High-performance networking (HPN) is of significance today in order to enable next-generation applications using wired and wireless networks. Some of the examples of HPN include low-latency industrial sensing, monitoring and automation using Wireless Sensor Networks (WSNs). HPN however requires protocol optimization at many layers of the open system interface (OSI) network model in order to meet the stringent performance constraints of the given applications. Furthermore, these protocols need to be impervious to denial of service (DoS) and distributed DoS (DDoS) attacks. Some of the key performance aspects of HPN are low point-to-point and end-to-end latency, high reliability of transmitted frames and performance predictability under various network load situations. This work focuses on two discrete issues in designing protocols for HPN applications. The first research issue looks at the Medium Access Control (MAC) layer of the OSI network model for designing of MAC protocols that provide low-latency and high reliability for point-to-point communication under a WSN. Existing standards in this area are governed by IEEE 802.15.4 specification which defines protocols for MAC and PHY layers for short-range, low bit-rate, and low-cost wireless networks. However, the IEEE 802.15.4 specification is inefficient in terms of latency and reliability performance and, as a result, is unable to meet the stringent operational requirements as defined by counterpart wired sensor networks. Work presented under current research issue describes new MAC protocols that are able to show low-latency transmission performance under strict timing constants for power limited WSNs. This enhancement of the MAC protocols is named extended GTS (XGTS) contained under extended CFP (ECFP) and is published under the IEEE's 802.15.4e standard. The second research issue focuses on the application layer of the OSI network model to design protocols that enhance the robustness of the text based protocols to various traffic inputs. The purpose of this is to increase the reliability of the given text based application layer protocol under a varied load. Session Initiation Protocol (SIP) is used as a case study and the work aims to build algorithms that ensure that SIP can continue to function under specific traffic conditions, which would otherwise deem the protocol useless due to DoS and DDoS attacks. Proposed algorithms investigate techniques that enhance the robustness of the SIP against parsing attacks without performing a deep parse of the protocol data unit (PDU). The desired effect of this is to reduce the time spent in parsing the SIP messages at a SIP router and as a result increase the number of SIP messages processed per unit time at a SIP router.

Serological discrepancies in matching blood group antigens between donors and patients for blood transfusion may lead to alloimmunisation, especially in multiply transfused patients. Blood group genotyping (BGG) has contributed in reducing this issue. ABO, Fy and Jk antigens are among those to be causative for alloimmunisation through transfusion or pregnancy. The number of alleles of these clinically significant blood groups is ever increasing. Currently, all commercially available high-throughput BGG platforms are only based on pre-defined polymorphisms. Consequently, novel or rare alleles that might have clinical significance are not identified. Next generation sequencing (NGS) circumvents this issue by providing high-throughput comprehensive genotyping of blood group genes in discovery mode to find all existing and novel mutations. Accordingly, a large number of individuals can be genotyped in a single run. Here, we describe an NGS-based method coupled with long-range polymerase chain reaction (LR-PCR) for high-throughput, rapid and extensive genotyping of FY, JK and ABO blood group genes. The Ion Torrent Personal Genome Machine (PGMTM) was used for sequencing the entire FY, JK and ABO blood group genes including flanking regions. Accordingly, high resolution genotyping was obtained. 53 genomic DNA samples were sequenced and genotyped for FY, 67 for JK and 47 for ABO. Sequencing data were aligned to the gene reference sequence derived from the human genome (hg19) to analyse variants. Analysis was accomplished by software packages, such as Ion Torrent SuiteTM plugins. Sanger sequencing of cDNA and cDNA clones was used to confirm findings in the JK gene. The sequencing data had a coverage depth of more than 5000x for FY, 700x for JK and 600x for ABO. NGS data matched with the serological phenotypes of FY alleles FY*A, FY*B and FY*02 Null main polymorphisms, such as FY*A/FY*B (125G > A) in exon 2 and (-67 T > C) in the promotor region. JK variant analysis revealed that the JK*01W.01 allele (130G > A) is common (10/67 samples) with normal antigenicity. The previously described silencing polymorphism (810G > A), leading to a purported JK*B null allele, restores a splice site and does not correlate with loss of Jkb antigenicity (10/67 samples). JK intron analysis revealed several new JK alleles described in this thesis. All 7 exons, introns and the flanking regions of the ABO gene were covered by only four amplicons. Several rare O alleles were found, such as O73 and O75, while one suggested novel O allele was characterised by a missense SNP 482G > A (Arg161His) in exon 7. The ABO reference sequence from hg19 appeared to resemble (O01 and O02) alleles. The intronic SNPs might be used to distinguish between alleles more accurately as a correlation of the intronic SNPs with the alleles was noted for the homozygous O alleles. It is predicted that NGS-based genotyping will replace not only microarray-based genotyping but also serology in the blood group typing of individuals, with great advancements in technology and molecular knowledge being expected in the near future.

