Domain Name System (DNS) is virtually the distributed directory of the Internet for obtaining the Internet Protocol (IP) addresses to access web resources. DNS has always been one of the prime targets for cyber attackers either to inundate different types of DNS servers with attack traffic and false records or to exploit the DNS protocol to perform targeted attacks to user machines. DNS amplification or reflection attacks are some of the most fundamental types of DNS specific Denial-of-Service (DoS) attacks. In this type of attack, users are denied service as the server needs to process spoofed DNS query from the attackers and victim machines receive unsolicited DNS response. Software Defined Networking (SDN) and Network Function Virtualization (NFV) are the technological breakthroughs which have brought transformational change in operating and maintaining network services. These have also opened new avenues to deal with those cyber-attacks along with introducing a whole new set of security threats or vulnerabilities that need to be taken care of. In this paper, we propose detection and mitigation strategies to combat DNS amplification or reflection attacks leveraging the functionalities of both SDN and NFV. We reviewed the existing literature of related approaches, incorporated Moving Target Defense (MTD) techniques into the security solutions, discussed the deployment options of vDNS (Virtual DNS) servers, and elaborated on the security issues involved with SDN and NFV. This work could potentially augment the security of the DNS infrastructure while improving the scalability and agility and provide future direction in research and practice.

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Nucleic-based acid technology (NAT) is a reliable and well-established method in molecular diagnosis for the detection of bacterial infection. Specifically, PCR (polymerase chain reaction) is the most popular technique to amplify the number of DNA or RNA copies in the sample. However, due to the thermal cycles in the PCR method, advanced equipment and technologies are required to precisely control the temperature during the cycles. To overcome this limitation, isothermal amplification methods have been developed which function at constant temperatures and help reduce the need for state-of-the-art machines to perform the amplification. Among isothermal amplification methods, LAMP (loop mediated isothermal amplification) has demonstrated robustness and sensitivity compared to PCR. Additionally, microfluidic lab-on-a-chip (LOC) technology can facilitate the intensive processes which have been used traditionally in laboratories by automating the required procedures, reducing the volume of the reagents and minimizing the cost and the time of experiments. Although many microfluidic LOC devices have been developed in order to be used in resource poor settings, there is still a need for a simple setup which is inexpensive, accurate and can be performed without the need for a trained technician. In this thesis, a disposable microfluidic device was developed which is capable of performing high-throughput DNA amplification by using a simple segmentation method in order to digitize the sample into multiple micro-wells. Moreover, design and fabrication of a disposable, inexpensive flexible heater which is an inevitable part of the setup using a direct write process was introduced in order to provide the required energy for the LAMP reaction. Parallel real-time DNA amplification with limit of detection down to few copies per micro-well in less than an hour was illustrated. Using E. coli 0157, it was demonstrated that the detection time of E.coli can be as quick as 11 to 55 minutes with sample concentrations varying from 700,000 copies/micro-well (11 minutes), 70,000 copies/micro-well (18 minutes), 700 copies/micro-well (31 minutes), 7 copies/micro-well (40 minutes) and 0.07 copies/micro-well (55 minutes). Finally, the capability of the device for on chip reagent storage up to 3 days without using any coating methods was illustrated. / Thesis / Master of Applied Science (MASc)

The development of easily fabricated, highly stable DNA-based microarray and continuous flow concentrating devices is vital for several biomedical and environmental applications. Nucleic acid biosensors can be used for genetic analysis, disease diagnosis, drug discovery, food and water quality control and more, however methods of fabrication are tedious, and the longevity of sensors is compromised by the fragility of the sensing component. In this report, the fabrication and characterization of two biosensing modalities – microarrays and microgels – composed of Rolling Circle Amplification (RCA) product in poly(oligoethylene glycol methacrylate) (POEGMA) hydrogels are investigated. RCA product microarrays were developed by the sequential printing of aldehyde and hydrazide functionalized POEGMA precursors on nitrocellulose paper, exploiting rapid gelling via hydrazone crosslinking to generate thin film hydrogel sensing arrays. POEGMA/RCA product microgels for affinity column applications were synthesized using an inverse emulsion polymerization technique. Inkjet printing evenly deposited RCA product in all wells, with POEGMA effectively stabilizing DNA on the cellulose substrate. Hybridization of complementary probe to the encapsulated RCA product was optimized, yielding a signal to noise ratio of ~4 for a large range of probe concentrations. Microgels were successfully synthesized in the size range of 10-60 μm diameter, and a linear model that can accurately predict size based on initiator and emulsifier concentration was developed. The encapsulation efficiency of RCA product in different sized microgels was explored, with larger microgels entrapping more product and the highest encapsulation efficiency calculated at 56%. These results demonstrate that POEGMA hydrogels can be utilized to encapsulate and stabilize RCA product in two distinct structures, providing a basis for the development of easily fabricated biosensors for more specific applications. / Thesis / Master of Applied Science (MASc)

