Baculovírus são vírus específicos de inseto que infectam principalmente membros da ordem Lepidoptera. Diatraea saccharalis granulovírus (DsGV) foi isolado de larvas de Diatraea saccharalis (Lepidoptera: Crambidae), a broca-da-cana-de-açúcar, um dos insetos-praga de maior importância na cultura de cana-de-açúcar no Brasil. O genoma completo de DsGV foi obtido através do sequenciamento 454 (Roche). O genoma de DsGV apresentou 98.463 pb e potencialmente codifica 116 genes. Foram identificados os 37 genes conservados em todos os baculovírus, 19 genes específicos de betabaculovírus e 17 genes únicos. DsGV é o primeiro betabaculovírus que possui o gene gp64, que codifica uma proteína de fusão, originalmente encontrado apenas em alfabaculovírus do grupo I. A análise filogenética utilizando a concatenação das sequências deduzidas de aminoácidos de 30 genes conservados em 61 baculovírus totalmente sequenciados sugere que DsGV está inserido no clado b do grupo dos betabaculovírus e parece estar mais estritamente relacionado a 5 GVs (ChocGV, PiraGV, ClanGV, CpGV e CrleGV). / Baculoviruses are insect specific viruses that infect mainly members of the Order Lepidoptera. Diatraea saccharalis granulovirus (DsGV) was isolated from Diatraea saccharalis (Lepidoptera: Crambidae), one of the most important insect pest of the sugar cane culture in Brazil. The genome of DsGV was obtained by the 454 sequencing system (Roche). Our results showed that the nucleotide sequence of the DsGV genome is 98.463 bp in length and potentially encodes 116 putative genes. It contains the 37 baculovirus core genes, a set of 19 betabaculovirus-specific genes and 17 putative DsGV genes were not found in any genome of the baculoviruses sequenced up to the present. DsGV is the first betabaculovirus sequenced so far that has the gp64 envelope fusion protein gene, originally found only in alphabaculovirus group I. Phylogenetic analysis performed with concatamers of 30 conserved proteins from 61 fully sequenced baculovirus genomes suggests that DsGV is a member of clade b of the betabaculovirus and seems to be closer to 5 GVs (ChocGV, PiraGV, ClanGV, CpGV e CrleGV).

The discovery of large DNA viruses has challenged the traditional perception of viral complexity due to their enormous genome size and physical dimensions. Previously, viruses were considered small, filterable agents until the discovery of large DNA viruses. Among large DNA viruses, the phylum Nucleocytoviricota and its members, which are often called "giant viruses" have large genome sizes (up to 2.5 Mbp) and virion sizes (up to 1.5 um). Due to having large virion and genome sizes, these viruses were often excluded from viral surveys and remained understudied for years. Luckily, the advancement of metagenomic analysis has facilitated the study of large DNA viruses by analyzing them directly from their environment without cultivating them in the lab, which could be challenging for viruses. In the first chapter of the thesis, I investigated 11 metagenome-assembled genomes (MAGs) of giant viruses previously surveyed from Station ALOHA in the Pacific Ocean. St. ALOHA is located near Hawaii and represents oligotrophic gyres which the majority of the ocean is made of them. I focused on 11 MAGs of giant viruses to get insight into their phylogenetic characteristics, genomic repertoire, and global distribution patterns. Despite the fact that metagenomic analysis has facilitated the study of genetic materials of microbes and viruses on a huge scale, it is essential to benchmark the performance of metagenomic tools and understand the associated biases, particularly in viral metagenomics. In the second chapter, I evaluated the performance of metagenomic tools (contigs assembler and binning tool) in recovering viral genomes using annotated dataset. We used a metagenome simulator (CAMISIM) to generate simulated short reads with known composition to assess these processes. Moreover, I emphasized the importance of binning contigs for viral genomes to fully recover the genomes of viruses along with discussing how diversity metrics were differed for contigs, bins populations. / Master of Science / Viruses are generally thought to be small biological agents with small genome (genetic material) sizes and tiny physical structures; for instance, the genome length of a Human Immunodeficiency Virus (HIV) is around 10 kilobase pair (a unit for measuring genetic material in an organism), and the virion size (physical dimension of a virus) can go up to 120 nm. The discovery of large DNA viruses has challenged the idea of considering viruses as small biological entities, as their genome sizes and physical dimensions can be up to 2.5 megabase pairs and 1500 nm, respectively. Famous members of large DNA viruses from the phylum Nucleocytoviricota are often known as "Giant Viruses'' because they have enormous genome sizes and physical dimensions. Due to having large viral particles, these viruses may usually be excluded from viral surveys. For instance, in field studies, samples must be filtered through a fraction (e.g., 0.2 um) to eliminate bacterial and archaeal genomes