Doctor of Philosophy / Department of Plant Pathology / Ari Jumpponen / Megan Kennelly / Soil microbial communities play fundamental and complex roles in the productivity of agriculture. However, we still have a limited understanding of the response of microbial communities to different farming systems, such as organic and conventional fertility management regimens. We applied high-throughput sequencing to develop a better understanding of how soil microbial communities (bacteria and fungi) in vegetable production respond to organic or conventional soil fertility management. Specifically, my three studies examined the following questions: 1. How do soil microbial communities from cDNA and DNA samples compare in organic and conventional fertility treatments? 2. How do soil microbial communities in a tomato cropping season respond to long-term organic vs. conventional soil fertility treatments? 3. How do soil bacterial and fungal communities respond to high tunnels, plastic mulch and organic amendments across a tomato cropping season? The first two questions were addressed at the Kansas State University Horticulture and Extension Center in Olathe, KS, using organic and conventional field plots with three levels of fertilizer. We sampled the plots during the development of a tomato crop. The third question was addressed at a commercial farm in Lawrence, KS, during its transition to organic vegetable production, during a tomato crop. The Lawrence experiment included as treatments field plots versus high tunnels, and three organic nutrient amendments. We used 454-pyrosequencing of bacterial and fungal ribosomal markers to compare total resident (DNA) and active microbial communities (cDNA, which is DNA synthesized from a single stranded RNA template) for our first question. We used Illumina MiSeq metabarcoding of bacterial and fungal ribosomal markers for our second and third questions. In all three studies we evaluated bacterial and fungal community responses using Simpson´s diversity index, Simpson´s evenness and richness for each experiment. For the first question, when we compared DNA and cDNA, bacterial diversity was higher in cDNA samples from organic compared to conventional management. In addition, fungal diversity from cDNA samples was higher than from DNA samples. In contrast, in the second question, bacterial and fungal diversity indices did not differ in the tomato crop under organic and conventional management systems. For our third question, high tunnels did not affect bacterial or fungal diversity. Use of plastic mulch for a tomato crop in open field plots did not affect bacterial richness, but decreased fungal richness compared to open field plots without plastic mulch. High-throughput sequencing provides a new perspective on the structure and dynamics of these communities. Information from this approach will ultimately improve our ability to manage soil for sustainable productivity by promoting beneficial microorganisms and suppressing pathogenic ones.

É conhecido que muitos softwares deixam de ser utilizados por sua complexa usabilidade. Mesmo ferramentas conhecidas por sua qualidade na execução de uma tarefa são abandonadas em favor de ferramentas mais simples de usar, de instalar ou mais rápidas. Na área da anotação funcional a ferramenta Sifter (v2.0) é considerada uma das com melhor qualidade de anotação. Recentemente ela foi considerada uma das melhores ferramentas de anotação funcional segundo o Critical Assessment of protein Function Annotation (CAFA) experiment. Apesar disso, ela ainda não é amplamente utilizada, provavelmente por questões de usabilidade e adequação do framework à larga escala. O workflow SIFTER original consiste em duas etapas principais: A recuperação das anotações para uma lista de genes e a geração de uma árvore de genes reconciliada para a mesma lista. Em seguida, a partir da árvore de genes o Sifter constrói uma rede bayesiana de mesma estrutura nas quais as folhas representam os genes. As anotações funcionais dos genes conhecidos são associadas a estas folhas e em seguida as anotações são propagadas probabilisticamente ao longo da rede bayesiana até as folhas sem informação a priori. Ao fim do processo é gerada para cada gene de função desconhecida uma lista de funções putativas do tipo Gene Ontology e suas probabilidades de ocorrência. O principal objetivo deste trabalho é aperfeiçoar o código-fonte original para melhor desempenho, potencialmente permitindo que seja usado em escala genômica. Durante o estudo do workflow de pré-processamento dos dados encontramos oportunidades para aperfeiçoamento e visualizamos estratégias para abordá-las. Dentre as estratégias implementadas temos: O uso de threads paralelas; balanceamento de carga de processamento; algoritmos revisados para melhor aproveitamento de disco, memória e tempo de execução; adequação do código fonte ao uso de bancos de dados biológicos em formato utilizado atualmente; aumento da acessibilidade do usuário; expansão dos tipos de entrada aceitos; automatização do processo de reconciliação entre árvores de genes e espécies; processos de filtragem de seqüências para redução da dimensão da análise; e outras implementações menores. Com isto