This thesis deals with the development of an environment and necessary set of tests for an evaluation of the DDoS Protector device in terms of functionality and performance. CESNET is developing device called DDoS Protector for protection against denial of service (DDoS) attacks with focus on volumetric and TCP SYN flood attacks. Current development environment does not support generation of stateful (TCP) network traffic and it's difficult to create complex evaluation tests in terms of interaction between various parts of the device. Goal of this work is to create an environment which enables complex evaluation of the device, including generation of both stateful and stateless network traffic combined with multi-vector DDoS attack, thus approaching real network traffic. Cisco TRex was chosen after examination of available traffic generators. Finally set of tests generating various combination of legitimate traffic and attacks was created and DDoS Protector was successfully evaluated.

As moléculas que compõem um fluído, devido à autodifusão, encontram-se em constante movimento de translação num meio poroso. Observar a migração dessas moléculas de um poro para outro é fundamental para análise das conectividades do meio, resultado importante para a prospecção de óleo e gás, qualidade de membranas filtros, entre outros processos. Se há distintos tempos de relaxações transversais, T2, para os poros, ocorre quando estes apresentam características físico-químicas ou tamanhos diferentes, um experimento capaz de observar esse efeito de troca entre poros é o chamado T2-T2 Exchange proposto em 1993. Esse experimento, na sua versão original, corresponde a um experimento tridimensional que consome muito tempo para ser executado, inviabilizando, por exemplo, o uso em perfilagem de poços petrolíferos. Desta forma, o grupo propôs diminuir o tempo de execução reduzindo uma dimensão do experimento. Este novo método, novo experimento, foi nomeado de T2-Filtered T2-T2 Exchange, o qual utiliza a primeira parte da sequência de pulsos original como um filtro de T2. Com o objetivo de validar o experimento proposto, surgiu a oportunidade de estudar a técnica T2-T2 Exchange como um todo. No decorrer do trabalho, surgiu mais uma nova aplicação da técnica T2-T2 Exchange, a execução simultânea. Tanto a versão tridimensional do T2-T2 Exchange quando a bidimensional, necessitam de uma ciclagem de fase especial. Neste contexto, foi proposto também a execução simultânea dos experimentos T2-Filtered T2-T2 Exchange e Saturation-Recovery-CPMG, adquirindo os sinais separados e empregando a ciclagem de fases distintas. A fim de validar as propostas T2-Filtered T2-T2 Exchange e execução simultânea, se optou por uma amostra padrão, uma cerâmica de alumina foi saturada com água e, então, estudado os núcleos de hidrogênios. A cerâmica foi manufaturada pelo método de prensagem a seco com adição de agentes porogênicos e sinterização, a qual foi caracterizada via porosimetria por intrusão de mercúrio e imagens por microscópio eletrônico de varredura. Em um campo de 2 tesla, frequência de 85 MHz para os núcleos de hidrogênios, foram executados os experimento Saturation-Recovery-CPMG, T2-T2 Exchange e T2-Filtered T2-T2 Exchange. A análise comparativa entre os mapas de correlação T1-T2 e as curvas de trocas obtidos deste, permitiu validar as propostas. Desta forma, se concluiu que a nova sequência T2-Filtered T2-T2 Exchange proposta, é uma poderosa ferramenta com potencial para aplicação em well-logging. / The molecules that make up a fluid inside a porous media are in constant motion due to self diffusion. Observing this migration inside the media is very interesting for analyzing the connectivity between different regions of the sample, which is of great importance to the field of oil and gas prospection. In the case the sample has pores with distinct transverse relaxation times, T2, which happens when they have distinct physical-chemical properties or sizes, an experiment capable of observing the movement from one distinct pore from the other is the T2-T2 Exchange proposed in 1993. This experiment, in its original version, corresponds to a three dimensional experiment which usually takes a very long time, making it unfeasible for well logging for example. Thus, this work proposes a method to drastically reduce the duration of the experiment by eliminating one of its dimensions. It was named T2-Filtered T2-T2 Exchange. It uses the first part of the original sequence as a T2 filter. To validate the filtered technique, the T2-T2 Exchange technique was vastly studied as a whole. Some phase cycling characteristics of the techniques were observed and in the end led to the development of new proposals. The proposal consists of simultaneously performing both the T2-Filtered T2-T2 Exchange and the Saturation-Recovery-CPMG. For the experimental tests of the sequences, a water saturated alumina ceramic sample was chosen as the standard sample. The ceramic was manufactured by a process of dry pressing with addition of some porogenic agents and followed by sinterization. The sample was characterized by mercury injection capillary pressure and scanning electron microscopy. The NMR experiments were performed on a 2 Tesla magnet corresponding to an 85 MHz frequency for protons and the experiments performed wereT2-T2 Exchange, T2-Filtered T2-T2 Exchange and Saturation-Recovery-CPMG. The comparative analysis between the T1-T2 correlation and the exchange curves obtained allowed the validation of the proposals. It was possible to conclude that the T2-Filtered T2-T2 Exchange technique is a powerful tool with potential application in the well-logging field.

