Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities

Dissertação de mestrado em Molecular Genetics

Biblioteca de referência de DNA barcodes de bivalves (Mollusca: Bivalvia) e gastrópodes (Mollusca: Gastropoda) da costa Portuguesa

Dissertação de mestrado em Ecologia

DNA barcodes de peixes marinhos da Europa: compilação de uma biblioteca de referência validada e investigação de padrões de divergência genética

Dissertação de mestrado em Ecologia

Hipometilação do LINE-1 está Associada ao Risco de Doença Cardíaca Coronariana na População Chinesa

Fundamentos: O nível de metilação global do ADN de leucócitos no sangue tem sido associado ao risco de doença arterial coronariana (DAC), com resultados inconsistentes em diferentes populações. Faltam dados semelhantes da população chinesa, onde diferentes fatores genéticos, de estilo de vida e ambientais podem afetar a metilação do ADN e sua relação com o risco de DCC. Objetivos: Analisar se a metilação global está associada ao risco de doença coronariana na população chinesa. Métodos: Foram incluídos um total de 334 casos de DCC e 788 controles saudáveis. A metilação global do ADN de leucócitos de sangue foi estimada por meio da análise das repetições do LINE-1 usando pirosequenciamento de bissulfito. Resultados: Em uma análise inicial restrita aos controles o nível do LINE-1 diminui significativamente com a idade avançada, colesterol total elevado, e diagnóstico de diabetes. Na análise de caso-controle, a redução da metilação do LINE-1 foi associada ao aumento do risco de DCC, tendo a análise por quartil revelado uma odds ratio (IC 95%) de 0,9 (0,6-1,4), 1,9 (1,3-2,9) e 2,3 (1,6 3.5) para o terceiro, segundo e primeiro (o mais baixo) quartil (P da tendência < 0,001), respectivamente, em comparação com o quarto (o mais alto) quartil. A metilação inferior (< mediana) do LINE-1 esteve associada a 2,2 vezes (IC 95% = 1,7-3,0) o aumento de risco de doença coronariana. As estimativas de risco de DCC menores relacionadas com o LINE-1 tenderam a ser mais fortes entre os indivíduos com maior tercil de homocisteína (P interação = 0,042) e naqueles com diagnóstico de hipertensão arterial (P interação = 0,012). Conclusão: A hipometilação do LINE-1 está associada ao risco de doença coronariana na população chinesa. Fatores de risco de DCC potenciais tais como a idade avançada, colesterol total elevado, e diagnóstico de diabetes podem ter impacto na metilação global do ADN, exercendo, portanto, o seu efeito sobre o risco de doença coronariana.

Kinetik des Auftretens fetaler DNA im mütterlichen Blut während und nach der Schwangerschaft

Magdeburg, Univ., Med. Fak., Diss., 2012

Logische Modellierung der DNA-Schadens-Antwort in humanen Epithelzellen

Magdeburg, Univ., Fak. für Naturwiss., Diss., 2013

mRNA metabolism: nonsense mediated mRNA decay as a tool for gene therapy and the role of human DIS3L2 in transcript degradation

Tese de mestrado em Biologia Humana e Ambiente, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2015

Untersuchungen molekularer Mechanismen und funktioneller Konsequenzen der DNA-Schädigung durch oxidativen Stress in Tumorzellen

Magdeburg, Univ., Fak. für Naturwiss., Diss., 2014

Estudos dos agrupamentos vegetativos relacionados com as áreas onde foram efetuadas as pesquisas sôbre a febre amarela silvestre no Município de Passos, Estado de Minas Gerais

