Telomeres are physical ends of chromosomes consisting of (TTAGGG)n DNA sequence and a specialized set of proteins that protect chromosomal ends from degradation and from eliciting DNA damage response. These specialized set of proteins, known as shelterin, directly bind to telomeric DNA. In addition, some DNA double-strand break (DSB) repair proteins such as, DNA-PKcs and KU70/80, play active roles in telomere maintenance. Mouse knock-out experiments have revealed that deletion of either DNA-PKcs or Ku70/80 resulted in elevated levels of telomeric fusion, indicative of dysfunctional telomeres. Artemis protein is involved in DNA DSB repair through non-homologous end joining (NHEJ) and it is phosphorylated by DNAPKcs. Human cells defective in Artemis have been identified and shown to be radiosensitive and patients with an Artemis defective gene suffer from radiosensitive severe-combined immune deficiency syndrome (RS-SCID). Mouse cells defective in Artemis have elevated levels of telomeric fusion. We have demonstrated in this thesis that Artemis defective human cell lines show a mild telomeric dysfunction phenotype detectable at the cytological level. The nature of telomere dysfunction phenotype appears to be similar to that observed in DNAPKcs defective cells as exemplified by the presence of IR induced chromatid telomeric fusions. We have also shown that (a) DNA damage occurring within the telomeric DNA is difficult to repair or irreparable in older cells and that (b) Artemis defective older cells show higher proportion of DNA damage at telomeres than their normal counterparts. Finally, we have demonstrated that inhibition of DNA-PKcs causes (a) an increase in telomeric fusions in Artemis defective cell lines relative to both normal cell lines after inhibition and Artemis cell lines before inhibition and (b)elevated levels of DNA damage at telomeres following exposure of cells to radiation relative to both irradiated normal cells exposed to a DNA-PKcs inhibitor and irradiated Artemis defective cells but not exposed to the DNA-PKcs inhibitor. These results suggest that the effects of Artemis and DNA-PKcs on telomeres are cumulative. We have also performed (a) experiments to examine telomere function in Artemis defective cell lines after knocking down DNA-PKcs levels by RNAi and b) preliminary experiments to knock-down Artemis in DNA-PKcs defective cells. Taken together, our results suggest that the Artemis defect causes mild telomere dysfunction phenotype in human cells.

DNA damage response (DDR) pathways are essential in maintaining genomic integrity in cells, but many DDR proteins have other important functions such as in the innate immune sensing of cytoplasmic DNA. Some DDR proteins are known to be beneficial or restrictive to viral infection, but most remain uncharacterised in this respect. Non-homologous end joining (NHEJ) is a mechanism of double stranded DNA (dsDNA) repair that functions to rapidly mend broken DNA ends. The NHEJ machinery is well characterised in the context of DDR but recent studies have linked the same proteins to innate immune DNA sensing and, hence, anti-viral responses. The aim of this thesis is to further investigate the interplay between herpes simplex virus 1 (HSV-1), a dsDNA virus, and two NHEJ proteins, DNA protein kinase catalytic subunit (DNA-PKcs) and paralogue of XRCC4 and XLF (PAXX). PAXX was first described in the literature as a NHEJ protein in 2015, but whether it has any role in the regulation of virus infection has not been established. Here we show that PAXX acts as a restriction factor for HSV-1 because PAXX-/- (KO) cells produce a consistently higher titre of HSV-1 than the respective wild type (WT) cells. We hypothesised that this could be due to a role of PAXX binding viral DNA and directly inhibiting HSV-1 replication or activating an anti-viral innate immune response. We have been able