perform propagation projects and appropriate management. Given the above, The objective of this study was to verify the existence of epigenetic variability due to DNA methylation in irradiated fig selections, with each other and when compared to the main commercial cultivar, Roxo-de-Valinhos, using MSAP and ELISA techniques, and subsequent DNA sequencing, treated with sodium bisulfite, for detection of the position of the polymorphic regions, analyzed by bioinformatics tools. Samples of genomic DNA were double-digested with the HpaII enzyme (sensitive to methylation) with its isoschizomer MspI (insensitive to methylation), together with the EcoRI enzyme. Fourteen primer combinations were tested and it was obtained 87.9%, 10.1% e 2.0%, respectively, unmethylated CCGG, methylated CmCGG and hemimethylated regions hmCCGG, from a total of 553 amplification products, displaying, the MSAP technique, efficient for detection of differentially methylated sites in the genomic material studied, demonstrating their epigenetic divergence. With the sequencing of DNA isolated of these differentially methylated sites, it was possible to verify different patterns of methylation in them by sequencing the DNA treated with sodium bisulfite, in coding regions of regulatory genes of the development and fruits ripening, besides they have been found in the mitochondrial DNA of treatments, which regulates the supply of energy in ATP form for the plants, being closely related to their development, justifying the different phenotypes found in both fruits and plant growth that suffered stress due to exposure to gamma radiation. By the technique of immunochemistry (ELISA), using 5-mC antibodies, significant differences were observed by Tukey test, at 95% of trustworthiness, in the global content methylation of the treatments DNA, indicating that this abiotic factor was responsible for the changes in the epigenome of the plants. Since the material used as control was found also methylated, a supposed demethylation of the genomic material may be responsible for phenotypic variation among treatments. Considering this, future study of gene expression between treatments becomes an extreme important strategy for understanding the complex regulatory systems, leading to the identification of genes with agronomic interest for the fig culture, allowing its subsequent manipulation and propagation of improved cultivars for commercial purposes.

Les objectifs de ce projet sont de mettre au point des pâtes de cellulose pour la synthèse de dérivés cellulosiques à haute valeur ajoutée : éthers de cellulose, nitrocelluloses et acétates de cellulose. La stratégie de recherche est générale car quelles que soient les applications visées, les caractéristiques chimiques recherchées sont très proches (viscosité en solution contrôlée, teneur en ?-cellulose élevée et haute blancheur). Les hémicelluloses, qui réagissent lors des réactions de fonctionnalisation de la cellulose pour former des composés insolubles, sont les principales impuretés à éliminer. Les caractéristiques physico-chimiques de la cellulose (cristallinité, teneur en éléments fins, densité de la feuille de pâte) ont aussi une influence considérable sur l’accessibilité et la réactivité de la cellulose. Différentes options ont alors été envisagées pour atteindre ces objectifs : modification des paramètres de cuisson bisulfite, élimination des éléments fins, préhydrolyse des copeaux de bois, ajout d’additifs lors de la purification et mise au point d’une nouvelle étape de purification alcaline à température modérée. La suppression des éléments fins conduit à une amélioration des qualités de la cellulose (baisse du taux d’hémicelluloses, faibles taux d’extrait et indice de cuivre) et de la nitrocellulose produite. Le traitement des pâtes de cellulose par des solutions de soude concentrées à température modérée permet d’atteindre des niveaux de pureté très élevés (haute teneur en ?