A probabilistic functional network of yeast genes

A conceptual framework for integrating diverse functional genomics data was developed by reinterpreting experiments to provide numerical likelihoods that genes are functionally linked. This allows direct comparison and integration of different classes of data. The resulting probabilistic gene network estimates the functional coupling between genes. Within this framework, we reconstructed an extensive, high-quality functional gene network for Saccharomyces cerevisiae, consisting of 4681 (approximately 81%) of the known yeast genes linked by approximately 34,000 probabilistic linkages comparable in accuracy to small-scale interaction assays. The integrated linkages distinguish true from false-positive interactions in earlier data sets; new interactions emerge from genes' network contexts, as shown for genes in chromatin modification and ribosome biogenesis.     

Microfluidic memory and control devices

We demonstrate microscopic fluidic control and memory elements through the use of an aqueous viscoelastic polymer solution as a working fluid. By exploiting the fluid's non-Newtonian rheological properties, we were able to demonstrate both a flux stabilizer and a bistable flip-flop memory. These circuit elements are analogous to their solid-state electronic counterparts and could be used as components of control systems for integrated microfluidic devices. Such miniaturized fluidic circuits are insensitive to electromagnetic interference and may also find medical applications for implanted drug-delivery devices.     

S-nitrosylation of matrix metalloproteinases: signaling pathway to neuronal cell death

Matrix metalloproteinases (MMPs) are implicated in the pathogenesis of neurodegenerative diseases and stroke. However, the mechanism of MMP activation remains unclear. We report that MMP activation involves S-nitrosylation. During cerebral ischemia in vivo, MMP-9 colocalized with neuronal nitric oxide synthase. S-Nitrosylation activated MMP-9 in vitro and induced neuronal apoptosis. Mass spectrometry identified the active derivative of MMP-9, both in vitro and in vivo, as a stable sulfinic or sulfonic acid, whose formation was triggered by S-nitrosylation. These findings suggest a potential extracellular proteolysis pathway to neuronal cell death in which S-nitrosylation activates MMPs, and further oxidation results in a stable posttranslational modification with pathological activity.     

Future Directions of Precision Agriculture

Precision Agriculture is advancing but not as fast as predicted 5years ago. The development of proper decision-support systems for implementing precision decisions remains a major stumbling block to adoption. Other critical research issues are discussed, namely, insufficient recognition of temporal variation, lack of whole-farm focus, crop quality assessment methods, product tracking and environmental auditing. A generic research programme for precision agriculture is presented. A typology of agriculture countries is introduced and the potential of each type for precision agriculture discussed.Invited paper, 7th International Conference on Precision Agriculture, Minneapolis, USA, July 2004.     

A Late Triassic dinosauromorph assemblage from New Mexico and the rise of dinosaurs

It has generally been thought that the first dinosaurs quickly replaced more archaic Late Triassic faunas, either by outcompeting them or when the more archaic faunas suddenly became extinct. Fossils from the Hayden Quarry, in the Upper Triassic Chinle Formation of New Mexico, and an analysis of other regional Upper Triassic assemblages instead imply that the transition was gradual. Some dinosaur relatives preserved in this Chinle assemblage belong to groups previously known only from the Middle and lowermost Upper Triassic outside North America. Thus, the transition may have extended for 15 to 20 million years and was probably diachronous at different paleolatitudes.     

Supernova shock breakout from a red supergiant

Massive stars undergo a violent death when the supply of nuclear fuel in their cores is exhausted, resulting in a catastrophic "core-collapse" supernova. Such events are usually only detected at least a few days after the star has exploded. Observations of the supernova SNLS-04D2dc with the Galaxy Evolution Explorer space telescope reveal a radiative precursor from the supernova shock before the shock reached the surface of the star and show the initial expansion of the star at the beginning of the explosion. Theoretical models of the ultraviolet light curve confirm that the progenitor was a red supergiant, as expected for this type of supernova. These observations provide a way to probe the physics of core-collapse supernovae and the internal structures of their progenitor stars.     

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia

Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications >100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia.     

Site-Specific Durum Wheat Quality and Its Relationship to Soil Properties in a Single Field in Northern New South Wales

The use of Precision Agriculture techniques to investigate agronomically significant soil factors and their relationship to wheat quality on a site-specific basis, was conducted during the winter 1996 wheat season in response to the growing concerns associated with wheat quality in Australia. A field of durum wheat was selected in Northern New South Wales, in which wheat and soil samples were taken from sites located within the field with the help of a Global Positioning System (GPS).Geostatistical methods were used to interpolate the data and produce maps of the field representing the spatial variability of all the soil and wheat properties. With the aid of these maps and empirical modeling techniques, relationships between the wheat and soil factors were determined.Areas within the field with lower soil profile available water capacities, caused by a combination of coarser soil texture and lower organic carbon content, probably contributed to water stress during grain-fill, which interacted with soil nitrogen to give higher protein levels. These areas of the field had lower yields and smaller 1000-kernel weights. Protein quality was found not to be compromised by increasing protein concentrations which resulted from water stress.The benefits of using precision agriculture techniques as a method for segregating wheat by protein at harvest to increase profits are described.