conquistamos aumento de performance de até 87 vezes para a recuperação de anotações e 73,3% para a reconstrução da árvore de genes em máquinas quad-core, e redução significante de consumo de memória na fase de realinhamento. O resultado desta implementação é apresentado como Sifter-T (Sifter otimizado para Throughput), uma ferramenta open source de melhor usabilidade, velocidade e qualidade de anotação em relação à implementação original do workflow de Sifter. Sifter-T foi escrito de forma modular em linguagem de programação Python; foi elaborado para simplificar a tarefa de anotação de genomas e proteomas completos; e os resultados são apresentados de forma a facilitar o trabalho do pesquisador. / It is known that many software are no longer used due to their complex usability. Even tools known for their task execution quality are abandoned in favour of faster tools, simpler to use or install. In the functional annotation field, Sifter (v2.0) is regarded as one of the best when it comes to annotation quality. Recently it has been considered one of the best tools for functional annotation according to the \"Critical Assessment of Protein Function Annotation (CAFA) experiment. Nevertheless, it is still not widely used, probably due to issues with usability and suitability of the framework to a high throughput scale. The original workflow SIFTER consists of two main steps: The annotation recovery for a list of genes and the reconciled gene tree generation for the same list. Next, based on the gene tree, Sifter builds a Bayesian network structure in which its leaves represent genes. The known functional annotations are associated to the aforementioned leaves, and then the annotations are probabilistically propagated along the Bayesian network to the leaves without a priori information. At the end of the process, a list of Gene Ontology functions and their occurrence probabilities is generated for each unknown function gene. This work main goal is to optimize the original source code for better performance, potentially allowing it to be used in a genome-wide scale. Studying the pre-processing workflow we found opportunities for improvement and envisioned strategies to address them. Among the implemented strategies we have: The use of parallel threads; CPU load balancing, revised algorithms for best utilization of disk access, memory usage and runtime; source code adaptation to currently used biological databases; improved user accessibility; input types increase; automatic gene and species tree reconciliation process; sequence filtering to reduce analysis dimension, and other minor implementations. With these implementations we achieved great performance speed-ups. For example, we obtained 87-fold performance increase in the annotation recovering module and 72.3% speed increase in the gene tree generation module using quad-core machines. Additionally, significant memory usage decrease during the realignment phase was obtained. This implementation is presented as Sifter-T (Sifter Throughput-optimized), an open source tool with better usability, performance and annotation quality when compared to the Sifter\'s original workflow implementation. Sifter-T was written in a modular fashion using Python programming language; it is designed to simplify complete genomes and proteomes annotation tasks and the outputs are presented in order to make the researcher\'s work easier.

Advances in combinatorial chemistry have facilitated the production of large chemical libraries that can be used as tools to discover biological probes and therapeutics. High-throughput screening (HTS) strategies have emerged as the standard method to assess the biological activity of small molecules. These screens involve the individual analysis of each small molecule in multi-well plates, often requiring expensive automated methods and development of robust assays that may not translate to physiologically relevant contexts. This problem of evaluating large numbers of reagents in physiologically relevant cell and animal models has been addressed for genetic reagents such as RNAi, CRISPR, and cDNA by creating barcoded retroviral libraries that can be used to infect target cells in culture or in animal models. Using these tools, effective reagents can be selected and decoded using a rapid and inexpensive procedure compared to testing of individual reagents one at a time in an arrayed fashion. In order to more efficiently analyze small molecules, a pooled approach would similarly be useful. This dissertation describes the studies towards developing a pooled screening strategy for small molecules in cellular contexts. Through an initial screen, we set to phenotypically profile small molecule biological activity in a pooled fashion, while simultaneously gain insight about an individual, active molecule’s mechanism of action. I first describe the design of the pooled screen and define the goals necessary for successful application. Next, I outline the steps taken and challenges encountered during the invention of each component of the technology. Finally, I discuss a computational, target-based approach to design small molecules appropriate for future applications of the new screening technology.