-cellulose, faible teneur en hémicelluloses et haute blancheur) et conduit à une amélioration des propriétés des acétates de cellulose produits avec ces pâtes. L’analyse de ces pâtes par diffraction des RX montre qu’elles sont faiblement mercerisées. De plus, nous avons mis au point un test d’acétylation rapide afin de pouvoir étudier l’influence des propriétés physiques et chimiques de la cellulose lors de la synthèse de l’acétate de cellulose Ce test d’acétylation permet de différencier l’origine de la ressource fibreuse, mais n’est pas encore assez sensible pour rendre compte de l’importance de l’état physique de la cellulose (densité de la feuille, taux de mâtons). Il apparaît au cours de cette étude que la pureté chimique ne suffit pas pour produire des dérivés cellulosiques de haute qualité : l’aspect physico-chimique de la cellulose (taux de cristallinité, accessibilité, réactivité) est aussi important. / The objectives of this project are to design high purity cellulose pulps for the synthesis of high added value cellulose derivatives : cellulose ethers, cellulose nitrate and cellulose acetates. The research strategy is general because whatever are the aimed applications, the desired chemical characteristics are very close (controlled viscosity in solution, high ?-cellulose content and high brightness). Hemicelluloses, which react during derivatization reaction to form insoluble compounds, appears to be the main impurities. Physico-chemical properties of cellulose (cristallinity index, content in fine elements, sheet density) have also a considerable influence on the accessibility and the reactivity react of the cellulose. Various ways have been envisaged to improve the purity of the cellulose : modification of bisulfite cooks parameters, removal of the fine elements, prehydrolysis of wood, addition of additives during the purification and the development of a new alkaline purification step at room temperature. Fines elements removal leads to a improvement of the qualities of the cellulose (low hemicelluloses content, low extract content and copper number) and of the synthesized nitrocellulose. The treatment of cellulose pulps by concentrated caustic soda solutions at mild temperature allows reaching very high levels of purity (high ?-cellulose content, low hemicelluloses content and high brightness) and led to an improvement of the properties of cellulose acetate produced with these pulps. X-Ray analyses of these pulps show no excessive mercerisation. The quick acetylation test could differentiate the origin of the fibrous resource, but it is not rather sensitive to report the importance of the physical state of the cellulose (density, knots level). During this study, it appears that high chemical purity of cellulose pulps is not enough for the production of high quality cellulose derivatives : the physico-chemical aspect of the cellulose (cristallinity index, accessibility, reactivity) is also very important.

Os programas de melhoramento de figueira (Ficus carica L.) por métodos convencionais tais como cruzamentos dirigidos, para a obtenção de novos cultivares, são inviáveis em muitos países, como no Brasil, principalmente pela pequena variabilidade genética encontrada, e pela dificuldade de obtenção de plantas originadas pela fusão de gametas, uma vez que a vespa Blastophaga psenes, responsável pela polinização natural, não existe no país. Desse modo, o melhoramento genético, com o uso de mutagênicos, se torna uma linha de pesquisa importante para a melhoria da cultura, sendo necessário reunir informações sobre essa espécie, principalmente, em relação à sua variabilidade genética, para que projetos de propagação e manejo adequados sejam realizados. Diante do exposto, o objetivo do presente trabalho foi verificar a existência de variabilidade epigenética devido à metilação do DNA em seleções irradiadas de figueiras, entre si e quando comparadas ao principal cultivar comercial, Roxo-de-Valinhos, utilizando as técnicas de MSAP e ELISA, e posterior sequenciamento do DNA, tratado com bissulfito de sódio, para detecção do posicionamento das regiões polimórficas, analisado por ferramentas de bioinformática. Amostras do DNA genômico foram duplamente digeridas com a enzima HpaII (sensível à metilação) ou com o seu isoesquizomero MspI (não sensível à metilação), juntamente com a enzima EcoRI. Foram testadas 14 combinações de primers e obteve-se 87.9%, 10.1% e 2.0%, respectivamente, de regiões não metiladas CCGG, regiões metiladas CmCGG e regiões hemimetiladas hmCCGG, de um total de 553 produtos de amplificação, demostrando que a técnica MSAP é eficiente para detecção de sítios diferencialmente metilados no material genômico estudado, evidenciando sua divergência epigenética. Com o sequenciamento do DNA isolado desses sítios diferencialmente metilados, foi possível verificar diferentes padrões de metilação nos mesmos pelo sequenciamento dos DNAs