and cellular debris, which also results in excluding larger viruses. Since these viruses remain understudied for several years because of biases associated with having large viral particles, there is a solid need to discover and investigate more about them. Growing and cultivating viruses in the laboratory may be challenging, as they need specific hosts to be dependent on to produce more viral progeny and some specific laboratory environments. Luckily, with the advancement of biotechnology, scientists could find ways to evade the need for cultivating viruses in the lab and study them with computational tools such as metagenomic analysis and bioinformatic tools. Metagenomics analysis helps to study the genetic materials of microbial or viral populations directly from their habitat without growing them in a laboratory. In short, metagenomic analysis has multiple steps, including collecting and filtering samples, fragmenting DNA within the samples, generating short DNA sequences (short-read sequences) with NGS (Next Generation Sequencing) technology, assembling short-read sequences into large DNA fragments which can be contigs (contiguous DNA fragments) and metagenome-assembled genome (MAGs). With metagenomic analysis, we can recover the genome of multiple organisms, and we name the recovered genome as metagenome-assembled genome (MAGs) as it is generated through metagenomic processes. The metagenomic analysis will allow us to study microbes and viruses in their environment and gain insight into their taxonomic details, genomic content, and how widespread they are. In the first chapter, I studied 11 MAGs of giant viruses previously surveyed from St. ALOHA, Hawaii. St. ALOHA is a good field site for examining microbial processes and diversity and a good representative of oligotrophic waters (low in nutrients). I examined 11 MAGs of giant viruses to investigate their taxonomic characteristics to clarify which order they belong to within their phylum, their genomic content, and their global distribution pattern. Although studies have successfully recovered the genome of large DNA viruses from their habitats and then analyzed them, all these metagenomic processes need to be evaluated so the results will be valid to consider as the genome of our interested organisms. In the second chapter, I developed a workflow for viral metagenomic analysis to assess metagenomic tools' performance in recovering reliable viral genomes, particularly for large DNA viruses. Most of these benchmarking workflows are done for bacterial and archaeal genomes, and in this thesis, I used these metagenomic tools and applied them to recover large DNA viruses genomes. Also, I emphasized the importance of using binning tools to fully recover large DNA viruses genomes, as due to their large genome size, their genomes might remain fragmented into different contigs, which are longer sequences than reads but shorter than MAGs.

Nucleocytoplasmic large DNA viruses (NCLDVs) have genome sizes that range from around 100 kilobases (kb) to up to 2.5 megabases, and virion sizes that can reach up to 1.5 μm. Their large size in both of these contexts is atypical and defies the traditional view that viruses are streamlined, "filterable infectious agents". NCLDVs include many diverse groups, including Poxviruses, Asfarviruses, Iridoviruses, Mimiviruses, and Marseilleviruses. Poxviruses are perhaps the most well-studied; these viruses have 135-360 kbp genomes with about half of the genes encoding essential replication genes and the other half encoding genes related to host-virus interactions. Many of the genes involved in host-virus interactions are involved in immunomodulatory processes and have homology to proteins encoded by the host. These viral genes, often referred to as "mimics", are therefore believed to be the result of host-to-virus gene transfer. In this study I sought to examine if common poxvirus immunomodulatory genes were found in other NCLDV lineages, and if so, to analyze the evolutionary history of these genes. I identified 5 protein families of immunomodulatory genes that were found in both poxviruses and other NCLDV lineages, and I used phylogenetic tools to compare viral immunomodulatory genes of NCLDVs to their eukaryotic orthologs to evaluate the number of times different NCLDV lineages have acquired these genes. Our phylogenetic analyses showed that several viral immunomodulatory genes were acquired multiple times by different NCLDV lineages, while others appear to have been transferred between viral groups. Interestingly, some NCLDV genes clustered together with homologs from the unrelated Herpesviridae family, suggesting that inter-viral gene exchange can traverse vast evolutionary distances. The vast diversity of hosts infected by different NCLDV lineages suggests that these immunomodulatory genes play key roles that are useful to viruses in a variety of contexts. This research provides insight into how giant viruses acquire host genes, which contribute to their large genome size, and how those genes evolved to subvert antiviral defenses. / Master of Science / Giant viruses are a relatively