Several wild-type poxviruses have emerged as potential oncolytic viruses (OVs), including orf virus (OrfV), and vaccinia virus (VV). Oncolytic VVs have been modified to include attenuating mutations that enhance their tumour selective nature, but these mutations also reduce overall viral fitness in cancer cells. Previous studies have shown that a VV (Western Reserve) with its E3L gene replaced with the E3L homologue from, OrfV (designated VV-E3LOrfV), maintained its ability to infect cells in vitro, but was attenuated compared to its parental VV in vivo. Our goal was to determine the safety and oncolytic potential VV-E3LOrfV, compared to wild type VV and other attenuated recombinants. VV-E3LOrfV, was unable to replicate to the same titers and was sensitive to IFN compared to its parental virus and other attenuated VVs in normal human fibroblast cells. The virus was also less pathogenic when administered in vivo. Viral replication, spread and cell killing, as measures of oncolytic potential in vitro, along with in vivo efficacy, were also observed.. The Parapoxvirus, OrfV has been shown to have a unique immune-stimulation profile, inducing a number of pro-inflammatory cytokines, as well as potently recruiting and activating a number of immune cells. Despite this unique profile, OrfV is limited in its ability to replicate and spread in human cancer cells. Various strategies were employed to enhance the oncolytic efficacy of wild-type OrfV. A transient transfection/infection screen was created to determine if any of the VV host-range genes (C7L, K1L, E3L or K3L) would augment OrfV oncolysis. Combination therapy, including the use of microtubule targeting agents, Viral Sensitizer (VSe) compounds and the addition of soluble VV B18R gene product were employed to see if they also enhance OrfV efficacy. Unfortunately, none of the strategies mentioned were able to enhance OrfV.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / Orf virus (ORFV), the type member of the genus Parapoxvirus of the family Poxviridae, is the etiologic agent of orf or contagious ecthyma, a contagious and ubiquitous disease of sheep and goats. ORFV genome consists of a double stranded DNA molecule with approximately 138 Kb, and contains 131 putative genes. Among those, 15 are novel genes, unique to parapoxviruses, which lack homology to other known viral or cellular genes. In the present study we describe the functional characterization of three of these genes, ORFV024, ORFV002, and ORFV121. Results presented here demonstrate that the proteins encoded by these genes inhibit the activation of the nuclear factor-kappa B (NF-κB) signaling pathway. ORFV-encoded ORFV024 inhibits activation of the NF-κB signaling pathway in the cell cytoplasm by inhibiting phosphorylation of the IκB kinases, IKKα and IKKβ, consequently inhibiting the activation of the IKK complex. Deletion of ORFV024 from the ORFV genome had no significant effect on disease severity, progression or time to resolution in sheep, indicating that ORFV024 does not contribute to ORFV virulence. ORFV-encoded ORFV002 functions in the cell nucleus, where it interacts with the NF-κB subunit NF-κB-p65, inhibiting its acetylation, a p300-mediated modification of NF-κB-p65 which modulates its transcriptional activity. Similarly to ORFV024, deletion of ORFV002 from the ORFV genome had no significant effect on ORFV virulence and disease pathogenesis in sheep. ORFV-encoded ORFV121 functions in the cell cytoplasm, where it binds to and inhibits phosphorylation and nuclear translocation of NF-κB-p65. Deletion of ORFV121 from the ORFV genome resulted in a marked attenuated disease phenotype in sheep, indicating that ORFV121 is a determinant of virulence of ORFV in the natural host. These results indicate that ORFV, like