GPU Accelerated Smith-Waterman

We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonstrate that our system's performance is competitive with current optimized software packages

Role of Cd and Cu on the Antioxidant Behaviour of Brachychiton populneus (Schott & Endl.) R.Br. (Sterculiaceae)

ROLE OF CD AND CU ON THE ANTIOXIDANT BEHAVIOUR OF BRACHYCHITON POPULNEUS (SCHOTT & ENDL.) R. BR. (STERCULIACEAE) Baycu, G.1* - Bakacak, S.A.1 - Rognes, S.E.2 1 Istanbul University 2 Oslo University *Corresponding author, e-mail: [email protected] Brachychiton populneus (Bottle tree) occurs naturally in southern Australia. Young seedlings distribute resources to form a large tap-rooted tuber that has considerable starch and water reserves, allowing the tree to survive in the dry and hot periods of Mediterranean environment. Brachychiton is commonly cultivated and is hardy in a range of climates and soils. Oxidative stress is induced by a wide range of environmental factors including drought, heat and trace metal stresses. The aim of this study was to examine the antioxidant behaviour of this drought tolerant plant to trace metal toxicity. Plant seeds were collected from Cyprus Island, which has a typical Mediterranean climate. We had some difficulties during the germination and plant growth in hydroponic cultures was impossible. For this reason sand & perlite cultures were set up and plants were grown for several months in the phytotrone conditions. The seedlings were then treated with 50-150μM Cd and 500-1500μM Cu for 2-week to investigate the role of Cd and Cu on the activity of catalase (CAT), glutathione reductase (GR) and guaiacol peroxidase (GPOX) in the leaves and roots. The activity of CAT was diminished both by Cd and Cu toxicity in the plant organs. GR activities were reduced by both metals in the leaves except a slight increase in the low Cd treatment. No changes in GR activity were observed in the roots. Conversely, both Cd and Cu produced a raise in GPOX activity in the leaves. Whereas an increase was observed with low Cd and low Cu treatments in the roots, high Cd and high Cu reduced the activity. GPOX could be exerting a stronger antioxidant function. These results suggest that antioxidant behaviours may change with various trace metal concentrations in different plant organs

An abandoned copper mining site in Cyprus and assessment of metal concentrations in plants and soil

Mining is an important source of metal pollution in the environment and abandoned mines are extremely restricted habitats for plants. Some plant species growing on metalliferous soils around mine tailings and spoil-heaps are metal-tolerant and accumulate high concentrations of metals. In this investigation, we aimed to perform a research in the CMC-abandoned copper mining area in Lefke-North Cyprus to assess the recent metal pollution in soil and plant systems. We collected 16 soil samples and 25 plant species from 8 localities around the vicinity of tailing ponds. Some concentrations of metals in soil samples varied from 185 to 1023mg kg(-1) Cu, 15.2 to 59.2mg kg(-1) Ni, 2.3 to 73.6mg kg(-1) Cd and metals for plants ranged from 0.135 to 283mg kg(-1) Cu, 0.26 to 31.2mg kg(-1) Ni, 0.143 to 277mg kg(-1) Cd. Atriplex semibaccata, Acacia cyanophylla, Erodium spp., Inula viscosa, Juncus sp., Oxalis pes-caprea, Pistacia lentiscus, Senecio vulgaris and Tragopogon sinuatus accumulated higher concentrations. BCF for Atriplex semibaccata was found very high, for this reason this plant can tentatively be considered as a hyperaccumulator of Cu and Cd, but it needs further investigation for its potential in phytoremediation

The motivic spectral sequence

Summary. We give an overview of the search for a motivic spectral sequence: a spectral sequence connecting algebraic K-theory to motivic cohomology that is analogous to the Atiyah-Hirzebruch spectral sequence that connects topological K-theory to singular cohomology