recent discovery, from the beginning of this century. Nucleocytoplasmic large DNA viruses (NCLDVs) are a classification of multiple giant virus families. These viruses have large genomes from around 100 kilobases to 2.5 megabases of DNA. For reference, the genome size of the flu virus is approximately 13 kilobases. Most viruses cannot be seen by the human eye, even with microscopes, but giant viruses can get as big as bacteria, which can be seen with microscopes. It is unknown how or why these viruses get so large. One explanation is that they steal genes from their host and those genes evolve to work against the host. In this thesis, I explored some of the genes that these viruses have picked up. I curated a set of 49 previously characterized viral genes to analyze in this context. These genes have to do with modulating the host immune system and are known as "immunomodulatory genes". Viral immunomodulatory genes are often mimics of the host genes which function to help the immune system. However, a virus evolves faster than a host and the virus mimic gene can evolve to work against the immune system. This change can be visualized using phylogenetic tools; the viral genes will be more similar to each other than to the host genes and cluster separately on a phylogenetic tree. About half of the genes of Poxviruses, a giant virus family that has viruses that infect humans, are related to virus-host interactions, and include viral mimic genes. Poxviruses have been far better studied than other NCLDV families because of their public health importance. Variola virus, the virus that causes smallpox, is a poxvirus. Other NCLDV infect animals, algae, and amoeba. Though their hosts are different, their genomes have similar features. I set out to discover whether some of these previously characterized viral immunomodulatory genes that exist in poxviruses also exist in other NCLDV families. I utilized phylogenetic tools and a database of giant virus sequences to figure out which genes are being picked up by which family of NCLDV. I also sought to determine whether the individual NCLDV families have their own acquired immunomodulatory gene or have a gene very similar to all other families, suggesting an ancient acquisition. If the gene is very similar, it suggests that an ancestor of the NCLDV acquired the gene and it has stuck around as the group diverged into families. It is also interesting if different families stole the same type of gene multiple times because that indicates the importance of that gene in subverting the antiviral immune system for viral replication. This work provides insight into how giant viruses acquire host genes, which contribute to their large genome size, and how they evolved those genes to subvert antiviral defenses.

Mesozooplankton are of critical importance to marine food webs by transferring energy from the microbial food web to higher trophic levels and depositing energy to the deeper ocean layers through fecal deposition. While decades of research have shown that viruses have significant impacts in the oceans, and infect a wide range of organisms from bacteria to whales, there is still little known about the impacts of viruses on the mesozooplankton community. As copepods are the most abundant mesozooplankton group, this study sought to characterize the viruses present in natural populations of the calanoid copepods Acartia tonsa and Labidocera aestiva in Tampa Bay, Florida. Viral metagenomics revealed two virus genomes, named Acartia tonsa copepod circovirus (AcCopCV) and Labidocera aestiva copepod circovirus (LaCopCV), which were discovered in their respective copepod species. Both viruses show amino-acid similarities to known circoviruses, and phylogenetic and genomic analyses suggest they may be divergent members of the Circoviridae family. LaCopCV was found to be extremely prevalent in the L. aestiva population, with up to 100% of individuals infected. High viral loads for LaCopCV were observed by quantitative PCR, with an average viral load of 1.3x105 copies per individual. In addition, transcription of the LaCopCV replication gene was detected in L. aestiva, demonstrating active viral replication. AcCopCV could be detected sporadically in A. tonsa populations throughout the year. The circoviruses were specific to their respective hosts, and were not detected in the other copepod species or surrounding seawater. Virus-like particles were observed in A. tonsa and L. aestiva under transmission electron microscopy, demonstrating that viruses were actively proliferating in copepod connective tissue, as opposed to gut tissue, parasites, or symbionts. Preliminary results from in-situ hybridization show that the AcCopCV genome can be detected in A. tonsa tissue, linking the discovered genomes to virus propagation in copepod tissue. This is the first study describing viruses in copepods, as well as the first discovery of circoviruses infecting marine organisms. These results suggest that viruses impact marine copepod populations, necessitating further studies to determine the ecological impacts of viruses on the mesozooplankton community.