other poxviruses, has evolved multiple strategies to modulate NF-κB, targeting different steps of the signaling pathway. Results obtained in the pathogenesis studies performed here suggest that multiple NF-κB inhibitors encoded by ORFV may exert complementary and/or redundant functions to effectively block host cell responses regulated by the NF-κB signaling pathway. Additionally, it is possible that ORFV-encoded NF-κB inhibitors modulate distinct cellular processes regulated by NF-κB in vivo. A better understanding of ORFV-host interactions may provide valuable insights for the development of improved vaccines against orf, or yet for the development of novel ORFV-based therapeutic agents and vaccine vectors with enhanced safety and efficacy, and a broader applicability. / O vírus da orf (ORFV), protótipo do gênero Parapoxvirus da família Poxviridae, é o agente etiológico da orf ou ectima contagioso, uma enfermidade contagiosa de distribuição mundial que afeta primariamente ovinos e caprinos. O genoma do ORFV consiste de uma molécula de DNA de fita dupla com aproximadamente 138 Kb, que contém presumidamente 131 genes. Dentre estes, 15 são genes novos, identificados apenas nos parapoxvírus e que não possuem homologia com outros genes de origem viral ou celular. O presente estudo descreve a caracterização funcional de três destes genes, ORFV024, ORFV002 e ORFV121. Os resultados apresentados no presente estudo demonstram que as proteínas codificadas pelos genes ORFV024, ORFV002 e ORFV121 inibem a ativação da via de sinalização do fator de transcrição nuclear-kappa B (NF-κB). O produto da ORFV024 bloqueia a ativação da via do NF-κB no citoplasma celular, inibindo a fosforilação das quinases IκB (IKK), IKKα e IKKβ e, consequentemente inibindo a ativação do complexo IKK. A deleção do gene ORFV024 do genoma do ORFV não alterou a severidade, a progressão, ou o tempo de resolução das lesões produzidas pelo ORFV em ovinos, indicando que o produto deste gene não contribui para a virulência do vírus. O gene ORFV002 codifica um inibidor do NF-κB que atua no núcleo das células. O produto do ORFV002 interage com a subunidade NF-κB-p65 do NF-κB, inibindo a sua acetilação, uma modificação pós-traducional do NF-κB-p65 mediada pela acetiltransferase p300 que regula a sua atividade transcripcional. Semelhante ao ORFV024, a deleção do gene ORFV002 do genoma do ORFV não afetou a virulência do vírus nem alterou a patogenia da enfermidade em ovinos. O produto do gene ORFV121 atua no citoplasma das células, onde esta proteína viral interage com o NF-κB-p65 inibindo sua fosforilação e translocação nuclear. A deleção do gene ORFV121 do genoma do ORFV reduziu significativamente a severidade, a progressão e o tempo de resolução da doença em ovinos, indicando que este produto viral constitui-se em um fator de virulência para o ORFV em seu hospedeiro natural. Estes resultados demonstram que, assim como outros poxvírus, o ORFV também desenvolveu múltiplas estratégias para modular a via de sinalização do NF-κB, codificando proteínas que atuam em diferentes eventos desta complexa via de sinalização intracelular. Os resultados obtidos nos estudos de patogenia sugerem que os inibidores do NF-κB codificados pelo ORFV desempenham funções complementares e/ou redundantes, provavelmente, para promover um bloqueio efficiente dos processos biológicos regulados pelo NF-κB. Além disso, estes produtos virais podem modular diferentes processos biológicos controlados pelo NF-κB in vivo. Um melhor entendimento das interações do ORFV com o seu hospedeiro pode favorecer o desenvolvimento de vacinas mais eficazes para o ectima contagioso, ou ainda, promover o desenvolvimento de vacinas vetoriais ou imunoterápicos, baseados no ORFV, mais eficazes e com uma maior espectro de aplicações.

