Efeito da suplementação com óleo de peixe, durante oito semanas, sobre o sistema imunitário inato de pacientes, pós-remoção tumoral e efeito in vitro do óleo de peixe sobre as células tumorais

Orientador: Luiz Claudio FernandesTese (doutorado) - Universidade Federal do Paraná, Setor de Ciências Biológicas, Programa de Pós-Graduação em Biologia Celular e Molecular. Defesa: Curitiba, 01/10/2008Inclui bibliografia e anexosO câncer é caracterizado por muitos passos, envolvendo alterações genéticas, que levam a progressiva transformação nas células normais, tornando-as malignas. Estimativas apontam para mais de 12 milhões de casos no mundo em 2008. Sendo que, aproximadamente, meio milhão será no Brasil. Na etiologia do câncer o ambiente tem papel relevante, sendo que alterações na dieta demonstraram ter grande importância. Vários estudos mostram que uma dieta rica em ácidos graxos poliinsaturados (AGPI) do tipo n-3 reduz a incidência de cânceres. O tratamento do câncer pode causar, geralmente, neutropenia. Isto leva a uma redução nas doses das terapias anticâncer e, na maior vulnerabilidade dos pacientes a infecções. Este estudo investigou se a suplementação com óleo de peixe, rico em AGPI n-3, é capaz de melhorar a atividade imunitária dos neutrófilos. Pacientes submetidos a tratamento quimioterápico foram divididos em dois grupos: suplementados com 2 g/dia de óleo de peixe durante oito semanas (T8 S) e os não suplementados (T8). Ambos os grupos tiveram o sangue coletado no primeiro dia de quimioterapia (ZERO) e também após as 8 semanas. Não houve diferença entre o peso corpóreo dos pacientes de ambos os grupos. No grupo T8 S houve: aumento da atividade fagocitária e da produção de ânion superóxido pelos neutrófilos quando comparado a T8; não houve alteração da retenção de vermelho neutro nem da produção de peróxido de hidrogênio em relação ao inicio da terapia anticâncer, porém quando comparado a T8 esta se elevou. Aumentou a incorporação de EPA e DHA e redução de ácido araquidônico (AA) nos neutrófilos e no plasma dos indivíduos T8 S, em relação ao início da quimioterapia. No plasma de T8 S não ocorreu alteração da concentração de colesterol total, LDL, VLDL e triacilgliceróis em relação ao período zero, porém estas foram mais elevadas nos indivíduos sem suplementação (T8). Ainda, em T8 S houve aumento do colesterol HDL e redução da lactatemia em relação aos demais grupos. In vitro foi observado redução da proliferação tumoral nas diluições de 1:5 e 1:10 nas culturas de células tumorais obtidas de mama e cólon;Cancer is a process characterized by many steps, which includes genetic alterations and gradual transformations in the normal cells, potentially leading them to malignancy. It is estimated that will be more than 12 million new cancer cases around the world in the year of 2008. For Brazil alone a half million cases are expected. The environment plays a key role in the etiology of cancer development, where diet habits are highlighted as main characters. Some studies show that diets rich in polyunsaturated fatty acids (PUFA) n-3 reduces the incidence of cancers. Cancer treatment can generally cause neutropenia. This study aimed to investigate whether fish oil, rich in PUFA n-3, supplementation to cancer patients’ plus tumor withdrawal is able to improve the function of blood neutrophils and the effect of fish oil in vitro in different tumor types, as well. Patients in chemotherapy treatment were randomly shared in to groups: intake of 2 g fish oil/day during eight weeks (T8 S) and not supplemented (T8). Blood was withdrawn right before the first chemotherapy session (ZERO) and 8 weeks after the beginning of the chemotherapy treatment. There were no differences in patients’ weights at the beginning of the trial. The T8 S group showed an increment of the phagocytic activity and anion superoxide production by neutrophils in relation to T8. No alterations in the neutral red uptake by secretion vesicles, neither in the production of hydrogen peroxide in the T8 S, when compared to the beginning of the anticancer therapy, were observed. However, all these parameters were increased in relation T8. The neutrophils and plasma’s concentration of EPA and DHA was increased by supplementation, otherwise the content of the arachidonic acid (AA) was reduced in relation to the beginning of the chemotherapy. There was no alteration in the plasma total cholesterol, LDL, VLDL and triacylglycerols in relation to the beginning of the supplementation; however these values were increased in the individuals without supplementation. In addition, there was an increase in the HDL cholesterol and a reduction in the lactatemia in the T8 S group. In vitro, a reduction in the cell proliferation using 1:5 and 1:10 dilutions into breast and colon tumors cells cultures was observed