The PhD research studied two aspects in tilapia, firstly the analysis of sex determination in Nile tilapia (evidence of complex sex-determining systems) and secondly the genetic management of the tilapia species, using different genomic analysis approaches. This research started with the development of two techniques: minimally invasive DNA sampling from fish mucus, which was found to be suitable for standard genotyping and double-digest restriction-site associated DNA sequencing – ddRADseq; and pre-extraction pooling of tissue samples for ddRADseq (BSA-ddRADseq), which was found to be suitable for identifying a locus linked to a trait of interest (sex in this case). The first molecular evidence concerning the sex determination in genetically improved farmed tilapia (GIFT) was described using BSA-ddRADseq. Given the multiple stock origin of GIFT, surprisingly only a single locus (in linkage group 23) was found to be associated with the phenotypic sex across the population. The first evidence of LG23 influence on phenotypic sex in the Stirling population of Nile tilapia was also found. Different combinations of estrogen hormones and high temperature were tested for feminising Nile tilapia: a combined treatment of estrogen hormone and high temperature was found to be more efficient in feminising Nile tilapia than the estrogen alone. A set of species-diagnostic SNP markers were tested which were found to be suitable to distinguish pure species (O. niloticus, O. mossambicus and O. aureus), and these were used to analyse species contribution to GIFT and a selected tilapia hybrid strain. The results of the current research added novel information to our understanding of sex determination in Nile tilapia, which will be helpful in the development of marker-assisted selection in GIFT and other Nile tilapia strains towards the production of all male offspring. The methods developed also have broader applicability in genetic and genomics research.

NOGUEIRA, Antonia Diana Braga. Uma proposta de integração das redes UMTS e IEEE 802.11 com suporte a mobilidade. 2007. 112 f. Dissertação (Mestrado em ciência da computação)- Universidade Federal do Ceará, Fortaleza-CE, 2007. / Submitted by Elineudson Ribeiro (elineudsonr@gmail.com) on 2016-07-08T18:49:42Z No. of bitstreams: 1 2007_dis_adbnogueira.pdf: 13756193 bytes, checksum: bb4a338bd2622ad6f90479ce37824ccd (MD5) / Approved for entry into archive by Rocilda Sales (rocilda@ufc.br) on 2016-07-18T13:41:19Z (GMT) No. of bitstreams: 1 2007_dis_adbnogueira.pdf: 13756193 bytes, checksum: bb4a338bd2622ad6f90479ce37824ccd (MD5) / Made available in DSpace on 2016-07-18T13:41:19Z (GMT). No. of bitstreams: 1 2007_dis_adbnogueira.pdf: 13756193 bytes, checksum: bb4a338bd2622ad6f90479ce37824ccd (MD5) Previous issue date: 2007 / Wireless Local Area Networks (WLANs) IEEE 802.11 reach relatively high data transmission rates when compared to other wireless networks, such as Bluetooth. These high data transmission rates have gained attention from the cellular networks operators, which have been considering IEEE 802.11 networks as a complement to their access networks. This interoperability between cellular systems and WLANs has been frequently discussed in the literature. For example, 3GPP (Third Generation Partnership Project) has defined six levels for the complete integration of the third generation cellular networks and WLANs. However, the mobility support has not been specified yet, which is necessary to make feasible voice and data transmission transparence for the final users. Thus, this work presents two approaches for the mobility management of the integration between UMTS and IEEE 802.11 networks: the first one is based on SIP (Session Initiation Protocol), and the other one is based on MIPv6 (Mobile IP version 6). This proposal extends the Loose Interworking architecture and uses the fourth level of the 3GPP specification. First, these approaches are modeled using sequence diagrams and, then, they are mapped to the SDL (Specification and Description Language) formal description technique. SDL, which is largely used to formally specify telecommunications systems, presents simulation and validation procedures that are applied to evaluate the specification and, consequently, the proposed approaches. / As redes locais sem fio (Wireless Local Area Networks - WLANs) IEEE 802.11 atingem taxas de transmissão de dados relativamente altas quando comparadas `a outras redes sem fio, por exemplo, Bluetooth. Essas altas taxas de transmissãao têm interessado as operadoras de redes celulares, as quais começam a ver as redes IEEE 802.11 como um complemento as suas redes de acesso. Esta interoperabilidade entre sistemas celulares e WLANs tem sido um tema bastante discutido na literatura. Por exemplo, o 3GPP (Third Generation Partnership Project) define seis n´ıveis para a total integração das redes celulares de terceira geração com as redes locais sem fio. No entanto, a integração com suporte a mobilidade ainda não foi especificada, o que é necessário para viabilizar a transparência de transmissão de voz e dados para os usuários finais. Esta dissertação apresenta então duas abordagens para o gerenciamento de mobilidade na integração do sistema 3G UMTS com as redes IEEE 802.11: uma baseada no SIP (Session Initiation Protocol ) e a outra no MIP versão 6 (Mobile IP version 6 - MIPv6). A proposta estende a arquitetura Loose Interworking e utiliza os requisitos do nível 4 do 3GPP. Para especificar a proposta, as abordagens de integração das redes UMTS e IEEE 802.11 foram modeladas em diagramas de seqüência e, em seguida, mapeadas para a técnica de descrição formal SDL (Specification and Description Language). SDL, que é bastante utilizada para especificar formalmente sistemas de telecomunicações, apresenta procedimentos de simulação e validação que são aplicados para avaliar a especificação e, em conseqüência, as abordagens propostas.

