The prevalence of antisense RNA in eukaryotes is not known and only a few naturally occurring antisense transcripts have been assigned a function. However, the recent identification of a large number of putative antisense transcripts strengthens the view that antisense RNAs might affect a wider variety of processes than previously thought. Here we show that in the model organism Neurospora crassa entrainment of the circadian clock, which is critical for the correct temporal expression of genes and their products, is controlled partly by an antisense RNA arising from a clock component locus. In a wild-type strain, levels of antisense frequency (frq) transcripts cycle in antiphase to sense frq transcripts in the dark, and are inducible by light. In mutant strains in which the induction of antisense frq RNA by light is abolished, the time of the internal clock is delayed relative to the wild-type strain, and resetting of the clock by light is altered. These data provide an unexpected link between antisense RNA and circadian timing and provide a new example of a eukaryotic cellular process regulated by naturally occurring antisense RNA.

The burrow emergence activity of the wild caught ragworm Nereis virens Sars associated with food prospecting was investigated under various photoperiodic (LD) and simulated tidal cycles (STC) using a laboratory based actograph. Just over half (57%) of the animals under LD with STC displayed significant tidal (approximately 12.4 h) and/or lunar-day (approximately 24.8 h) activity patterns. Under constant light (LL) plus a STC, 25% of all animals were tidal, while one animal responded with a circadian (24.2 h) activity rhythm suggestive of cross-modal entrainment where the environmental stimulus of one period entrains rhythmic behavior of a different period. All peaks of activity under a STC, apart from that of the individual cross-modal entrainment case, coincided with the period of tank flooding. Under only LD without a STC, 49% of the animals showed nocturnal (approximately 24 h) activity. When animals were maintained under free-running LL conditions, 15% displayed significant rhythmicity with circatidal and circadian/circalunidian periodicities. Although activity cycles in N. virens at the population level are robust, at the individual level they are particularly labile, suggesting complex biological clock-control with multiple clock output pathways.

Researchers working on environmentally relevant organisms, populations, and communities are increasingly turning to the application of OMICS technologies to answer fundamental questions about the natural world, how it changes over time, and how it is influenced by anthropogenic factors. In doing so, the need to capture meta-data that accurately describes the biological "source" material used in such experiments is growing in importance. Here, we provide an overview of the formation of the "Env" community of environmental OMICS researchers and its efforts at considering the meta-data capture needs of those working in environmental OMICS. Specifically, we discuss the development to date of the Env specification, an informal specification including descriptors related to geographic location, environment, organism relationship, and phenotype. We then describe its application to the description of environmental transcriptomic experiments and how we have used it to extend the Minimum Information About a Microarray Experiment (MIAME) data standard to create a domain-specific extension that we have termed MIAME/Env. Finally, we make an open call to the community for participation in the Env Community and its future activities.

Errant polychaete worms in the Orders Eunicida (family Eunicidae) and Phyllodocida (families Nereidae and Polynoidae) exhibit a highly developed biorhythmic capability. The Pacific palolo worms are well known for a precisely timed annual breeding event in which mass spawning occurs at a particular time of day, on one day per year, that day having a fixed relationship to the lunar period. Nereidae and Polynoidae exhibit photoperiodic responses that determine the breeding season by regulation of oocyte growth. Nereis virens shows short-term cycles of foraging activity; automated recording of these patterns has revealed four distinct behaviour rhythm phenotypes: circadian, tidal, lunidian and arrhythmic, the last phenotype being expressed during the photoperiod induced growth diapause. The Eunicids and Phyllodocids are represented in the fossil record by scolecodonts, their fossilised jaws. There was a major radiation of these polychaetes during the Ordovician and the earliest suggested polychaete fossils are from the Cambrian. The simultaneous expression of tidal and circadian rhythmicity is characteristic of intertidal animals and it is likely that this complex behavioural repertoire was found in the ancestors of modern terrestrial forms, such as tetrapods and arthropods, prior to their emergence onto land during the Carboniferous and Silurian periods at least 400 Ma. The period of the earth's rotation, and hence day length and tidal period, has long been known to be increasing, and additionally the moon to be retreating from the earth, due to the phenomenon of tidal friction caused by the gravitational interactions between the moon and the earth. These changes are significant over a geological time scale. Consequently, the length of day was substantially less (and the number of days in a year more) than at present in the Cambrian and Ordovician periods. Recent theoretical analysis of the period of the earth's rotation suggests that the day length prior to a critical period (t crit ) around 1800 Ma may have been stable, with a length of only 4 h. At that time a period of more rapid change in the dynamics of the rotation was initiated. The implications of this theory for the evolution of the biological clock are discussed.

In filamentous fungi, including the model organism Neurospora crassa, plentiful biological tissue from which RNA can be extracted may be obtained by allowing fungal spores to germinate and form a mycelium in liquid culture. The mycelium constitutes a mosaic of multinuclear, tubular filaments known as hyphae or mycelia. In general, when exposed to air, fungal hyphae quickly start to develop spores, which are often colorful. However, when submerged in liquid under rapid agitation large amounts of vegetatively growing mycelium can be obtained, which can be easily harvested by means of filtration. To preserve the physiological state of the culture, the mycelium is snap-frozen, and then to free its contents, the mycelium is ground under liquid nitrogen to break all hyphal structures. Here a method to extract high-quality total RNA from Neurospora mycelium using TRIzol reagent is described.