The work reported here was carried-out on the invitation of Dr. Henry Kumm, Director of the Rockefeller Foundation, and by appointment from Dr. Henrique Aragão, Director of the Instituto Oswaldo Cruz. It was done during the investigation of sylvan yellow fever, in June 1947, with a view to establishing the phyto-ecological conditions of the county of Passos. The pe¬riod was, however, too short for definite conclusions to be reached. Thanks are due to Dr. O. R. Causey, Chief of Research on Yellow Fever for transpor¬tation and other help. THE REGIONAL VEGETATION. Aerial photographs of the county of Passos shoto that it is covered by three great types of vegetation: Rain Forest, Secondary Pasture Land and Scrub.1 Detailed investigation, however, brings out the fact that these correspond to different seres; furthermore, each type presents not only the specific, characteristics of the biological form dominant for the climate, but also are at various stages, which express HABITATS differing from those of the normal sere. The phytogeographic survey of the region shows that most of it is now covered by secondary pasture land (disclimax) in which Melinis minutiflora, v. "fat grass" (fig. 1), predominates. The mosaic of Rain Forest and of small patches of Scrub reveals the effects of human intervention (BARRETO, H. L. de Mello 1); consequently, all the formations have to be regarded as secon¬dary, though some of them probably include relicts of the primitive climax (WARMING, E. 2). On close examination, the Scrub cannot be considered as the climax, because of the following facts: 1. In the zone of Rain-Forest stretches of forest are present in very varied topographic conditions and the reconstitution of the associations show that man has destroyed an ecological unit (fig. 2). 2. In the zone of Scrub the characteristic patches are small. The banks of rivers and brooks, the valleys and ravine and whatever the soil has retained some humidity, is being invaded fry Rain Forest, which seems to be growing under optimum conditions. The Scrub is thus limited to small belts on the calcareous mountains and on sandy soils with alcaline depths (pH abo¬ve 7) which do not retain enough moisture for the Rain Forest that is progres¬sively restricting the area occupied by Scrub. In view of the topographic and present climatic conditions the Rain Forest must consequently be regarded as the regional climax. The presence of ecologically contradictory elements and associations shows that the real problem is that of the fluctuations of the climate of Passos or even of Minas Geraes during the quaternary and recent periods (DAN-SEREAU, P. : 3), a subject on which little is known and which is tied to the evolution of the climate of Brazil (OLIVEIRA, E. : 4) . The transformation of Scrub into Rain Forest has been - observed by the author before, in other parts of Brazil (VELOSO, PL P.: 5) . It seems probable that the Rio Grande has also greatly influenced the change of the regional vegetation, by invading areas of Scrub and dislocating the limit of the Pluvial climate towards the Canastra Range, though there are remnants of Scrub (postclimax) transfor¬med into secondary open country (disclimax, fig. 5) by human devastation and the setting of fire to the land. VEGETATION GROUPS OF THE PLUVIAL TYPE. The map of the region also shows that at the present time the small patches of forest (whether devasted or intact) occupy the least accessible places, such as valleys, peaks and abrupt slopes (fig. 2). Even these are now being destroyed, so that in the near future this forested region will be en¬tirely reduced to poor pasture land unless energetic measures of conservation are undertaken in time. The Special Service for Prophylaxis against Yellow Fever installed two of their four Stations for the Capture of Mosquitos in this area, one of them at Batatal and the other at Cachoeira, which have separate formations each of them composed of several associations. Other vegetation formations were also analysed, from the synecological point of view, so as to ascertain of which degree of succession their associations belong. These phytosociological sur¬veys give an idea of the principal characteristics of each station. BATATAL FORMATION. The abrupt nature of the valley has rendered this location inappropriate for agricultural purposes since colonial times. The relict of the primitive forest climax saved by this circumstance has expanded gradually to zones whose paedologic conditions favour the eatablishment of mesophilous species. The aerial photograph shows two small stretches of forest, one apparently primi¬tive, the other composed of associations belonging to the subclimax of the subsere. CACHOEIRA FORMATION. Aerial photographs show that this station is crossed by a small river, which divides it into two separate parts. The first, which presents ecological conditions similar, though not identical to those of Batatal, is favoured by topography and apparently remains primitive forest. Though the topography of the other, on the whole, favours the establishment of groups belonging to the normal sere of the climax, is has been partly devastated recently and the aspect of the associations has been completely modified. It was is this part that the four posts for the capturing of mosquitos were set up. The first forest is favoured by deposition of organic matter, washed out from the nearby devasted areas by torrential rains, and thus provides, an appropriate HABITAT for the climax species with certain hygrophilous trends of the ecological quasiclimax type. This association seems to have reached a biological equilibrium, as the dominates. Gallesia gorarema and Cariniana legalis (fig. 10), present an optimum vitality with a vigorous habit and a normal evolutionary cycle. The Cariniantum legalis Gallesiosum equilibrium, corresponds however, to a provisory association, because if the moving of soil by torrential rains should cease it would become possible…

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Array de DNA per identificar espècies de Fusarium: ampliació d'un array existent per incloure espècies del Sud d'Europa