Bacteria have been the causative agents of major infectious disease pandemics throughout human history. Over the past 4 decades, a combination of changing medical practices, industrialization, and globalisation have led to a number of emergences and re-emergences of bacterial pathogens. The design of rational control programs and bespoke therapies will require an enhanced understanding of the dynamics underpinning the emergence and transmission of pathogenic clones. The recent development of new technologies for sequencing bacterial genomes rapidly and economically has led to a greatly enhanced understanding of the diversity of bacterial populations. This thesis describes the application of whole genome sequencing of 2 bacterial pathogens, Staphylococcus aureus and Legionella pneumophila, in order to understand the dynamics of bacterial infections on different temporal and spatial scales. The first study involves the examination of S. aureus evolution during a chronic infection of a single patient over a period of 26 months revealing differences in antibiotic resistance profiles and virulence factor expression over time. The genetic variation identified correlated with differences in growth rate, haemolytic activity, and antibiotic sensitivity, implying a profound effect on the ecology of S. aureus. Importantly, polymorphisms were identified in global regulators of virulence, with a high frequency of polymorphisms within the SigB locus identified, suggesting this region may be under selection in this patient. The identification of genes under diversifying selection during long-term infection may inform the design of novel therapeutics for the control of refractory chronic infections. Secondly, the emergence and transmission of 3 pandemic lineages derived from S. aureus clonal complex 30 (CC30) were investigated. Independent origins for each pandemic lineage were identified, with striking molecular correlates of hospital- or community-associated pandemics represented by mobile genetic elements, such as bacteriophage and Staphylococcal pathogenicity islands, and non-synonymous mutations affecting antibiotic resistance and virulence. Hospitals in large cities were identified as hubs for the transmission of MRSA to regional health care centres. In addition, comparison of whole genome sequences revealed that at least 3 independent acquisitions of TSST-1 have occurred in CC30, but a single distinct clade of diverse community-associated CC30 strains was responsible for the TSS epidemic of the late 1970s, and for subsequent cases of TSS in the UK and USA. Finally, whole genome sequencing was used as a tool for investigating a recent outbreak of legionellosis in Edinburgh. An unexpectedly high level of genomic diversity was identified among the outbreak strains, with respect to core genome polymorphisms, and accessory genome content. The data indicate that affected individuals may be infected with heterogeneous strains. The findings highlight the complexities in identifying environmental sources and suggest possible differences in pathogenic potential among isolates from a single outbreak. Taken together, the findings demonstrate applications of bacterial genome sequencing leading to enhanced understanding of bacterial pathogen evolution, emergence, and transmission, which may ultimately inform appropriate infection control measures.

High-throughput sequencing is a powerful tool to study diverse aspects of biology and applies to genome, transcriptome, and small RNA profiling. Ever increasing sequencing throughput and more specialized sequencing assays demand more sophisticated bioinformatics approaches. In this thesis, I present 4 studies for which I developed computational methods to handle high-throughput sequencing data to gain insights into biology. The first study describes the genome of High Five (Hi5) cells, originally derived from Trichoplusia ni eggs. The chromosome-level assembly (scaffold N50 = 14.2 Mb) contains 14,037 predicted protein-coding genes. Examination and curation of multiple gene families, pathways, and small RNA-producing loci reveal species- and order-specific features. The availability of the genome sequence, together with genome editing and single-cell cloning protocols, enables Hi5 