The internet is one of the most widely used mediums for communication in modern society and it has become an everyday necessity for many. It is therefore of utmost importance that it remains as secure as possible. SSL and TLS are the backbones of internet security and an integral part of these technologies are the certificates used. Certificate authorities (CAs) can issue certificates that validate that domains are who they claim to be. If a user trusts a CA they can in turn also trust domains that have been validated by them. CAs can in turn trust other CAs and this, in turn, creates a chain of trust called a certificate chain. In this thesis, the structure of these certificate chains is analysed and a longitudinal dataset is created. The analysis looks at how the certificate chains have changed over time and puts extra focus on the domains of big tech companies. The dataset created can also be used for further analysis in the future and will be a useful tool in the examination of historical certificate chains. Our findings show that the certificate chains of the domains studied do change over time; both their structure and the lengths of them vary noticeably. Most of the observed domains show a decrease in average chain length between the years of 2013 and 2020 and the structure of the chains vary significantly over the years.

Bacterial DNA replication can stall at DNA lesions, leading to cell death if the damage fails to be repaired. To circumvent this, bacteria possess a mechanism called translesion DNA synthesis (TLS) to allow DNA damage bypass. The ImuABC TLS mutasome comprises the RecA domain-containing protein ImuA, the inactive polymerase ImuB, and the error-prone polymerase ImuC. ImuA and ImuB are necessary for the mutational function of ImuC that can lead to antimicrobial resistance (AMR) as seen in high-priority pathogens Pseudomonas aeruginosa and Mycobacterium tuberculosis. Understanding how ImuA and ImuB contribute to this function can lead to new targets for antimicrobial development. This research aims to discover the molecular functions of ImuA and ImuB homologs from Myxococcus xanthus through structural modelling and biochemical analyses. ImuA was discovered to be an ATPase whose activity is enhanced by DNA. Based on predicted structural models of the ATPase active site, I identified the critical residues needed for ATP hydrolysis, and found that the ImuA C-terminus regulates ATPase activity. Further, ImuA and ImuBNΔ34 (a soluble truncation of ImuB) display a preference for longer single-stranded DNA and overhang DNA substrates, and their affinity for DNA was quantified in vitro. To better understand how ImuA and ImuB assemble in the TLS mutasome, bacterial two-hybrid assays determined that ImuA and ImuB can self-interact and bind one another. Mass photometry revealed that ImuA is a monomer and ImuBNΔ34 is a trimer in vitro. ImuA and ImuBNΔ34 binding affinity was quantified in vitro at 1.69 μM ± 0.21 by microscale thermophoresis, and removal of the ImuA C-terminus weakens this interaction. Lastly, ImuA and ImuBNΔ34 secondary structures were quantified using circular dichroism spectroscopy, and ImuA was modified to enable crystallization for future structural studies. Together, this research provides a better understanding of ImuABC-mediated TLS, potentially leading to novel antibiotics to reduce the clinical burden of AMR. / Thesis / Master of Science (MSc) / The antimicrobial resistance (AMR) crisis is fueled by the emergence of multi-drug resistant microbes, posing a major threat to global health and disease treatment. Bacteria can develop resistance to antibiotics through mutations in the genome. When the genome becomes damaged, bacteria can acquire these mutations by an error-prone replication mechanism called translesion DNA synthesis (TLS). In some bacteria, TLS involves a specialized enzyme complex, consisting of proteins ImuA, ImuB and ImuC, allowing replication past bulky DNA damage and lesions. The goal of this thesis is to investigate how the ImuA and ImuB proteins contribute to the functioning of this mistake-making machinery. I used biochemical and biophysical methods to identify ImuA and ImuB interactions with each other and themselves. I discovered that ImuA is an enzyme that uses energy to enhance its binding to DNA, and determined the specific amino acids involved in this function.