NOGUEIRA, Antonia Diana Braga. Uma proposta de integração das redes UMTS e IEEE 802.11 com suporte a mobilidade. 2007. 91 f. : Dissertação (mestrado) - Universidade Federal do Ceará, Centro de Ciências, Departamento de Computação, Fortaleza-CE, 2007. / Submitted by guaracy araujo (guaraa3355@gmail.com) on 2016-05-30T19:51:57Z No. of bitstreams: 1 2007_dis_adbnogueira.pdf: 13756193 bytes, checksum: bb4a338bd2622ad6f90479ce37824ccd (MD5) / Approved for entry into archive by guaracy araujo (guaraa3355@gmail.com) on 2016-05-30T19:52:27Z (GMT) No. of bitstreams: 1 2007_dis_adbnogueira.pdf: 13756193 bytes, checksum: bb4a338bd2622ad6f90479ce37824ccd (MD5) / Made available in DSpace on 2016-05-30T19:52:27Z (GMT). No. of bitstreams: 1 2007_dis_adbnogueira.pdf: 13756193 bytes, checksum: bb4a338bd2622ad6f90479ce37824ccd (MD5) Previous issue date: 2007 / Wireless Local Area Networks (WLANs) IEEE 802.11 reach relatively high data transmission rates when compared to other wireless networks, such as Bluetooth. These high data transmission rates have gained attention from the cellular networks operators, which have been considering IEEE 802.11 networks as a complement to their access networks. This interoperability between cellular systems and WLANs has been frequently discussed in the literature. For example, 3GPP (Third Generation Partnership Project) has defined six levels for the complete integration of the third generation cellular networks and WLANs. However, the mobility support has not been specified yet, which is necessary to make feasible voice and data transmission transparence for the final users. Thus, this work presents two approaches for the mobility management of the integration between UMTS and IEEE 802.11 networks: the first one is based on SIP (Session Initiation Protocol), and the other one is based on MIPv6 (Mobile IP version 6). This proposal extends the Loose Interworking architecture and uses the fourth level of the 3GPP specification. First, these approaches are modeled using sequence diagrams and, then, they are mapped to the SDL (Specification and Description Language) formal description technique. SDL, which is largely used to formally specify telecommunications systems, presents simulation and validation procedures that are applied to evaluate the specification and, consequently, the proposed approaches. / As redes locais sem fio (Wireless Local Area Networks - WLANs) IEEE 802.11 atingem taxas de transmissão de dados relativamente altas quando comparadas `a outras redes sem fio, por exemplo, Bluetooth. Essas altas taxas de transmissãao têm interessado as operadoras de redes celulares, as quais começam a ver as redes IEEE 802.11 como um complemento as suas redes de acesso. Esta interoperabilidade entre sistemas celulares e WLANs tem sido um tema bastante discutido na literatura. Por exemplo, o 3GPP (Third Generation Partnership Project) define seis n´ıveis para a total integração das redes celulares de terceira geração com as redes locais sem fio. No entanto, a integração com suporte a mobilidade ainda não foi especificada, o que é necessário para viabilizar a transparência de transmissão de voz e dados para os usuários finais. Esta dissertação apresenta então duas abordagens para o gerenciamento de mobilidade na integração do sistema 3G UMTS com as redes IEEE 802.11: uma baseada no SIP (Session Initiation Protocol ) e a outra no MIP versão 6 (Mobile IP version 6 - MIPv6). A proposta estende a arquitetura Loose Interworking e utiliza os requisitos do nível 4 do 3GPP. Para especificar a proposta, as abordagens de integração das redes UMTS e IEEE 802.11 foram modeladas em diagramas de seqüência e, em seguida, mapeadas para a técnica de descrição formal SDL (Specification and Description Language). SDL, que é bastante utilizada para especificar formalmente sistemas de telecomunicações, apresenta procedimentos de simulação e validação que são aplicados para avaliar a especificação e, em conseqüência, as abordagens propostas.