to, at least partially, rule out both of these initial hypotheses by showing that there was a reduced number of viral genomes present in KO cells during active lytic infection, and that an identical level of type I interferons are produced from WT and KO cells during HSV-1 infection. Although further characterisation of HSV-1 infection in WT and KO cells has not defined the molecular mechanism of restriction of HSV-1 by PAXX, we have uncovered a potential role for PAXX in mitogen-activated protein kinase (MAPK) signalling. In addition, and consistent with its function in restriction of HSV-1 infection, we show that infection with this virus in WT cells induces a loss of nuclear PAXX protein. Preliminary data suggest that these changes in localisation may occur as a result of stimulation of the cells with DNA, but not the RNA analogue poly(I:C). The role of PAXX in the regulation of HSV-1 infection in vivo was investigated by studying KO mice. Despite previous observations that mice lacking NHEJ proteins have brain defects related to autoinflammatory pathology, there were no obvious defects in the development of Paxx-/- mice, and they had brains of normal weight. No significant difference in viral spread or viral protein expression was observed between WT and KO HSV-1 infected mice, and KO mice did not exhibit abnormal pathology. There were, however, small but significant differences in the cellular immune response to infection which might be explained by reduced MAPK signalling in KO cells. DNA-PKcs is another component of the NHEJ machinery that acts to assist in dsDNA break repair in the nucleus and as an innate sensor of cytoplasmic viral DNA, but the effect of DNA-PKcs on HSV-1 infection has not been fully explored. Murine skin fibroblasts (MSFs) derived from wild type and PRKDC-/- (DNA-PKcs deficient) mice were cultured ex vivo and used for innate immune studies. Although HSV-1 was able to infect and stimulate these cells, no differences in the stimulation of innate immune gene expression between the two genotypes was observed, suggesting that DNA-PKcs does not contribute to HSV-1 sensing in MSFs. It has previously been reported that the HSV-1 protein ICP0 targets DNA-PKcs for degradation, although the reason for this is unknown. We confirmed these data, although found it to be cell-type specific and explored this interaction further using PRKDC-/- RPE-1 cells created using CRISPR/Cas9. HSV-1 infection in these cells followed unusual dynamics, and the development of cytopathic effect was accelerated as compared to WT cells. Together these observations confirm that DNA-PKcs regulates HSV-1 infection, but more work is required to fully understand the mechanisms involved.

ATM (Ataxia-Telangiectasia Mutated) i DNA-PKcs (DNA-dependent Protein Kinase, catalytic subunit) són dues proteïnes que pertanyen a la família de les PIKKs (PhosphatidylInositol 3-Kinase-related Kinase) i ambdues desenvolupen funcions importants en la via de resposta al dany en el DNA (DDR). ATM i DNA-PKcs són activades en resposta als trencaments de doble cadena del DNA (DSBs) que es produeixen a conseqüència de l'actuació de múltiples factors, entre ells les radiacions ionitzants. Un cop activades, les dues cinases realitzen funcions diferents -però significativament complementàries- en aquesta via: ATM és capaç de: (1) aturar el cicle cel·lular en qualsevol fase; (2) activar diverses proteïnes implicades en la via de reparació homòloga (HR) del DNA i (3) induir l'activació de la via de l'apoptosi cel·lular en cas que el dany sigui massiu i/o irreparable. Per la seva part DNA-PKcs és una proteïna mestra de la via de reparació no homòloga del DNA (NHEJ), on activa i regula a la resta de factors participants d'aquesta via. Finalment DNA-PKcs també pot induir la via de l'apoptosi en resposta a un dany massiu. L'absència d'alguna d'aquestes dues cinases comporta, en