Submitted by (edna.saturno@ufrpe.br) on 2016-11-03T13:19:37Z No. of bitstreams: 1 Rosana Leo de Santana.pdf: 1515110 bytes, checksum: 27fa86f8f333295d8921b44bc59f3dcb (MD5) / Made available in DSpace on 2016-11-03T13:19:37Z (GMT). No. of bitstreams: 1 Rosana Leo de Santana.pdf: 1515110 bytes, checksum: 27fa86f8f333295d8921b44bc59f3dcb (MD5) Previous issue date: 2012-02-13 / Contagious ecthyma is a severe and proliferative viral disease affecting ovine and caprine species, and eventually men, caused by the contagious ecthyma virus (ECV) of the Parapoxvirus genus. The disease is spread worldwide, including in Brazil, where in the state of Pernambuco, due to its endemicity, can be mistaken by other vesicular diseases such as the Foot and mouth Disease, which requires its diagnostic differentiation. Meanwhile, the control of the infection in endemic regions is limited due to the difficulties in replicating the virus in cell cultures, for the development of vaccines. The purpose of this work is to evaluate the behavior of ECV samples in primary cultures of fetal caprine cornea cells, and also to establish an efficient molecular diagnostic method for field samples, and to analyze the phylogenetic profile of the virus samples studied. Crust samples from twenty-two sheep and seven goats from the states of Pernambuco, Bahia, Sergipe and Paraiba presenting the clinical symptoms of EC were inoculated in cell monolayers, during seven consecutive passages at weekly intervals. During all passages, starting at 24 hours post-infection was observed a cytopathic effect (CE) characterized by cell rounding, cell fusion with the formation of small syncytia, cytoplasmic inclusion and vacuolization. The intensity of cell detachment from the layers ranged from 25% to 100% which varied according to the viral sample. We concluded that the primary cultures of the fetal caprine cornea cell appeared highly permissible to replication of ECV and the isolated samples of ECV seemed to adapt to the utilized culture with a slight variation among samples, and the identification by PCR showed to be an applicable method to the differential diagnosis of vesicular diseases, especially to support the actions of PNEFA, where goats and sheep are considered sentinel animals. The phylogenetic analysis showed that ORFV sequences from the northeastern of Brazil are highly correlated showing identical sequences up to 99%. In addition, they present more than 80% sequence identity with other isolates of ORFV worldwide. / Ectima contagioso (EC) ou orf é uma doença infecto-contagiosa da pele causada pelo vírus do ectima contagioso (ECV) ou ORFV, que acomete principalmente ovinos e caprinos, e ocasionalmente o homem. Protótipo do gênero Parapoxvírus da família Poxviridae, está amplamente disseminado em todo mundo, inclusive no Brasil, especialmente na Região Nordeste, onde a caprinovinocultura é amplamente praticada para a produção de pele, carne e leite. Em Pernambuco, a doença ocorre de forma endêmica e pode ser confundida com enfermidades vesiculares, como a Febre Aftosa (FA), havendo a necessidade de diferenciação, sobretudo como suporte às ações do Programa Nacional de Erradicação da Febre Aftosa (PNEFA). Uma grande limitação no controle da doença é a dificuldade de replicação do vírus em cultivo celular, visando sua manipulação biotecnológica para a produção de vacinas. O objetivo deste trabalho é isolar e avaliar o comportamento de amostras de ECV em cultura primária de células de córnea fetal caprina, além de estabelecer um diagnóstico molecular eficiente para amostras de campo e avaliar o perfil filogenético das amostras de campo estudadas. Amostras de crostas de 22 ovinos e de sete caprinos que apresentavam sinais clínicos de EC, originários dos Estados de Pernambuco, Bahia, Sergipe e Paraíba, foram inoculadas em monocamadas de células epiteliais de córnea de feto caprino, durante sete passagens consecutivas, a intervalos semanais. Para realização do diagnóstico molecular foi utilizado para amplificação de um fragmento de 235pb do gene do envelope B2L o par de primers, PPP-3 e PPP-4 denominados pan-parapoxvirus. Observou-se em todas as passagens, a partir de 24 horas pós-infecção, efeito citopático (ECP) caracterizado pelo arredondamento celular, fusão com formação de pequenos sincícios, vacuolização e corpúsculos de inclusão citoplasmática, com intensidade de 25% a 100% de desprendimento da camada celular, que variou de acordo com a amostra viral. Conclui-se que as culturas de células primárias de córnea fetal caprina mostraram-se altamente permissíveis à replicação do ECV e que as amostras virais isoladas mostraram-se adaptadas ao cultivo utilizado, com pequena variação entre as amostras virais, e que, a identificação viral através da PCR é um método aplicável ao diagnóstico diferencial de enfermidades vesiculares, sobretudo como suporte às ações do PNEFA, no qual caprinos e ovinos são considerados animais sentinelas. A análise filogenética mostrou que as seqüências de ORFV do Nordeste do Brasil estão altamente relacionadas entre si, com seqüências idênticas acima de 99%. Além de apresentarem mais de 80% de identidade com seqüências de outros isolados de ORFV em todo mundo.

