Identificação e caracterização de sequências repetidas de DNA no genoma de peixes ciclídeos do gênero Cichla

Pós-graduação em Biologia Geral e Aplicada - IBB

Identificação e caracterização de sequências repetidas de DNA no genoma do ciclídeo Astronotus ocellatus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Low levels of genetic diversity depicted from mitochondrial DNA sequences in a heavily exploited marine fish (Cynoscion acoupa, Sciaenidae) from the Northern coast of Brazil

The acoupa weakfish (Cynoscion acoupa - Sciaenidae) is a marine species of croaker with estuarine-dependent behavior, found in the western Atlantic from Panama to Argentina. It is one of the most exploited food fish on the northern coast of Brazil. In this study, DNA sequences were determined from the entire control region (D-loop) of the mitochondrial genome of 297 individuals collected during seven different months between December 2003 and August 2005 on the northern coast of Brazil (Amapá and Pará). Genetic variability expressed by haplotype (h = 0,892) and nucleotide (p = 0,003) diversities were low compared to other heavily exploited marine fish species from the western Atlantic and eastern Asia. AMOVA depicted a lack of genetic structuring among the samples from different years, indicating the presence of a single stock of C. acoupa within the sample area. The possible reasons for the low levels of genetic diversity are discussed. These results demonstrate a need for the monitoring of C. acoupa harvesting and the preservation of the estuaries within its geographic range, considering that this large fish depends on estuarine ecosystems during part of its life cycle.

Evolutionary Relationships of the Triatoma matogrossensis Subcomplex, the Endemic Triatoma in Central-Western Brazil, Based on Mitochondrial DNA Sequences

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Repetitive DNA chromosomal organization in the cricket Cycloptiloides americanus: a case of the unusual X(1)X(2)0 sex chromosome system in Orthoptera

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Tandem repetitive DNA: Stabilität und Wirkung auf die Genexpression im transgenen System