cells as a new tool for studying small RNAs. The second study focuses on just one type of piRNAs that are produced at the pachytene stage of mammalian spermatogenesis. Despite their abundance, pachytene piRNAs are poorly understood. I find that pachytene piRNAs cleave transcripts of protein-coding genes and further target transcripts from other pachytene piRNA loci. Subsequently, systematic investigation of piRNA targeting by integrating different types of sequencing data uncovers the piRNA targeting rule. The third study describes computational procedures to map splicing branchpoints using high-throughput sequencing data. Screening >1.2 trillion RNA-seq reads determines >140,000 BPs for both human and mouse. Such branchpoints are compiled into BPDB (BranchPoint DataBase) to provide a comprehensive branchpoint catalog. The final study combines novel experimental and computational procedures to handle PCR duplicates that are prevalent in high-throughput sequencing data. Incorporation of unique molecular identifiers (UMIs) to tag each read enables unambiguous identification of PCR duplicates. Both simulated and experimental datasets demonstrate that UMI incorporation increases the reproducibility of RNA-seq and small RNA-seq. Surveying 7 common variables in high-throughput sequencing reveals that the amount of starting material and sequencing depth, but not the number of PCR cycles, determine the PCR duplicate frequency. Finally, I show that removing PCR duplicates without UMIs leads to substantial bias into data analysis. / 2020-12-11T00:00:00Z

Le travail présenté dans ce manuscrit porte sur la recherche de nouveaux membres de la famille des dioxygénases α-cétoglutarate et fer dépendantes (α-KAO) et leur application en synthèse organique. Dans un premier, ce travail a consisté à chercher de nouvelles enzymes selon une approche génomique basée sur l’homologie de séquence et le partage d’un motif InterPro. Deux criblages haut débit avec 79 et 127 enzymes candidates ont ensuite été effectués sur des panels constitués respectivement de 23 et 36 substrats, structurellement plus ou moins proches des substrats métaboliques. Huit nouvelles α-KAO ont ainsi pu être découvertes. Parmi ces huit nouvelles α-KAO, quatre ont été étudiées plus en détail. Après optimisation des conditions de réaction pour chaque enzyme, des montées en échelle ont été réalisées pour caractériser les produits formés. A partir de ces quatre enzymes, la (3S)-3-hydroxy-L-lysine, un dérivé cyclisé de la (4R)-4-hydroxy-L-lysine, (3S)-3-hydroxy-L-ornithine et un dérivé de la (3S)-3-hydroxy-L-arginine ont pu être produits. Nous avons proposé une synthèse biocatalytique de mono et dihydroxydiamines en couplant une ou deux α-KAO avec une décarboxylase. Les (2S)-1,5-diamino-2-pentanol, 1,5-diamino-3-pentanol, (2S)-1,4-diamino-2-butanol et (2S,3S)-1,5-diamino-2,3-pentanediol ont ainsi été obtenus avec de bonnes conversions. / The work described in this manuscript deals with the search of new members of the α-ketoglutarate and Iron-dependent dioxygenases family (α-KAO) and their applications in organic synthesis. The first part of this work presents the search of new enzymes through a genomic approach based on sequence homology and InterPro motif sharing. Two high-throughput screenings with 79 and 127 candidate enzymes have been performed on 23 and 36 substrates more or less structurally close to known metabolic substrates. 8 new α-KAOs have been discovered. Among these new enzymes, four were studied in more details. After optimization of the enzymatic reaction conditions for each enzyme, scale-up allowed to obtain compounds for isolation and characterization. With these four enzymes, (3S)-3-hydroxy-L-lysine, (4R)-4-hydroxy-L-lysine as its cyclic derivative, (3S)-3-hydroxy-L-ornithine and a derivative of (3S)-3-hydroxy-L-arginine were produced. Two of the new α-KAO were combined in a cascade process to afford the (3R,4R)-3,4-dihydroxy-L-lysine as its cyclic derivative. We proposed a biocatalytic synthesis of mono and hydroxydiamines by coupling one or two α-KAO with a decarboxylase enzyme. (2S)-1,5-diamino-2-pentanol, 1,5-diamino-3-pentanol, (2S)-1,4-diamino-2-butanol and (2S,3S)-1,5-diamino-2,3-pentanediol were obtained with good overall conversions.