Projecte de recerca elaborat a partir d’una estada al Department for Feed and Food Hygiene del National Veterinary Institute, Noruega, entre novembre i desembre del 2006. Els grans de cereal poden estar contaminats amb diferents espècies de Fusarium capaces de produir metabolits secundaris altament tòxics com trichotecenes, fumonisines o moniliformines. La correcta identificació d’aquestes espècies és de gran importància per l’assegurament del risc en l’àmbit de la salut humana i animal. La identificació de Fusarium en base a la seva morfologia requereix coneixements taxonòmics i temps; la majoria dels mètodes moleculars permeten la identificació d’una única espècie diana. Per contra, la tecnologia de microarray ofereix l’anàlisi paral•lel d’un alt nombre de DNA dianes. En aquest treball, s’ha desenvolupat un array per a la identificació de les principals espècies de Fusarium toxigèniques del Nord i Sud d’Europa. S’ha ampliat un array ja existent, per a la detecció de les espècies de Fusarium productores de trichothecene i moniliformina (predominants al Nord d’Europa), amb l’addició de 18 sondes de DNA que permeten identificar les espècies toxigèniques més abundants al Sud d’Europa, les qual produeixen majoritàriament fumonisines. Les sondes de captura han estat dissenyades en base al factor d’elongació translació- 1 alpha (TEF-1alpha). L’anàlisi de les mostres es realitza mitjançant una única PCR que permet amplificar part del TEF-1alpha seguida de la hibridació al xip de Fusarium. Els resultats es visualitzen mitjançant un mètode de detecció colorimètric. El xip de Fusarium desenvolupat pot esdevenir una eina útil i de gran interès per a l’anàlisi de cereals presents en la cadena alimentària.

A glycine-arginine domain in control of the human MRE11 DNA repair protein.

Human MRE11 is a key enzyme in DNA double-strand break repair and genome stability. Human MRE11 bears a glycine-arginine-rich (GAR) motif that is conserved among multicellular eukaryotic species. We investigated how this motif influences MRE11 function. Human MRE11 alone or a complex of MRE11, RAD50, and NBS1 (MRN) was methylated in insect cells, suggesting that this modification is conserved during evolution. We demonstrate that PRMT1 interacts with MRE11 but not with the MRN complex, suggesting that MRE11 arginine methylation occurs prior to the binding of NBS1 and RAD50. Moreover, the first six methylated arginines are essential for the regulation of MRE11 DNA binding and nuclease activity. The inhibition of arginine methylation leads to a reduction in MRE11 and RAD51 focus formation on a unique double-strand break in vivo. Furthermore, the MRE11-methylated GAR domain is sufficient for its targeting to DNA damage foci and colocalization with gamma-H2AX. These studies highlight an important role for the GAR domain in regulating MRE11 function at the biochemical and cellular levels during DNA double-strand break repair.

Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts.

A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in order to evaluate the distribution of mitochondrial DNA (mtDNA) heteroplasmy amongst the hairs of an individual who displays point heteroplasmy in blood and buccal cells. A second aim of the exercise was to study reproducibility of mtDNA sequencing of hairs between laboratories using differing chemistries, further to the first mtDNA reproducibility study carried out by the EDNAP group. Laboratories were asked to type 2 sections from each of 10 hairs, such that each hair was typed by at least two laboratories. Ten laboratories participated in the study, and a total of 55 hairs were typed. The results showed that the C/T point heteroplasmy observed in blood and buccal cells at position 16234 segregated differentially between hairs, such that some hairs showed only C, others only T and the remainder, C/T heteroplasmy at varying ratios. Additionally, differential segregation of heteroplasmic variants was confirmed in independent extracts at positions 16093 and the poly(C) tract at 302-309, whilst a complete A-G transition was confirmed at position 16129 in one hair. Heteroplasmy was observed at position 16195 on both strands of a single extract from one hair segment, but was not observed in the extracts from any other segment of the same hair. Similarly, heteroplasmy at position 16304 was observed on both strands of a single extract from one hair. Additional variants at positions 73, 249 and the HVII poly(C) region were reported by one laboratory; as these were not confirmed in independent extracts, the possibility of contamination cannot be excluded. Additionally, the electrophoresis and detection equipment used by this laboratory was different to those of the other laboratories, and the discrepancies at position 249 and the HVII poly(C) region appear to be due to reading errors that may be associated with this technology. The results, and their implications for forensic mtDNA typing, are discussed in the light of the biology of hair formation.