Zusammenfassung In der vorliegenden Arbeit wurden unterschiedliche Eigenschaften von tandem repetitiver DNA (trDNA) analysiert. Drei der untersuchten trDNA-Familien (Cla-Elemente, Alu-Elemente, 1,688-Satelliten-DNA) stammen aus der genomischen DNA von Insekten, während ein trDNA-Cluster artifiziell aus Hsp70 Promotoren hergestellt wurde. Untersucht wurde die Stabilität dieser trDNA-Sequenzfamilien innerhalb eines Plasmidvektors in E. coli bzw. nach Integration der trDNA auch im Genom von D. melanogaster. Der Schwerpunkt der Arbeit liegt jedoch in der Analyse des Einflusses von trDNA auf die Expression eines benachbarten Reportergens in D. melanogaster.Ziel der Untersuchungen zur Stabilität war es, Eigenschaften von trDNA-Clustern und Mechanismen aufzuzeigen, die die Stabilität derselben in E. coli und im Genom von D. melanogaster beeinflussen. Mit Ausnahme der Alu-Elemente zeigen alle trDNA-Familien eine deutliche Instabilität in E. coli. Am Beispiel der Cla-Elemente wurde gezeigt, daß spezifische Eigenschaften der trDNA-Familie, wie etwa die sequenzbedingte Krümmung der Helixachse, keinen Einfluß auf die Stabilität des trDNA-Clusters haben, sondern die Orientierung des trDNA-Clusters innerhalb des Vektors ausschlaggebend ist. Ein entscheidender Faktor könnte die Orientierung des trDNA-Clusters relativ zur Wanderungsrichtung der Replikationsgabel in E. coli sein. Am Beispiel des trDNA-Clusters aus artifiziellen Hsp70 Promotoren konnte gezeigt werden, daß verschiedene Rekombinationssysteme an der Instabilität in E. coli beteiligt sind. Die meisten beobachteten Deletionen von trDNA sind RecA-abhängig. Zusätzlich findet jedoch in einem kleinen Teil der Plasmide auch eine RecA-unabhängige Rekombination statt. Sowohl in E. coli als auch in D. melanogaster wurde als vorherrschender Mechanismus der trDNA-Instabilität die homologe Rekombination identifiziert. TrDNA-Cluster, die in E. coli deutlich instabil sind, können jedoch im Genom von D. melanogaster weitgehend stabil sein. Auch Faktoren, die in E. coli die Stabilität eines trDNA-Clusters beeinflussen, wie etwa die Orientierung, zeigen in D. melanogaster keinen Einfluß auf die Stabilität der trDNA-Cluster. Ergebnisse aus Stabilitätsuntersuchungen in E. coli können damit nicht ohne Überprüfung auf andere Organismen übertragen werden. Im Hauptteil der Arbeit sollte geklärt werden, ob trDNA generell die Expression benachbarter Gene beeinflußt und welche Eigenschaften der trDNA für diesen inhibitorischen oder stimulierenden Effekt verantwortlich sind. Keine der untersuchten trDNA-Familien zeigt einen inhibitorischen Effekt auf ein benachbartes Reportergen. Entgegen dem Modell von Dorer und Henikoff (1994) führen trDNA-Cluster nicht per se zu der Entstehung von Heterochromatin. Die Ergebnisse der vorliegenden Arbeit zeigen, daß sowohl ein trDNA-Cluster aus Cla-Elementen als auch aus Hsp70 Promotor-Elementen eine deutliche Steigerung der Expression des miniwhite-Reportergens bewirken. Diese Steigerung ist für beide trDNA-Familien unabhängig von der chromosomalen Lage des Transgens im Euchromatin. In beiden Fällen ist der Effekt von der Orientierung des trDNA-Clusters abhängig und verstärkt sich mit wachsender Kopienzahl der trDNA-Einheiten. Während eines der trDNA-Cluster aus trDNA-Einheiten besteht, die bekanntermaßen eine Promotoraktivität aufweisen (Hsp70 Promotoren), war für die Cla-Elemente kein Einfluß auf die Expression eines benachbarten Gens bekannt. Damit wurde für eine trDNA-Familie aus Chironomus nachgewiesen, daß sie auf ein benachbartes Gen ähnlich wirkt wie zusätzliche Promotoren. Die experimentellen Befunde unterstützen ein Modell, demzufolge die Cla-Elemente in gleicher Weise wie tandem repetitive Promotoren auf ein benachbartes Gen expressionssteigernd wirken. Die TATA-Box ist für das Modell ein wichtiges Strukturelement, da diese in beiden expressionssteigernden DNA-Sequenzen der trDNA-Cluster vorkommt und ausschließlich in einer Orientierung wirkt. Das Modell besagt, daß durch die Verbindung einer offenen Chromatinstruktur mit korrekt orientierten Bindungsstellen für TBP der Aufbau von vollständigen Transkriptionskomplexen an den tandem repetitiven Promotoren initiiert wird. Einer Perlenschnur ähnlich wären die Transkriptionskomplexe direkt verfügbar, nachdem ein Transkriptionskomplex den Promotor zur Transkription verlassen hat (Abb. 32). Dies würde zu der beobachteten Steigerung der Expression des Reportergens sowohl durch die tandem repetitiven Hsp70 Promotoren als auch durch die Cla-Elemente führen.

Statistical methods for the analysis of DNA sequences: application to dinucleotide distribution in the human genome

Questa tesi si inserisce nell'ambito delle analisi statistiche e dei metodi stocastici applicati all'analisi delle sequenze di DNA. Nello specifico il nostro lavoro è incentrato sullo studio del dinucleotide CG (CpG) all'interno del genoma umano, che si trova raggruppato in zone specifiche denominate CpG islands. Queste sono legate alla metilazione del DNA, un processo che riveste un ruolo fondamentale nella regolazione genica. La prima parte dello studio è dedicata a una caratterizzazione globale del contenuto e della distribuzione dei 16 diversi dinucleotidi all'interno del genoma umano: in particolare viene studiata la distribuzione delle distanze tra occorrenze successive dello stesso dinucleotide lungo la sequenza. I risultati vengono confrontati con diversi modelli nulli: sequenze random generate con catene di Markov di ordine zero (basate sulle frequenze relative dei nucleotidi) e uno (basate sulle probabilità di transizione tra diversi nucleotidi) e la distribuzione geometrica per le distanze. Da questa analisi le proprietà caratteristiche del dinucleotide CpG emergono chiaramente, sia dal confronto con gli altri dinucleotidi che con i modelli random. A seguito di questa prima parte abbiamo scelto di concentrare le successive analisi in zone di interesse biologico, studiando l’abbondanza e la distribuzione di CpG al loro interno (CpG islands, promotori e Lamina Associated Domains). Nei primi due casi si osserva un forte arricchimento nel contenuto di CpG, e la distribuzione delle distanze è spostata verso valori inferiori, indicando che questo dinucleotide è clusterizzato. All’interno delle LADs si trovano mediamente meno CpG e questi presentano distanze maggiori. Infine abbiamo adottato una rappresentazione a random walk del DNA, costruita in base al posizionamento dei dinucleotidi: il walk ottenuto presenta caratteristiche drasticamente diverse all’interno e all’esterno di zone annotate come CpG island. Riteniamo pertanto che metodi basati su questo approccio potrebbero essere sfruttati per migliorare l’individuazione di queste aree di interesse nel genoma umano e di altri organismi.