Thesis (MSc (Medical Virology )--University of Stellenbosch, 2004. / 150 leaves printed on single pages, preliminary pages i-vii and numberd pages 1-143. Includes bibliography and figures digitized at 300 dpi grayscale and 300 dpi 24-bit Color to pdf format (OCR), using a Hp Scanjet 8250 Scanner and digitized at 600 dpi grayscale to pdf format (OCR), using a Bizhub 250 Konica Minolta Scanner. / ENGLISH ABSTRACT: The first episode of HIV-1 in South Africa was documented in 1982. Homosexual transmission of the virus was the predominate mode of transmission in an epidemic of mainly HIV-1 subtype Band D infections. To date, no full-length sequences of Subtype D strains from South Africa has been reported. Here we describe the characterization and some of the unique features of the Tygerberg HIV-1 subtype D strains. A near full-length 9 kb fragment was obtained through a one step PCR using high molecular weight DNA. Cloning was done successfully with the pCR-XLTapa cloning kit. Large quantities of plasmid DNA was grown and sequenced on both strands of the DNA. ORF determination and subtyping was followed by standard phylogenetic methods to construct evolutionary phylogenetic trees. Subtyping and similarity plots revealed that the sequences from Tygerberg are pure subtype D. All the Tygerberg strains had intact genes with no premature stop codons. At the tip of the V3 loop, the Tygerberg strains have the GOGO motif. R214 has a more variable vpu gene than the rest of the Tygerberg strains, but is still subtype D in this region. No premature stop codons have been observed in the tat gene and the glycosilation of the strains are less than the subtype D consensus. We are the first to report full-length sequences of HIV-1 subtype D strains from South Africa. The sequences represent non-mosaic genomes of subtype D. Our results confirm that the subtype D sequences from the beginning of the HIV-1 epidemic differ from the Subtype D sequences from recent isolates. / AFRIKAANSE OPSOMMING: Die eerste episode van HIV-1 infeksie in Suid Afrika is in 1982 gedokumenteer. Die epidemie het hoofsaaklik uit subtipe B en D bestaan en was deur homoseksuele kontak oorgedra. Geen vollengte subtipe D DNS volgordes van Suid-Afrika is tans beskryf nie. Hier beskryf ons die karakterisering van vollengte subtipe D stamme asook sommige van die unieke eienskappe van die virusse. Die vollengte 9 kb genoom volgorde was verkry deur 'n eenstap PKR reaksie met hoë molekulêre gewig DNS uit te voer. Die 9 kb fragment was suksesvol gekloneer met behulp van die peR-Xl-TOPO klonerings toetsstel. Groot hoeveelhede plasmied DNS was opgegroei en die nukleotied volgorde bepaal op beide stringe van die genoom. Die stamme was gesubtipeer en filogenetiese analise was uitgevoer met standaard metodes. Die volledige DNS volgordes was bepaal en subtipering het daarop gedui dat die stamme van Tygerberg suiwer subtipe D is. Geen premature stop kodons is in die nukleotied volgordes van die Tygerberg stamme gevind nie. By die draai van die varieerbare deel (V3) het al die Tygerberg stamme die GQGQ motief gehad. R214 het 'n meer varieerbare vpu geen, maar behoort steeds tot die subtipe D groep in die gedeelte. Daar was geen premature stop kodons in die tat geen gevind nie en die glikosilasie van die stamme is minder as die van die konsensus subtipe D stam. Ons is die eerste groep om vollengte subtipe D stamme van Suid-Afrika te karakteriseer. Die DNS volgordes verteenwoordig suiwer subtipe D genome. Ons resultate bevestig die van ander dat die nukleotied volgordes van die ouer subtipe D stamme verskil van die nuwer stamme.