Submitted by LIVIA MARIA GONÇALVES ROSSI null (liv.rossi@yahoo.com) on 2016-01-25T14:04:25Z No. of bitstreams: 1 TESE_HCV Multi-region_LIVIA ROSSI.pdf: 6853283 bytes, checksum: d2ce231bc1292f9fa0469f971cf0856b (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-01-25T17:23:43Z (GMT) No. of bitstreams: 1 rossi_lmg_dr_sjrp.pdf: 6853283 bytes, checksum: d2ce231bc1292f9fa0469f971cf0856b (MD5) / Made available in DSpace on 2016-01-25T17:23:43Z (GMT). No. of bitstreams: 1 rossi_lmg_dr_sjrp.pdf: 6853283 bytes, checksum: d2ce231bc1292f9fa0469f971cf0856b (MD5) Previous issue date: 2016-01-18 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O vírus da Hepatite C (HCV) afeta cerca de 3% da população mundial. A cada ano, 3-4 milhões de novos casos são diagnosticados. A identificação de redes transmissão é complexa devido ao longo período de incubação, à falta de sintomas na fase aguda da doença e à heterogeneidade do HCV, que dificulta o estabelecimento de vínculos entre casos relacionados. Uma ampla caracterização das populações intra-hospedeiros pode ser realizada de forma eficiente através do sequenciamento de nova geração (NGS). Com base neste contexto, o sequenciamento de múltiplas regiões subgenômicas é uma solução às limitações impostas pela rápida evolução molecular do HCV. Variantes virais das regiões HVR1 e NS5A de 16 pacientes cronicamente infectados com o HCV, genótipos 1a e 1b, foram sequenciadas com a técnica de NGS. Os pacientes 1-7 compartilhavam fatores de risco, pertencendo ao mesmo grupo de usuários de drogas injetáveis, porém o parentesco genético desses casos não pode ser estabelecido com base apenas no sequenciamento da HVR1 (distância nucleotídica mínima entre 16-23). A amplificação de um fragmento maior (~450 pb), correspondente a um segmento da região NS5A, aprimorou a relação epidemiológica entre os pacientes 1-5, onde as distancias genéticas mínimas foram consideravelmente menores (9-13). Os pacientes 6 e 7 não compartilharam sequências com os outros cinco pacientes dessa rede, apresentando populações virais mais homogêneas. Adicionalmente, Median Joining Networks foram construídas para melhor analisar a variabilidade genética intra-hospedeiro. Em geral, observou-se que as sequências derivadas da NS5A formaram comunidades mais homogêneas e menos divergentes geneticamente. Assim, a tecnologia NGS e o sequenciamento das regiões subgenômicas HVR1 e NS5A podem ajudar a restaurar elos perdidos quando somente a região HVR1 é analisada, aprimorando portanto, a resolução de estudos de associação genética entre populações de HCV. / The hepatitis C virus (HCV) affects approximately 3% of the world's population. Each year 3-4 million new cases are diagnosed. The identification of transmission networks is complicated due to the characteristic long incubation period, the lack of symptoms during the acute phase of the disease and the heterogeneity of HCV, making it challenging to link related cases to a common source of infection. Extensive characterization of intra-host populations can be reliably archived using next generation sequencing (NGS) approaches. Sequencing of multiple and longer subgenomic regions has been proposed as an alternative to overcome the limitations imposed by the rapid molecular evolution of the HCV HVR1. Thus, the NS5A and HVR1 regions of 16 chronically infected individuals, genotypes 1a and 1b, were sequenced using a NGS platform. Patients 1-7 shared risk factors and belonged to the same injection drug users network. However, genetic relatedness could not be established based on the HVR1 sequences (minimal nucleotide distance ranging from 16-23). Amplification and sequencing of a larger PCR fragment (~450 bp) targeting the NS5A region reestablished lost epidemiological links between patients 1-5. The minimum genetic distances in those patients were considerable smaller than the HVR1 counterparts (9-13). Patients 6 and 7 displayed a rather homogeneous viral population and were clearly not sharing any sequences with all other five patients in this network. Additionally, Median Joining Networks analysis was carried out to further analyze the intrahost genetic variability of all seven patients. Overall, NS5A sequences were significantly less diverse than their HVR1 equivalents. Thus, NGS technology and use of both HVR1 and NS5A sequences might help restored otherwise lost links when the HVR1 region alone is analyzed, improving the resolution of HCV genetic relatedness studies. / CAPES: 33004153079P9

