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

Alteração precoce da matriz extracelular e parâmetros diastólicos na síndrome metabólica

FUNDAMENTOS: Síndrome Metabólica (SM) está associada com maior risco cardiovascular, porém não está claro se as alterações miocárdicas presentes nessa condição, como a disfunção diastólica, são consequência de mecanismos sistêmicos ou de efeitos diretos no miocárdio. OBJETIVOS: Comparar função diastólica, biomarcadores de atividade da Matriz Extracelular (MEC), inflamação e estresse hemodinâmico, em pacientes com SM e controles saudáveis. MÉTODOS: Pacientes com SM (n = 76) e controles saudáveis (n = 30) foram avaliados clinicamente e submetidos a exame ecocardiográfico e mensuração dos níveis plasmáticos de metaloproteinase-9 (MMP9), inibidor tecidual da metaloproteinase-1 (TIMP1), proteína C reativa ultrassensível (PCR-us), resistência insulínica (HOMA-RI) e NT-proBNP. RESULTADOS: O grupo SM apresentou menor onda E' (10,1 ± 3,0 cm/s vs. 11,9 ± 2,6 cm/s, p = 0,005), maiores valores para onda A (63,4 ± 14,1 vs. 53,1 ± 8,9 cm/s, p < 0,001), razão E/E'(8,0 ± 2,2 vs. 6,3 ± 1,2; p < 0,001), MMP9 (502,9 ± 237,1 vs. 330,4 ± 162,7 ng/mL, p < 0,001), PCR-us (p = 0,001) e HOMA-RI (p < 0,001), sem diferença nos níveis de TIMP1 e NT-proBNP. Na análise multivariada, apenas MMP9 foi independentemente associada a SM. CONCLUSÃO: Pacientes com SM apresentaram diferenças em medidas ecocardiográficas de função diastólica, na atividade da MEC, PCR-us e HOMA-RI em relação aos controles. Porém, somente MMP9 foi independentemente associada com SM. Esses achados sugerem que os efeitos precoces da SM sobre a atividade da MEC podem não ser detectados nas medidas ecocardiográficas de função diastólica usuais.

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

Influência da época de seleção do rebento sobre o desenvolvimento e produção da planta matriz de bananeira (Musa cavendishii) cultivar nanicão

No presente trabalho foram feitos os tratamentos: planta matriz sem rebentos; planta matriz com rebentos de janeiro, março e maio e testemunha com todos os rebentos, sendo estudada sua influência no desenvolvimento e produção da planta matriz de bananeira. Os resultados mostraram diferença significativa entre os tratamentos, com relação ao número de dias do plantio ao florescimento, ciclo de produção, número de folhas na colheita e peso do cacho. Não houve diferença significativa em relação ao diâmetro do pseudo-caule no florescimento e colheita, número de pencas e frutos.

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

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

Acumulação de matéria seca e micronutrientes pela planta matriz da bananeira cv. prata (Musa AAB, subgrupo prata) em diferentes estádios de desenvolvimento

Visando estabelecer a curva de crescimento da matéria seca, marcha de absorção, quantidade exportada e reciclada de boro, zinco e cobre, instalou-se um ensaio no Estado do Espírito Santo, em solo cambissólico distrófico com declividade média de 40%. Sorteou-se três plantas matrizes, bimensalmente até 300 dias e mensalmente até 465 dias após o plantio, que foram separadas em folha, pecíolo, pseudo-caule, rizoma, engaço, botão floral e fruto. Determinou-se a massa de matéria seca e o teor de micronutrientes destes órgãos, cujos dados foram ajustados em programa de regressão, obtendo-se as curvas de acumulação de matéria seca e de absorção dos micronutrientes. Dos resultados conclui-se que: a absorção do boro, zinco e cobre pelos órgãos estudados, acompanha a acumulação de matéria seca, exceto o cobre, no pecíolo; 70% dos micronutrientes analisados são absorvidos a partir de 240 dias após o plantio; ocorre uma razão de absorção de 5 Zn, 2,5 B, 1 Cu; podem ser exportados com a colheita cerca de 10% B, 5,5% Zn e 3% Cu.

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.

Use of DNA profiles for investigation using a simulated national DNA database: Part I. Partial SGM Plus profiles.

In traditional criminal investigation, uncertainties are often dealt with using a combination of common sense, practical considerations and experience, but rarely with tailored statistical models. For example, in some countries, in order to search for a given profile in the national DNA database, it must have allelic information for six or more of the ten SGM Plus loci for a simple trace. If the profile does not have this amount of information then it cannot be searched in the national DNA database (NDNAD). This requirement (of a result at six or more loci) is not based on a statistical approach, but rather on the feeling that six or more would be sufficient. A statistical approach, however, could be more rigorous and objective and would take into consideration factors such as the probability of adventitious matches relative to the actual database size and/or investigator's requirements in a sensible way. Therefore, this research was undertaken to establish scientific foundations pertaining to the use of partial SGM Plus loci profiles (or similar) for investigation.