Hijacking, hitchhiking and burglary behaviors of pelagic octopuses

Cephalopod International Advisory Council Conference: Recent Advances in Cephalopod Science, November 6-14, 2015, Hakodate, Japan.

Hitchhiking Trypanosoma cruzi minicircle DNA affects gene expression in human host cells via LINE-1 retrotransposon

The horizontal transfer of Trypanosoma cruzi mitochondrial minicircle DNA to the genomes of naturally infected humans may play an important role in the pathogenesis of Chagas disease. Minicircle integrations within LINE-1 elements create the potential for foreign DNA mobility within the host genome via the machinery associated with this retrotransposon. Here we document integration of minicircle DNA fragments in clonal human macrophage cell lines and their mobilization over time. The movement of an integration event in a clonal transfected cell line was tracked at three months and three years post-infection. The minicircle sequence integrated into a LINE-1 retrotransposon; one such foreign fragment subsequently relocated to another genomic location in association with associated LINE-1 elements. The p15 locus was altered at three years as a direct effect of minicircle/LINE-1 acquisition, resulting in elimination of p15 mRNA. Here we show for the first time a molecular pathology stemming from mobilization of a kDNA/LINE-1 mutation. These genomic changes and detected transcript variations are consistent with our hypothesis that minicircle integration is a causal component of parasite-independent, autoimmune-driven lesions seen in the heart and other target tissues associated with Chagas disease.

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, interpopulation differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.

Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae).

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species-rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species-rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non-neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.

Ampliació i millora d'un sistema avançat de compartició de vehicle

Actualment el cotxe és un dels mitjans de transport més utilitzats,comportant problemes de trànsit i aparcament, contaminació acústica i ambiental i una important despesa econòmica. Ja fa uns anys, i davant d'aquesta nova realitat, va sorgir la idea del carpooling, un sistema de transport privat compartit protagonitzat per particulars i que pot esdevenir una molt bona alternativa de mobilitat sostenible. Tot i això, els projectes de carpooling són actualment poc dinàmics I majoritàriament acotats a portals web. Molt pocs disposen de portals adaptats adispositius mòbils i, encara menys, disposen d’aplicacions natives. Amb tot, avui en dia elsaparells mòbils, ja siguin smartphones o PDAs, obren un ventall de possibilitats encara noexplotat en aquest camp.Per altra banda, compartir un viatge amb algú desconegut i de qui no se’n tenenreferències és quelcom que ens fa sentir insegurs, però això es pot resoldre gràciesal trust i reputation, un sistema basat en les valoracions dels usuaris que ja han viscutl’experiència, i que per tant, ens permet conèixer la reputació i confiança de que disposaun usuari dins el sistema. A tots aquests punts, cal afegir-hi la importància que té avui endia rebre en tot moment una informació clara i actualitzada.Aquest projecte vol exprimir aquestes oportunitats donant una plataforma d’accésusable per aquesta mena de dispositius, per tal de que no hi hagi cap barrera per estarconnectat al sistema en qualsevol lloc i moment. A més a més, aquests terminals donen lapossibilitat de saber la seva localització en temps real, cosa que pot resultar molt útil per agent que comparteix viatges i que s’està movent d’un lloc a un altre.Així doncs, partint de totes aquestes possibilitats de millora, es van idear una sèried’estratègies per a un projecte de carpooling ja existent anomenat e-hitchhiking, dotant aaquest sistema d’una major comunicació, protecció i seguretat per a que l’experiència del’usuari sigui molt més gratificant, on a més, hi ha la possibilitat de rebre informaciótotalment veraç i actualitzada en certs dispositius mòbils.Per tant la motivació principal per dur a terme aquest projecte és, a part de lesesmentades anteriorment, la de dotar un sistema de compartició de vehicle d’un majordinamisme, més realisme, més fiabilitat i fer-lo més sociable. El sistema s’implanta oficialment al setembre del 2011 amb la creació de lacomunitat UdG

Análise das ações preventivas executadas pelo DETRAN/AM e imtrans na cidade de Manaus durante o carnaval dos anos de 2007 e 2008: um estudo de caso

Atualmente, os acidentes de trânsito têm se constituído como um grave problema sócio-econômico e de saúde pública, sendo responsáveis por 1,2 milhões de óbitos e 50 milhões de feridos por ano em todo mundo. Muitas são as causas que geram esses acidentes. O Brasil é tido como um dos líderes mundiais em acidentes de trânsito há mais de 30 anos. O custo desses acidentes de trânsito é muito elevado. Manaus, é uma cidade da Região Norte, considerada pólo regional, é uma das 49 aglomerações urbanas do país, e apresenta uma população de 1.688.524 habitantes aproximadamente. Como a maioria dos municípios brasileiros, o trânsito urbano é violento, vez que apresenta um alto índice de acidentes de trânsito. Durante os anos de 2007 e 2008, o Departamento Estadual de Trânsito do Amazonas(Detran/AM), colocou em funcionamento o programa educativo de prevenção de acidentes de trânsito denominado “Carona Solidária”, conhecido popularmente como “Disk Pileque”. Este trabalho consistiu em analisar as ações preventivas levadas a efeito durante os períodos carnavalescos de 2007 e 2008, com a execução do carona solidária, demonstrando sua efetividade na redução de acidentes de trânsito com vítimas fatais. A execução do programa se deu através do próprio Detran, que montou esquema no sentido de proporcionar melhor atendimento ao cidadão. Os dados foram obtidos através de relatórios emitidos pelo Detran/AM, de sorte que mostrassem as especificidades relacionadas aos acidentes. Os resultados mostraram que a execução do programa foi positiva, pois, o número de solicitações feitas superou as expectativas, gerando com isso redução de custos e principalmente redução da quantidade de vítimas fatais na cidade por ocasião dos períodos analisados.Foi sugerido que o programa seja executado em outros períodos do ano.