Submitted by TATIANE CRISTINA SELEGUIM CHUD null (tatischud@gmail.com) on 2018-03-13T20:36:16Z No. of bitstreams: 1 Tese_Tatiane_Cristina_Seleguim_Chud.pdf: 4849443 bytes, checksum: b950a6891cf2829637cfa58f2ae8367a (MD5) / Approved for entry into archive by Neli Silvia Pereira null (nelisps@fcav.unesp.br) on 2018-03-16T18:20:58Z (GMT) No. of bitstreams: 1 chud_tcs_dr_jabo.pdf: 4849443 bytes, checksum: b950a6891cf2829637cfa58f2ae8367a (MD5) / Made available in DSpace on 2018-03-16T18:20:58Z (GMT). No. of bitstreams: 1 chud_tcs_dr_jabo.pdf: 4849443 bytes, checksum: b950a6891cf2829637cfa58f2ae8367a (MD5) Previous issue date: 2018-02-23 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Com o avanço das tecnologias genômicas, permitiu-se detectar no genoma de humanos e animais domésticos elevado número de variações estruturais cromossômicas, como variação no número de cópias (CNV). No melhoramento genético de animais domésticos, CNVs podem auxiliar no entendimento da variabilidade genética de características de importância econômica, pois a maioria dessas regiões influenciam a expressão de genes com funções biológicas específicas. Com a finalidade de verificar possíveis relações de CNVs com características de sanidade, reprodutivas e produtivas em rebanhos leiteiros, o objetivo deste trabalho foi detectar e caracterizar CNVs em bovinos da raça composta Girolando (Gir X Holandês), identificar CNVs específicas em animais Girolando oriundas de animais da raça Gir e Holandês e investigar a diferenciação populacional entre as três raças por meio da variação no número de cópias nas regiões próximas aos genes anotados no genoma bovino. Para detecção das CNVs por meio dos dados de painel de polimorfismo de nucleotídeo único (SNP), no capítulo 2, foram utilizados registros de 1.607 vacas genotipadas com painel de SNP de média densidade (50K SNP) e de 280 touros genotipados com painel de alta densidade (HD SNP). A detecção foi realizada por meio do modelo oculto de Markov implementado pelo programa PennCNV. Foram utilizados dois touros ressequenciados para identificação das CNVs pelo método “read -depth” por meio dos dados de sequenciamento de nova-geração (NGS). Um total de 203 e 213 regiões candidatas de CNVs foram selecionadas pelos painéis de 50K e HD, respectivamente. Deleções e duplicações relacionadas a resistência a parasitas, susceptibilidade à doenças e reprodução, foram encontradas principalmente nos cromossomos BTA 5 e BTA 17. A detecção e caracterização das CNVs realizadas em bovinos de leite de raça composta demonstrou melhor entendimento das características de adaptabilidade ao clima tropical, como resistência à doenças e eficiência reprodutiva. No capítulo 3, foram utilizados cinco animais da raça Holandês, 14 animais da raça Gir e dois animais da raça Girolando. Após o alinhamento do genoma foi realizada a detecção das CNVs pela metodologia baseada em “read-depth”. A estatística VST.foi calculada pela média do número de cópias nas regiões próximas aos genes anotados no genoma bovina. Genes relacionados com fertilidade (MEPCE, ASB3) e susceptibilidade às doenças (HLX, MIR-455) foram anotados nas regiões específicas compartilhadas entre Girolando e as raças formadoras (Gir e Holandês). Os valores de VST variaram de -0,37 a 0,98. Os genes AOX1, SLBP, TACC3 e PRAME, apresentaram elevado VST, indicando diferenciação populacional pelo número de cópias, possivelmente originárias durante os processos de domesticação das subespécies. Regiões especificas de CNVS foram identificadas nos animais Girolando provenientes do Gir e do Holandês. O estudo de diferenciação populacional evidenciou seleção positiva no genoma de animais da raça Gir e Girolando para características relacionadas à adaptação desses animais aos ambientes de clima tropical, possivelmente originadas do processo de domesticação. / The advances of the genomic technologies has enabled to identify a high number of chromosomal structural variations in human and domestic animal genomes, such as copy number variation (CNV). In animal breeding, CNVs may assist to understand genetic variability of the economic important traits due most of the CNVs influence gene expression with specific biological functions. To identify possible CNVs linked to health, reproductive and productive traits in dairy cattle, the objective of this work was to detect and to describe CNVs in Girolando cattle (Gir x Holstein), to identify breed-specific CNV regions in Girolando from Gir and Holstein, and to investigate the population differentiation among the breeds using the copy number located on regions within annotated genes. In chapter 2, the CNV detection using single-nucleotidepolymorphism (SNP) panel was