els individus afectes, l'aparició de síndromes d'inestabilitat cromosòmica caracteritzats per una major probabilitat de desenvolupar processos cancerígens. Les cèl·lules derivades dels individus afectes són extremadament radiosensibles i acumulen aberracions cromosòmiques. L'objectiu d'aquesta tesi doctoral és determinar quins factors contribueixen de manera específica a la radiosensibilitat i a la inestabilitat cromosòmica de les cèl·lules deficients en ATM i en DNA-PKcs. Per assolir aquest objectiu es va analitzar: (1) l'espectre d'aberracions radio-induïdes en ambdós tipus cel·lulars; (2) l'evolució i resolució d'aquestes aberracions al llarg del temps; (3) la possible implicació del metabolisme telomèric en aquestes aberracions i (4) la cinètica de reunió de DSBs de les cèl·lules deficients en ATM i la de les cèl·lules deficients en DNA-PKcs. Després de ser irradiats, ambdós tipus cel·lulars acumulen un nombre significativament elevat d'aberracions cromosòmiques. El metabolisme telomèric només contribueix de manera marginal a la inestabilitat cromosòmica en cèl·lules deficients en DNA-PKcs i no té repercussions en la línia cel·lular deficient en ATM emprada en aquest estudi. En analitzar la cinètica de reunió dels DSBs radio-induïts es va fer palès que la deficiència en DNA-PKcs indueix un alentiment de la mateixa. Una reparació més lenta de les lesions en el DNA afavoreix (1) l'acumulació de fragments cromosòmics i, alhora, (2) la reunió il·legítima dels mateixos. La cinètica alentida explica l'ampli espectre d'aberracions radio-induïdes obtingut en aquestes cèl·lules així com la seva persistència en el temps, esdevenint el principal factor responsable de la radiosensibilitat i inestabilitat cromosòmica en cèl·lules deficients en DNA-PKcs. En canvi les cèl·lules deficients en ATM reparen la majoria dels DSBs radio-induïts amb una cinètica comparable a la de les cèl·lules normals, però una fracció dels trencaments roman sense reparar inclús a llargs temps post-irradiació. Per tant, l'acumulació de trencaments pendents de ser reparats a llargs temps post-irradiació (48 i 72 h) apareix com el principal factor responsable de la radiosensibilitat i inestabilitat cromosòmica d'aquestes cèl·lules. Però com s'explica la persistència d'aquests trencaments durant vàries divisions post-irradiació? Un cop descartat un alentiment de la cinètica de reparació ens varem plantejar la possibilitat de que l'absència d'ATM impedís la correcta detecció d'aquests DSBs. Per tal d'avaluar aquesta hipòtesi es va realitzar un anàlisi de la presència de γH2AX i Mre11 en els extrems cromosòmics trencats. La majoria de les delecions cromosòmiques presents en les cèl·lules deficients en ATM presenten marcatge amb les dues proteïnes en el punt de trencament, però una fracció considerable de les mateixes (25%) no presenta cap tipus de marcatge. El resultat obtingut suggereix que els trencaments no senyalitzats no estan essent correctament detectats i que la maquinària de reparació no és activa en ells. Proposem que l'acumulació de trencaments pendents de reparar són una característica de les cèl·lules deficients en ATM, i que aquesta acumulació contribueix de manera important a la seva radiosensibilitat i inestabilitat cromosòmica. Mentre que la fracció de trencaments correctament senyalitzats per γH2AX i Mre11 podrà ser reparada al llarg del temps, la fracció de trencaments sense senyalitzar podria romandre sense reparar durant temps indefinit, contribuint especialment a la inestabilitat cromosòmica d'aquestes cèl·lules. / ATM (Ataxia-Telangiectasia Mutated) and DNA-PKcs (DNA-dependent Protein Kinase, catalytic subunit) belong to the PIKKs (PhosphatidylInositol 3-Kinase-related Kinase) family, and both proteins develop important functions in the DNA damage response pathway (DDR). ATM and DNA-PKcs are activated by the presence of DNA double strand breaks (DSBs), which