Sleep in Drosophila is regulated by adult mushroom bodies

Sleep is one of the few major whole-organ phenomena for which no function and no underlying mechanism have been conclusively demonstrated. Sleep could result from global changes in the brain during wakefulness or it could be regulated by specific loci that recruit the rest of the brain into the electrical and metabolic states characteristic of sleep. Here we address this issue by exploiting the genetic tractability of the fruitfly, Drosophila melanogaster, which exhibits the hallmarks of vertebrate sleep. We show that large changes in sleep are achieved by spatial and temporal enhancement of cyclic-AMP-dependent protein kinase (PKA) activity specifically in the adult mushroom bodies of Drosophila. Other manipulations of the mushroom bodies, such as electrical silencing, increasing excitation or ablation, also alter sleep. These results link sleep regulation to an anatomical locus known to be involved in learning and memory.     

The redox state of arc mantle using Zn/Fe systematics

Many arc lavas are more oxidized than mid-ocean-ridge basalts and subduction introduces oxidized components into the mantle. As a consequence, the sub-arc mantle wedge is widely believed to be oxidized. The Fe oxidation state of sub-arc mantle is, however, difficult to determine directly, and debate persists as to whether this oxidation is intrinsic to the mantle source. Here we show that Zn/Fe(T) (where Fe(T) = Fe(2+)?+?Fe(3+)) is redox-sensitive and retains a memory of the valence state of Fe in primary arc basalts and their mantle sources. During melting of mantle peridotite, Fe(2+) and Zn behave similarly, but because Fe(3+) is more incompatible than Fe(2+), melts generated in oxidized environments have low Zn/Fe(T). Primitive arc magmas have identical Zn/Fe(T) to mid-ocean-ridge basalts, suggesting that primary mantle melts in arcs and ridges have similar Fe oxidation states. The constancy of Zn/Fe(T) during early differentiation involving olivine requires that Fe(3+)/Fe(T) remains low in the magma. Only after progressive fractionation does Fe(3+)/Fe(T) increase and stabilize magnetite as a fractionating phase. These results suggest that subduction of oxidized crustal material may not significantly alter the redox state of the mantle wedge. Thus, the higher oxidation states of arc lavas must be in part a consequence of shallow-level differentiation processes, though such processes remain poorly understood.     

Demographic compensation and tipping points in climate-induced range shifts

To persist, species are expected to shift their geographical ranges polewards or to higher elevations as the Earth's climate warms. However, although many species' ranges have shifted in historical times, many others have not, or have shifted only at the high-latitude or high-elevation limits, leading to range expansions rather than contractions. Given these idiosyncratic responses to climate warming, and their varied implications for species' vulnerability to climate change, a critical task is to understand why some species have not shifted their ranges, particularly at the equatorial or low-elevation limits, and whether such resilience will last as warming continues. Here we show that compensatory changes in demographic rates are buffering southern populations of two North American tundra plants against the negative effects of a warming climate, slowing their northward range shifts, but that this buffering is unlikely to continue indefinitely. Southern populations of both species showed lower survival and recruitment but higher growth of individual plants, possibly owing to longer, warmer growing seasons. Because of these and other compensatory changes, the population growth rates of southern populations are not at present lower than those of northern ones. However, continued warming may yet prove detrimental, as most demographic rates that improved in moderately warmer years declined in the warmest years, with the potential to drive future population declines. Our results emphasize the need for long-term, range-wide measurement of all population processes to detect demographic compensation and to identify nonlinear responses that may lead to sudden range shifts as climatic tipping points are exceeded.     

2'-O methylation of the viral mRNA cap evades host restriction by IFIT family members

Cellular messenger RNA (mRNA) of higher eukaryotes and many viral RNAs are methylated at the N-7 and 2'-O positions of the 5' guanosine cap by specific nuclear and cytoplasmic methyltransferases (MTases), respectively. Whereas N-7 methylation is essential for RNA translation and stability, the function of 2'-O methylation has remained uncertain since its discovery 35 years ago. Here we show that a West Nile virus (WNV) mutant (E218A) that lacks 2'-O MTase activity was attenuated in wild-type primary cells and mice but was pathogenic in the absence of type I interferon (IFN) signalling. 2'-O methylation of viral RNA did not affect IFN induction in WNV-infected fibroblasts but instead modulated the antiviral effects of IFN-induced proteins with tetratricopeptide repeats (IFIT), which are interferon-stimulated genes (ISGs) implicated in regulation of protein translation. Poxvirus and coronavirus mutants that lacked 2'-O MTase activity similarly showed enhanced sensitivity to the antiviral actions of IFN and, specifically, IFIT proteins. Our results demonstrate that the 2'-O methylation of the 5' cap of viral RNA functions to subvert innate host antiviral responses through escape of IFIT-mediated suppression, and suggest an evolutionary explanation for 2'-O methylation of cellular mRNA: to distinguish self from non-self RNA. Differential methylation of cytoplasmic RNA probably serves as an example for pattern recognition and restriction of propagation of foreign viral RNA in host cells.     

