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.

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.

Lamprey (Lampetra fluviatilis and Lampetra planeri) ammocoete habitat associations at regional, catchment and microhabitat scales in Northern Ireland

Habitat characteristics associated with lamprey ammocoetes (Lampetra spp.) were investigated at three different spatial scales: regional (Northern Ireland), catchment (Ballinderry River) and microhabitat. At the regional scale, ammocoetes were more abundant in rivers with a pH >= 8.2, while within a catchment, abundance was negatively related to the number of potential lamprey barriers and distance upstream. At the microhabitat scale, at sites where ammocoetes were present, ammocoetes were more abundant where median phi >= 1.94 (very coarse sand), where sediment depth >= 11.5 cm, and where kurtosis was >1.71. This study provides information on habitat associations of lamprey in the UK which may be of use in their conservation, in particular it highlights the negative association of migration barriers with lamprey abundance.

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

Differential physico-chemical tolerances of amphipod species revealed by field transplantations

Physico-chemical regimes of river systems are major determinants of the distributions and relative abundances of macroinvertebrate taxa. Other factors, however, such as biotic interactions, may co-vary with changes in physico-chemistry and concomitant changes in community composition. Thus, direct cause and effect relationships may not always be established from field surveys. Equally, however, laboratory studies may suffer from lack of realism in extrapolation to the field. Here, we use balanced field transplantation experiments to elucidate the role of physico-chemical regime in determining the generally mutually exclusive distributions of two amphipod taxa, Gammarus (two species) and Crangonyx pseudogracilis. Within two river systems in Ireland, the former species dominate stretches of well oxygenated, high-quality water, whereas the latter dominates stretches of poorly oxygenated, low-quality water. G. pulex and G. duebeni celticus did not survive in bioassay tubes in areas dominated by C. pseudogracilis, which itself survived in tubes in such areas. However, both C. pseudogracilis and Gammarus spp. survived equally well in tubes in areas dominated by Gammarus spp. Physicochemical regime thus limits the movement of Gammarus spp. into C. pseudogracilis areas, but some other factor excludes C. pseudogracilis from Gammarus spp. areas. Since previous laboratory experiments showed high predation rates of Gammarus spp. on C. pseudogracilis, we propose that predation by the former causes exclusion of the latter. Hence, presumed effects of physico-chemical regime on macroinvertebrate presence/abundance may often require experimental field testing and appreciation of alternative explanations.