are produced by multiple factors, ionizing radiations among these. Once activated, both kinases display different -but significantly complementary- functions in the DDR: ATM is able to: (1) halt the cell cycle; (2) activate several proteins implicated in the homologous repair pathway (HR) and (3) if the cell harbours massive and/or irreparable damage, ATM can initiate the apoptosis pathway. Meanwhile, DNA-PKcs is a master protein belonging to the non homologous end joining repair pathway (NHEJ), where it activates and regulates the remaining factors implied in this repair pathway. Finally, if the cell carries extensive damage DNA-PKcs can also induce the apoptosis pathway. Individuals affected by the absence of either kinase develop chromosomal instability syndromes, which are characterized by a special cancer predisposition. Cells obtained from the affected individuals are extremely radiosensitive and accumulate chromosomal aberrations.The main goal of this doctoral thesis is to determine which factors specifically contribute to the radiosensitivity and chromosomal instability of ATM and DNA-PKcs deficient cells. In order to attain this goal we analyzed: (1) the spectrum of radio-induced aberrations in both cell types; (2) the evolution and resolution of these aberrations over time; (3) the possible implication of telomeric metabolism in these aberrations and (4) the DSBs joining kinetics of ATM and DNA-PKcs deficient cells.After irradiation both cellular types accumulate a significant number of chromosomal aberrations. While telomeric metabolism contributes -although only marginally- to the chromosomal instability in DNA-PKcs deficient cells, it has no influence on the ATM deficient cell line employed in this study. Analysis of the DSBs joining kinetics demonstrates that DNA-PKcs deficiency induces a delay in the repair kinetics of radio-induced lesions. Slower DNA repair favours the accumulation of chromosomal fragments as well as their illegitimate joining displayed by DNA-PKcs deficient cells. Thus, the slower repair kinetics explain the broad aberration spectrum obtained in these cells, as well as their persistence in time, revealed to be the main factor responsible for radiosensitivity and chromosomal instability in DNA-PKcs deficient cells. On the other hand, ATM deficient cells are able to repair the majority of the radio-induced DSBs with normal joining kinetics except for a fraction of breaks, which remain unrepaired even at long post-irradiation times. Therefore, the accumulation of unrepaired breaks at long post-irradiation times (48 and 72 hr) is revealed to be the main factor responsible for the radiosensitivity and chromosomal instability of AT cells. But how can the persistence of these breaks in an unrepaired state during several cell divisions be explained? After discarding a delayed DSBs joining kinetic, we reflected upon the possibility of the absence of ATM preventing proper detection of unrepaired DSBs. In order to evaluate this hypothesis we analysed the presence of γH2AX and Mre11 signalling in the broken chromosome ends scored in AT cells. The majority of the chromosome deletions displayed both γH2AX and Mre11 labelling at the break point, but a significant fraction (25%) was devoid of any labelling. The results obtained suggest that unlabelled breaks are not being correctly detected and that the cell repair machinery is not active on them. We propose that the accumulation of breaks waiting for efficient repair is a hallmark of ATM deficient cells, and that this accumulation makes a major contribution to their radiosensitivity and chromosomal instability. While the fraction of correctly γH2AX and Mre11-labelled breaks will eventually be repaired, the fraction of unlabelled breaks remains invisible to the DNA damage repair machinery, thus especially contributing to the chromosomal instability of these cells.