PCR identification of HIV-1 DNA sequences in brain tissue of patients with AIDS encephalopathy.

We analyzed brain tissue from 39 patients for the presence of proviral HIV-1 sequences, using the polymerase chain reaction (PCR) for the amplification of segments of the viral LTR and gag genes. A novel primer extension procedure allowed the detection of a single HIV-1 copy in 1 micrograms DNA. We detected proviral HIV-1 DNA in 16 of 25 brain samples from AIDS patients. Semiquantitative evaluation of the amplified DNAs indicated considerable variation in viral load. Highest levels of proviral DNA were present in brain samples from six patients with clinical evidence of HIV-associated cognitive/motor complex and the histopathologic correlate of HIV leukoencephalopathy or HIV encephalitis. An additional 11 brain samples contained smaller amounts of proviral DNA. In these patients, clinical data were inconclusive regarding the diagnosis of HIV-1 encephalopathy and histopathologically there was no evidence of HIV-1-induced tissue lesions. In nine of 25 seropositive patients with AIDS (36%), brain samples scored negative or did not contain an unequivocal signal indicating the presence of proviral DNA. HIV-1 sequences were not detected in any of 14 control brain samples from HIV-1 seronegative patients. Our data indicate that HIV-1 is present in the central nervous system of the majority (two thirds) of AIDS patients and that the highest levels of proviral DNA in brain tissue are associated with HIV encephalopathy.

A DNA probe for the detection of Dicrocoelium dendriticum in ants of Formica spp. and Lasius spp

Repetitive DNA sequences present in the genome of Dicrocoelium dendriticum were identified by hybridization of genomic DNA that had been digested with different restriction enzymes with 32P-labeled genomic D. dendriticum DNA. DNA fragments containing repetitive sequences were isolated from PstI-digested D. dendriticum DNA and were subcloned into a plasmid vector. Plasmids containing repetitive sequences were identified by colony hybridization. One of these plasmids, designated Ddr-IV, was isolated and used as a probe in further studies. Ddr-IV is specific for D. dendriticum since it does not hybridize to DNA isolated from other trematodes. In addition, Ddr-IV was capable of detecting D. dendriticum metacercariae in ants (Formica cunicularia, F. rufibarbis, and Lasius sp.), which act as second intermediate hosts in the parasite's life cycle. Since metacercariae constitute the infectious stage of the parasite for grazing animals, Ddr-IV will provide a useful tool for epidemiology studies of dicrocoeliosis.

MATHEMATICAL STUDIES ON THE EVOLUTIONARY CHANGE OF DNA SEQUENCES

With the aim of understanding the mechanism of molecular evolution, mathematical problems on the evolutionary change of DNA sequences are studied. The problems studied and the results obtained are as follows: (1) Estimation of evolutionary distance between nucleotide sequences. Studying the pattern of nucleotide substitution for the case of unequal substitution rates, a new mathematical formula for estimating the average number of nucleotide substitutions per site between two homologous DNA sequences is developed. It is shown that this formula has a wider applicability than currently available formulae. A statistical method for estimating the number of nucleotide changes due to deletion and insertion is also developed. (2) Biases of the estimates of nucleotide substitutions obtained by the restriction enzyme method. The deviation of the estimate of nucleotide substitutions obtained by the restriction enzyme method from the true value is investigated theoretically. It is shown that the amount of the deviation depends on the nucleotides in the recognition sequence of the restriction enzyme used, unequal rates of substitution among different nucleotides, and nucleotide frequences, but the primary factor is the unequal rates of nucleotide substitution. When many different kinds of enzymes are used, however, the amount of average deviation is generally small. (3) Distribution of restriction fragment lengths. To see the effect of undetectable restriction fragments and fragment differences on the estimate of nucleotide differences, the theoretical distribution of fragment lengths is studied. This distribution depends on the type of restriction enzymes used as well as on the relative frequencies of four nucleotides. It is shown that undetectability of small fragments or fragment differences gives a serious underestimate of nucleotide substitutions when the length-difference method of estimation is used, but the extent of underestimation is small when the site-difference method is used. (4) Evolutionary relationships of DNA sequences in finite populations. A mathematical theory on the expected evolutionary relationships among DNA sequences (nucleons) randomly chosen from the same or different populations is developed under the assumption that the evolutionary change of nucleons is determined solely by mutation and random genetic drift. . . . (Author's abstract exceeds stipulated maximum length. Discontinued here with permission of author). UMI ^

