Genome-level longitudinal expression of signaling pathways and gene networks in pediatric septic shock

We have conducted longitudinal studies focused on the expression profiles of signaling pathways and gene networks in children with septic shock. Genome-level expression profiles were generated from whole blood-derived RNA of children with septic shock (n=30) corresponding to day one and day three of septic shock, respectively. Based on sequential statistical and expression filters, day one and day three of septic shock were characterized by differential regulation of 2,142 and 2,504 gene probes, respectively, relative to controls (n=15). Venn analysis demonstrated 239 unique genes in the day one dataset, 598 unique genes in the day three dataset, and 1,906 genes common to both datasets. Functional analyses demonstrated time-dependent, differential regulation of genes involved in multiple signaling pathways and gene networks primarily related to immunity and inflammation. Notably, multiple and distinct gene networks involving T cell- and MHC antigen-related biology were persistently downregulated on both day one and day three. Further analyses demonstrated large scale, persistent downregulation of genes corresponding to functional annotations related to zinc homeostasis. These data represent the largest reported cohort of patients with septic shock subjected to longitudinal genome-level expression profiling. The data further advance our genome-level understanding of pediatric septic shock and support novel hypotheses.     

Apoptotic DNA fragmentation is not related to the phosphorylation state of histone H1

Changes in chromatin structure, histone phosphorylation and cleavage of DNA into nucleosome-size fragments are characteristic features of apoptosis. Since H1 histones bind to the site of DNA cleavage between nucleosomal cores, the question arises as to whether the state of H1 phosphorylation influences the rate of internucleosomal cleavage. Here, we tested the relation between DNA fragmentation and H1 phosphorylation both in cultured cells and in vitro. In Jurkat cells, hyperosmotic mannitol concentration resulted in apoptosis, including nucleosomal fragmentation, whereas apoptosis induction by increased NaCl concentration was not accompanied by DNA fragmentation. However, both treatments induced dephosphorylation of H1 histones. In contrast, treatment of Raji cells with alkylphosphocholine led to induction of apoptosis with internucleosomal fragmentation, albeit without notable histone H1 dephosphorylation. These results demonstrate that dephosphorylation of H1 histones is neither a prerequisite for nor a consequence of internucleosomal cleavage. Moreover, we observed with an in vitro assay that the known enhancing effect of H1 histones on the activity of the apoptosis-induced endonuclease DFF40 is independent of the subtype or the phosphorylation state of the linker histone.     

Chemotaxis in shallow gradients is mediated independently of PtdIns 3-kinase by biased choices between random protrusions

Current models of eukaryotic chemotaxis propose that directional sensing causes localized generation of new pseudopods. However, quantitative analysis of pseudopod generation suggests a fundamentally different mechanism for chemotaxis in shallow gradients: first, pseudopods in multiple cell types are usually generated when existing ones bifurcate and are rarely made de novo; second, in Dictyostelium cells in shallow chemoattractant gradients, pseudopods are made at the same rate whether cells are moving up or down gradients. The location and direction of new pseudopods are random within the range allowed by bifurcation and are not oriented by chemoattractants. Thus, pseudopod generation is controlled independently of chemotactic signalling. Third, directional sensing is mediated by maintaining the most accurate existing pseudopod, rather than through the generation of new ones. Finally, the phosphatidylinositol 3-kinase (PI(3)K) inhibitor LY294002 affects the frequency of pseudopod generation, but not the accuracy of selection, suggesting that PI(3)K regulates the underlying mechanism of cell movement, rather than control of direction.     

Duration of colonization and interactions between early and late colonists determine the effects of patch colonization history on patch biodiversity

Patches can vary in their colonization history as the result of many factors, including differences in patch size and isolation, which alter the timing and duration in which one or more species colonize a patch. Prior work has found that the particular time that a species colonizes a patch can affect the performance of co‐occurring species, but it is less clear whether it affects the biodiversity of the patch. Our objective was to evaluate how two components of colonization history affect biodiversity – the total duration of the colonization window in which a predator is able to colonize the patch and the particular time in the patch's colonization history (i.e. early versus late in community development) that colonization by a predator occurs. We conducted an experiment to examine how the duration and timing in which predatory dragonflies colonize recently filled ephemeral ponds affects insect biodiversity. Dragonfly colonization history had an important effect on insect biodiversity. Ponds with a longer colonization history by dragonflies had fewer insect morphotypes than ponds with a shorter colonization history. The timing of dragonfly colonization (i.e. early versus late in community development) had no effect on the number of insect morphotypes present despite altering both the rate of dragonfly metamorph production and the abundance of larval dragonflies present at the end of the study. The effect of duration of long‐term dragonfly colonization on biodiversity stemmed from early colonists weakening the influence of later colonists on insect biodiversity. Though colonization by dragonflies reduced adult insect abundance, differences in the time in which dragonflies colonized ponds had no effect on total insect abundance. Moreover, differences in patch biodiversity appears to be affected more by variation in the duration a patch was colonized by a predator than variation in the time in which a patch was colonized by a predator.