Os papilomavírus são pequenos vírus de DNA dupla-fita, não envelopados, mucoepiteliotrópicos, capazes de infectar inúmeros vertebrados superiores de maneira espécie-específica. A infecção por estes vírus está associada a uma série de desordens proliferativas que levam desde de a formação de verrugas comuns até a do carcinoma invasivo. Aproximadamente 200 tipos de papilomavírus humano (HPVs) foram identificados, sendo que cerca de 40 deles infectam o trato genital. Dentre estes, os chamados HPVs de alto-risco estão associados etiologicamente ao carcinoma de colo de útero, enquanto que os de baixo-risco estão relacionados às lesões epiteliais benignas. A infecção por HPVs de alto-risco é muito comum, no entanto, a maioria destas é transitória e somente uma pequena proporção de mulheres desenvolvem o carcinoma. Entretanto, algumas mulheres são incapazes de eliminar esta infecção, levando a persistência viral e o conseqüente desenvolvimento da neoplasia. Para que a infecção pelo HPV persista é necessário um mecanismo de escape ao sistema imune do hospedeiro. O mecanismo de escape à resposta imune inata parece ser característico da infecção pelo HPV, pois o ciclo infeccioso deste vírus não promove inflamação. A infecção por HPV promove a liberação de citocinas, tal como o fator de necrose tumoral (TNF). Esta citocina possui um potente efeito citostático em queratinócitos normais e imortalizados com HPV, enquanto que em queratinóctos imortalizados com HPV18 este efeito não é observado. Do mesmo modo, observamos que a expressão do oncogene E6 de HPV16 ou 18 é suficiente para promover resistência ao efeito antiproliferativo do TNF em culturas em monocamada e organotípica. A expressão aumentada e contínua destes ocogenes é sabidamente o principal evento favorável ao desenvolvimento do câncer de colo de útero. Estas proteínas são essenciais na indução da transformação celular, visto que interferem na regulação do ciclo celular e apoptose. O produto dos genes E6 e E7 se liga ao produto dos genes supressores de tumor p53 e pRb, respectivamente, levando a sua degradação pela via de proteólise dependente de ubiquitina. As bases moleculares desta resistência ao TNF ainda são pouco conhecidas. Neste estudo, comparamos o efeito desta citocina em queratinócitos normais e que expressam E6 ou E7. Observamos através de cDNA Microarray a expressão de um grupo de genes, entre eles TCN1, DEK, HMGB2, INHBA, MCM2, MCM5 e MMP9, com expressão diferencial entre as células sensíveis e as resistentes ao TNF. / Papillomaviruses are small, non-enveloped, epitheliotropic, double-stranded DNA viruses that infect mucosal and cutaneous epithelia in a wide variety of higher vertebrates in a species-specific manner. Papillomavirus infections are associated to a series of proliferative disorders that range from common warts to invasive carcinomas. Almost 200 types of human papillomaviruses (HPVs) have been identified and approximately 40 of them infect the genital tract. Only the so-called high-risk HPV types mediate human carcinogenesis, whereas the low-risk HPVs have been linked to benign epithelial lesions. High-risk genital HPV infection is very common, and the majority of individuals clear their infection with time. However, a proportion of women cannot effectively clear the virus, and the persistence of a high-risk HPV is the major risk factor for the development of anogenital malignancies. To persist, HPV must escape the host immune system. Effective evasion of innate immune recognition seems to be the hallmark of HPV infections, since the infectious cycle is one in which viral replication and virion release is not associated with inflammation. Furthermore, HPV infections promote cytokine release, as tumor necrosis factor-alpha (TNF). This cytokine has a potent cytostatic effect on normal and HPV16 immortalized keratinocytes, while it does not affect HPV18 immortalized keratinocytes proliferation. In addition, we have observed that expression of HPV 16 or 18 E7 oncogene is sufficient to overcome TNF antiproliferative effect in monolayer and organotypic cell cultures. The increased and sustained expression of HPV oncogenes, E6 and E7, is the main contributor to the development of cervical cancer. Both E6 and E7 proteins are essential to induce and maintain cellular transformation, due to their interference with cell-cycle and apoptosis regulation. The most manifest function of the E6 protein is to promote the degradation of p53, while E7 is known to bind to and promote the proteasomal degradation of the retinoblastoma tumor suppressor gene product, pRb, and its family members. The molecular basis of TNF resistance is not well understood. In this study we compared the effect of TNF between normal and HPV16 E6 or E7 expressing keratinocytes. We observed by cDNA Microarray the differential expression of a common set of genes in TNF-sensitive cell lines, including TCN1, DEK, HMGB2, INHBA, MCM2, MCM5 and MMP9, that differs from those modulated in TNF-resistant cells.

