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Ecological genomics is the study of adaptation of natural populations to their environment, and therefore seeks to link organism and population level processes through an understanding of genome organization and function. The planktonic microcrustacean Daphnia, which has long been an important system for ecology, is now being used as a genomic model as well. Here we review recent progress in selected areas of Daphnia genomics research. Production of parthenogenetic male offspring occurs through environmental cues, which clearly involves endocrine regulation and has also been studied as a toxicological response to juvenoid hormone analog insecticides. Recent progress has uncovered a putative juvenoid cis-response element, which together with microarray analysis will stimulate further research into nuclear hormone receptors and their associated transcriptional regulatory networks. Ecotoxicological studies indicate that mRNA profiling is a sensitive and specific research tool with promising applications in environmental monitoring and for uncovering conserved cellular processes. Rapid progress is expected to continue in these and other areas, as genomic tools for Daphnia become widely available to investigators.Heredity (2008) 100, 184–190; doi:10.1038/sj.hdy.6800999; published online 23 May 2007 [ABSTRACT FROM AUTHOR]

Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are “off” and survival/growth pathways “on.” Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common “cell line“ gene expression pattern., Organismic and Evolutionary Biology

Optimal conditions were developed for an in organello transcriptional run-on assay using mitochondria isolated from Artemia franciscana embryos to investigate potential regulatory features of RNA synthesis under conditions of anoxia-induced quiescence. Transcription is not dependent on oxidative phosphorylation for maximal activity when exogenous ATP is available. Bona fide transcription products, as assessed by hybridization with specific mitochondrial cDNAs from A. franciscana, are produced in an inhibitor-sensitive manner. Transcription rate measured at pH 7.9 is reduced 80% when pH is lowered to 6.3, a pH range that mimics the in vivo change seen on exposure of embryos to anoxia. The proton sensitivity of mitochondrial RNA synthesis may provide a mechanism to depress this significant energy expenditure during quiescence. The influence of nucleotide concentration on kinetics is complicated by an interdependence among nucleotide species. ATP inhibition observed at subsaturating UTP concentrations is relieved when UTP is at saturating, physiologically relevant levels. Taken together, these data suggest that local (versus nuclear mediated) control is important in dictating mitochondrial transcription during rapid modulations in gene expression, such as those observed under anoxia-induced quiescence.