A Reevaluation of the Native American MtDNA Genome Diversity and Its Bearing on the Models of Early Colonization of Beringia

The Americas were the last continents to be populated by humans, and their colonization represents a very interesting chapter in our species' evolution in which important issues are still contentious or largely unknown. One difficult topic concerns the details of the early peopling of Beringia, such as for how long it was colonized before people moved into the Americas and the demography of this occupation. A recent work using mitochondrial genome (mtDNA) data presented evidence for a so called “three-stage model” consisting of a very early expansion into Beringia followed by ∼20,000 years of population stability before the final entry into the Americas. However, these results are in disagreement with other recent studies using similar data and methods. Here, we reanalyze their data to check the robustness of this model and test the ability of Native American mtDNA to discriminate details of the early colonization of Beringia. We apply the Bayesian Skyline Plot approach to recover the past demographic dynamic underpinning these events using different mtDNA data sets. Our results refute the specific details of the “three-stage model”, since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes. Nevertheless, they are consistent with a moderate population bottleneck in Beringia associated with the Last Glacial Maximum followed by a strong population growth around 18,000 years ago as suggested by other recent studies. We suggest that this bottleneck erased the signals of ancient demographic history from recent Native American mtDNA pool, and conclude that the proposed early expansion and occupation of Beringia is an artifact caused by the misincorporation of non-Native American haplotypes

Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty

Phylogenetic inferences under the maximum likelihood criterion deploy heuristic tree search strategies to explore the vast search space. Depending on the input dataset, searches from different starting trees might all converge to a single tree topology. Often, though, distinct searches infer multiple topologies with large log-likelihood score differences or yield topologically highly distinct, yet almost equally likely, trees. Recently, Haag et al. introduced an approach to quantify, and implemented machine learning methods to predict, the dataset difficulty with respect to phylogenetic inference. Easy multiple sequence alignments (MSAs) exhibit a single likelihood peak on their likelihood surface, associated with a single tree topology to which most, if not all, independent searches rapidly converge. As difficulty increases, multiple locally optimal likelihood peaks emerge, yet from highly distinct topologies. To make use of this information, we introduce and implement an adaptive tree search heuristic in RAxML-NG, which modifies the thoroughness of the tree search strategy as a function of the predicted difficulty

Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers

South American racers of the tribe Philodryadini are a widespread and diverse group of Neotropical snakes with a complex taxonomic and systematic history. Recent studies failed to present a robust phylogenetic hypothesis for the tribe, mainly due to incomplete taxon sampling. Here we provide the most extensive molecular phylogenetic analysis of Philodryadini available so far, including 20 species (83% of the known diversity) from which six were not sampled previously. Our results reveal that Philodryadini is not monophyletic, but instead includes a central Andean clade formed by Philodryas simonsii, P. tachymenoides, and P. amaru, and a southern and cis-Andean clade including all remaining philodryadines. This discovery requires resurrection of two genera as well as erection of a new tribe of Xenodontinae for the central Andean clade. Within the southern and cis-Andean radiation, our analyses resolve a basal dichotomy separating two main lineages: Clade A, containing the Common Green Racers P. laticeps and P. viridissima and the South American Vine snakes P. georgeboulengeri and P. argentea; and Clade B, including the remaining species of Philodryas sensu stricto. We resurrect the genera Chlorosoma and Xenoxybelis to better represent the monophyly of lineages within the southern and cis-Andean cladeFil: Arredondo, Juan Camilo. Universidad Ces. Facultad de Ciencias y Biotecnologia.; ColombiaFil: Grazziotin, Felipe G.. Instituto Butantan; BrasilFil: Scrocchi Manfrini, Gustavo Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico - Tucumán. Unidad Ejecutora Lillo; ArgentinaFil: Trefaaut Rodriguez, Miguel. Universidade de Sao Paulo; BrasilFil: Bonatto, Sandro Luis. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Zaher, Husam. Museu de Zoologia - Usp; Brasi

Gone With the Water: The Loss of Genetic Variability in Black and Gold Howler Monkeys (Alouatta caraya) Due to Dam Construction