carried out on 1.607 females genotyped with the medium-density SNP panel (50K SNP) and 280 bulls genotyped with high-density panel (HD SNP) using Hidden Markov model implemented by PennCNV software. CNV calling also was perform using read-depth method applied on next-generation sequencing (NGS) data from two bulls resenquenced. A total of 203 and 213 CNVs candidate’s regions were picked using 50K e HD panels, respectively. Deletions and duplications related to parasite resistance, to disease susceptibility, and to reproductive efficiency was observed mainly located on chromosome BTA 5 and BTA 17. The detection and characterization of the CNVs in composite dairy cattle breed demonstrated better understanding of the traits, such disease resistance and reproductive efficiency. In chapter 3, the CNV calling was carried out on three Girolando bulls, 14 Gir bulls, and five Holstein bulls resequenced using the “readdepth” method implemented by CNVnator software. The VST statistic was calculated for the average of the copy number in regions located near annotated genes. Genes linked to fertility (MEPCE, ASB3) and disease susceptibility (HLX, MIR-455) were mapped on specific regions shared between Girolando and the pure-breeds (Gir ans Holstein). VST values ranged from -0.37 to 0.98. The genes AOX1, SLBP, TACC3 and PRAME, showed high VST, indicating high level of the population differentiation for the copy number located on the regions near of these genes. We found CNVR regions in Girolando specific from Gir and Holstein. The population differentiation study evidenced positive selection in genome of the Gir and Girolando animals for traits related to the adaptability of the breeds in tropical environmental may have originated from the domestication process. / FAPESP : 15/08939-0

La prévalence de la déficience intellectuelle est estimée entre 1 à 3% de la population. En France, la déficience intellectuelle légère concerne entre 10 et 20 pour 1 000 personnes et la déficience intellectuelle sévère entre 3 à 4 pour 1 000 personnes. La déficience intellectuelle fait partie d’un groupe hétérogène de pathologies syndromiques et non syndromiques ayant en commun la limitation importante du fonctionnement intellectuel et du comportement adaptatif, apparaissant avant 18 ans et entrainant un handicap. Les causes de la déficience intellectuelle affectent la neurogénèse et/ou le fonctionnement neuronal. Environ 50% des déficiences intellectuelles sont encore à l’heure actuelle d’étiologie indéterminée. Les étiologies génétiques expliquent un grand nombre de déficiences intellectuelles et plus particulièrement les formes sévères. Les nouvellestechnologies, telles que les analyses chromosomiques sur puce à ADN et le séquençage à haut débit de l’ADN, ont permis d’augmenter le rendement diagnostique à 55-70% dans les déficiences intellectuelles modérées à sévères. C’est grâce à ces techniques que nous avons pu identifier puis caractériser deux nouveaux gènes impliqués dans des déficiences intellectuelles sévères syndromiques autosomiques récessives: le gène WDR73 responsable du syndrome de Galloway Mowat associant un déficience intellectuelle sévère et un syndrome néphrotique cortico-résistant et le gèneUBA5, impliqué dans le processus d’ufmylation, dans une encéphalopathie précoce. / The prevalence of intellectual disability is estimated between 1% and 3% of the population. In France, mild intellectual disability affects between 10 and 20 per 1,000 people and severe intellectual disability between from 3 to 4 per 1,000 people. Intellectual disability is part of a heterogeneous group of syndromic and nonsyndromic pathologies with limitation in intellectual functioning and adaptive behavior appearing before the age of 18 and causing a disability. The causes of intellectual disability affect neurogenesis and / or neuronal functions. About 50% of intellectual disabilities are still undetermined. Genetic etiologies explain a large number of intellectual disabilities and more particularly the severe forms. New technologies, such as Array- Based Comparative Genomic Hybridization and next generation sequencing, have increased the diagnostic yield to 55-70% in moderate to severe intellectualdisability. Thanks to these techniques, we have been able to identify and characterize two new genes involved in severe autosomal recessive syndrome: the WDR73 gene responsible for Galloway Mowat syndrome which associates severe intellectual disability with corticosteroid-resistant nephrotic syndrome, and the UBA5 gene, involved in the ufmylation process in early encephalopathy.