Les ADN-Topoisomérases (Topo) de type I et II sont des enzymes essentielles à la suppression des surenroulements de engendrés par la plupart des transactions de l’ADN. Elles sont des cibles de médicaments anticancéreux très utilisés en clinique. Parmi eux, les inhibiteurs de Topo1 de la famille des camptothécines (CPT) exercent leur cytotoxicité en produisant des cassures double-brin de l’ADN provenant de la collision des fourches de réplications avec les complexes ADN-Topo1 stabilisés par ces inhibiteurs. Les dérivés de CPT sont approuvés pour le traitement des cancers coliques, de l’ovaire et du poumon, mais il existe de multiples mécanismes de résistance à ces agents qui sont à l’origine de l’échec du traitement. Les cancers de la prostate sont réfractaires aux CPT, mais très peu d’études ont été réalisées pour expliquer cette résistance « intrinsèque ». Ce travail de thèse visait à identifier les mécanismes de cette résistance en nous appuyant (1) sur des résultats antérieurs de l’équipe montrant que l’interaction entre la DNA-PKcs, une kinase impliquée dans la réparation de l’ADN par recombinaison non-homologue, et la Topo1 pouvait réguler la sensibilité aux CPT de manière indépendante de la réparation de l’ADN et (2) sur une étude ayant mis en évidence une interaction entre DNA-PKcs et le facteur de transcription ERG dont le gène est remanié dans plus de 50% des tumeurs de prostate. Nos résultats montrent pour la première fois que ERG est effectivement impliqué dans la régulation de la réponse aux CPT dans la lignée VCaP présentant un gène de fusion TMPRSS2-ERG. La répression de ERG dans la lignée VCaP induit une sensibilisation à la CPT mais pas à l’étoposide (un inhibiteur de Topo2) et est accompagnée d’une augmentation du nombre de complexes ADN/Topo1. Ce mécanisme peut-être soit lié à un effet de ERG sur l’interaction DNA-PKcs/Topo1 ou à une régulation transcriptionnelle de gènes impliqués dans la réponse aux CPT incluant la Topo1 elle-même. Nous avons confirmé cette deuxième hypothèse, en démontrant que ERG régule la transcription du micro ARN miR-24 et que l’expression de Topo1 est également sous contrôle de miR-24 dans la lignée VCaP. Des résultats similaires ont été obtenus dans la lignée LNCaP (présentant le gène de fusion TMPRSS2-ETV1) dans laquelle la répression de ETV1 confère aussi une sensibilisation à la CPT. Au cours de notre travail nous avons également recherché des inhibiteurs de l’interaction entre la DNA-PKcs et Topo1 afin de pouvoir utiliser ces composés comme agents de potentialisation des dérivés de CPT en clinique. Les résultats du criblage d’une banque de 320 composés naturels réalisé par la technologie AlphaScreen n’ont malheureusement pu identifier que des inhibiteurs catalytiques de Topo1. Nous avons néanmoins pu montrer que l’un d’entre eux, la mahanimbine, présentait une forte activité cytotoxique vis-à-vis de lignées résistantes aux dérivés de CPT et vis-à-vis de la lignée VCaP ce qui permet d’envisager le développement de nouvelles classes d’inhibiteurs catalytiques Topo1 pouvant contourner la résistance des dérivés de CPT en clinique. / Type I and II DNA Topoisomerases (Top) are essential enzymes involved in the removal of DNA torsional constraints induced by most DNA transactions. They are the targets of various anticancer agents used in the clinic. Among them, Top1 inhibitors from the camptothecins (CPT) family exert their cytotoxicity by producing DNA double-strand breaks that are generated by the collision of advancing replication forks with DNA-Top1 complexes that are stabilized by these inhibitors. CPT derivatives are approved for the treatment of colon, ovary and lung cancers but resistance mechanisms are developed and lead to treatment failure. Prostate cancers are refractory to CPT, but few studies have addressed the mechanisms of such “intrinsic” resistance. This work was aimed at identifying such mechanisms based on (1) previous results from the laboratory showing that interaction of Top1 with DNA-PKcs, a kinase that is essential for non-homologous end-joining, could regulate cell sensitivity to CPT independently of DNA repair and (2) a study that showed an interaction of DNA-PKcs with ERG, a transcription factor from the ETS family which is rearranged in more than 50% of prostate tumors. Our results show for the first time that ERG is indeed involved in the regulation of prostate cancer cell response to CPT as its repression sensitized VCaP cells displaying the TMPRSS2-ERG gene fusion to CPT but not to the Top2 inhibitor etoposide. This effect is accompanied with an increase in Top1-DNA complexes. This could be due to either an effect of ERG on DNA-PKcs/Top1 interaction, or to the transcriptional regulation of genes involved in cell response to CPT, including Top1 itself. We confirmed the latter hypothesis by showing that ERG can regulate the transcription levels of the microRNA miR-24 and that Top1 expression relies, at least in part, on miR24 levels in VCaP cells. We obtained similar results in LNCaP cells (characterized by a TMPRSS2-ETV1 gene fusion), in which ETV1 repression also sensitizes cells to CPT. In parallel, we also searched for inhibitors of DNA-PKcs/Top1 interaction in order to use these compounds to potentiate CPT derivatives in the clinic. We screened a chemical library of 320 natural compounds using the AlphaScreen technology. The results were disappointing as we only identified compounds that are catalytic inhibitors of Top1. Nevertheless, we could show that among them, mahanimbine displayed a potent cytotoxic activity towards CPT-resistant colon cancer cell lines and could efficiently inhibit the growth of VCaP cells that are highly resistant to CPT. This opens new avenues for the development of new classes of Top1 catalytic inhibitors that could be used to circumvent the clinical resistance to CPT derivatives.