Plasma- und Serumproben waren in früheren epidemiologischen Studien häufig das einzige biologische Material, das gesammelt und untersucht wurde. Diese Studien besitzen gerade durch ihren sehr langen Untersuchungszeitraum einen riesigen Informationsgehalt und wären ein unbezahlbarer Schatz für genetische Analysen. Oft ist aufgrund damals mangelnder Akquirierung jedoch keine genomische DNA verfügbar. Um die in Plasmaproben in geringer Menge vorkommende DNA verwenden zu können, extrahierten wir die DNA mit Hilfe von magnetischen Partikeln und setzten sie in eine Whole Genome Amplification (WGA) mittels Φ29-DNA-Polymerase ein. Wir stellten 88 Probenpärchen, bestehend aus einer WGA-Plasma-DNA und der korrespondierenden Vollblut-DNA derselben Person, zusammen und genotypisierten bei diesen neun hochpolymorphe Short Tandem Repeats (STR) und 25 SNPs. Die durchschnittliche innerhalb der Probenpaare auftretende Diskordanzrate betrug 3,8% für SNPs sowie 15,9% für STRs. Basierend auf den Ergebnissen der Hälfte der Probenpaare entwickelten wir einen Ausschlussalgorithmus und validierten diesen in der anderen Hälfte der Probenpaare. Mit diesem ist es möglich, zum Einen diejenigen Proben mit einer guten DNA-Qualität herauszufiltern, um Genotypisierungsfehler zu vermeiden, und zum Anderen jene Proben mit insuffizienter DNA-Qualität auszuschließen. Nachdem Proben, die fünf oder mehr homozygote Loci in dem 9-STR-Markerset aufwiesen, ausgeschlossen wurden, resultierte dies in einer Ausschlussrate von 22,7% und senkte die durchschnittliche Diskordanzrate auf 3,92% für STRs bzw. 0,63% für SNPs. Bei SNPs entspricht dieser Wert ungefähr der Fehlerquote, wie er auch bei Genotypisierungen mit Vollblut-DNA in vielen Laboratorien auftritt. Unsere Methode und das Ausschlusskriterium bieten damit neue Möglichkeiten, um zuverlässige DNA aus archivierten Plasmaproben wiederzugewinnen. Dieser Algorithmus ist auch besser geeignet, als nur die eingesetzte DNA-Menge in die WGA-Reaktion als Kriterium zu benützen. / Plasma and serum samples were often the only biological material collected for earlier epidemiological studies. These studies have a huge informative content, especially due to their long follow-up and would be an invaluable treasure for genetic investigations. However, often no banked DNA is available. To use the small amounts of DNA present in plasma, in a first step, we applied magnetic bead technology to extract this DNA, followed by a whole-genome amplification (WGA) using phi29-polymerase. We assembled 88 sample pairs, each consisting of WGA plasma DNA and the corresponding whole-blood DNA. We genotyped nine highly polymorphic short tandem repeats (STRs) and 23 SNPs in both DNA sources. The average within-pair discordance was 3.8% for SNPs and 15.9% for STR genotypes, respectively. We developed an algorithm based on one-half of the sample pairs and validated on the other one-half to identify the samples with high WGA plasma DNA quality to assure low genotyping error and to exclude plasma DNA samples with insufficient quality: excluding samples showing homozygosity at five or more of the nine STR loci yielded exclusion of 22.7% of all samples and decreased average discordance for STR and SNP markers to 3.92% and 0.63%, respectively. For SNPs, this is very close to the error observed for genomic DNA in many laboratories. Our workflow and sample selection algorithm offers new opportunities to recover reliable DNA from stored plasma material. This algorithm is superior to testing the amount of input DNA.