Messenger RNAs (mRNAs) have to undergo a series of post-transcriptional processing steps before translation. One of the post-transcriptional steps - 3' end processing, which consists of cleavage and polyadenylation, is critical for delimiting the 3' end of mRNA and determining regulatory elements for downstream post-transcriptional/translational regulation. Like another well-characterized mRNA processing step - splicing, 3' end processing is very flexible due to the diversity of trans-acting factors and cis-acting elements in the 3' end of mRNA. In recent years, the differential usage of alternative polyA sites (APA) of the same gene, which leads to mRNA isoforms of different 3' UTR, has been increasingly revealed by both experimental and computational studies. More significantly, the global changes of 3' UTR length have been observed in multiple clinical settings, particularly in the cancer cells. However, the depiction of APA phenomenon does not synchronize the efforts to study the mechanism underlying APA biogenesis. In this thesis, we first describe general principle and pipeline to identify APA in different biological or clinical conditions using various high throughput sequencing techniques. After that, we present the work about the global impacts of two RNA binding proteins (ESRP/aCP) and one core 3' end processing factor (CstF64 and its paralog CstF64τ) on the regulation of APA. The APA identification analyses and motif analyses suggest a wide range of APA associated with the expression change of those proteins in different cell lines. In addition, for each protein, we have collect substantial evidence about the mechanism underlying the APA induction. Our findings could provide significant insights into the APA regulation mechanisms. In addition, we also conducted a research on the induction of APA in JEG-3 cells as a response to the change of oxygen supply (Hypoxia and Normoxia). Using a robustness protocol for specifically sequencing 3' end of mRNA, we identified more than 500 APA events and revealed a global shortening pattern of 3' UTR length as a result of hypoxia. The work on APA in this thesis largely increases the understanding of APA regulation by various proteins and provided new evidence for the APA in clinical condition.

Transkriptionsfaktoren (TF) sind wichtige Regulatoren der Genexpression. In Arabidopsis kodieren ca. 1500-2000 Gene für TF, von denen die Mehrheit bis heute nicht funktionell charakterisiert ist. Um die Aufklärung der TF-Funktionen weiter voranzutreiben, werden daher Analyse-Plattformen für Hochdurchsatzverfahren immer wichtiger. In den letzten Jahren sind umfangreiche Gateway® -kompatible ORF (open-reading-frame)-Kollektionen für Arabidopsis aufgebaut worden, die nun als nützliche Ressourcen für genetische Analysen zur Verfügung stehen. Auf Grundlage dieser Kollektionen wurde in dieser Arbeit eine neue Screening-Plattform etabliert, mit der trans-regulatorische Eigenschaften von TF in einem Hochdurchsatzverfahren untersucht werden können. Ein Mikrotiterplatten-System für Protoplastentransformationen erlaubt die transiente Koexpression von 96 verschiedenen TF-Expressionsvektoren mit einem Promotor:Luciferase-Reporter der Wahl. Das Transaktivierungspotential jedes einzelnen TF kann über die Luciferaseaktivität bestimmt werden, indem emittierte Lumineszenz in einem Luminometer detektiert wird. Die Funktionalität des PTA (Protoplast Trans Activation)-Systems wurde anhand einer Transaktivierungsstudie der bereits gut charakterisierten Promotoren von RD29A und PDF1.2 und der ERF (Ethylene Response Factor)-TF-Familie überprüft, wobei bekannte Bindungsspezifitäten der TF bestätigt werden konnten. Für das System wurde eine umfassende Arabidopsis TF-Kollektion aufgebaut. Ca. 950 verschiedene Gateway® -kompatible TF-Expressionsvektoren stehen für Screening-Ansätze zur Verfügung. Für das PTA-System wurden verschiedene Anwendungen etabliert. Neben transaktivierenden, konnten beispielsweise auch repressive Eigenschaften von TF bestimmt werden. Darüber hinaus wurde gezeigt, dass es möglich ist, (I) die Expression von Promotoren gezielt durch verschiedene Stimuli, wie Salz oder Pflanzenhormone zu modulieren, (II) Protein-Protein-Interaktionen zu bestimmen, sowie (III) den Einfluss von Signalmolekülen (wie z. B. Kinasen) auf ihre Aktivierungseigenschaften zu untersuchen. Das PTA-System wurde in verschiedenen Screening-Ansätzen zur Identifizierung transkriptioneller Regulatoren pflanzlicher Stressantworten eingesetzt. In einer Analyse des Auxin-induzierbaren GH3.3-Promotors wurde dabei gezeigt, dass weit mehr bZIP-TF Einfluss auf die Auxin-vermittelte GH3.3-Expression