Journal of Computer Science & Systems Biology

In order to improve capability of some traditional algorithms for 3D virtual reality animation, this article comes up with a new improved algorithm, which can improve traditional ones and is more suitable for 3-D graphic environment. There are two steps. The first step is to break down the entire 3-D scene and then setup the Octree structure. The second step is to transform the Octree onto 2-D plane, and write down nodes which are modified and then render the modified ones. Many experiments demonstrate the superiority of the algorithm. Especially, in the process of blanking, the quadrants are shown from far to near and achieve 3-D display more effectively, according to the given object and the location of view.

The enzyme carbonic anhydrase isoform II (CAII), catalyzing the hydration and dehydration of CO2, enhances transport activity of the monocarboxylate transporter isoform I (MCT1, SLC16A1) expressed in Xenopus oocytes by a mechanism that does not require CAII catalytic activity. In the present study, we have investigated the mechanism of the CAII induced increase in transport activity by using electrophysiological techniques and mathematical modeling of the MCT1 transport cycle. The model consists of six states arranged in cyclic fashion and features an ordered, mirrorsymmetric, binding mechanism, where binding and unbinding of the proton to the transport protein is considered to be the rate limiting step under physiological conditions. An explicit rate expression for the substrate flux is derived using model reduction techniques. By treating the pools of intra-and extracellular MCT1 substrates as dynamic states, the time dependent kinetics are obtained by integration, using the derived expression for the substrate flux. The simulations were compared with experimental data obtained from MCT1-expressing oocytes injected with different amounts of CAII. The model suggests that CAII increases the effective rate constants of the proton reactions, possibly by working as a proton antenna.

Biological Engineering involves global DNA sampling and modular design from genetic parts. A new approach reflected by natural history is based on the recognition of interchangeable DNA fragments that move around the world due to horizontal gene transfer. According to the large scale, metagenomics provide opportunities to sequence whole genomes within environmental populations. Annotated gene sequences, protein structures, and metabolic data can be used to design small biosystems from interchangeable genetic parts, the same as from functional modules. To illustrate this, the 21 genes for sulfur metabolism were inferred from the genome of bacterium Vesicomyosocius okutanii HA, and the distribution of two gene clusters (dissimilatory sulfite reductase - dsr and sulfur-oxidation - sox) within environmental samples was investigated. The correlation between the dsr and sox clusters for the experimental set of 41 stations was R = 0.86 which demonstrates the complementarity of dsr and sox metabolic pathways in environmental populations. Hypothetical functions were assigned using comparisons with known proteins. The 18 reads from symbionts of gutless worm Olavius algarvensis showed a high identity to large AprA protein from V.okutanii. In addition, comparative 3D modeling of hypothetical DsrB protein revealed sulfite reductase ferredoxin-like half domain, sulfite reductase 4Fe-4S domain, and a repressor of phase-1 flagellin. The simplistic reconstruction of sulfur metabolism from parts and examples of hierarchical modularity in nature are given. The origin of modularity is considered in the context of minimal cell and horizontal gene transfer. The role of ancient sulphur metabolism in modularization is discussed under the umbrella of iron-sulfur world theory (Wächtershäuser, 1988), deep-hot biosphere model (Gold, 1992), and radiolysis hypothesis (Garzón and Garzón, 2001). The reverse engineering approach based on natural genetic modules is proposed for understanding early life.