Background: Therapy resistance is a great challenge in cancer treatment. Among numerous factors, cell adhesion to extracellular matrix is a well-known determinant of radiochemo-resistance. It has been shown that targeting focal adhesion proteins (FAPs), e.g. β1 integrin, enhances tumor cell radio(chemo)sensitivity in various entities such as head and neck squamous cell carcinoma (HNSCC), lung carcinoma, glioblastoma, breast carcinoma and leukemia. Previous studies demonstrated a functional crosstalk between specific FAPs and DNA repair processes; however, the molecular circuitry underlying this crosstalk remains largely unsolved. Hence, this study in HNSCC aimed to identify alternative FAPs associated with DNA damage repair mechanisms and radioresistance. Materials and Methods: A novel 3D High Throughput RNAi Screen (3DHT-RNAi-S) using laminin-rich extracellular matrix (lrECM) was established to determine radiation-induced re-sidual DNA double strand breaks (DSBs; foci assay) and clonogenic radiation survival. In the screen, we used UTSCC15 HNSSC cells stably expressing the DSB marker protein 53BP1 tagged to pEGFP. Validations were performed in 10 additional HNSCC cell lines (Cal33, FaDu, SAS, UTSCC5, UTSCC8, UTSCC14, UTSCC15, UTSCC45 and XF354fl2) grown in 3D lrECM. Immunofluorescence staining, immunoblotting, chromatin fractionation were utilized to evaluate protein expression, dynamics and kinetics post irradiation. Investigations of molecular mechanisms of DNA repair and radio(chemo)resistance employed DSB repair reporter assays for non-homologous end joining (NHEJ) and homologous recombination (HR), cell cycle analysis, chromatin fractionation levels evaluation and kinase activity profiling (PamGene) upon protein knockdown in combination with/-out X-ray exposure. Foci assay and clonogenic survival assay were performed after single or multiple knockdowns of synemin and associated proteins such as DNA-PKcs and c-Abl. Protein-protein interactions between synemin and associated proteins were determined using immunoprecipitation and proximity ligation assay. Mutant/depletion constructs of synemin (ΔLink-Tail, ΔHead-Link, Synemin_301-961, Synemin_962-1565, S1114A and S1159A) were generated in order to identify essential synemin’s sites controlling DNA repair functions. Results: Among the targets found in the 3DHT-RNAi-S, synemin was one of the most promising FAP candidates to determine HNSCC cell survival and DNA damage repair. Synemin silencing radiosensitized HNSCC cells, while its exogenous overexpression induced radio-protection. Radiation induced an increased synemin/chromatin interaction and a marked ac-cumulation of synemin in the perinuclear area. Intriguingly, synemin depletion elicited a 40% reduction in NHEJ activity without affecting HR or Alt-EJ. In line, ATM, DNA-PKcs and c-Abl phosphorylation as well as Ku70 expression strongly declined in synemin depleted and irra-diated cells relative to controls, whereas an opposite effect was observed under synemin overexpression. Single, double and triple depletion of synemin, DNA-PKcs and c-Abl resulted in a similar radiosensitizing effect and DSB levels as detected upon single knockdown of synemin, describing its upstream role. In kinome analysis, tyrosine kinases showed signifi-cantly reduced activity after synemin silencing relative to controls. Furthermore, immunoprecipitation assays revealed a protein complex formed between synemin, DNA-PKcs and c-Abl under pre- and post-irradiation conditions. This protein complex dispersed when ATM was pharmacologically inhibited, implying synemin function to be dependent on ATM kinase activity. By means of the different mutation/deletion constructs of synemin, the phosphorylation site at serine 1114 located on the distal portion of synemin’s tail was identified as essential protein-protein interaction site for synemin’s function in DNA repair. Conclusions: The established 3DHT-RNAi-S provides a robust screening platform for identifying novel targets involved in therapy resistance. Based on this screen and detailed mechanistic analyses, the intermediate filament synemin was discovered as a novel important determinant of DNA repair, tyrosine kinase activity and radiochemoresistance of HNSCC cells. These results further support the notion that DNA repair is controlled by cooperative interactions between nuclear and cytoplasmic proteins.

