Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.     

Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus

The influenza pandemic of 1918-19 was responsible for about 50 million deaths worldwide. Modern histopathological analysis of autopsy samples from human influenza cases from 1918 revealed significant damage to the lungs with acute, focal bronchitis and alveolitis associated with massive pulmonary oedema, haemorrhage and rapid destruction of the respiratory epithelium. The contribution of the host immune response leading to this severe pathology remains largely unknown. Here we show, in a comprehensive analysis of the global host response induced by the 1918 influenza virus, that mice infected with the reconstructed 1918 influenza virus displayed an increased and accelerated activation of host immune response genes associated with severe pulmonary pathology. We found that mice infected with a virus containing all eight genes from the pandemic virus showed marked activation of pro-inflammatory and cell-death pathways by 24 h after infection that remained unabated until death on day 5. This was in contrast with smaller host immune responses as measured at the genomic level, accompanied by less severe disease pathology and delays in death in mice infected with influenza viruses containing only subsets of 1918 genes. The results indicate a cooperative interaction between the 1918 influenza genes and show that study of the virulence of the 1918 influenza virus requires the use of the fully reconstructed virus. With recent concerns about the introduction of highly pathogenic avian influenza viruses into humans and their potential to cause a worldwide pandemic with disastrous health and economic consequences, a comprehensive understanding of the global host response to the 1918 virus is crucial. Moreover, understanding the contribution of host immune responses to virulent influenza virus infections is an important starting point for the identification of prognostic indicators and the development of novel antiviral therapies.     

The distillation and volatility of ionic liquids

It is widely believed that a defining characteristic of ionic liquids (or low-temperature molten salts) is that they exert no measurable vapour pressure, and hence cannot be distilled. Here we demonstrate that this is unfounded, and that many ionic liquids can be distilled at low pressure without decomposition. Ionic liquids represent matter solely composed of ions, and so are perceived as non-volatile substances. During the last decade, interest in the field of ionic liquids has burgeoned, producing a wealth of intellectual and technological challenges and opportunities for the production of new chemical and extractive processes, fuel cells and batteries, and new composite materials. Much of this potential is underpinned by their presumed involatility. This characteristic, however, can severely restrict the attainability of high purity levels for ionic liquids (when they contain poorly volatile components) in recycling schemes, as well as excluding their use in gas-phase processes. We anticipate that our demonstration that some selected families of commonly used aprotic ionic liquids can be distilled at 200-300 degrees C and low pressure, with concomitant recovery of significant amounts of pure substance, will permit these currently excluded applications to be realized.     

High-throughput synthesis and catalytic properties of a molecular sieve with 18- and 10-member rings

Crystalline molecular sieves with large pores and high adsorption capacities have many potential applications. Of these materials, zeolites are of particular interest owing to their stability in a wide range of experimental conditions. An aluminophosphate with very large circular channels(5) containing 18 oxygen atoms (18-ring channels) has been synthesized, but in the search for large-pore zeolites, most of the materials which have been synthesized up to now contain only 14-ring channels; the synthesis of zeolites with larger ring structures has been believed to be hindered by the low Si-O-Si bond angles available. A silicogaloaluminate (ECR-34) with unidirectional 18-ring channels was recently reported, but exhibited low micropore volume, thus rendering the material less attractive for catalytic applications. Here we report the structure and catalytic activity of the silicogermanate zeolite ITQ-33; this material exhibits straight large pore channels with circular openings of 18-rings along the c axis interconnected by a bidirectional system of 10-ring channels, yielding a structure with very large micropore volume. The conditions for synthesis are easily accessible, but are not typical, and were identified using high-throughput techniques.     

Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex

RNA degradation is a determining factor in the control of gene expression. The maturation, turnover and quality control of RNA is performed by many different classes of ribonucleases. Ribonuclease II (RNase II) is a major exoribonuclease that intervenes in all of these fundamental processes; it can act independently or as a component of the exosome, an essential RNA-degrading multiprotein complex. RNase II-like enzymes are found in all three kingdoms of life, but there are no structural data for any of the proteins of this family. Here we report the X-ray crystallographic structures of both the ligand-free (at 2.44 A resolution) and RNA-bound (at 2.74 A resolution) forms of Escherichia coli RNase II. In contrast to sequence predictions, the structures show that RNase II is organized into four domains: two cold-shock domains, one RNB catalytic domain, which has an unprecedented alphabeta-fold, and one S1 domain. The enzyme establishes contacts with RNA in two distinct regions, the 'anchor' and the 'catalytic' regions, which act synergistically to provide catalysis. The active site is buried within the RNB catalytic domain, in a pocket formed by four conserved sequence motifs. The structure shows that the catalytic pocket is only accessible to single-stranded RNA, and explains the specificity for RNA versus DNA cleavage. It also explains the dynamic mechanism of RNA degradation by providing the structural basis for RNA translocation and enzyme processivity. We propose a reaction mechanism for exonucleolytic RNA degradation involving key conserved residues. Our three-dimensional model corroborates all existing biochemical data for RNase II, and elucidates the general basis for RNA degradation. Moreover, it reveals important structural features that can be extrapolated to other members of this family.     

No supernovae associated with two long-duration gamma-ray bursts

It is now accepted that long-duration gamma-ray bursts (GRBs) are produced during the collapse of a massive star. The standard 'collapsar' model predicts that a broad-lined and luminous type Ic core-collapse supernova accompanies every long-duration GRB. This association has been confirmed in observations of several nearby GRBs. Here we report that GRB 060505 (ref. 10) and GRB 060614 (ref. 11) were not accompanied by supernova emission down to limits hundreds of times fainter than the archetypal supernova SN 1998bw that accompanied GRB 980425, and fainter than any type Ic supernova ever observed. Multi-band observations of the early afterglows, as well as spectroscopy of the host galaxies, exclude the possibility of significant dust obscuration and show that the bursts originated in actively star-forming regions. The absence of a supernova to such deep limits is qualitatively different from all previous nearby long-duration GRBs and suggests a new phenomenological type of massive stellar death.     

Participative Methodology for Local Development: The Contribution of Engineers Without Borders from Italy and Colombia: Towards the Improvement of Water Quality in Vulnerable Communities

This paper presents a systemic methodology by which engineering is put to use in vulnerable communities through applied technological research and the main results of its application. The methodology presented corresponds to one implemented and designed by two groups of Engineers without Borders in Europe and Latin America, to integrate technical know-how with local context in communities with water problems in Colombia and the Democratic Republic of Congo. The main results of this methodology are related to the improvement of the living conditions of vulnerable groups thanks to the integration of the communities?? knowledge with engineering know-how, leading to autonomous communities and engineering professors and students learning from real life problems to enrich applied sciences.