haben, als bisher angenommen. Beispielsweise zeigten bZIP16 und bZIP68 ein höheres Transaktivierungspotential, als die bisher beschriebenen bZIP-Regulatoren der GH3.3-Expression. In einem zweiten Ansatz wurde die koordinierte Regulation der Biosynthese von Tryptophan-abgeleiteten antimikrobiellen Sekundärmetaboliten (Indol-Glukosinolate, Camalexin) untersucht. Dabei konnten ERF-TF der phylogenetischen Gruppen VIII und IX als potentielle Regulatoren mehrerer wichtiger Gene der Biosynthesewege identifiziert werden. Mit einem zusätzlichen Screening-Ansatz der gesamten TF-Expressionsvektor-Kollektion und einem Markerpromotor des Camalexin-Biosynthesewegs wurden weitere potentielle Regulatoren identifiziert, von denen einige bereits in der Pathogenantwort beschrieben sind. In einem weiteren Schwerpunkt dieser Arbeit wurde die von Weiste et al. (2007) etablierte Arabidopsis thaliana TF-ORF-Überexpressions-Kollektion (AtTORF-EX) erweitert. Mit Hilfe des dafür entwickelten Hochdurchsatzverfahrens zur Generierung stabil transformierter Pflanzenlinien wurden neue Überexpressionssamen-Kollektionen hergestellt und anschließend in einem Screening-Ansatz auf erhöhte Toleranz gegenüber oxidativem Stress getestet, wobei die Chemikalie Paraquat als oxidativer Stress-Geber eingesetzt wurde. Die TF bZIP1 und OBP1 konnten dabei als Resistenz-vermittelnd identifiziert werden. Zusammenfassend wurden in dieser Arbeit mit Hilfe beider Systeme neue potentielle Regulatoren pflanzlicher Stressantworten identifiziert. / Transcription factors (TFs) are important cellular regulators of gene expression. In Arabidopsis approximately 1500-2000 genes encode for TFs. Until now, the majority of these genes has not been functionally characterized. To further promote the evaluation of TF function, high-throughput tools are required. In recent years, comprehensive Arabidopsis open reading frame (ORF) collections have been established, which are valuable resources for functional genomics. Based on these collections a high-throughput microtiter plate based Protoplast Trans Activation (PTA) system has been established to screen for TFs which regulate a given promoter:Luciferase construct in planta. 96 protoplast transfection experiments can be performed simultaneously in a standard microtiter plate. Transactivation of a promoter:Luciferase reporter is measured via luciferase imaging. A screening collection of roughly 950 TFs expression vectors has been assembled using Gateway® technology and can be tested in various screening approaches. In this respect, it is possible to analyze transactivating as well as repressive properties. Moreover (I) stimulus induced transcription, (II) studies of protein-protein interaction and (III) the impact of signaling molecules (e.g. kinases) on the promoters activation potential can be measured. To demonstrate the feasibility of the high-throughput system, the transactivating properties of the Ethylene Response Factor (ERF) TF family were studied in combination with the well-characterized RD29A and PDF1.2 promoters. By this means, known binding specificities of the TF family were confirmed. Furthermore, the PTA-System was applied to identify transcriptional regulators involved in plant stress responses. In one approach the influence of bZIP TFs on the auxin-inducibility of the GH3.3-promoter was studied. In particular, bZIP16 and bZIP68 showed a stronger transactivation potential than those bZIPs which were previously described to regulate this auxin-responsive promoter. In an independent approach the transcriptional regulation of tryptophan-derived antifungal compounds (indol-glycosinolates, camalexin) biosynthesis has been studied. ERF TFs of the groups VIII and IX were identified as potential regulators of several biosynthetic genes. A subsequent screening approach of a key promoter of the camalexin biosynthetic pathway disclosed further potential regulators. Among these TFs, many have been described previously in plant pathogen responses. As a second approach to examine TF function the Arabidopsis thaliana TF ORF-EXpression-library (AtTORF-EX) established by Weiste et al. (2007) was extended. The developed high-throughput transformation procedure was used to generate new TF overexpression seed collections. Afterwards the library was applied in a screening approach to identify regulators which mediate enhanced tolerance towards the oxidative stress inducing chemical Paraquat. Thus, the TFs bZIP1 and OBP1 were found to promote resistance against Paraquat when overexpressed in Arabidopsis. In summary, using both approaches novel putative regulators of plant stress response signaling were identfied.

