A statistical framework for the design of microarray experiments and effective detection of differential gene expression

Motivation: Microarray experiments generate a high data volume. However, often due to financial or experimental considerations, e.g. lack of sample, there is little or no replication of the experiments or hybridizations. These factors combined with the intrinsic variability associated with the measurement of gene expression can result in an unsatisfactory detection rate of differential gene expression (DGE). Our motivation was to provide an easy to use measure of the success rate of DGE detection that could find routine use in the design of microarray experiments or in post-experiment assessment.

Inductive reasoning and semantic cognition: More than just different names for the same thing?

We describe evidence that certain inductive phenomena are associated with IQ, that different inductive phenomena emerge at different ages, and that the effects of causal knowledge on induction are decreased under conditions of memory load. On the basis of this evidence we argue that there is more to inductive reasoning than semantic cognition.

Differential Effect of IL-27 on Developing versus Committed Th17 Cells

IIL-27 counters the effect of TGF-beta+IL-6 on naive CD4(+) T cells, resulting in near complete inhibition of de novo Th17 development. In contrast, little is known about the effect of IL-27 on already differentiated Th17 cells. A better understanding of how IL-27 regulates these cells is needed to evaluate the therapeutic potential of IL-27 in Th17 cells-associated diseases. In this study, we show that IL-27 had surprisingly little effect on committed Th17 cells, despite its expression of a functional IL-27R. Contrary to de novo differentiation of Th17 cells, IL-27 did not suppress expression of retinoid-related orphan receptor (ROR)gammat or RORalpha in committed Th17 cells. Consistent with this finding, the frequency of committed Th17 cells and their cytokine secretion remained unaffected by IL-27. Both memory Th17 cells (CD4(+)CD25(-)CD62L(low)) that developed in vivo and encephalitogenic Th17 cells infiltrating the CNS of mice developing experimental autoimmune encephalomyelitis produced similar amounts of IL-17A when reactivated with IL-23 in the absence and presence of exogenous IL-27. Finally, IL-27 failed to suppress encephalitogenicity of Th17 cells in an adoptive transfer of experimental autoimmune encephalomyelitis. Analysis ex vivo of transferred Th17 cells in the spleen and CNS of recipient mice showed that cells retained similar phenotype irrespective of whether cells were treated or not with IL-27. Our data demonstrate that in contrast to inhibition of de novo differentiation of Th17 cells, IL-27 has little or no effect on committed Th17 cells. These findings indicate that therapeutic applications of IL-27 might have a limited efficacy in inflammatory conditions where aggressive Th17 responses have already developed.

Echinostoma caproni: Differential tegumental responses to growth in compatible and less compatible hosts

The topography of the tegument of Echinostoma caproni adults collected from high (mice) and low (rats) compatible hosts was compared by SEM. In the oral (OS) and the ventral sucker (VS) areas, a worm age-host species interaction was found with regard to the density of spines. There was a decrease in the density of spines in the adults collected from mice, whereas an increase occurred in the OS area in worms from rats over time. The tegumentary spines in adults from mice became larger and blunter. Some spines from the VS area in adults from mice at 4 wpi were multipointed. The spines of adults from rats were sharper, not covered by the tegument and no multipointed spines were observed. We detected a greater level of actin gene expression in the adults collected from rats. These facts suggest that the low compatible host induces an increased turnover of tegumentary spines. (C) 2010 Elsevier Inc. All rights reserved.

Potential roles for differential body size and microhabitat complexity in mediating biotic interactions within invasive freshwater amphipod assemblages

Cannibalism and intraguild predation (IGP) are common amongst freshwater amphipod crustacean aswsemblages, particularly between individuals of different body size, with IGP of smaller by larger species. The decline of Gammarus tigrinus Populations in mainland Europe has been accompanied by the arrival of the Ponto-Caspian invader Dikerogammarus villosus and previous studies have implicated IGP of G. tigrinus by the larger D. villosus as the principal driving force in this replacement. We examined how factors such as microhabitat and body size may mediate both cannibalism within G. tigrinus populations and IGP by D. villosus and thus contribute to field patterns of coexistence and exclusion. A field Survey of an invaded Dutch fake indicated that G. tigrinus and D. villosus differed in distribution. with D. villosus being the numerically dominant amphipod (80-96 %) on the rocky boulder Substrate of the shoreline and G. tigrinus being the dominant amphipod (100 %) in the crushed shell/sand matrix immediately adjacent to this. Laboratory microcosm experiments indicated that G. tigrinus cannibalism, particularly of smaller by larger size classes, may be common. In addition, although D. villosus predation of all G. tigrinus size classes was extreme, the smallest size classes Suffered the highest predation. Indeed, when exposed to D. villosus, predation of larger G. tigrinus was lowest when smaller G. tigrinus were also present. Increasing microhabitat complexity from a simple bare substrate littered with Dreissena polymorpha zebra mussels to a Crushed shell/sand matrix significantly reduced both cannibalism and IGP. Our Study emphasizes the need to consider both life history stages and habitat template, when considering the impacts of biotic interactions and it also emphasizes that complex, interacting factors may be mediating the range expansion of D. villosus.

Differential drift and parasitism in invading and native Gammarus spp. (Crustacea : Amphipoda)

Invading and native species often interact directly, such as by predation, producing patterns of exclusion and coexistence. Less direct factors, such as interactions with the broader abiotic and biotic environment, may also contribute to such patterns, but these have received less recognition. In Northern Ireland, the North American Gammarus tigrinus has invaded freshwaters populated with the native Gammarus duebeni celticus, with intraguild predation between the two implicated in their relative success. However, these species also engage in day and night