As moléculas que compõem um fluído, devido à autodifusão, encontram-se em constante movimento de translação num meio poroso. Observar a migração dessas moléculas de um poro para outro é fundamental para análise das conectividades do meio, resultado importante para a prospecção de óleo e gás, qualidade de membranas filtros, entre outros processos. Se há distintos tempos de relaxações transversais, T2, para os poros, ocorre quando estes apresentam características físico-químicas ou tamanhos diferentes, um experimento capaz de observar esse efeito de troca entre poros é o chamado T2-T2 Exchange proposto em 1993. Esse experimento, na sua versão original, corresponde a um experimento tridimensional que consome muito tempo para ser executado, inviabilizando, por exemplo, o uso em perfilagem de poços petrolíferos. Desta forma, o grupo propôs diminuir o tempo de execução reduzindo uma dimensão do experimento. Este novo método, novo experimento, foi nomeado de T2-Filtered T2-T2 Exchange, o qual utiliza a primeira parte da sequência de pulsos original como um filtro de T2. Com o objetivo de validar o experimento proposto, surgiu a oportunidade de estudar a técnica T2-T2 Exchange como um todo. No decorrer do trabalho, surgiu mais uma nova aplicação da técnica T2-T2 Exchange, a execução simultânea. Tanto a versão tridimensional do T2-T2 Exchange quando a bidimensional, necessitam de uma ciclagem de fase especial. Neste contexto, foi proposto também a execução simultânea dos experimentos T2-Filtered T2-T2 Exchange e Saturation-Recovery-CPMG, adquirindo os sinais separados e empregando a ciclagem de fases distintas. A fim de validar as propostas T2-Filtered T2-T2 Exchange e execução simultânea, se optou por uma amostra padrão, uma cerâmica de alumina foi saturada com água e, então, estudado os núcleos de hidrogênios. A cerâmica foi manufaturada pelo método de prensagem a seco com adição de agentes porogênicos e sinterização, a qual foi caracterizada via porosimetria por intrusão de mercúrio e imagens por microscópio eletrônico de varredura. Em um campo de 2 tesla, frequência de 85 MHz para os núcleos de hidrogênios, foram executados os experimento Saturation-Recovery-CPMG, T2-T2 Exchange e T2-Filtered T2-T2 Exchange. A análise comparativa entre os mapas de correlação T1-T2 e as curvas de trocas obtidos deste, permitiu validar as propostas. Desta forma, se concluiu que a nova sequência T2-Filtered T2-T2 Exchange proposta, é uma poderosa ferramenta com potencial para aplicação em well-logging. / The molecules that make up a fluid inside a porous media are in constant motion due to self diffusion. Observing this migration inside the media is very interesting for analyzing the connectivity between different regions of the sample, which is of great importance to the field of oil and gas prospection. In the case the sample has pores with distinct transverse relaxation times, T2, which happens when they have distinct physical-chemical properties or sizes, an experiment capable of observing the movement from one distinct pore from the other is the T2-T2 Exchange proposed in 1993. This experiment, in its original version, corresponds to a three dimensional experiment which usually takes a very long time, making it unfeasible for well logging for example. Thus, this work proposes a method to drastically reduce the duration of the experiment by eliminating one of its dimensions. It was named T2-Filtered T2-T2 Exchange. It uses the first part of the original sequence as a T2 filter. To validate the filtered technique, the T2-T2 Exchange technique was vastly studied as a whole. Some phase cycling characteristics of the techniques were observed and in the end led to the development of new proposals. The proposal consists of simultaneously performing both the T2-Filtered T2-T2 Exchange and the Saturation-Recovery-CPMG. For the experimental tests of the sequences, a water saturated alumina ceramic sample was chosen as the standard sample. The ceramic was manufactured by a process of dry pressing with addition of some porogenic agents and followed by sinterization. The sample was characterized by mercury injection capillary pressure and scanning electron microscopy. The NMR experiments were performed on a 2 Tesla magnet corresponding to an 85 MHz frequency for protons and the experiments performed wereT2-T2 Exchange, T2-Filtered T2-T2 Exchange and Saturation-Recovery-CPMG. The comparative analysis between the T1-T2 correlation and the exchange curves obtained allowed the validation of the proposals. It was possible to conclude that the T2-Filtered T2-T2 Exchange technique is a powerful tool with potential application in the well-logging field.