A rubéola é uma doença infecciosa aguda, normalmente com um curso clínico suave. Porém quando adquirida nas primeiras 12 semanas de gestação, pode causar severos defeitos de nascimento, conhecida como Síndrome da Rubéola Congênita (SRC). A caracterização genética do vírus da rubéola é feita analisando a seqüência da região hipervariável do gene da glicoproteína E1. Este estudo, apresenta a primeira caracterização molecular de do vírus da rubéola isolados no estado de São Paulo, Brasil. As amostras (sangue, urina, swab de orofaringe, explante de fígado, produto de aborto e fluido cerebrospinal) foram coletados entre 1997 e 2004 de pacientes com sintomas clínicos de rubéola. O gene E1 vírus da rubéola foi amplificado pela reação em cadeia da polimerase em cadeia diretamente de espécimes clínicos e isolados, e os fragmentos de DNA obtidos foram seqüenciados. As seqüências foram alinhadas para a analise filogenética, com seqüências representativas dos diferentes genótipos do vírus da rubéola. Vinte e nove isolados foram obtidos, incluindo isolados relacionados com insuficiência hepática aguda, encefalite e infecções congênitas. A análise filogenética mostrou que 19 dos 29 virus da rubéola isolados pertencem ao genótipo 1a, e 10 pertencem ao genótipo 1G. Este trabalho demonstrou dois genótipos do vírus da rubéola circularam simultaneamente entre os anos de 1997-2004. / Rubella is an acute infectious disease with normally a mild clinical course. However, infections during pregnancy, especially before week 12 of gestation (WG), can cause severe birth defects known as congenital rubella syndrome (CRS). Genetic characterization of wild-type rubella virus is based on sequence analysis of a hypervariable region of the glycoprotein E1 gene. This study presents the first molecular characterization of isolates from São Paulo, Brazil. Samples (blood, urine, oropharyngeal swab, explanted liver, product of conception and cerebrospinal fluid) were collected between 1997 and 2004 from patients with clinical symptoms of rubella. The rubella virus E1 gene coding region was amplified by reverse transcriptase polymerase chain reaction directly from clinical specimens and isolates, and the resulting DNA fragments were sequenced. Sequences were assigned to genotypes by phylogenetic analysis with rubella virus reference sequences. Twenty-nine isolates were obtained, including isolates from acute liver failure, encephalitis and congenital infections. Phylogenetic analysis showed that 19 out of 29 isolated in the São Paulo strains of rubella virus belonged to genotype 1a, and 10 strains to genotype 1G. This work demonstrated two genotypes of RV circulated simultaneously between years 1997 and 2004 in the state of São Paulo. The information reported in this paper may be useful for contributes to understand better the molecular epidemiology of RV in São Paulo, Brazil.

Os papilomavírus são pequenos vírus de DNA dupla-fita, não envelopados, mucoepiteliotrópicos, capazes de infectar inúmeros vertebrados superiores de maneira espécie-específica. A infecção por estes vírus está associada a uma série de desordens proliferativas que levam desde de a formação de verrugas comuns até a do carcinoma invasivo. Aproximadamente 200 tipos de papilomavírus humano (HPVs) foram identificados, sendo que cerca de 40 deles infectam o trato genital. Dentre estes, os chamados HPVs de alto-risco estão associados etiologicamente ao carcinoma de colo de útero, enquanto que os de baixo-risco estão relacionados às lesões epiteliais benignas. A infecção por HPVs de alto-risco é muito comum, no entanto, a maioria destas é transitória e somente uma pequena proporção de mulheres desenvolvem o carcinoma. Entretanto, algumas mulheres são incapazes de eliminar esta infecção, levando a persistência viral e o conseqüente desenvolvimento da neoplasia. Para que a infecção pelo HPV persista é necessário um mecanismo de escape ao sistema imune do hospedeiro. O mecanismo de escape à resposta imune inata parece ser característico da infecção pelo HPV, pois o ciclo infeccioso deste vírus não promove inflamação. A infecção por HPV promove a liberação de citocinas, tal como o fator de necrose tumoral (TNF). Esta citocina possui um potente efeito citostático em queratinócitos normais e imortalizados com HPV, enquanto que em queratinóctos imortalizados com HPV18 este efeito não é observado. Do mesmo modo, observamos que a expressão do oncogene E6 de HPV16 ou 18 é suficiente para promover resistência ao efeito antiproliferativo do TNF em culturas em monocamada e organotípica. A expressão aumentada e contínua destes ocogenes é sabidamente o principal evento favorável ao desenvolvimento do câncer de colo de útero. Estas proteínas são essenciais na indução da transformação celular, visto que interferem na regulação do ciclo celular e apoptose. O