Karyotypic abnormalities create discordance of germline genotype and cancer cell phenotypes

The nature of mendelian inheritance assumes that all tissues in which a phenotype of interest is expressed have a uniform diploid karyotype, which is often not the case in cancer cells. Owing to nonrandom gains of chromosomes, trisomies are present in many cases of leukemia and other malignances. We used polymorphisms in the genes encoding thiopurine S-methyltransferase (TPMT), gamma-glutamyl hydrolase (GGH) and the reduced folate carrier (SLC19A1) to assess the nature of chromosomal acquisition and its influence on genotype-phenotype concordance in cancer cells. TPMT and GGH activities in somatic cells were concordant with germline genotypes, whereas activities in leukemia cells were determined by chromosomal number and whether the acquired chromosomes contained a wild-type or variant allele. Leukemia cells that had acquired an additional chromosome containing a wild-type TPMT or GGH allele had significantly lower accumulation of thioguanine nucleotides or methotrexate polyglutamates, respectively. Among these genes, there was a comparable number of acquired chromosomes with wild-type and variant alleles. Therefore, chromosomal gain can alter the concordance of germline genotype and cancer cell phenotypes, indicating that allele-specific quantitative genotyping may be required to define cancer pharmacogenomics unequivocally.     

Tree use by koalas in a chemically complex landscape

Although defence against herbivores is often argued to be the main action of plant secondary metabolites (PSMs), very few examples have demonstrated that intraspecific variation in PSM concentrations influences foraging by wild vertebrate herbivores. Experiments with captive animals often indicate that PSM concentrations influence how much herbivores eat from individual plants, but these experiments do not replicate the subtle trade-offs in diet selection faced by wild animals, which must avoid predators and extremes of weather, interact with conspecifics, and achieve a balanced, nutritious diet, while avoiding intoxication by PSMs. We characterized the foliar chemistry of every tree from two Eucalyptus species available to a population of koalas (Phascolarctos cinereus) and considered rates of tree visitation over a ten-year period. We show that visitation rate was most strongly influenced by tree size, but that koalas also visited trees less frequently if the foliage contained either high concentrations of deterrent PSMs known as formylated phloroglucinol compounds, or low concentrations of nitrogen. Consequently, plant chemistry restricts the use of trees by this herbivore, and thus limits the food available to koalas and potentially influences koala populations.     

Mutation of ARX causes abnormal development of forebrain and testes in mice and X-linked lissencephaly with abnormal genitalia in humans

Male embryonic mice with mutations in the X-linked aristaless-related homeobox gene (Arx) developed with small brains due to suppressed proliferation and regional deficiencies in the forebrain. These mice also showed aberrant migration and differentiation of interneurons containing gamma-aminobutyric acid (GABAergic interneurons) in the ganglionic eminence and neocortex as well as abnormal testicular differentiation. These characteristics recapitulate some of the clinical features of X-linked lissencephaly with abnormal genitalia (XLAG) in humans. We found multiple loss-of-function mutations in ARX in individuals affected with XLAG and in some female relatives, and conclude that mutation of ARX causes XLAG. The present report is, to our knowledge, the first to use phenotypic analysis of a knockout mouse to identify a gene associated with an X-linked human brain malformation.     

A 'periodic table' for protein structures

Current structural genomics programs aim systematically to determine the structures of all proteins coded in both human and other genomes, providing a complete picture of the number and variety of protein structures that exist. In the past, estimates have been made on the basis of the incomplete sample of structures currently known. These estimates have varied greatly (between 1,000 and 10,000; see for example refs 1 and 2), partly because of limited sample size but also owing to the difficulties of distinguishing one structure from another. This distinction is usually topological, based on the fold of the protein; however, in strict topological terms (neglecting to consider intra-chain cross-links), protein chains are open strings and hence are all identical. To avoid this trivial result, topologies are determined by considering secondary links in the form of intra-chain hydrogen bonds (secondary structure) and tertiary links formed by the packing of secondary structures. However, small additions to or loss of structure can make large changes to these perceived topologies and such subjective solutions are neither robust nor amenable to automation. Here I formalize both secondary and tertiary links to allow the rigorous and automatic definition of protein topology.     

Recovery of 16S ribosomal RNA gene fragments from ancient halite

During the last decade, sensitive techniques for detecting DNA have been successfully applied to archaeological and other samples that were a few hundred to a few thousand years old. Nevertheless, there is still controversy and doubt over claims of exceptionally ancient DNA. Additional accounts stretching back nearly a century suggest that microorganisms may survive over geological time in evaporite deposits. There is, however, often doubt over the age relationship between evaporite formation and the incorporation of microorganisms. Here, we have used petrographic and geochemical techniques (laser ablation microprobe inductively coupled plasma mass spectrometry) to verify the estimated geological age of halite (NaCl) evaporite samples. Fragments of 16S ribosomal RNA genes were detected by polymerase chain reaction amplification of DNA extracted from halite samples ranging in age from 11 to 425 Myr (millions of years). Haloarchaeal 16S rDNA amplicons were present in one sample (11 16 Myr), whereas other samples (65 425 Myr) yielded only bacterial 16S rDNA amplicons. Terminal restriction fragment length polymorphism analyses indicate complex and different populations of microorganisms or their free DNA in ancient halites of different ages.