Several wild-type poxviruses have emerged as potential oncolytic viruses (OVs), including orf virus (OrfV), and vaccinia virus (VV). Oncolytic VVs have been modified to include attenuating mutations that enhance their tumour selective nature, but these mutations also reduce overall viral fitness in cancer cells. Previous studies have shown that a VV (Western Reserve) with its E3L gene replaced with the E3L homologue from, OrfV (designated VV-E3LOrfV), maintained its ability to infect cells in vitro, but was attenuated compared to its parental VV in vivo. Our goal was to determine the safety and oncolytic potential VV-E3LOrfV, compared to wild type VV and other attenuated recombinants. VV-E3LOrfV, was unable to replicate to the same titers and was sensitive to IFN compared to its parental virus and other attenuated VVs in normal human fibroblast cells. The virus was also less pathogenic when administered in vivo. Viral replication, spread and cell killing, as measures of oncolytic potential in vitro, along with in vivo efficacy, were also observed.. The Parapoxvirus, OrfV has been shown to have a unique immune-stimulation profile, inducing a number of pro-inflammatory cytokines, as well as potently recruiting and activating a number of immune cells. Despite this unique profile, OrfV is limited in its ability to replicate and spread in human cancer cells. Various strategies were employed to enhance the oncolytic efficacy of wild-type OrfV. A transient transfection/infection screen was created to determine if any of the VV host-range genes (C7L, K1L, E3L or K3L) would augment OrfV oncolysis. Combination therapy, including the use of microtubule targeting agents, Viral Sensitizer (VSe) compounds and the addition of soluble VV B18R gene product were employed to see if they also enhance OrfV efficacy. Unfortunately, none of the strategies mentioned were able to enhance OrfV.

No description available.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Orf virus (ORFV) belongs to the family Poxviridae, subfamily Chordopoxvirinae and genus Parapoxvirus and is the agent of contagious ecthyma, a mucocutaneous disease that affects mainly young sheep and goats and, occasionally, may affect people. The clinical lesions progress through stages of hyperemia, papules, vesicles, pustules, ulcers and proliferative and scabby lesions, located mainly on the labial commissure, lips and nostrils. Variable clinical lesions with different degrees of severity often occur in sheep and goats, and may be associated with host and/or viral genetics. The present study aimed to investigate the phenotype in vivo and to characterize virulence genes of four ORFV isolates recovered from contagious ecthyma outbreaks in Rio Grande do Sul State, Brazil. Twenty sheep, aged 6 and 8 months, were divided into five groups of four animals each and inoculated in the labial commissure with homogenates of scabs (viral titers 105.6TCID50/ml) obtained from different outbreaks: SV269/11, SV252/11, SV581/11 and SV820/10-Canguçu. The animals were evaluated for 30 days in clinical and virological aspects by clinical inspection and swab collection for virus isolation. A clinical score was established for each animal and group. All ORFV inoculated animals developed classical ecthyma contagious lesions, characterized by hyperemia, papules, macules, vesicles, pustules and scabs in varied degrees and duration. SV269/10 and SV820/10-Canguçu isolates induced more severe lesions resulting in higher clinical scores and longer duration of lesions. The animals inoculated with SV581/11 developed milder lesions and clinical scores significantly lower than other groups, but they shed virus for a longer period of time. For genetic analyses, PCR amplification and nucleotide sequencing of three virulence genes (VEGF, VIR and IL-10v) were performed. Deletion and mutations on VEGF and IL-10v amino acid sequence of SV581/11 and SV252/11 isolates were identified. The degree of amino acid identity among ORFV sequences was variable, and the lowest homology was found in the VEGF gene of SV581/11 when compared with the standard strains and other viruses. Thus, the present results showed that SV581/11 and SV252/11 isolates, particularly the former, are less virulent in sheep than SV269/11 and SV820/10-Canguçu. Possibly, the variable phenotypic observed in vivo is due to genetic alterations detected in the analyzed virulence genes. / O vírus da orf (ORFV) pertence à família Poxviridae, subfamília Chordopoxvirinae gênero Parapoxvirus e é o agente etiológico do ectima contagioso, uma doença mucocutânea que afeta principalmente ovinos e caprinos jovens e pode, ocasionalmente, afetar pessoas. Clinicamente, a enfermidade evolui com a formação de áreas hiperêmicas, vesículas, pústulas, úlceras e lesões proliferativas e crostosas sobre a pele dos lábios, comissura labial e narinas. Apresentações clínicas variáveis, com