produto dos genes E6 e E7 se liga ao produto dos genes supressores de tumor p53 e pRb, respectivamente, levando a sua degradação pela via de proteólise dependente de ubiquitina. As bases moleculares desta resistência ao TNF ainda são pouco conhecidas. Neste estudo, comparamos o efeito desta citocina em queratinócitos normais e que expressam E6 ou E7. Observamos através de cDNA Microarray a expressão de um grupo de genes, entre eles TCN1, DEK, HMGB2, INHBA, MCM2, MCM5 e MMP9, com expressão diferencial entre as células sensíveis e as resistentes ao TNF. / Papillomaviruses are small, non-enveloped, epitheliotropic, double-stranded DNA viruses that infect mucosal and cutaneous epithelia in a wide variety of higher vertebrates in a species-specific manner. Papillomavirus infections are associated to a series of proliferative disorders that range from common warts to invasive carcinomas. Almost 200 types of human papillomaviruses (HPVs) have been identified and approximately 40 of them infect the genital tract. Only the so-called high-risk HPV types mediate human carcinogenesis, whereas the low-risk HPVs have been linked to benign epithelial lesions. High-risk genital HPV infection is very common, and the majority of individuals clear their infection with time. However, a proportion of women cannot effectively clear the virus, and the persistence of a high-risk HPV is the major risk factor for the development of anogenital malignancies. To persist, HPV must escape the host immune system. Effective evasion of innate immune recognition seems to be the hallmark of HPV infections, since the infectious cycle is one in which viral replication and virion release is not associated with inflammation. Furthermore, HPV infections promote cytokine release, as tumor necrosis factor-alpha (TNF). This cytokine has a potent cytostatic effect on normal and HPV16 immortalized keratinocytes, while it does not affect HPV18 immortalized keratinocytes proliferation. In addition, we have observed that expression of HPV 16 or 18 E7 oncogene is sufficient to overcome TNF antiproliferative effect in monolayer and organotypic cell cultures. The increased and sustained expression of HPV oncogenes, E6 and E7, is the main contributor to the development of cervical cancer. Both E6 and E7 proteins are essential to induce and maintain cellular transformation, due to their interference with cell-cycle and apoptosis regulation. The most manifest function of the E6 protein is to promote the degradation of p53, while E7 is known to bind to and promote the proteasomal degradation of the retinoblastoma tumor suppressor gene product, pRb, and its family members. The molecular basis of TNF resistance is not well understood. In this study we compared the effect of TNF between normal and HPV16 E6 or E7 expressing keratinocytes. We observed by cDNA Microarray the differential expression of a common set of genes in TNF-sensitive cell lines, including TCN1, DEK, HMGB2, INHBA, MCM2, MCM5 and MMP9, that differs from those modulated in TNF-resistant cells.

A rubéola é uma doença infecciosa aguda, normalmente com um curso clínico suave. Porém quando adquirida nas primeiras 12 semanas de gestação, pode causar severos defeitos de nascimento, conhecida como Síndrome da Rubéola Congênita (SRC). A caracterização genética do vírus da rubéola é feita analisando a seqüência da região hipervariável do gene da glicoproteína E1. Este estudo, apresenta a primeira caracterização molecular de do vírus da rubéola isolados no estado de São Paulo, Brasil. As amostras (sangue, urina, swab de orofaringe, explante de fígado, produto de aborto e fluido cerebrospinal) foram coletados entre 1997 e 2004 de pacientes com sintomas clínicos de rubéola. O gene E1 vírus da rubéola foi amplificado pela reação em cadeia da polimerase em cadeia diretamente de espécimes clínicos e isolados, e os fragmentos de DNA obtidos foram seqüenciados. As seqüências foram alinhadas para a analise filogenética, com seqüências representativas dos diferentes genótipos do vírus da rubéola. Vinte e nove isolados foram obtidos, incluindo isolados relacionados com insuficiência hepática aguda, encefalite e infecções congênitas. A análise filogenética mostrou que 19 dos 29 virus da rubéola isolados pertencem ao genótipo 1a, e 10 pertencem ao genótipo 1G. Este trabalho demonstrou dois genótipos do vírus da rubéola circularam simultaneamente entre os anos de 1997-2004. / Rubella is an acute infectious disease with normally a mild clinical course. However, infections during pregnancy, especially before week 12 of gestation (WG), can cause severe birth defects known as congenital rubella syndrome (CRS). Genetic characterization of wild-type rubella virus is based on sequence analysis of a hypervariable region of the glycoprotein E1 gene. This study presents the first molecular