Fotogrammetri är en viktig metod för att skapa 3D-representationer av terräng och strukturer, men utmaningar kvarstår när det gäller noggrannheten på grund av faktorer som bildkvalitet, kamerakalibrering och positionsdata. Användningen av drönare för byggnadsdetaljmätning möjliggör snabb och kostnadseffektiv datainsamling, men noggrannheten kan påverkas av bildkvalitet och skuggning. Avhandlingen syftar till att jämföra noggrannheten och kvaliteten hos punktmoln genererade med två olika tekniker: terrester laserskanning (TLS) och struktur-från-rörelse (SfM) fotogrammetri med drönare. För att testa båda metodernas osäkerhet och noggrannhet vid detaljmätning av bostäder. Genom att utföra mätningar på en villa har data samlats in med både TLS och drönare utrustade med 48 MP kamera, samt georeferering med markstöd (GCP). SfM-punktmoln bearbetades med Agisoft Metashape. Jämförelser gjordes mellan SfM- och TLS-punktmoln avseende täckning, lägesskillnad och lägesosäkerhet. Genom att följa riktlinjer från HMK - Terrester Laserskanning och tillämpa HMK Standardnivå 3 säkerställs hög noggrannhet i mätningarna. Kontroll av lägesosäkerhet av båda punktmolnen resulterade i en lägesosäkerhet som understeg toleranser satta enligt HMK - Terrester laserskanner Standardnivå 3.  Kontrollen av lägesosäkerheten visade att kvadratiska medelfelet(RMSE) i plan och höjd var 0.011m respektive 0.007m för TLS-punktmolnet, och 0.02m respektive 0.015m för drönar-SfM-punktmolnet, vilket låg under toleransen enligt HMK- Terrester Detaljmätning 2021. Resultaten tyder på att Structure-from-Motion fotogrammetri med drönare kan generera punktmoln med god detaljrikedom, inte lika noggrann som med terrester laserskanner på sin lägsta inställning. TLS uppvisade mindre osäkerhet enligt kontrollen av lägesosäkerhet, ungefär en halvering av RMSE i både plan och höjd. I studien framgick det att TLS presterar sämre vid svåråtkomliga ytor med skymd sikt och ogynnsamma infallsvinklar, där effekten blir en lägre punkttäthet för punktmolnet. Vid gynnsamma förhållanden erbjuder TLS en högre noggrannhet och detaljnivå jämfört med SfM punktmoln. Enligt M3C2 punktmoln analys, med TLS punktmolnet som referens, antydde det att SfM punktmolnet genererade största felen vid takfot samt vid buskage. De större felen vid takfot tyder på att SfM presterar sämre gällande detaljnivå och fel vid buskageområdet varierar inte från det som dokumenterats om fotogrammetriska fel vid mappning av vegetation. SfM kan utföra en effektiv datainsamling för större samt svåråtkomliga ytor men kräver lång bearbetningstid med diverse hjälpmedel för att uppnå hög noggrannhet. TLS kräver istället en lång datainsamlingsprocess men kan generera ett detaljerat och noggrant punktmoln direkt utan långa bearbetningsprocesser. Val av metod styrs därmed baserat på specifika projektkrav. Långsiktiga implikationer inkluderar förbättrad effektivitet och säkerhet inom bygg- och anläggningsprojekt, samt potentialen för kostnadsbesparingar och mer detaljerade inspektioner. / Photogrammetry is a crucial method for creating 3D representations of terrain and structures, yet challenges remain regarding accuracy due to factors such as image quality, camera calibration, and positional data. The use of drones for building detail measurements enables rapid and cost-effective data collection, but accuracy can be affected by image quality and shading. This thesis aims to compare the accuracy and quality of point clouds generated using two different techniques: terrestrial laser scanning (TLS) and Structure-from-Motion (SfM) photogrammetry with drones. The objective is to test the uncertainty and accuracy of both methods in residential surveying. Data collection was performed on a villa using both TLS and a drone equipped with a 48 MP camera, along with georeferencing with ground control points (GCP). SfM point clouds were processed with Agisoft Metashape. Comparisons were made between SfM and TLS point clouds in terms of coverage, positional difference, and positional uncertainty. By following guidelines from HMK - Terrester laserskanning 2021 and applying HMK Standard Level 3, high measurement accuracy was ensured. Positional uncertainty checks of both point clouds resulted in positional uncertainty within tolerances set by HMK - Terrestrial Laser Scanning Standard Level 3. The positional uncertainty, with a sample of 41 points showed that the root mean square error (RMSE) in plane and height was 0.011m and 0.007m respectively for the TLS point cloud, and 0.02m and 0.015m for the drone-SfM point cloud, both within the tolerance according to HMK - Terrestrial Detail Measurement 2021. The results suggest that Structure-from-Motion photogrammetry with drones can generate point clouds with good detail, although not as accurate as terrestrial laser scanning at its lowest setting. TLS showed less uncertainty according to the positional uncertainty check, with approximately half the RMSE in both plan and height. The study found that TLS performs worse on difficult-to-access surfaces with obstructed views and unfavorable angles, resulting in lower point cloud density. Under favorable conditions, TLS offers higher accuracy and detail compared to SfM point clouds. According to M3C2 point cloud analysis, using the TLS point cloud as a reference, SfM point clouds showed the largest errors at eaves and shrubbery. The larger errors at eaves indicate that SfM performs worse in terms of detail level, and errors in the shrubbery area are consistent with documented photogrammetric errors in vegetation mapping. SfM can effectively collect data for larger and difficult-to-access areas but requires extensive processing time with various aids to achieve high accuracy. Conversely, TLS requires a long data collection process but can generate a detailed and accurate point cloud directly without lengthy processing. The choice of method thus depends on specific project requirements. Long-term implications include improved efficiency and safety in construction and infrastructure projects, as well as potential cost savings and more detailed inspections.