L'intégrité de l'information génétique est essentielle aux fonctions cellulaires et pour éviter l'instabilité génomique, qui est une des caractéristique du cancer. Suite à des cassures double brin (Double Strand Breaks; DSBs), la voie de signalisation de réponse aux dommages de l'ADN est activée dans la cellule qui comprend deux sous voies de signalisation : la jonction d'extrémités non-homologues et la recombinaison homologue. Le complexe TREX-2 associé au pore nucléaire est impliqué dans l'export des ARNm. Chez la levure, TREX-2 est impliqué dans le maintien de la stabilité génomique. Nous nous sommes intéressés au rôle de TREX-2 dans la réparation de DSBs dans les cellules humaines. La déplétion du complexe TREX-2 entraine une réparation de l'ADN par recombinaison homologue insuffisante. De plus, nos résultats démontrent que la protection contre les dommages de l'ADN par TREX-2 dépend aussi de l'équilibre entre H2B an H2Bub1 contrôlé par le module de deubiquitination de SAGA. / The maintenance of proper genetic information is essential to avoid genomic instability, which is a hallmark of cancer. In response to Double Strand Breaks (DSBs), cells initiate the DNA Damage Response (DDR), that acts through two main sub-pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). The nuclear pore-associated TREX-2 complex is involved in mRNA export and has been implicated, in yeast, in genome stability maintenance. Here we investigated the role of TREX-2 in DSB repair in human cells. We find that loss of the scaffold subunit of TREX-2 (GANP) results in DNA repair deficiency by HR. Moreover, we showed that the mechanism through which TREX-2 protects human cells from DNA damage is dependent on an interplay with the co-activator complex SAGA that regulates H2Bub1 histone mark. Our results demonstrate a functional cross-talk between human TREX-2 and the SAGA deubiquitination activity that is important to ensure correct DSB repair during HR.

Traffic generators, as an indispensable tool to test devices under test and networking protocols, help researchers to execute performance inspection and optimization. Among all traffic generators, TRex is an open-source, high-performance, and low-cost traffic generator which is built on Data Plane Development Kit (DPDK). It supports stateless traffic generation patterns and the modification of fields and length for each packet. More importantly, it can emulate realistic TCP stateful traffic. Although DPDK can greatly improve the packet processing speed, the maximum throughput of the system is limited by the bandwidth of network interface cards (NICs). This thesis combines TRex traffic generator and a P4 programmable switch to construct a high-speed, feature-rich, and cost-effective traffic generation system. Our basic idea is to ”shift” the bottleneck of NICs’ bandwidth to a P4 programmable switch. In particular, TRex only generates small packet headers while the payloads of the packets are generated on the P4 programmable switch by fast recirculations. Since sending small packets consumes less bandwidth, TRex can reach a higher packet rate. Thanks to the enormous bandwidth provided by the programmable switches and the higher packet rate, our design can generate traffic beyond the bandwidth of the NICs. Besides, we build upon the original TRex and completely inherit its toolchain, which exhibits high transparency. That is to say, the users do not need to modify the profiles that generate traffic to use our system. We establish and test our design on Virtual Machines, and then perform a real-world performance evaluation on a physical server with 2×100Gbps Mellanox NICs. The evaluation results show that our system can achieve more than 2x throughput for Advanced Stateful mode than the TRex without any modification when the average packet size reaches 1367 bytes. / Trafikgeneratorer, som är ett oumbärligt verktyg för att testa testade enheter och nätverksprotokoll, hjälper forskare att utföra prestandainspektion och optimering. TRex är en trafikgenerator med öppen källkod, hög prestanda och låg kostnad som bygger på Data Plane Development Kit (DPDK). Den stöder statslösa trafikgenereringsmönster och modifiering av fält och längd för varje paket. Ännu viktigare är att den kan emulera realistisk TCP stateful-trafik. Även om DPDK kan förbättra paketbehandlingshastigheten avsevärt, begränsas systemets maximala genomströmning av bandbredden hos nätverksgränssnittskorten (NIC). Denna avhandling kombinerar TRex trafikgenerator och en P4 programmerbar switch för att konstruera ett höghastighets, funktionsrikt och kostnadseffektivt system för trafikgenerering. Vår grundläggande idé är att ”flytta” flaskhalsen i NIC:s bandbredd till en programmerbar P4-switch. TRex genererar endast små paketrubriker medan paketens nyttolast genereras på den programmerbara P4-växeln genom snabba återcirkulationer. Eftersom små paket förbrukar mindre bandbredd kan TRex nå en högre paketfrekvens. Tack vare den enorma bandbredd som de programmerbara switcharna ger och den högre paketfrekvensen kan vår design generera trafik som överskrider NIC:ernas bandbredd. Dessutom bygger vi vidare på den ursprungliga TRex och ärver helt dess verktygskedja, som uppvisar hög transparens. Det innebär att användarna inte behöver ändra de profiler som genererar trafik för att använda vårt system. Vi etablerar och testar vår design på virtuella maskiner och utför sedan en verklig prestandautvärdering på en fysisk server med 2×100Gbps Mellanox NIC. Utvärderingsresultaten visar att vårt system kan uppnå mer än 2x genomströmning för Advanced Stateful-läge än TRex utan någon modifiering när den genomsnittliga paketstorleken når 1367 byte.

