between theoretical (mathematical) considerations when analysing microarray data, and the approach taken by life scientists. For example, there is a complex interplay between experimental setup and hybridization design in microarray studies. Although more complex designs than a simple control versus exposed design have been worked out, these are not commonly applied despite the fact that often all conditions for doing so have been met, resulting in poor analysis and interpretation of microarray data. Furthermore, it has become apparent that the major advantage of microarray technology is – at the same time – its most important drawback: the amount of information resulting from microarray analyses is too large and too complex to lead to one single, statistically sound conclusion. Due to this statistical and computational complexity of microarray data analysis recent studies have restricted themselves to assessing relatively simple questions, based on simple mathematical models. However, more complex biological questions, such as those relating to time dynamics of gene expression patterns, remain more difficult to address. This paper therefore aims at summarizing the knowledge available in the mathematics and bioinformatics fields, and distill the information that is relevant to toxicologists for practical use. Current toxicological literature using microarray technology will be reviewed comparing the methods used, focusing on the gap between the suggested ideal mathematical approach and the contemporary real- life approach. To conclude, a short list of best practices will be provided that can easily and realistically be implemented in most experimental setups in order to improve the scientific yield of microarray analyses. doi:10.1016/j.cbpa.2008.05.140 3. Acclimatory responses of the Daphnia pulex proteome to changes in oxygen and temperature conditions B. Zeis, S. Schwerin, R. Pirow, T. Lamkemeyer, R.J. Paul (University of Muenster, Germany) Freshwater planktonic crustaceans of the genus Daphnia show a remarkable plasticity to cope with environmental changes in oxygen concentration and temperature. In both cases, a mismatch of oxygen supply and demand limits the animals' tolerance for stressful O 2 and temperature conditions. Within the tolerable range, one central response is the induction of hemoglobin to restore oxygen homeostasis. To explore further elements of adaptive protein expression in response to low-oxygen conditions and temperature changes, two- dimensional gel electrophoresis and mass spectrometry were used to analyze the proteome composition of Daphnia pulex acclimated to different oxygen and temperature conditions in long-term laboratory cultures. The release of the genome information for this species (Daphnia genomics consortium; https://dgc.cgb.indiana.edu) in 2007 allowed protein identification. Among up-regulated proteins under hypoxia, several enzymes of carbohydrate metabolism indicated sup- port from anaerobic pathways to energy metabolism. At cold tem- perature conditions, an induction of vitellogenin revealed effects on reproductive processes, whereas a reduction of secretory enzymes involved in protein digestion reflects shifts in protein metabolism (Zeis et al, 2008 BMC Physiology, in press). The complex patterns of shifts in protein expression observed can help to estimate the impact of oxygen and temperature changes to the animals' physiology and give insight into the mechanism of acclima- tory processes to environmental stressors. doi:10.1016/j.cbpa.2008.05.141 4. Hypotonic stress alters expression of genes encoding transcription factors, protein homeostasis enzymes, mitochondrial proteins, and transport proteins in gills of the euryhaline green crab (Carcinus maenas) D.W. Towle (Mt. Desert Island Biological Laboratory, Salsbury Cove, Maine USA); N.B. Terwilliger (Oregon Institute of Marine Biology, Charleston, Oregon, USA); R.P. Henry (Auburn University, Alabama, USA) The green crab Carcinus maenas is an invasive species originating in Europe and inhabiting many coastal areas around the world. Tolerant of many types of environmental stress, it is particularly capable of withstanding a wide range of salinities. Previous single- gene studies of expression changes following salinity dilution identified several transporters and transport-related proteins whose mRNA levels are altered in gills following an abrupt change in salinity. In this study, in order to identify additional targets for future study, we used a 4462-feature oligonucleotide microarray based on 15,637 expressed sequence tags that were derived from a normalized multiple-tissue cDNA library. Two time-course experiments sampled mitochondria-rich posterior gills following transfer of crabs from 32 ppt to 10 ppt seawater, a condition in which the animals effectively hyperosmoregulate the hemolymph. Transcripts encoding Na + /K + - ATPase α-subunit and carbonic anhydrase increased significantly, while Rh-like ammonium transporter mRNA decreased, confirming previous data obtained via quantitative PCR. Other membrane proteins showing increased mRNA expression included γ-amino butyric acid and dopamine receptors, sodium/glucose cotransporter, and chloride/ bicarbonate exchanger. Aquaporin-encoding transcripts decreased. Among transcripts encoding stress-related proteins, ubiquitin-con- jugating enzyme E2 and proteasome α-subunit increased while heat shock cognate protein 70 decreased. A large suite of mitochondrial proteins exhibited increased mRNA expression, including cytochromes b and c, ATP synthase subunits, and cytochrome c oxidase. Transiently up-regulated transcription factors included MAX binding protein, methyl-CpG binding domain protein 4, and transcription factor IIe. Thus, in addition to targets previously investigated by single-gene studies, microarray results point to a number of additional transcrip- tional changes elicited by hypotonic stress in this strongly euryhaline species. Supported by NSF (IOB-0543860 to DWT and IBN-0230005 to RPH), NIH (P20 RR016463), and an MDIBL New Investigator Award to NBT. doi:10.1016/j.cbpa.2008.05.142 5. Transcriptomic approach to study the response to rapid changes of temperature in the hydrothermal vent mussel Bathymodiolus azoricus I. Boutet, A. Tanguy, D. Le Guen, P. Piccino, S. Hourdez, D. Jollivet (CNRS-UPMC, UMR 7144 Adaptation et Diversité en Milieu Marin, France); J. Ravaux, B. Shillito (CNRS-UPMC UMR 7138 ‘Systématique, Adaptation et Evolution, France) Temperature, and especially thermal gradients, is one of the major environmental factors influencing vertical and latitudinal distribu- tions of marine organisms by constraining many biological processes. In particular marine ecosystems such as deep-sea hydrothermal vents, organisms are often exposed to strong and variable environmental gradients (temperature and oxygen, sulphide) and long periods of stressful conditions. Among species that are living in hydrothermal vents, the hydrothermal vent mussel belonging to the genus S38 Abstracts / Comparative Biochemistry and Physiology, Part A 151 (2008) S37–S43