The genome sequence of the filamentous fungus Neurospora crassa

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.     

Impedance-optimized photo-acoustic spectroscopy

We have examined the basic assumptions leading to optimized performance of small photo-acoustic resonators. Previous attempts at miniaturizing photo-acoustic systems have found the loading of the microphone on the cavity to be insignificant. We have shown theoretically and tested experimentally the fact that the microphone loading can have a dramatic effect on the resonator behavior. Treatment of the pressure and volume velocity of the sound waves as analogs of voltage and current facilitates the use of standard electrical engineering techniques and leads to techniques that enable one to efficiently optimize the impedance match between the cavity and the microphone. PACS 43.35.Ud; 43.20.Ks; 43.20.Mv     

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the production of sake, miso and soy sauce. Our analysis of genome structure provided a quantitative evaluation of forces driving long-term eukaryotic genome evolution. It also led to an experimentally validated model of mating-type locus evolution, suggesting the potential for sexual reproduction in A. fumigatus and A. oryzae. Our analysis of sequence conservation revealed over 5,000 non-coding regions actively conserved across all three species. Within these regions, we identified potential functional elements including a previously uncharacterized TPP riboswitch and motifs suggesting regulation in filamentous fungi by Puf family genes. We further obtained comparative and experimental evidence indicating widespread translational regulation by upstream open reading frames. These results enhance our understanding of these widely studied fungi as well as provide new insight into eukaryotic genome evolution and gene regulation.     

A histone H3 methyltransferase controls DNA methylation in Neurospora crassa.

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. We have demonstrated previously that dim-2 encodes a DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora crassa. Here we report that another Neurospora gene, dim-5, is required for DNA methylation, as well as for normal growth and full fertility. We mapped dim-5 and identified it by transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a gene related to histone methyltransferases that are involved in heterochromatin formation in other organisms. Transformation of a wild-type strain with a segment of dim-5 reactivated a silenced hph gene, apparently by 'quelling' of dim-5. We demonstrate that recombinant DIM-5 protein specifically methylates histone H3 and that replacement of lysine 9 in histone H3 with either a leucine or an arginine phenocopies the dim-5 mutation. We conclude that DNA methylation depends on histone methylation.     

The methylated component of the Neurospora crassa genome

Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals and the fungus Neurospora crassa have about 2-3% of cytosines methylated. In mammals, methylation is almost exclusively in the under-represented CpG dinucleotides, and most CpGs are methylated whereas in Neurospora, methylation is not preferentially in CpG dinucleotides and the bulk of the genome is unmethylated. DNA methylation is essential in mammals but is dispensable in Neurospora, making this simple eukaryote a favoured organism in which to study methylation. Recent studies indicate that DNA methylation in Neurospora depends on one DNA methyltransferase, DIM-2 (ref. 6), directed by a histone H3 methyltransferase, DIM-5 (ref. 7), but little is known about its cellular and evolutionary functions. As only four methylated sequences have been reported previously in N. crassa, we used methyl-binding-domain agarose chromatography to isolate the methylated component of the genome. DNA sequence analysis shows that the methylated component of the genome consists almost exclusively of relics of transposons that were subject to repeat-induced point mutation--a genome defence system that mutates duplicated sequences.     

Thermodynamic Correction for Salts in Variably Saturated Porous Media

Using thermodynamic principles, the general relationship describing the equilibrium vapor content in the gas phase above a saline liquid and across a curved liquid–gas interface is developed. Since high salt concentration affects the intensive and extensive liquid properties, it is also necessary to account for these effects in liquid water content/liquid water pressure relationship curves so that experimentally derived curves for pure water may be useful for elevated salt concentrations. The appropriate thermodynamic relationships are derived to describe the salt effects on liquid and vapor properties. The resulting equations are valid for salt concentrations between zero and saturation, and for any temperatures that nominally occur in nearsurface geologic materials.     

The Local Geometry of Gas Injection into Saturated Homogeneous Porous Media

The injection of gases into liquid saturated porous media is of theoretical and practical interest (e.g., air sparging for the removal of volatile organic compounds from contaminated aquifer sediments). The influence of the rate of gas delivery and the vertical distance from the source are developed. The concept of a “near-injection region” is presented in which the pressure gradients exceed buoyant gradients and thus exhibits largely radial flow. The near-injection size is shown to have an area required to carry the injected gas flow under unit gradient. The parabolic movement of gas outside of this area which has often been observed is explained as reflecting the sum of many realizations of gas channels following random lateral movements as they precede upward independent of flux. These concepts are confirmed through comparison with published and experimental data of air injection into slabs consisting of saturated sands of a range of textures.     

Numerical estimation of multicomponent adsorption isotherms in preparative chromatography: implications of experimental error.

Since experimental methods for measuring multicomponent adsorption isotherms are extremely tedious, numerical approaches are an attractive alternative. Here, the variance in isotherm parameters as a function of experimental error in measured effluent concentrations is quantified. The number of experimental replicates needed to obtain isotherm parameters to a desired level of accuracy is calculated explicitly. After the covariance matrix of the parameters has been determined, Monte Carlo methods are found to be rapid and effective. The use of different kinds of experiments, the effect of resolution and loading, and the impact of the number of measured data points are described.