abstract: Exome sequencing was used to identify novel variants linked to amyotrophic lateral sclerosis (ALS), in a family without mutations in genes previously linked to ALS. A F115C mutation in the gene MATR3 was identified, and further examination of other ALS kindreds identified an additional three mutations in MATR3; S85C, P154S and T622A. Matrin 3 is an RNA/DNA binding protein as well as part of the nuclear matrix. Matrin 3 interacts with TDP-43, a protein that is both mutated in some forms of ALS, and found in pathological inclusions in most ALS patients. Matrin 3 pathology, including mislocalization and rare cytoplasmic inclusions, was identified in spinal cord tissue from a patient carrying a mutation in Matrin 3, as well as sporadic ALS patients. In an effort to determine the mechanism of Matrin 3 linked ALS, the protein interactome of wild-type and ALS-linked MATR3 mutations was examined. Immunoprecipitation followed by mass spectrometry experiments were performed using NSC-34 cells expressing human wild-type or mutant Matrin 3. Gene ontology analysis identified a novel role for Matrin 3 in mRNA transport centered on proteins in the TRanscription and EXport (TREX) complex, known to function in mRNA biogenesis and nuclear export. ALS-linked mutations in Matrin 3 led to its re-distribution within the nucleus, decreased co-localization with endogenous Matrin 3 and increased co-localization with specific TREX components. Expression of disease-causing Matrin 3 mutations led to nuclear mRNA export defects of both global mRNA and more specifically the mRNA of TDP-43 and FUS. Our findings identify ALS-causing mutations in the gene MATR3, as well as a potential pathogenic mechanism attributable to MATR3 mutations and further link cellular transport defects to ALS. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2018

The Piwi interacting RNA pathway (piRNA) transcriptionally and post-transcriptionally silences transposons in the germline to maintain host genome integrity and faithful transmission of the genetic materials. In Drosophilaovaries, maternally loaded piRNAs kick-start piRNA biogenesis and convert precursor transcripts into piRNAs to replenish the piRNA pool during oogenesis. piRNA clusters are the genomic source of piRNA precursors, which are determined by the HP1 homolog Rhino and accessary factors. Rhino specifically binds to piRNA cluster chromatin. I was intrigued by how Rhino localizes to piRNA clusters to specify piRNA precursors. TREX is a conserved mRNA biogenesis complex composed of UAP56 and the THO complex. Identification of UAP56 as a cluster transcript-processing factor established the link between piRNA biogenesis and the general mRNA processing machinery. In my thesis, I investigated the functions of UAP56 and THO in piRNA cluster transcript processing. I characterized an RNP specific to cluster transcripts, defined by binding with both factors, which is distinct from RNP of bulk mRNA transcripts, and found that assembly of these RNPs depends on Rhino. These findings imply that piRNA precursors are specified co-transcriptionally. Additionally, I found that TREX mutants lead to a loss of Rhino binding specificity. I propose that Rhino and TREX co-transcriptionally scan for cluster and transposon sequences to establish loci that produce piRNA precursors. Surprisingly, I also discovered a piRNA-independent function for TREX in transposon silencing. I showed that TREX mutants lead to transcriptionally activation of a number of transposon families without affecting their piRNA biogenesis and piRNA mediated repressive histone modifications. I propose that TREX could mediate a conserved transposon silencing mechanism.