The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.     

A resource for large-scale RNA-interference-based screens in mammals

Gene silencing by RNA interference (RNAi) in mammalian cells using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) has become a valuable genetic tool. Here, we report the construction and application of a shRNA expression library targeting 9,610 human and 5,563 mouse genes. This library is presently composed of about 28,000 sequence-verified shRNA expression cassettes contained within multi-functional vectors, which permit shRNA cassettes to be packaged in retroviruses, tracked in mixed cell populations by means of DNA 'bar codes', and shuttled to customized vectors by bacterial mating. In order to validate the library, we used a genetic screen designed to report defects in human proteasome function. Our results suggest that our large-scale RNAi library can be used in specific, genetic applications in mammals, and will become a valuable resource for gene analysis and discovery.     

Diatom carbon export enhanced by silicate upwelling in the northeast Atlantic

Diatoms are unicellular or chain-forming phytoplankton that use silicon (Si) in cell wall construction. Their survival during periods of apparent nutrient exhaustion enhances carbon sequestration in frontal regions of the northern North Atlantic. These regions may therefore have a more important role in the 'biological pump' than they have previously been attributed, but how this is achieved is unknown. Diatom growth depends on silicate availability, in addition to nitrate and phosphate, but northern Atlantic waters are richer in nitrate than silicate. Following the spring stratification, diatoms are the first phytoplankton to bloom. Once silicate is exhausted, diatom blooms subside in a major export event. Here we show that, with nitrate still available for new production, the diatom bloom is prolonged where there is a periodic supply of new silicate: specifically, diatoms thrive by 'mining' deep-water silicate brought to the surface by an unstable ocean front. The mechanism we present here is not limited to silicate fertilization; similar mechanisms could support nitrate-, phosphate- or iron-limited frontal regions in oceans elsewhere.     

A mesoporous germanium oxide with crystalline pore walls and its chiral derivative

Microporous oxides are inorganic materials with wide applications in separations, ion exchange and catalysis. In such materials, an important determinant of pore size is the number of M (where M = Si, Ge and so on) atoms in the rings delineating the channels. The important faujasite structure exhibits 12-ring structures while those of zeolites, germanates and other materials can be much larger. Recent attention has focused on mesoporous materials with larger pores of nanometre scale; however, with the exception of an inorganic-organic hybrid, these have amorphous pore walls, limiting many applications. Chiral porous oxides are particularly desirable for enantioselective sorption and catalysis. However, they are very rare in microporous and mesoporous materials. Here we describe a mesoporous germanium oxide, SU-M, with gyroidal channels separated by crystalline walls that lie about the G (gyroid) minimal surface as in the mesoporous MCM-48 (ref. 9). It has the largest primitive cell and lowest framework density of any inorganic material and channels that are defined by 30-rings. One of the two gyroidal channel systems of SU-M can be filled with additional oxide, resulting in a mesoporous crystal (SU-MB) with chiral channels.     

Semisynthesis and biological properties of the [B24-leucine]-, [B25-leucine]- and [B24-leucine,B25-leucine]-analogues of human insulin

Summary Trypsin-catalyzed coupling of porcine desoctapeptide-insulin with synthetic octapeptides produced the [Leu^B24]-(I), [Leu^B25]- (II) and [Leu^B24, Leu^B25]- (III)analogues of human insulin. I, II and III displayed respectively 20–30%, 1–2% and 0.5% of the receptor binding activity of the normal hormone. Biological activities of these analogues seemed to be proportional to their binding potencies when assayed in vitro, while in an in vivo assay analogue I was fully active and II exhibited 10–20% of normal activity. III was less active than II in all assays tested.     

A micrococcal nuclease homologue in RNAi effector complexes

RNA interference (RNAi) regulates gene expression by the cleavage of messenger RNA, by mRNA degradation and by preventing protein synthesis. These effects are mediated by a ribonucleoprotein complex known as RISC (RNA-induced silencing complex). We have previously identified four Drosophila components (short interfering RNAs, Argonaute 2 (ref. 2), VIG and FXR) of a RISC enzyme that degrades specific mRNAs in response to a double-stranded-RNA trigger. Here we show that Tudor-SN (tudor staphylococcal nuclease)--a protein containing five staphylococcal/micrococcal nuclease domains and a tudor domain--is a component of the RISC enzyme in Caenorhabditis elegans, Drosophila and mammals. Although Tudor-SN contains non-canonical active-site sequences, we show that purified Tudor-SN exhibits nuclease activity similar to that of other staphylococcal nucleases. Notably, both purified Tudor-SN and RISC are inhibited by a specific competitive inhibitor of micrococcal nuclease. Tudor-SN is the first RISC subunit to be identified that contains a recognizable nuclease domain, and could therefore contribute to the RNA degradation observed in RNAi.