Les gènes TDP-43 (TAR DNA Binding Protein 43) et FUS/TLS (Fused in Sarcoma/Translocated in Liposarcoma) sont actuellement à l’étude quant à leurs rôles biologiques dans le développement de diverses neuropathies telles que la Sclérose Latérale Amyotrophique (SLA). Étant donné que TDP-43 et FUS sont conservés au cours de l’évolution, nous avons utilisé l’organisme modèle C. elegans afin d’étudier leurs fonctions biologiques. Dans ce mémoire, nous démontrons que TDP-1 fonctionne dans la voie de signalisation Insuline/IGF pour réguler la longévité et la réponse au stress oxydatif. Nous avons développé des lignées C. elegans transgéniques mutantes TDP-43 et FUS qui présentent certains aspects de la SLA tels que la dégénérescence des motoneurones et la paralysie adulte. La protéotoxicité causée par ces mutations de TDP- 43 et FUS associées à la SLA, induit l’expression de TDP-1. À l’inverse, la délétion de tdp-1 endogène protège contre la protéotoxicité des mutants TDP-43 et FUS chez C. elegans. Ces résultats suggèrent qu’une induction chronique de TDP-1/TDP-43 sauvage propagerait la protéotoxicité liée à la protéine mutante. Nous avons aussi entrepris un criblage moléculaire pilote afin d’isoler des suppresseurs de toxicité neuronale des modèles transgéniques mutants TDP-43 et FUS. Nous avons ainsi identifié le bleu de méthylène et le salubrinal comme suppresseurs potentiels de toxicité liée à TDP-43 et FUS via réduction de la réponse au stress du réticulum endoplasmique (RE). Nos résultats indiquent que l’homéostasie de repliement des protéines dans le RE représente une cible pour le développement de thérapies pour les maladies neurodégénératives. / Two recently discovered causative genes for ALS, TDP-43 (TAR DNA Binding Protein 43) and FUS/TLS (Fused in Sarcoma/Translocated in Liposarcoma) are under further investigation regarding their biological roles in neuropathies such as Amyotrophic Lateral Sclerosis (ALS). Since TDP-43 and FUS are evolutionarily conserved we turned to the model organism C. elegans to learn more about their biological functions. Here we report that TDP-1 functions in the Insulin/IGF pathway to regulate longevity and the oxidative stress response. We have generated mutant TDP-43 and FUS transgenic lines in C. elegans that recapitulate certain aspects of ALS including motor neuron degeneration and adult-onset paralysis. Proteotoxicity caused by ALS- associated mutations in TDP-43 or FUS also induce TDP-1 expression and consistently, deletion of endogenous tdp-1 rescues mutant TDP-43 and FUS proteotoxicity in C. elegans. These results suggest that chronic induction of wild type TDP-1/TDP-43 by proteotoxicity may actively promote neurodegeneration. We also screened for small- molecule suppressors of mutant TDP-43 and FUS neuronal toxicity in transgenic C. elegans and identified methylene blue and salubrinal as potent suppressors of TDP-43 and FUS toxicity in our models through induction of the endoplasmic reticulum (ER) stress response. Our results indicate that protein folding homeostasis in the ER may be an important target for therapeutic development in neurodegenerative diseases.

