Biological networks and epistasis in genome-wide association studies

Over the last few years, technological improvements have made possible the genotyping of hundreds of thousands of SNPs, enabling whole-genome association studies. The first genome-wide association studies have recently been completed to detect causal variant for complex traits. Although increasing evidence suggests that interaction between loci, such as epistasis between two loci, should be considered, most of these studies proceed by considering each SNP independently. One reason for this choice is that looking at all pairs of SNPs increases dramatically the number of tests (approximatively 50 billions of tests for a 300,000 SNPs data set) that faces with computational limitation and strong multiple testing correction.
We proposed to reduce the number of tests by focusing on pairs of SNPs that belong to genes known to interact in some metabolic network. Although some interactions might be missed, these pairs of genes are good candidates for epistasis. Furthermore the use of protein interaction databases (such as the STRING database) may reduce the number of tests by a factor of 5,000.
Results using this approach will be presented on simulated data sets and on public data sets.
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Chapter 6 Making or unmaking a movement?

This article discusses dilemmas of global civic activism from a neo-Gramscian perspective as both subordinated and a potential challenge to hegemonic neoliberal order. With the investigational focus on the People’s Global Action on Migration, Development and Human Rights (PGA) event, the space for civic activism relating to the intergovernmental Global Forum on Migration and Development (GFMD) and its associated Civil Society Days and Common Space is analysed. The article asks how the future of PGA activism may be influenced by its formalized representation within the GFMD. It posits that the PGA has landed at a crossroad between becoming a global activist counterhegemonic movement to a dominant neoliberal migration policy and being captured in a tokenist subordinated inclusion within a truncated ‘invited space’ for interchange. This ambiguous position jeopardizes its impact on global migration governance, discussed with reference to theories of transversal politics and issues of counterhegemonic alliance-building

The Role of Cultural Memory in Contemporary Migrant Activism: Staging Gender in a Transforming Welfare State

Contemporary scientific and media debates about cultural conflict and gender relations have consolidated stereotypical categorisations of female migrants as passive victims of traditional cultural values. This risks veiling agency against ethnic, gender and other kinds of discrimination inherent in contemporary transformation of Swedish welfare state. In the light of a critical review of the current debate on gender and culture, the authors discuss an alternative understanding of past memories in contemporary activism for gender equality and social inclusion. They illustrate how civic agency echoes a dynamic interplay between the past and the present

Leaf vegetables for use in integrated hydroponics and aquaculture systems: Effects of root flooding on growth, mineral composition and nutrient uptake

In recirculating aquaculture and hydroponics systems, the waste products from fish production are used to produce vegetables or other crops of economic value, and the water is recirculated to the fish tanks. We studied growth, productivity and nutrient uptake of four leaf vegetable species (Lactuca sativa, Ipomoea aquatica, Brassica rapa var. chinensis and Brassica rapa var. parachinensis) in a controlled growth experiment with three root flooding treatments (drained, half-flooded and flooded) toassess their preferred hydroponic growth requirements, biomass production and nutrient removal capacities. Growth of the two Brassica varieties was clearly best at drained root conditions, while L. sativa and I. aquatica grew best with half-flooded and flooded roots. I. aquatica took up 3 times more N, P and K per plant than L. sativa, and 4 to 6 times more than the two Brassica varieties. At a plant density of 30 plants/m2, I. aquatica produced 146 g DW/m2 aboveground biomass during a 30-day cultivation period containing 2.8, 0.9 and 6.8 g/m2 of N, P and K, respectively. L. sativa produced 115 g DW/m2 of aboveground DW during a 60-day cultivation period, containing 2.2, 0.6 and 4.6 g/m2 of N, P and K, respectively. The two Brassica varieties produced much less aerial biomass (50-54 g DW/m2 during a 60-day period). Both I. aquatica and L. sativa are promising species to be included in integrated hydroponic and aquaculture facilities, with I. aquatica showing the most promise because of its higher growth and nutrient uptake capacity

Chapter 6 Making or unmaking a movement?

This article discusses dilemmas of global civic activism from a neo-Gramscian perspective as both subordinated and a potential challenge to hegemonic neoliberal order. With the investigational focus on the People’s Global Action on Migration, Development and Human Rights (PGA) event, the space for civic activism relating to the intergovernmental Global Forum on Migration and Development (GFMD) and its associated Civil Society Days and Common Space is analysed. The article asks how the future of PGA activism may be influenced by its formalized representation within the GFMD. It posits that the PGA has landed at a crossroad between becoming a global activist counterhegemonic movement to a dominant neoliberal migration policy and being captured in a tokenist subordinated inclusion within a truncated ‘invited space’ for interchange. This ambiguous position jeopardizes its impact on global migration governance, discussed with reference to theories of transversal politics and issues of counterhegemonic alliance-building

Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection

Recently diverged species typically have incomplete reproductive barriers, allowing introgression of genetic material from one species into the genomic background of the other. The role of natural selection in preventing or promoting introgression remains contentious. Because of genomic co-adaptation, some chromosomal fragments are expected to be selected against in the new background and resist introgression. In contrast, natural selection should favor introgression for alleles at genes evolving under multi-allelic balancing selection, such as the MHC in vertebrates, disease resistance, or self-incompatibility genes in plants. Here, we test the prediction that negative, frequency-dependent selection on alleles at the multi-allelic gene controlling pistil self-incompatibility specificity in two closely related species, Arabidopsis halleri and A. lyrata, caused introgression at this locus at a higher rate than the genomic background. Polymorphism at this gene is largely shared, and we have identified 18 pairs of S-alleles that are only slightly divergent between the two species. For these pairs of S-alleles, divergence at four-fold degenerate sites (K = 0.0193) is about four times lower than the genomic background (K = 0.0743). We demonstrate that this difference cannot be explained by differences in effective population size between the two types of loci. Rather, our data are most consistent with a five-fold increase of introgression rates for S-alleles as compared to the genomic background, making this study the first documented example of adaptive introgression facilitated by balancing selection. We suggest that this process plays an important role in the maintenance of high allelic diversity and divergence at the S-locus in flowering plant families. Because genes under balancing selection are expected to be among the last to stop introgressing, their comparison in closely related species provides a lower-bound estimate of the time since the species stopped forming fertile hybrids, thereby complementing the average portrait of divergence between species provided by genomic data

Insertion and Deletion Processes in Recent Human History

Background: Although insertions and deletions (indels) account for a sizable portion of genetic changes within and among species, they have received little attention because they are difficult to type, are alignment dependent and their underlying mutational process is poorly understood. A fundamental question in this respect is whether insertions and deletions are governed by similar or different processes and, if so, what these differences are. Methodology/Principal Findings: We use published resequencing data from Seattle SNPs and NIEHS human polymorphism databases to construct a genomewide data set of short polymorphic insertions and deletions in the human genome (n = 6228). We contrast these patterns of polymorphism with insertions and deletions fixed in the same regions since the divergence of human and chimpanzee (n = 10546). The macaque genome is used to resolve all indels into insertions and deletions. We find that the ratio of deletions to insertions is greater within humans than between human and chimpanzee. Deletions segregate at lower frequency in humans, providing evidence for deletions being under stronger purifying selection than insertions. The insertion and deletion rates correlate with several genomic features and we find evidence that both insertions and deletions are associated with point mutations. Finally, we find no evidence for a direct effect of the local recombination rate on the insertion and deletion rate. Conclusions/Significance: Our data strongly suggest that deletions are more deleterious than insertions but that insertion