International Telemetering Conference Proceedings / October 27-30, 1997 / Riviera Hotel and Convention Center, Las Vegas, Nevada / Last year the design and implementation of a secure World Wide Web based data sharing tool which could enable geographically remote contractor teams to access flight and test telemetry data securely over the Internet was presented [1]. Key technologies facilitating this capability were the Hypertext Transfer Protocol (HTTP) and the Secure Sockets Layer (SSL) capable web browsers and web servers. This year the applicability of the Secure Multipurpose Internet Mail Extension (S/MIME) specification is being evaluated for the transport of telemetry data via secure E-mail.

The term 'Retinitis pigmentosa' (RP) represents a group of inherited, late-onset diseases characterised by progressive retinal degeneration due to photoreceptor death. Mutations in the RP2 gene are found in 7-18% of patients with X-linked RP, one of the most severe forms. The RP2 gene product is a membrane-associated protein which encompasses two distinct domains. The N-terminal domain is well characterised as possessing GTPase-activating protein (GAP) activity towards the small GTPase ARL3 and thus regulate the transport of lipid-modified proteins within the photoreceptor cell. However, it is not known if the loss of this particular function of RP2 is the sole reason that causes the disease, while the role of the protein's C-terminus remains unknown. This thesis focuses on the characterisation of two novel protein-protein interactions of RP2 with the aim to investigate novel roles of the protein. Firstly, evidence is provided that a highly-conserved cluster of RP2 residues that span both the N- and C-terminus participate in direct interaction with Osteoclast-stimulating factor 1 (OSTF1). Two hypotheses are explored about the potential role of the complex in SRC-mediated RP2 phosphorylation and the regulation of cell motility. Secondly, the catalytic subunit of DNA-dependent protein kinase (DNA PK) is identified as a novel interaction partner of RP2 in cultured cells. The two proteins are shown to co-localise in the nuclear and membrane compartments of a retinal-derived cell line and might engage in a kinase-substrate relationship. So far, no evidence was found that RP2 participates in the canonical function of DNA PK which is the regulation of DNA double-stranded breaks. Finally, the CRISPR/Cas9 genome editing method was applied on zebrafish embryos to generate a novel vertebrate animal model for the loss of RP2 function. One out of three different zebrafish lines with rp2 mutations was shown by histology to have mild late-onset thinning of the photoreceptor outer segments. The present thesis reports previously unexplored aspects of RP2's function and will, therefore, contribute to understanding the molecular mechanisms that underlie RP. Moreover, this thesis will contribute to the discussion about the usefulness of zebrafish as an RP model.