Les gènes TDP-43 (TAR DNA Binding Protein 43) et FUS/TLS (Fused in Sarcoma/Translocated in Liposarcoma) sont actuellement à l’étude quant à leurs rôles biologiques dans le développement de diverses neuropathies telles que la Sclérose Latérale Amyotrophique (SLA). Étant donné que TDP-43 et FUS sont conservés au cours de l’évolution, nous avons utilisé l’organisme modèle C. elegans afin d’étudier leurs fonctions biologiques. Dans ce mémoire, nous démontrons que TDP-1 fonctionne dans la voie de signalisation Insuline/IGF pour réguler la longévité et la réponse au stress oxydatif. Nous avons développé des lignées C. elegans transgéniques mutantes TDP-43 et FUS qui présentent certains aspects de la SLA tels que la dégénérescence des motoneurones et la paralysie adulte. La protéotoxicité causée par ces mutations de TDP- 43 et FUS associées à la SLA, induit l’expression de TDP-1. À l’inverse, la délétion de tdp-1 endogène protège contre la protéotoxicité des mutants TDP-43 et FUS chez C. elegans. Ces résultats suggèrent qu’une induction chronique de TDP-1/TDP-43 sauvage propagerait la protéotoxicité liée à la protéine mutante. Nous avons aussi entrepris un criblage moléculaire pilote afin d’isoler des suppresseurs de toxicité neuronale des modèles transgéniques mutants TDP-43 et FUS. Nous avons ainsi identifié le bleu de méthylène et le salubrinal comme suppresseurs potentiels de toxicité liée à TDP-43 et FUS via réduction de la réponse au stress du réticulum endoplasmique (RE). Nos résultats indiquent que l’homéostasie de repliement des protéines dans le RE représente une cible pour le développement de thérapies pour les maladies neurodégénératives. / Two recently discovered causative genes for ALS, TDP-43 (TAR DNA Binding Protein 43) and FUS/TLS (Fused in Sarcoma/Translocated in Liposarcoma) are under further investigation regarding their biological roles in neuropathies such as Amyotrophic Lateral Sclerosis (ALS). Since TDP-43 and FUS are evolutionarily conserved we turned to the model organism C. elegans to learn more about their biological functions. Here we report that TDP-1 functions in the Insulin/IGF pathway to regulate longevity and the oxidative stress response. We have generated mutant TDP-43 and FUS transgenic lines in C. elegans that recapitulate certain aspects of ALS including motor neuron degeneration and adult-onset paralysis. Proteotoxicity caused by ALS- associated mutations in TDP-43 or FUS also induce TDP-1 expression and consistently, deletion of endogenous tdp-1 rescues mutant TDP-43 and FUS proteotoxicity in C. elegans. These results suggest that chronic induction of wild type TDP-1/TDP-43 by proteotoxicity may actively promote neurodegeneration. We also screened for small- molecule suppressors of mutant TDP-43 and FUS neuronal toxicity in transgenic C. elegans and identified methylene blue and salubrinal as potent suppressors of TDP-43 and FUS toxicity in our models through induction of the endoplasmic reticulum (ER) stress response. Our results indicate that protein folding homeostasis in the ER may be an important target for therapeutic development in neurodegenerative diseases.