Ionisierende Strahlung (IR) ist in der medizinischen Diagnostik und in der Tumortherapie von zentraler Bedeutung, kann aber Genominstabilität und Krebs auslösen. Strahleninduzierte Genominstabilität (RIGI) ist in den klonalen Nachkommen bestrahlter Zellen zu beobachten, die zugrundeliegenden Mechanismen sind jedoch noch unverstanden. Zur Erforschung von verzögerten Strahleneffekten wurden primäre embryonale Fibroblastenkulturen mit 2 Gray bestrahlt und für 20 Populationsverdopplungen klonal expandiert. Zellen, die keiner Strahlung ausgesetzt waren, dienten als Kontrolle für normale Alterungsprozesse. Die Klone wurden durch klassische Chromosomenbänderungstechniken analysiert und in Abhängigkeit der Stabilität ihres Genoms in Gruppen eingeteilt. Ein Klon wurde als stabil gewertet, wenn die analysierten Metaphasen keinerlei Auffälligkeiten zeigten, während instabile Klone ein Mosaik aus normalen und abnormalen Metaphasen waren. Die Zellen von zwei Spendern wurden untersucht, um interindividuelle Strahleneffekte zu beurteilen. Nach Bestrahlung hatten mehr als die Hälfte der Klone Metaphasen mit strukturellen Aberrationen und wurden dementsprechend als instabil eingestuft. Drei Klone zeigten zudem numerische Aberrationen, die ausschließlich das Y Chromosom betrafen. Fluoreszenz in situ Hybridisierungen verifizierten diese Beobachtung in weiteren Klonen und deuteten an, dass der Verlust des Y Chromosoms mit RIGI assoziiert ist. Molekulare Karyotypisierungen mit SNP Arrays ergaben, dass IR in den Klonen Veränderungen der Kopienzahl auslöst. Ein Unterschied zwischen chromosomal stabilen und instabilen Klonen konnte jedoch nicht detektiert werden. Chromosomale Regionen, in denen sich bekanntermaßen fragile Stellen befinden, zeigten eine Anhäufung von CNVs. Ein RIGI Effekt konnte für die fragile Stelle 3B, in der sich das Gen FHIT befindet, identifiziert werden. Exom Sequenzierungen von Klonen und der entsprechenden Massenkultur zeigten eine alterungsassoziierte Entstehung von Varianten. Der Effekt wurde durch die Einwirkung von Strahlung erhöht. Auf Ebene von einzelnen Nukleotiden konnten ebenfalls Anhäufungen von Schäden in bestimmten genomischen Bereichen detektiert werden, dieser Effekt ging ohne die typischen RIGI Endpunkte einher. Die Ergebnisse der vorliegenden Arbeit zeigen, dass strahlenbedingte Veränderungen auf verschiedenen Ebenen (Chromosomen, Genkopienzahl und einzelnen Nukleotiden) beobachtet werden können, welche, unabhängig von RIGI, die Tumorentstehung begünstigen. Speziell Veränderungen im FRA3B Lokus und der Verlust des Y Chromosoms scheinen jedoch über die Destabilisierung des Genoms zur Krebsentstehung beizutragen. / Ionizing radiation is important in medical diagnosis and cancer treatment but can lead to genomic instability and secondary malignancies as a late effect. Radiation induced genomic instability (RIGI) can be observed in the progeny of irradiated cells but the underlying cellular processes remain to be elucidated. To study delayed genetic radiation effects, single cell fibroblast clones from two different male donors were established after a single X ray dose of 2 Gray. Non irradiated cells were used as controls to account for aging related effects. Clones were characterized using chromosome banding analysis. Stable clones were endowed with no karyotype abnormalities in all analysed metaphases after 20 Population doublings, whereas unstable clones showed both normal and abnormal metaphases. Two fibroblast strains were used to detect differences in radiation sensitivity. More than half of the irradiated clones were chromosomally abnormal and thus classified as unstable. Both banding analysis and fluorescence in situ hybridization revealed an increased rate of Y chromosome loss in irradiated clones which might be associated with RIGI. Using SNP Arrays, an increased rate of de novo copy number variations (CNVs) was detected in the progeny of irradiated cells when compared to non irradiated controls. However, a significant difference between chromosomally stable and unstable clones was not found. CNVs clustered in chromosomal regions that are associated with known fragile sites. The fragile site 3B, which encompasses the gene FHIT, was found to be affected by CNVs in unstable clones suggesting a RIGI related effect. Exome sequencing of clones and the respective primary cultures revealed an increased rate of variants during in vitro aging. This effect was further increased by radiation exposure. Analysis of single nucleotides showed a RIGI independent accumulation of damage in specific regions. The results of the present study show that radiation induced changes can manifest as chromosomal abnormalities, copy number variations and DNA sequence mutations promoting tumorigenesis independent from RIGI. However, changes in FRA3B and loss of Y chromosome might trigger cancer through destabilizing the genome.