Orientador: Paula Rahal / Resumo: O vírus da Hepatite C (HCV) afeta cerca de 3% da população mundial. A cada ano, 3-4 milhões de novos casos são diagnosticados. A identificação de redes transmissão é complexa devido ao longo período de incubação, à falta de sintomas na fase aguda da doença e à heterogeneidade do HCV, que dificulta o estabelecimento de vínculos entre casos relacionados. Uma ampla caracterização das populações intra-hospedeiros pode ser realizada de forma eficiente através do sequenciamento de nova geração (NGS). Com base neste contexto, o sequenciamento de múltiplas regiões subgenômicas é uma solução às limitações impostas pela rápida evolução molecular do HCV. Variantes virais das regiões HVR1 e NS5A de 16 pacientes cronicamente infectados com o HCV, genótipos 1a e 1b, foram sequenciadas com a técnica de NGS. Os pacientes 1-7 compartilhavam fatores de risco, pertencendo ao mesmo grupo de usuários de drogas injetáveis, porém o parentesco genético desses casos não pode ser estabelecido com base apenas no sequenciamento da HVR1 (distância nucleotídica mínima entre 16-23). A amplificação de um fragmento maior (~450 pb), correspondente a um segmento da região NS5A, aprimorou a relação epidemiológica entre os pacientes 1-5, onde as distancias genéticas mínimas foram consideravelmente menores (9-13). Os pacientes 6 e 7 não compartilharam sequências com os outros cinco pacientes dessa rede, apresentando populações virais mais homogêneas. Adicionalmente, Median Joining Networks foram construídas para ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The hepatitis C virus (HCV) affects approximately 3% of the world's population. Each year 3-4 million new cases are diagnosed. The identification of transmission networks is complicated due to the characteristic long incubation period, the lack of symptoms during the acute phase of the disease and the heterogeneity of HCV, making it challenging to link related cases to a common source of infection. Extensive characterization of intra-host populations can be reliably archived using next generation sequencing (NGS) approaches. Sequencing of multiple and longer subgenomic regions has been proposed as an alternative to overcome the limitations imposed by the rapid molecular evolution of the HCV HVR1. Thus, the NS5A and HVR1 regions of 16 chronically infected individuals, genotypes 1a and 1b, were sequenced using a NGS platform. Patients 1-7 shared risk factors and belonged to the same injection drug users network. However, genetic relatedness could not be established based on the HVR1 sequences (minimal nucleotide distance ranging from 16-23). Amplification and sequencing of a larger PCR fragment (~450 bp) targeting the NS5A region reestablished lost epidemiological links between patients 1-5. The minimum genetic distances in those patients were considerable smaller than the HVR1 counterparts (9-13). Patients 6 and 7 displayed a rather homogeneous viral population and were clearly not sharing any sequences with all other five patients in this network. Additionally, Median Joining... (Complete abstract click electronic access below) / Doutor

An interdisciplinary approach integrating micro and macroevolution, genomic, morphometric and morphological variation, systematics, quantitative genetics, and biogeography was employed to investigate the evolutionary history of the genus Holochilus (Rodentia: Sigmodontinae). Holochilus presents poorly defined species, with nomenclatural problems and phylogenetic relationships on species level unknown. The current species number possibly does not reflect its real diversity, and no work combining genetic and morphometric evidences from all its geographic range was performed. This genus belongs to the tribe Oryzomyini, and along with other 14 genera constitute the Oryzomyini clade D, the most comprehensive generic diversity of the tribe, occupying distinct environments. The internal phylogenetic relationship within this clade is still unclear and variable. Due to its broad geographic distribution, Holochilus also represents a key piece on the study of the evolution of oryzomines of open formations of South America. Based on a comprehensive sampling, I analyzed patterns of morphometric and genomic variation within Holochilus, in order to delimit the species belonging to this genus, as well as access the phylogenetic relationship between these lineages. I investigated the sexual and ontogenetic variation in this group, comparing natural and captive populations, seeking for understand the effect of the environmental differences in the pattern of variation and ontogenetic trajectories (Chapter 1). I also evaluated and compared the genomic variation among three species of Holochilus to verify the influence of the biomes and the climatic changes in the genomic signatures (Chapter 2). I applied a model-based approach to delimit species (Chapter 3). And finally, additional investigations were made to propose the phylogenetic relationship between members of clade D, and provide date intervals for the main diversifications