Ensuring personal data ownership and interoperability for decentralized social Web applications is currently a debated topic, especially when taking into consideration the aspects of privacy and access control. Since the user's data are such an important asset of the current business models for most social Websites, companies have no incentive to share data among each other or to offer users real ownership of their own data in terms of control and transparency of data usage. We have concluded therefore that it is important to improve the social Web in such a way that it allows for viable business models while still being able to provide increased data ownership and data interoperability compared to the current situation. To this regard, we have focused our research on three different topics: identity, authentication and access control. First, we tackle the subject of decentralized identity by proposing a new Web standard called "Web Identity and Discovery" (WebID), which offers a simple and universal identification mechanism that is distributed and openly extensible. Next, we move to the topic of authentication where we propose WebID-TLS, a decentralized authentication protocol that enables secure, efficient and user friendly authentication on the Web by allowing people to login using client certificates and without relying on Certification Authorities. We also extend the WebID-TLS protocol, offering delegated authentication and access delegation. Finally we present our last contribution, the Social Access Control Service, which serves to protect the privacy of Linked Data resources generated by users (e.g. pro le data, wall posts, conversations, etc.) by applying two social metrics: the "social proximity distance" and "social contexts"

Third-party authentication services are becoming more common since it eases the login procedure by not forcing users to create a new login for every website thatuses authentication. Even though it simplifies the login procedure the users still have to be conscious about what data is being shared between the identity provider (IDP) and the relying party (RP). This thesis presents a tool for collecting data about third-party authentication that outperforms previously made tools with regards to accuracy, precision and recall. The developed tool was used to collect information about third-party authentication on a set of websites. The collected data revealed that third-party login services offered by Facebook and Google are most common and that Twitters login service is significantly less common. Twitter's login service shares the most data about the users to the RPs and often gives the RPs permissions to perform write actions on the users Twitter account.  In addition to our large-scale automatic data collection, three manual data collections were performed and compared to previously made manual data collections from a nine-year period. The longitudinal comparison showed that over the nine-year period the login services offered by Facebook and Google have been dominant.It is clear that less information about the users are being shared today compared to earlier years for Apple, Facebook and Google. The Twitter login service is the only IDP that have not changed their permission policies. This could be the reason why the usage of the Twitter login service on websites have decreased.  The results presented in this thesis helps provide a better understanding of what personal information is exchanged by IDPs which can guide users to make well educated decisions on the web.

The Master’s Thesis deals with the design and implementation of a web application for testing the security of SSL/TLS protocols on a remote server. The web application is developed in the Nette framework. The theoretical part describes SSL/TLS protocols, vulnerabilities, recommendations and technologies used in the practical part. The practical part is devoted to the creation of a web application with the process of using automatic scripts to test and display the results on the website with a rating of A+~to~C. The web application also displays a list of detected vulnerabilities and their recommendations.

The goal of the Master thesis on the topic of the Client application of DNS protocol with graphical interface for teaching purposes is to create a program with the features of sending, receiving DNS, MDNS and LLMNR protocols with optional parameters. Additionally, compare the created application with available tools such as Nslookup, Dig and create examples of application for teaching.

The aim of this thesis is to study and describe the theme of Public Key Infrastructure (PKI). Within the scope of minute PKI characterization there is a gradual depiction of particular structural elements, which are above all represented by cryptographic operations (asymetric and symetric cryptography, hash function and digital signature); then, there are also individual PKI subjects that are dealt with, like eg. certification authority, certificates, security protocols, secure heap etc. Last but not least there are a few complete Public Key Infrastructure implementation solutions described (OpenSSL, Microsft CA). The practical part of the thesis, a lab exercise, gives potential students the knowledge of installing OpenSSL system based certification authority. The next task educate students how to secure web server with certificate signed with own CA and also how to secure web server users‘ access control through certificates signed by the previously installed CA.