diferentes graus de severidade, ocorrem frequentemente e podem estar associadas a características do hospedeiro e, principalmente, a características genéticas do agente. O presente trabalho teve como objetivo investigar o fenótipo in vivo e caracterizar genes de virulência de quatro amostras de ORFV oriundas de surtos no Estado do Rio Grande do Sul, Brasil. Para isso, foram utilizados vinte ovinos, com idade entre 6 e 8 meses, divididos em cinco grupos de quatro animais cada. Os ovinos foram inoculados na comissura labial com homogeneizados de crostas (títulos virais 105,6 DICC50/ml) obtidas dos surtos (amostras SV269/11, SV252/11, SV581/11 e SV820/10-Canguçu). Os animais foram avaliados durante 30 dias com relação aos aspectos clínicos e virológicos, por inspeção clínica e coleta de suabes das lesões para detecção da excreção viral. As manifestações clínicas foram convertidas em um escore clínico, para cada animal e para os grupos. Os animais inoculados com os as quatro amostras desenvolveram lesões típicas de ectima contagioso, caracterizadas por hiperemia, pápulas, máculas, vesículas e pústulas, e formação de crostas em diferentes graus de intensidade e duração. As amostras SV269/10 e SV820/10-Canguçu induziram lesões mais graves, escores clínicos maiores e maior tempo de duração das lesões. Os animais inoculados com a amostra SV581/11 desenvolveram lesões e escores clínicos significativamente inferiores aos demais grupos, mas excretaram o vírus por período mais longo. Para a caracterização genética, foi realizada a amplificação por PCR e sequenciamento de nucleotídeos de três genes de virulência (VEGF, VIR e IL-10v). Foram identificadas deleções e mutações nas sequências dos genes VEGF e IL-10v das amostras SV581/11 e SV252/11. O grau de identidade de aminoácidos entre as amostras foi variável, sendo que a menor homologia foi encontrada no gene VEGF da amostra SV581/11, quando comparado com os demais vírus e a cepa padrão. Assim, os resultados obtidos demonstram que as amostras SV581/11 e SV252/11, em especial a primeira, foram menos virulentas em ovinos do que as amostras SV269/11 e SV820/10-Canguçu. Possivelmente essa diferença fenotípica observada in vivo seja resultado das alterações genéticas detectadas nos genes de virulência.

Les mitochondries sont généralement transmises de façon strictement maternelle. Chez les animaux, il existe une seule exception à ce mode de transmission mitochondriale : la transmission doublement uniparentale (DUI). La DUI est retrouvée uniquement chez certaines espèces de bivalves. Les mâles possèdent dans leurs gamètes le génome mitochondrial paternel, alors que les femelles ont dans leurs oeufs le génome mitochondrial maternel. Ces génomes possèdent respectivement m-orf ou f-orf, un cadre de lecture supplémentaire (outre les 13 codant pour les protéines mitochondriales de référence) potentiellement codant. La présence de ces ORF étant liée au sexe de l’animal, l’hypothèse a été avancée que ces protéines pourraient jouer un rôle dans le maintien de la DUI ou dans le déterminisme sexuel chez ces espèces. Ce projet consiste donc à mieux cerner les fonctions potentielles de ces orfs chez la moule bleue Mytilus edulis. Pour caractériser leur expression, nous avons procédé à des tests d’immunobuvardage sur des lysats de tissus gamétiques et somatiques mâles et femelles, ainsi qu’à des tests d’immunofluorescence sur des cultures cellulaires des deux sexes. Aussi, nous avons effectué des co-immunoprécipitation et des essais pull-down pour préciser les fonctions des protéines par l’entremise des partenaires d’interaction. Nous avons pu observer la présence de M-ORF dans les gonades mâles uniquement, plus particulièrement dans les mitochondries des spermatozoïdes et dans l’acrosome, et ce, uniquement durant la saison de reproduction des moules. F-ORF, cependant, était produite dans tous les tissus à tous les moments de l’année, encore une fois dans les mitochondries des cellules. Les deux protéines ont de nombreux partenaires d’interactions possibles, dont plusieurs sont liés à des processus spécifiques au sexe ou encore aux acides nucléiques. Les protéines M-ORF et F-ORF sont donc bien fonctionnelles. Leurs partenaires potentiels sont multiples, et d’autres essais doivent être effectués afin de préciser les fonctions des protéines. La présence dans l’acrosome de M-ORF est toutefois d’un grand intérêt en lien avec son rôle potentiel dans le DUI et le déterminisme sexuel. / Mitochondria are usually transmitted by strict maternal inheritance. In animals, there is only one exception to this: doubly uniparental inheritance (DUI). DUI can be found only in some bivalve species. Males have in their sperm a paternal mitochondrial genome whereas females have in their eggs the maternal mitochondrial genome. Both genomes possess an orf (other than the 13 coding for annotated mitochondrial proteins) that