Genetic diversity of the HLA-G coding region in Amerindian populations from the Brazilian Amazon: a possible role of natural selection

HLA-G has an important role in the modulation of the maternal immune system during pregnancy, and evidence that balancing selection acts in the promoter and 3′UTR regions has been previously reported. To determine whether selection acts on the HLA-G coding region in the Amazon Rainforest, exons 2, 3 and 4 were analyzed in a sample of 142 Amerindians from nine villages of five isolated tribes that inhabit the Central Amazon. Six previously described single-nucleotide polymorphisms (SNPs) were identified and the Expectation-Maximization (EM) and PHASE algorithms were used to computationally reconstruct SNP haplotypes (HLA-G alleles). A new HLA-G allele, which originated in Amerindian populations by a crossing-over event between two widespread HLA-G alleles, was identified in 18 individuals. Neutrality tests evidenced that natural selection has a complex part in the HLA-G coding region. Although balancing selection is the type of selection that shapes variability at a local level (Native American populations), we have also shown that purifying selection may occur on a worldwide scale. Moreover, the balancing selection does not seem to act on the coding region as strongly as it acts on the flanking regulatory regions, and such coding signature may actually reflect a hitchhiking effect.Genes and Immunity advance online publication, 3 October 2013; doi:10.1038/gene.2013.47.

Balancing immunity and tolerance: genetic footprint of natural selection in the transcriptional regulatory region of HLA-G

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

The patterns of genomic divergence during ecological speciation are shaped by a combination of evolutionary forces. Processes such as genetic drift, local reduction of gene flow around genes causing reproductive isolation, hitchhiking around selected variants, variation in recombination and mutation rates are all factors that can contribute to the heterogeneity of genomic divergence. On the basis of 60 fully sequenced three-spined stickleback genomes, we explore these different mechanisms explaining the heterogeneity of genomic divergence across five parapatric lake and river population pairs varying in their degree of genetic differentiation. We find that divergent regions of the genome are mostly specific for each population pair, while their size and abundance are not correlated with the extent of genome-wide population differentiation. In each pair-wise comparison, an analysis of allele frequency spectra reveals that 25–55% of the divergent regions are consistent with a local restriction of gene flow. Another large proportion of divergent regions (38–75%) appears to be mainly shaped by hitchhiking effects around positively selected variants. We provide empirical evidence that alternative mechanisms determining the evolution of genomic patterns of divergence are not mutually exclusive, but rather act in concert to shape the genome during population differentiation, a first necessary step towards ecological speciation.

Complexities in the genetic structure of Anopheles gambiae populations in west Africa as revealed by microsatellite DNA analysis

Chromosomal forms of Anopheles gambiae, given the informal designations Bamako, Mopti, and Savannah, have been recognized by the presence or absence of four paracentric inversions on chromosome 2. Studies of karyotype frequencies at sites where the forms occur in sympatry have led to the suggestion that these forms represent species. We conducted a study of the genetic structure of populations of An. gambiae from two villages in Mali, west Africa. Populations at each site were composed of the Bamako and Mopti forms and the sibling species, Anopheles arabiensis. Karyotypes were determined for each individual mosquito and genotypes at 21 microsatellite loci determined. A number of the microsatellites have been physically mapped to polytene chromosomes, making it possible to select loci based on their position relative to the inversions used to define forms. We found that the chromosomal forms differ at all loci on chromosome 2, but there were few differences for loci on other chromosomes. Geographic variation was small. Gene flow appears to vary among different regions within the genome, being lowest on chromosome 2, probably due to hitchhiking with the inversions. We conclude that the majority of observed genetic divergence between chromosomal forms can be explained by forces that need not involve reproductive isolation, although reproductive isolation is not ruled out. We found low levels of gene flow between the sibling species Anopheles gambiae and Anopheles arabiensis, similar to estimates based on observed frequencies of hybrid karyotypes in natural populations.

Male fitness increases when females are eliminated from gene pool: Implications for the Y chromosome

Because the two sexes share a common gene pool while performing many different biological functions, mutations benefiting one sex may not accumulate due to counter selection in the other sex. In these experiments 99% of a haploid genome of Drosophila melanogaster was constrained to segregate like a male-limited Y chromosome for 41 generations, thereby eliminating potential counter selection in females. The synthetic Y chromosomes rapidly accumulated genetic variation that increased male fitness and decreased female fitness. The survival and fertility of females declined when they were mated to males expressing the synthetic Y chromosomes. These results suggests that opposing selection between the sexes may substantially interfere with sex-specific adaptation. They also demonstrate how intersexual evolutionary conflict can lead to perpetual degeneration of the Y via genetic hitchhiking of deleterious mutations.