<p>In this report hardware based alternatives to password authentication in a Windows domain are evaluated for the needs of a certain company. In order to investigate the demands on such alternatives interviews with people concerned have been carried out. The demands which resulted from the interviews have been used to select types of hardware tokens for evaluation. Two products which offer authentication with smart cards and USB tokens have been selected and closer evaluated. These are RSA Passage which offers both hardware options and Rainbow iKey which uses USB tokens. Both products are evaluated based on the demands and additional evaluation criteria. The information from the evaluations is used to compare the products.</p>

This thesis examines the vulnerabilities due to low-level implementation deficiencies of otherwise secure communication protocols in smart-cards. Smart-cards are considered to be one of the most secure, tamper-resistant, and trusted devices for implementing confidential operations, such as authentication, key management, encryption and decryption for financial, communication, security and data management purposes. The self-containment of smart-cards makes them resistant to attacks as they do not depend on potentially vulnerable external resources. As such, smart-cards are often incorporated in formally-verified protocols that require strong security of the cryptographic computations. Such a setting consists of a smart-card which is responsible for the execution of sensitive operations, and an Application Programming Interface (API) which implements a particular protocol. For the smart-card to execute any kind of operation there exists a confidential low-level communication with the API, responsible for carrying out the protocol specifications and requests. This communication is kept secret on purpose by some vendors, under the assumption that hiding implementation details enhances the system’s security. The work presented in this thesis analyses such low-level protocol implementations in smart-cards, especially those whose implementation details are deliberately kept secret. In particular, the thesis consists of a thorough analysis of the implementation of PKCS#11 and Bitcoin smart-cards with respect to the low-level communication layer. Our hypothesis is that by focusing on reverse-engineering the low-level implementation of the communication protocols in a disciplined and generic way, one can discover new vulnerabilities and open new attack vectors that are not possible when looking at the highest levels of implementation, thereby compromising the security guarantees of the smart-cards. We present REPROVE, a system that automatically reverse-engineers the low-level communication of PKCS#11 smart-cards, deduces the card’s functionalities and translates PKCS#11 cryptographic functions into communication steps. REPROVE deals with both standard-conforming and proprietary implementations, and does not require access to the card. We use REPROVE to reverse-engineer seven commercially available smart-cards. Moreover, we conduct a security analysis of the obtained models and expose a set of vulnerabilities which would have otherwise been unknown. To the best of our knowledge, REPROVE is the first system to address proprietary implementations and the only system that maps cryptographic functions to communication steps and on-card operations. To that end, we showcase REPROVE’s usefulness to a security ecosystem by integrating it with an existing tool to extract meaningful state-machines of the card’s implementations. To conduct a security analysis of the results we obtained, we define a threat model that addresses low-level PKCS#11 implementations. Our analysis indicates a series of implementation errors that leave the cards vulnerable to attacks. To that end, we showcase how the discovered vulnerabilities can be exploited by presenting practical attacks. The results we obtained from the PKCS#11 smart-card analysis showed that proprietary implementations commonly hide erroneous behaviours. To test the assumption that the same practice is also adopted by other protocols, we further examine the low-level implementation of the only available smart-card based Bitcoin wallets, LEDGER. We extract the different protocols that the LEDGER wallets implement and conduct a through analysis. Our results indicate a set of vulnerabilities that expose the wallets as well as the processed transactions to multiple threats. To that end, we present how we successfully mounted attacks on the LEDGER wallets that lead to the loss of the wallet’s ownership and consequently loss of the funds. We address the lack of well-defined security properties that Bitcoin wallets should conform to by introducing a general threat model. We further use that threat model to propose a lightweight fix that can be adopted by other, not necessarily smart-card-based, wallets.

In this report hardware based alternatives to password authentication in a Windows domain are evaluated for the needs of a certain company. In order to investigate the demands on such alternatives interviews with people concerned have been carried out. The demands which resulted from the interviews have been used to select types of hardware tokens for evaluation. Two products which offer authentication with smart cards and USB tokens have been selected and closer evaluated. These are RSA Passage which offers both hardware options and Rainbow iKey which uses USB tokens. Both products are evaluated based on the demands and additional evaluation criteria. The information from the evaluations is used to compare the products.