can potentially code for a protein, called respectively m-orf and f-orf. These genes are sex-specific in gametes, which brought the possibility that there is a link between the orfs and the maintenance of DUI or with sex determination in DUI species. Therefore, this project aims to have a better understanding of the potential functions of these proteins in the blue mussel Mytilus edulis. To demonstrate the proteins' existence, we did Western blot assays on gametic and somatic tissues from males and females, along with immunohistochemistry on cellular cultures of both sexes. To look for possible interaction partners, we did co-immunoprecipitation assays and pull-downs assays. Our results show expression of M-ORF in the male mantle only, more specifically in sperm mitochondria and acrosome. This is found only during the reproductive season of Mytilus edulis. However, F-ORF is expressed in all tissues all year in both sexes, in cells mitochondria. Both proteins have numerous possible interaction partners. Several are linked to sex-specific processes or to interactions with nucleic acids. Both M-ORF and F-ORF are expressed. Potential partners are multiple, and other assays have to be done to further ascertain these proteins' functions. However, the presence of M-ORF in acrosome is of great interest toward a potential function in DUI or in sex determination.

Motivation: As the human genome project progresses and some microbial and eukaryotic genomes are recognized, numerous biotechnological processes have attracted increasing number of biologists, bioengineers and computer scientists recently. Biotechnological processes profoundly involve production and analysis of highthroughput experimental data. Numerous sequence libraries of DNA and protein structures of a large number of micro-organisms and a variety of other databases related to biology and chemistry are available. For example, microarray technology, a novel biotechnology, promises to monitor the whole genome at once, so that researchers can study the whole genome on the global level and have a better picture of the expressions among millions of genes simultaneously. Today, it is widely used in many fields- disease diagnosis, gene classification, gene regulatory network, and drug discovery. For example, designing organism specific microarray and analysis of experimental data require combining heterogeneous computational tools that usually differ in the data format; such as, GeneMark for ORF extraction, Promide for DNA probe selection, Chip for probe placement on microarray chip, BLAST to compare sequences, MEGA for phylogenetic analysis, and ClustalX for multiple alignments. Solution: Surprisingly enough, despite huge research efforts invested in DNA array applications, very few works are devoted to computer-aided optimization of DNA array design and manufacturing. Current design practices are dominated by ad-hoc heuristics incorporated in proprietary tools with unknown suboptimality. This will soon become a bottleneck for the new generation of high-density arrays, such as the ones currently being designed at Perlegen [109]. The goal of the already accomplished research was to develop highly scalable tools, with predictable runtime and quality, for cost-effective, computer-aided design and manufacturing of DNA probe arrays. We illustrate the utility of our approach by taking a concrete example of combining the design tools of microarray technology for Harpes B virus DNA data.

Ogre elements represent a distinct group of Ty3/gypsy LTR retrotransposons occurring in a range of dicot plants. They are characterized by two specific features ? presence of long extra open reading frame in 5´ untranslated region with unknown function and a non-coding sequence containing several stop codons separating protease and reverse transcriptase domains which was proposed to be removed by splicing. This thesis describes the functional analysis of intron splicing in Ogre retrotransposons. Further, it investigates additional coding information not only in Ogre retrotransposons but in the whole group of Ty3/gypsy retroelements.

This thesis provides theoretical resources for the design of a new bioinformatics tool for transposon annotation with focus on their additional structural elements. There is a biological description of transposons, the mobile elements in DNA, their classification and structure. It further deals with the overview and classification of available transposon identification and annotation bioinformatics tools, description of function and implementation of a select few. Next we state the scheme of a new bioinformatics tool for LTR retrotransposon identification and annotation with a focus on extra ORFs and tandem repeats. The functionality of this new tool was tested on the A. thaliana genome. We identified 95 groups of conserved extra ORFs and 10 groups of conserved tandem repeats.