Minimal DNA sequences that control the cell lineage-specific expression of the pro$\alpha$2(I) collagen promoter in transgenic mice

The pattern of expression of the pro$\alpha$2(I) collagen gene is highly tissue-specific in adult mice and shows its strongest expression in bones, tendons, and skin. Transgenic mice were generated harboring promoter fragments of the mouse pro$\alpha$2(I) collagen gene linked to the Escherichia coli $\beta$-galactosidase or firefly luciferase genes to examine the activity of these promoters during development. A region of the mouse pro$\alpha$2(I) collagen promoter between $-$2000 and +54 exhibited a pattern of $\beta$-galactosidase activity during embryonic development that corresponded to the expression pattern of the endogenous pro$\alpha$2(I) collagen gene as determined by in situ hybridization. A similar pattern of activity was also observed with much smaller promoter fragments containing either 500 or 350 bp of upstream sequence relative to the start of transcription. Embryonic regions expressing high levels of $\beta$-galactosidase activity included the valves of the developing heart, sclerotomes, meninges, limb buds, connective tissue fascia between muscle fibers, osteoblasts, tendon, periosteum, dermis, and peritoneal membranes. The pattern of $\beta$-galactosidase activity was similar to the extracellular immunohistochemical localization of transforming growth factor-$\beta$1 (TGF-$\beta$1). The $-$315 to $-$284 region of the pro$\alpha$2(I) collagen promoter was previously shown to mediate the stimulatory effects of TGF-$\beta$1 on the pro$\alpha$2(I) collagen promoter in DNA transfection experiments with cultured fibroblasts. A construct containing this sequence tandemly repeated 5$\sp\prime$ to both a very short $\alpha$2(I) collagen promoter ($-$40 to +54) and a heterologous minimal promoter showed preferential activity in tail and skin of 4-week old transgenic mice. The pattern of expression mimics that of the $-$350 to +54 pro$\alpha$2(I) collagen promoter linked to a luciferase reporter gene in transgenic mice. ^

Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences

Homobasidiomycete fungi display many complex fruiting body morphologies, including mushrooms and puffballs, but their anatomical simplicity has confounded efforts to understand the evolution of these forms. We performed a comprehensive phylogenetic analysis of homobasidiomycetes, using sequences from nuclear and mitochondrial ribosomal DNA, with an emphasis on understanding evolutionary relationships of gilled mushrooms and puffballs. Parsimony-based optimization of character states on our phylogenetic trees suggested that strikingly similar gilled mushrooms evolved at least six times, from morphologically diverse precursors. Approximately 87% of gilled mushrooms are in a single lineage, which we call the “euagarics.” Recently discovered 90 million-year-old fossil mushrooms are probably euagarics, suggesting that (i) the origin of this clade must have occurred no later than the mid-Cretaceous and (ii) the gilled mushroom morphology has been maintained in certain lineages for tens of millions of years. Puffballs and other forms with enclosed spore-bearing structures (Gasteromycetes) evolved at least four times. Derivation of Gasteromycetes from forms with exposed spore-bearing structures (Hymenomycetes) is correlated with repeated loss of forcible spore discharge (ballistospory). Diverse fruiting body forms and spore dispersal mechanisms have evolved among Gasteromycetes. Nevertheless, it appears that Hymenomycetes have never been secondarily derived from Gasteromycetes, which suggests that the loss of ballistospory has constrained evolution in these lineages.

Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes

The positions of ≈4,800 individual miniature inverted-repeat transposable element (MITE)-like repeats from four families were mapped on the Caenorhabditis elegans chromosomes. These families represent 1–2% of the total sequence of the organism. The four MITE families (Cele1, Cele2, Cele14, and Cele42) displayed distinct chromosomal distribution profiles. For example, the Cele14 MITEs were observed clustering near the ends of the autosomes. In contrast, the Cele2 MITEs displayed an even distribution through the central autosome domains, with no evidence for clustering at the ends. Both the number of elements and the distribution patterns of each family were conserved on all five C. elegans autosomes. The distribution profiles indicate chromosomal polarity and suggest that the current genetic and physical maps of chromosomes II, III, and X are inverted with respect to the other chromosomes. The degree of conservation of both the number and distribution of these elements on the five autosomes suggests a role in defining specific chromosomal domains.