events, as well as the possible process responsible for the biogeographic pattern current observed related with the forest and open areas occupation (Chapter 4). Sexual dimorphism exhibited small degree of variation among populations. The greater ontogenetic variation is found in the younger age classes, but oldest individuals also show larger degree of differentiation. There are also great differences in the ontogenetic trajectories among samples, where individuals from the captive population exhibited the lower degree of variation between all age classes. The quantitative genetic analysis showed that genomic differences are observed across the taxa, and it was associated with geography. Ecological niche models revealed that biomes with larger areas of stability also presented more genomic structure, suggesting that historical dimension impacted population isolation/connectivity. Results also shows that biomes not only differ geographically and environmentally (based on past climatic conditions), but also show significant association between the environmental space and the genetic variation that is not related with geography. Eight independent lineages within Holochilus were recovered, and the phylogenetic arrangement partially corroborates previous studies. Finally, the phylogeny proposed for the clade D presented some differences in comparisons with other previously reported, and suggest that most of the cladogenetic events happened during the Pleistocene, being the expansion of open environments an important driver of diversification in this group. / Uma abordagem interdisciplinar integrando micro e macroevolução, variação genômica, morfométrica e morfológica, sistemática, genética quantitativa e biogeografia foi empregada para investigar a história evolutiva do gênero Holochilus (Rodentia: Sigmodontinae). O gênero Holochilus apresenta espécies mal definidas, com problemas nomenclaturais e relações desconhecida. O número atual de espécies possivelmente não reflete a sua diversidade real e, até o momento, não foi realizado nenhum trabalho combinando evidências genéticas e morfométricas englobando toda a distribuição geográfica desse grupo. Este gênero pertence à tribo Oryzomyini, e juntamente com outros 14 gêneros (a diversidade genérica mais abrangente da tribo) formam o clado D. A relação filogenética interna dentro deste clado ainda é variável. Devido à sua ampla distribuição geográfica, Holochilus também representa uma peça chave no estudo da evolução dos oryzomíneos de formações abertas da América do Sul. Com base em uma amostragem abrangente, analisei padrões de variação morfométrica e genômica dentro de Holochilus, a fim de delimitar as espécies pertencentes a este gênero, bem como acessar a relação filogenética entre essas linhagens. Investiguei a variação sexual e ontogenética deste grupo, comparando populações naturais e de cativeiro, buscando entender o efeito das diferenças ambientais no padrão de variação e nas trajetórias ontogenéticas (Capítulo 1). Eu também avaliei e comparei a variação genômica entre três espécies de Holochilus a fim de verificar a influência dos biomas e das mudanças climáticas nas assinaturas genômicas das espécies (Capítulo 2). Em seguida eu apliquei uma abordagem baseada em modelos para delimitar as espécies (Capítulo 3). Finalmente, investigações adicionais foram realizadas para propor as relações filogenéticas entre os membros do clade D, fornecendo datas para os principais eventos de diversificação, e inferências sobre possíveis processos responsáveis pelo padrão biogeográfico atual, relacionado os mesmos com a ocupação florestal e áreas abertas (Capítulo 4). O dimorfismo sexual apresentou pequeno grau de variação entre as populações. A maior variação ontogenética é encontrada nas classes etárias mais jovens e mais velhas. Há também grandes diferenças nas trajetórias ontogenéticas entre as amostras, onde indivíduos da população cativeiro exibiram o menor grau de variação entre todas as classes etárias. A análise genética quantitativa mostrou que diferenças genômicas são observadas em todos os táxons e essa diferença está associada à geografia. Modelos de nichos ecológicos revelaram que os biomas com maiores áreas de estabilidade também apresentaram maior estruturação genômica, sugerindo que uma dimensão histórica impactou o isolamento/conectividade entre as populações. Os resultados também mostram que os biomas não só diferem geograficamente e ambientalmente (baseado em condições climáticas passadas), mas também mostram associação significativa entre o espaço ambiental e a variação genética que não está relacionada com a geografia. Adicionalmente, foi recuperado oito linhagens independentes dentro de Holochilus, e o arranjo filogenético parcialmente corrobora estudos anteriores. Finalmente, a filogenia proposta para o clado D apresentou algumas diferenças em comparação com outros estudos, e sugeriu que a maioria dos eventos cladogenéticos ocorreram durante o Pleistoceno, sendo a expansão dos ambientes abertos um importante motor de diversificação neste grupo.