tratados com bissulfito de sódio, em regiões codificadoras de genes regulatórios do desenvolvimento e amadurecimento dos frutos, além de terem sido encontrados no DNA mitocondrial dos tratamentos, o qual regula o fornecimento de energia em forma de ATP para as plantas, estando intimamente relacionado com o desenvolvimento das mesmas, justificando os diferentes fenótipos encontrados, tanto nos frutos, quanto no crescimento das plantas que sofreram estresse devido à exposição à radiação gama. Pela técnica de imunoquímica (ELISA), utilizando anticorpos anti 5-mC, foram observadas diferenças significativas pelo teste de Tukey, a 95 % de confiabilidade, no conteúdo global de metilação dos DNAs dos tratamentos, indicando que este fator abiótico foi responsável pelas alterações no epigenoma das plantas. Como o material utilizado como controle se encontrou também metilado, uma possível desmetilação dos materiais genômicos pode ser a responsável pela variação fenotípica entre os tratamentos. Diante disso, o estudo futuro da expressão gênica entre os tratamentos torna-se uma estratégia de extrema importância para o entendimento dos complexos sistemas regulatórios, levando à identificação de genes de interesse agronômico para a cultura da figueira, possibilitando a sua manipulação subsequente e propagação de cultivares melhorados para fins comerciais. / The fig tree (Ficus carica L.) breeding programs by conventional methods such as directed crosses, in order to obtain new cultivars, are unworkable in many countries, as in Brazil, mainly by small genetic variability found, and by the difficulty for obtaining plants originated from the fusion of gametes, since the wasp Blastophaga psenes, responsible for natural pollination, doesn`t exist in the country. In this way, the genetic breeding, with the use of mutagenic, becomes an important research line for the improvement of culture, being necessary to gather information about this species, mainly in relation to its genetic variability, for perform propagation projects and appropriate management. Given the above, The objective of this study was to verify the existence of epigenetic variability due to DNA methylation in irradiated fig selections, with each other and when compared to the main commercial cultivar, Roxo-de-Valinhos, using MSAP and ELISA techniques, and subsequent DNA sequencing, treated with sodium bisulfite, for detection of the position of the polymorphic regions, analyzed by bioinformatics tools. Samples of genomic DNA were double-digested with the HpaII enzyme (sensitive to methylation) with its isoschizomer MspI (insensitive to methylation), together with the EcoRI enzyme. Fourteen primer combinations were tested and it was obtained 87.9%, 10.1% e 2.0%, respectively, unmethylated CCGG, methylated CmCGG and hemimethylated regions hmCCGG, from a total of 553 amplification products, displaying, the MSAP technique, efficient for detection of differentially methylated sites in the genomic material studied, demonstrating their epigenetic divergence. With the sequencing of DNA isolated of these differentially methylated sites, it was possible to verify different patterns of methylation in them by sequencing the DNA treated with sodium bisulfite, in coding regions of regulatory genes of the development and fruits ripening, besides they have been found in the mitochondrial DNA of treatments, which regulates the supply of energy in ATP form for the plants, being closely related to their development, justifying the different phenotypes found in both fruits and plant growth that suffered stress due to exposure to gamma radiation. By the technique of immunochemistry (ELISA), using 5-mC antibodies, significant differences were observed by Tukey test, at 95% of trustworthiness, in the global content methylation of the treatments DNA, indicating that this abiotic factor was responsible for the changes in the epigenome of the plants. Since the material used as control was found also methylated, a supposed demethylation of the genomic material may be responsible for phenotypic variation among treatments. Considering this, future study of gene expression between treatments becomes an extreme important strategy for understanding the complex regulatory systems, leading to the identification of genes with agronomic interest for the fig culture, allowing its subsequent manipulation and propagation of improved cultivars for commercial purposes.