Classic Galactosemia (CG) is an autosomal recessive disorder caused by deleterious mutations of galactose-1-phosphate uridyltransferase (E.C. 2.7.7.12) (GALT) gene, which results in the inability to metabolize galactose and the accumulation of galactose-1-phosphate (gal-1-p) in patients' cells. Newborn screening has resulted in presymptomatic diagnosis and treatment. Although a galactose-restricted diet prevents the neonatal lethality of this disorder, many well-treated patients continue to develop debilitating complications such as premature ovarian insufficiency (POI), dyspraxic speech, ataxia and other neurological defects. The causes of these unsatisfactory outcomes remain unclear, but accumulation of gal-1-p is regarded as the major factor responsible for these chronic complications. In previous studies we found that gal-1-p was a competitive inhibitor of the UTP dependent, glucose-1-phosphate pyrophosphorylase (EC 2.7.7.9) and inositol monophosphatase (EC 3.1.3.25). As a result there were deficiencies in cellular UDP-glucose and UDP-galactose as well as impaired G-protein-stimulated inositol responses of Ca++ release, respectively. In this study, we found that when we challenged GALT-deficient yeast and GALT-deficient human diploid fibroblasts with galactose, these cells exhibited environmental stress and endoplasmic reticulum (ER) stress, which was characterized by the up-regulation of the gene encoding the master regulator of ER stress, GRP78/BiP. In separate studies using GALT-deficient diploid fibroblasts and comparative expression arrays, we found that the expression level of a tumor suppressor gene called aplysia ras homolog I (ARHI) was significantly higher in patient cells under galactose challenge. This ARHI gene was lost in rodents during evolution and GALT knockout mice did not express the human phenotype for galactosemia whereas over-expression of this gene in transgenic mice resulted in phenotypes characteristic of those seen in patients with galactosemia. We therefore propose here that ARHI could be an important target of galactose toxicity in Classic Galactosemia, and also explain the absence of patient phenotypes in GALT knock-out mice. In order to prevent accumulation of gal-1-p caused by GALT-deficiency, we experimentally screened over 300,000 chemical compounds against human galactokinase (GALK) in vitro. To date, we obtained from two high-throughput screenings (HTS), 200 GALK inhibitors with IC50s ranging from 700nM to 35μM. We subsequently established selectivity and toxicity profiles of 34 selected GALK inhibitors. Based on these results, we selected four compounds for further characterization, which included kinetic studies, site-directed mutagenesis and molecular docking experiments. From these experiments, we learned how these compounds interacted with the GALK enzyme and built detailed binding models for each of them. We demonstrated that three of the in vitro inhibitors of GALK could lower intracellular gal-1-p accumulation in GALT-deficient cells. Of considerable interest to us was that one of the compounds, cluster 25-1, not only reduced gal-1-p accumulation, but also corrected the level of GRP78/BiP back to background in the galactose-challenged GALT-deficient cells. These results were the first to demonstrate a direct link between GALT-deficiency and ER stress and provided proof of concept that we could prevent both gal-1-p accumulation and ER stress with GALK inhibitors in GALT deficient human cells. Lastly, we developed a new, virtual method of identifying novel GALK inhibitors by combining software-based, high-throughput virtual screening (HTVS) and fragment-based linkage using docking software. The initial HTVS validation experiments with compounds from the "ZINC" database identified four active GALK inhibitors with IC50s ranging from 70μM to 400μM. We then used HTVS to identify chemical fragments which bind to the active site of the human GALK enzyme. Using fragment-linking software, we identified chemical fragments which could potentially result in high-affinity inhibitors when chemically joined.