Black and gold howler monkeys (Alouatta caraya) inhabit several eco-regions in South America with the highest population densities in riverine forests. Dam construction for electricity production represents a severe human alteration of ecosystems with consequences for primate conservation. To evaluate the possible loss of genetic diversity in A. caraya, we analysed and compared the genetic structure of the species across 22 study sites in Argentina (14), Paraguay (1), and Brazil (7). Four of these study sites (referred to as flooded) were sampled before dam-linked flooding which most likely caused a drastic decline or functional extinction of these populations. The genetic variability of 256 individuals was evaluated using 10 autosomal microsatellites (STRs) and 112 individuals by sequencing a fragment of 507 bp of mtDNA. DNA was extracted from tissue, blood, and faecal samples. Significantly higher values of genetic variability were observed for the flooded populations both in mtDNA and STRs. Population genetic structure showed a K = 1, 2, or 5 depending on the method, separating Argentinian and Paraguayan sites from Brazilian sites and, in the case of K = 5, two clusters were mostly represented by flooded populations. Isolation-by-distance analyses showed that geographic distances influence gene flow. Analytical methods, such as Pairwise Fst’s and Nei’s and regression model of Harpending and Ward, were concordant in detecting significant genetic structuring between flooded and remaining sites examined. Although some sites have very low sample sizes, these samples are of great importance since these sampling sites are currently flooded. Our results show that the study sites where dams were built had the greatest genetic diversity. As A. caraya is currently severely threatened by yellow fever outbreaks, the remaining populations may be more vulnerable to disease outbreaks due to impoverished genetic variability. Accordingly, it is essential to implement management actions to conserve the remaining populations. Our results underline the importance for Environmental Impact Assessments (EIA) to include data on the genetic structure of species in the affected sites prior to their alteration or destruction. These genetic data are also remarkably important for determining where to relocate specific individuals to help avoid biodiversity loss.Fil: Oklander, Luciana Inés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Caputo, Mariela. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Genética y Biología Molecular; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; ArgentinaFil: Fernández, Gabriela Paula. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Bioinvestigaciones (Sede Pergamino); Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires. Universidad Nacional del Noroeste de la Provincia de Buenos Aires. Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires; ArgentinaFil: Jerusalinsky, Leandro. Centro Nacional de Pesquisa e Conservação de Primatas Brazileiros; BrasilFil: de Oliveira, Silviene F.. Universidade do Brasília; BrasilFil: Bonatto, Sandro Luis. Pontificia Universidade Católica do Rio Grande do Sul; BrasilFil: Corach, Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay; Argentina. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Departamento de Microbiología, Inmunología y Biotecnología. Cátedra de Genética y Biología Molecular; Argentin

A Bayesian Approach to Genome/Linguistic Relationships in Native South Americans

The relationship between the evolution of genes and languages has been studied for over three decades. These studies rely on the assumption that languages, as many other cultural traits, evolve in a gene-like manner, accumulating heritable diversity through time and being subjected to evolutionary mechanisms of change. In the present work we used genetic data to evaluate South American linguistic classifications. We compared discordant models of language classifications to the current Native American genome-wide variation using realistic demographic models analyzed under an Approximate Bayesian Computation (ABC) framework. Data on 381 STRs spread along the autosomes were gathered from the literature for populations representing the five main South Amerindian linguistic groups: Andean, Arawakan, Chibchan-Paezan, Macro-Je? , and Tupı´. The results indicated a higher posterior probability for the classification proposed by J.H. Greenberg in 1987, although L. Campbell?s 1997 classification cannot be ruled out. Based on Greenberg?s classification, it was possible to date the time of Tupı´-Arawakan divergence (2.8 kya), and the time of emergence of the structure between present day major language groups in South America (3.1 kya).Fil: Guerra Amorim, Carlos Eduardo. Departamento de Genética, Instituto de Biociencias. Universidade Federal do Rio Grande do Sul; Brazil;Fil: Bisso-Machado, Rafael. Departamento de Genética, Instituto de Biociencias. Universidade Federal do Rio Grande do Sul; Brazil;Fil: Ramallo, Virginia. UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL; . Consejo Nacional de Invest.cientif.y Tecnicas. Centro Cientifico Tecnol.conicet - la Plata. Instituto Multidiscipl.de Biologia Celular (i); ArgentinaFil: Bortolini, María Cátira. UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL;Fil: Bonatto, Sandro L.. PONTIFICIA UNIVERSIDADE CATOLICA DO RIO GRANDE DO SUL;Fil: Salzano, Francisco Mauro. UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL;Fil: Hunemeier, Tábita. UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL

