Mitochondrial metagenomics: letting the genes out of the bottle

‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity

Investigation of possible hydrogen shielding effect on epithermal neutron activation analysis - a computation and experimental approach

Neutron activation is a popular analytical technique used to determine the presence and concentration of certain elements. It has several variations, including thermal neutron, epithermal neutron, fast neutron activation, etc, for different applications; all of those variations are non-destructive, and sensitive to small quantity. While trying to determine the concentration of Cl and Br in the light water solution, Dr. Landsberger’s team found the epithermal neutron activation analysis results were 25% lower than the conventional chemical method. They were not able to determine the cause of such discrepancy. This study was motivated to re-examine such discrepancy, and to study its possible causes. Furthermore, the study tries to determine if such discrepancy, if it exists, was linked with thermal neutron cut off or hydrogen absorption of neutrons. A computer simulation using the Monte Carlo radiation transport software MCNPX was developed to radiate sample Cl & Br solutions of known mass concentrations in a simulated TRIGA reactor core at 500 KW steady state power. [1] The neutron activation rate of Br, Cl at each concentration was then calculated. Such procedure was then repeated for heavy water solutions. Finally, a cadmium shield was added to eliminate thermal neutrons; all samples were tested again using epithermal neutron activation. The actual neutron activation experiment was also carried out in the University of Texas’s TRIGA Mark II reactor. A total of 40 samples of Br & Cl solution (with and without Cd, in light water and in heavy water) were irradiated in the reactor at 500 KW steady state power.Physic

An Efficient Parallel Solver for SDD Linear Systems

We present the first parallel algorithm for solving systems of linear equations in symmetric, diagonally dominant (SDD) matrices that runs in polylogarithmic time and nearly-linear work. The heart of our algorithm is a construction of a sparse approximate inverse chain for the input matrix: a sequence of sparse matrices whose product approximates its inverse. Whereas other fast algorithms for solving systems of equations in SDD matrices exploit low-stretch spanning trees, our algorithm only requires spectral graph sparsifiers