De nombreuses applications militaires ou civiles, telles que la spectroscopie dans les bandes de transmission de l’atmosphère (bandes 3-5µm et 8-12µm), nécessitent de disposer de sources émettant dans le moyen infrarouge (IR). Les travaux de cette thèse portent sur la génération de rayonnement dans la bande 3-5µm par amplification paramétrique (mélange à quatre ondes) dans les fibres optiques en verres fluorés et en verres de chalcogénures. La première partie de ce travail a été consacrée à l’étude théorique et à la modélisation des conditions d’accord de phase et du gain paramétrique dans des fibres à saut d’indice monomodes en verres fluorés ZBLAN et verres de chalcogénures As2S3 et As2Se3. La nature des résultats obtenus nous a conduit à étudier théoriquement le potentiel de l’accord de phase multimode dans les fibres en verres de chalcogénures. La deuxième partie de ce travail a porté sur la modélisation de l’amplification paramétrique dans des fibres en verres de chalcogénures microstructurées à géométrie hexagonale. Pour ce faire, un modèle simplifié de la propagation dans les fibres microstructurées hexagonales a été développé : le modèle de l’indice effectif de gaine (EIM). Il a ensuite été comparé à une méthode de résolution aux éléments finis. Grâce à cette comparaison, nous avons pu améliorer la précision du modèle EIM en déterminant la valeur de plusieurs paramètres empiriques. Ce modèle nous a alors permis de prédire l’efficacité du processus d’amplification paramétrique dans les fibres microstructurées. L’ensemble de ces études théoriques a permis d’identifier les fibres les plus adaptées à la conversion de fréquence vers la bande 3-5µm. Enfin, nous avons réalisé un banc de mesure de la dispersion chromatique des fibres, ainsi que le dimensionnement d’un convertisseur de fréquence utilisant les fibres identifiées dans l’étude théorique. / Various civil or military applications, such as spectroscopy in the atmospheric transparency windows (3 – 5 µm and 8 – 12 µm ranges), require the use of mid-infrared emitting laser sources.The work presented in this thesis is about light generation in the 3 – 5 µm range by parametric amplification (four-wave mixing) in fluoride and chalcogenide fibers. The first part of the study is devoted to modelizations of phase-matching condition and parametric gain in monomode step-index ZBLAN fluoride fibers as well as As2S3 and As2Se3 chalcogenide fibers. The results obtained in this modelization led to the theoretical study of multimode phase-matching conditions in chalcogenide fibers.The second part of the study presents the modelization of parametric amplification in hexagonal microstructured chalcogenide fibers. A simplified model, called the effective index method (EIM), has been developed and compared to the finite element method. Thanks to this comparison, the accuracy of the EIM model was improved through the determination of several empirical parameters. Using the improved EIM model, we have been able to predict the parametric amplification efficiency in microstructured fibers. Thus, all those theoretical studies allowed us to identify the most adapted fibers for frequency conversion in the 3 – 5 µm range. Eventually, we realized an experimental bench to measure the chromatic dispersion of optical fibers, and we suggested an experimental architecture using the fibers we had indentified in the theoretical study.

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Généralement, diagnostiquer une pathologie donnée à un stade de développement précoce favorise le pronostic vital du patient atteint. Une telle performance nécessite de détecter des marqueurs présents à des seuils de concentrations bas dans des fluides biologiques souvent complexes. Pour détecter ces concentrations extrêmement faibles en analyte donné, la stratégie employée au cours de ce travail est l’amplification moléculaire du signal. Pour cela, différentes approches sont possibles (i) amplifier le signal issu de l’évènement de reconnaissance cible/sonde, (ii et iii) amplifier le signal par régénération ou réplication de la cible. Les stratégies conçues au cours de ce travail de thèse se focalisent principalement sur la détection de petites molécules, telles que l’eau oxygénée ou encore l’anion fluorure, mais avec à terme l’idée de les étendre à la détection indirecte de biomarqueurs ou protéines d’intérêts. La première partie de cette thèse se focalise sur l’amplification moléculaire d’un signal par une catalyse allostérique en utilisant la réaction de reconstitution d’une apoenzyme donnée avec son cofacteur tandis que la seconde partie de cette thèse repose sur la mise en place de systèmes d’amplification catalytique et auto-catalytique pour la détection d’H2O2, grâce à des dérivés pro-quinoniques porteurs de groupement acide/ester boronique. La distinction entre les systèmes catalytique et auto-catalytique se fait selon qu’H2O2 est régénéré ou amplifié au cours de la réaction. / Generally, diagnosing a given pathology at an early stage of development promotes the patient's prognosis. Such a performance requires the detection of specific markers which are present in complex biological fluids at low concentration level. To detect these extremely low analyte concentrations, the strategy employed in this work is the molecular amplification of the signal. To this end, different approaches are possible (i) amplifying the signal resulting from the target / probe recognition event, (ii and iii) amplifying the signal by regeneration or replication of the target. The strategies conceived during this thesis work mainly focus on the detection of small molecules, such as hydrogen peroxide or fluoride anion, but with the idea of extending them to the indirect detection of biomarkers or proteins of interest. The first part of this thesis focuses on the molecular amplification of a signal by allosteric catalysis using the reconstitution reaction of a given apoenzyme with its cofactor. The second part of this thesis is based on the implementation of catalytic and auto-catalytic amplification systems for the detection of H2O2, thanks to pro-quinonic derivatives bearing boronic acid/ester group. The distinction between catalytic and auto-catalytic systems is based on whether H2O2 is regenerated or amplified during the reaction.