How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data

In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population

Does Variation in Genome Sizes Reflect Adaptive or Neutral Processes? New Clues from Passiflora

One of the long-standing paradoxes in genomic evolution is the observation that much of the genome is composed of repetitive DNA which has been typically regarded as superfluous to the function of the genome in generating phenotypes. In this work, we used comparative phylogenetic approaches to investigate if the variations in genome sizes (GS) should be considered as adaptive or neutral processes by the comparison between GS and flower diameters (FD) of 50 Passiflora species, more specifically, within its two most species-rich subgenera, Passiflora and Decaloba. For this, we have constructed a phylogenetic tree of these species, estimated GS and FD of them, inferred the tempo and mode of evolution of these traits and their correlations, using both current and phylogenetically independent contrasted values. We found significant correlations among the traits, when considering the complete set of data or only the subgenus Passiflora, whereas no correlations were observed within Decaloba. Herein, we present convincing evidence of adaptive evolution of GS, as well as clues that this pattern is limited by a minimum genome size, which could reduce both the possibilities of changes in GS and the possibility of phenotypic responses to environment changes

An alternative model for the early peopling of Southern South America revealed by analyses of three mitochondrial DNA haplogroups

After several years of research, there is now a consensus that America was populated from Asia through Beringia, probably at the end of the Pleistocene. But many details such as the timing, route(s), and origin of the first settlers remain uncertain. In the last decade genetic evidence has taken on a major role in elucidating the peopling of the Americas. To study the early peopling of South America, we sequenced the control region of mitochondrial DNA from 300 individuals belonging to indigenous populations of Chile and Argentina, and also obtained seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies and are basically restricted to populations from the extreme south of South America. The estimated ages of D1g and B2l, about ∼ 15,000 years BP, together with their similar population dynamics and the high haplotype diversity shown by the networks, suggests that they probably appeared soon after the arrival of the first settlers and agrees with the dating of the earliest archaeological sites in South America (Monte Verde, Chile, 14,500 BP). One further sub-haplogroup, D4h3a5, appears to be restricted to Fuegian-Patagonian populations and reinforces our hypothesis of the continuity of the current Patagonian populations with the initial founders. Our results indicate that the extant native populations inhabiting South Chile and Argentina are a group which had a common origin, and suggest a population break between the extreme south of South America and the more northern part of the continent. Thus the early colonization process was not just an expansion from north to south, but also included movements across the Andes.Instituto Multidisciplinario de Biología Celula

Were sea level changes during the pleistocene in the south atlantic coastal plain a driver of speciation in Petunia (Solanaceae)?

Background: Quaternary climatic changes led to variations in sea level and these variations played a significant role in the generation of marine terrace deposits in the South Atlantic Coastal Plain. The main consequence of the increase in sea level was local extinction or population displacement, such that coastal species would be found around the new coastline. Our main goal was to investigate the effects of sea level changes on the geographical structure and variability of genetic lineages from a Petunia species endemic to the South Atlantic Coastal Plain. We employed a phylogeographic approach based on plastid sequences obtained from individuals collected from the complete geographic distribution of Petunia integrifolia ssp. depauperata and its sister group. We used population genetics tests to evaluate the degree of genetic variation and structure among and within populations, and we used haplotype network analysis and Bayesian phylogenetic methods to estimate divergence times and population growth. Results: We observed three major genetic lineages whose geographical distribution may be related to different transgression/regression events that occurred in this region during the Pleistocene. The divergence time between the monophyletic group P. integrifolia ssp. depauperata and its sister group (P. integrifolia ssp. integrifolia) was compatible with geological estimates of the availability of the coastal plain. Similarly, the origin of each genetic lineage is congruent with geological estimates of habitat availability. Conclusions: Diversification of P. integrifolia ssp. depauperata possibly occurred as a consequence of the marine transgression/regression cycles during the Pleistocene. In periods of high sea level, plants were most likely restricted to a refuge area corresponding to fossil dunes and granitic hills, from which they colonized the coast once the sea level came down. The modern pattern of lineage geographical distribution and population variation was established by a range expansion with serial founder effects conditioned on soil availability