characterization of isolates from São Paulo, Brazil. Samples (blood, urine, oropharyngeal swab, explanted liver, product of conception and cerebrospinal fluid) were collected between 1997 and 2004 from patients with clinical symptoms of rubella. The rubella virus E1 gene coding region was amplified by reverse transcriptase polymerase chain reaction directly from clinical specimens and isolates, and the resulting DNA fragments were sequenced. Sequences were assigned to genotypes by phylogenetic analysis with rubella virus reference sequences. Twenty-nine isolates were obtained, including isolates from acute liver failure, encephalitis and congenital infections. Phylogenetic analysis showed that 19 out of 29 isolated in the São Paulo strains of rubella virus belonged to genotype 1a, and 10 strains to genotype 1G. This work demonstrated two genotypes of RV circulated simultaneously between years 1997 and 2004 in the state of São Paulo. The information reported in this paper may be useful for contributes to understand better the molecular epidemiology of RV in São Paulo, Brazil.

Wild-type viruses with intrinsic oncolytic capacity in human includes DNA viruses like some autonomous parvoviruses and many RNA viruses. Recent advances in molecular biology have allowed the design of several genetically modified viruses, such as adenovirus and herpes simplex virus that specifically replicate in, and kill tumor cells. However, still several hurdles regarding clinical limitations and safety issues should be overcome before this mode of therapy can become of clinical relevance. It includes limited virus spread in tumor masses, stability of virus in the blood, trapping within the liver sinusoids, transendothelial transfer, and/or vector diffusion of viral particles to tumor cells, limited tumor transduction, immune-mediated inactivation or destruction of the virus. For replication-competent vectors without approved antiviral agents, suicide genes might be used as fail-safe mechanism. Cancer stem cells are a minor population of tumor cells that possess the stem cell property of self-renewal. Therefore, viruses that target the defective self-renewal pathways in cancer cells might lead to improved outcomes.<p>In this thesis, data we generated in the field of oncolytic autonomous parvoviruses are presented.<p>We replaced capsid genes by reporter genes and assessed expression in different types of human cancer cells and their normal counterparts, either at the level of whole cell population, (CAT ELISA) or at the single cell level, (FACS analysis of Green Fluorescent Protein). Cat expression was substantial (up to 10000 times background) in all infected tumor cells, despite variations according to the cell types. In contrast, no gene expression was detected in similarly infected normal cells, (with the exception of an expression slightly above background in fibroblasts.). FACS analysis of GFP expression revealed that most tumor cells expressed high level of GFP while no GFP positive normal cells could be detected with the exception of very few (less than 0.1%) human fibroblast cells expressing high level of GFP. We also replace capsid genes by genes coding for the costimulatory molecules B7-1 and B7-2 and show that, upon infection with B7 recombinant virions, only tumor cells display the costimulatory molecules and their immunogenicity was increased without any effect on normal cells. Using a recombinant MVM containig the Herpes Simplex thymidine kinase gene, we could get efficient killing of most tumor cell types in the presence of ganciclovir, whithout affecting normal proliferating cells. We also produced tetracycline inducible packaging cell lines in order to improve recombinant vectors yields. The prospects and limitations of these different strategies will be discussed.<p>An overview is given of the general mechanisms and genetic modifications by which oncolytic viruses achieve tumor cell-specific replication and antitumor efficacy. However, as their therapeutic efficacy in clinical trials is still not optimal, strategies are evaluated that could further enhance the oncolytic potential of conditionally replicating viruses in conjunction with other standard therapies. <p>Another exciting new area of research has been the harnessing of naturally tumor-homing cells as carrier cells to deliver oncolytic viruses to tumors. The trafficking of these tumor-homing cells (stem cells, immune cells and cancer cells), which support proliferation of the viruses, is mediated by specific chemokines and cell adhesion molecules and we are just beginning to understand the roles of these molecules. Finally, we will explore some ways deserving further study in order to be able to utilize various oncolytic viruses for effective cancer treatment. <p><p> / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished