计算机科学与系统生物学杂志

If biological objects are created by natural selection, why are they composed of discrete modules? What has been the nature of mutations since the Darwinian epoch? This paper presents examples of genetic circuits in terms of stochastic
-calculus; a new mathematical language for nanosystems. The author used a constructor of five elements such as decay, null gate, gene product, and negative and positive gates. These primitives were applied to design genetic switches, oscillators, feedforward and feedback loops, pulse generators, memory elements, and combinatorial logics. The behaviors of those circuits were investigated – functions, such as oscillations or a spontaneous pulse generation were performed simply, flip-flops between stable states occurred in the noisy environment. The modular essence of
-calculus and the following up features of Stochastic Pi Machine (SPiM) programming language allowed us to change the topology of networks that resembled a gene exchange in nature. Other types of mutations were considered as variations in parameters. Perturbations modified system behavior in unpredictable ways that generated diversity for a possible future design by selection of appropriative variants.

Service-Oriented Architecture (SOA) is being one of the widely accepted methodologies in software market for building and integrating different kinds of software systems. This acceptance comes from the extreme benefits that it offers to their adopters including agility, dynamicity, and loose-coupling. These benefits are usually missed in traditional software terminologies and practices. XML Web Services is the most used technology for applying SOA because it is easy to use and it allows high interoperability between different systems due to its dependency on standards that are widely accepted and supported by almost all large software vendors. However, XML Web Services suffer from a number of drawbacks such as low performance, bad utilization for hardware resources, and high network latency. These pitfalls may prevent some adopters from utilizing SOA in large and complex systems. So, these issues should be first addressed and resolved before leveraging it into real-time systems. This paper presents an experimental evaluation for the performance of XML Web Services in real-time business systems. Furthermore, it offers some tactics and strategies that might be used to enhance the overall performance of XML Web Services.

The amount of glycomics data being generated is rapidly increasing as a result of improvements in analytical and computational methods. Correlation and analysis of this large, distributed data set requires an extensible and flexible representational standard that is also ‘understood’ by a wide range of software applications. An XML-based data representation standard that faithfully captures essential structural details of a glycan moiety along with additional information (such as data provenance) to aid the interpretation and usage of glycan data, will facilitate the exchange of glycomics data across the scientific community. We reviewed importance of data warehouse, showing a method of applying data mining techniques using XML, and some of the data issues, analysis problems, and results.

Hypoxanthin-guanine phosphoribosyltransferase (HPRT) is responsible for catalyzing a reaction which breaks down uric acid in the body. The lack of this enzyme creates a build-up of uric-acid, leading to a neurological problem, joint pain and kidney problem. The condition is called Lesch-Nyhan Syndrome. A comparative modelling of the protein Hypoxanthin-guanine phosphoribosyltransferase is performed using the modeling program modeller9v3.The following structure validation programs PROCHECK, PROSA, VERIFY3D and WHATIF are used. Descret Optimized Protein Energy (DOPE), is a statistical potential used to asses homology model in protein structure prediction. Predicted model can be useful to develop new inhibitor against Lesch-Nyhan Syndrome. CASTp can be used to study surface features and functional regions of proteins.

Meningococcal disease is a life-threatening illness with annual incidence rates varying from 1 to 1000 per 100 000 persons in different parts of the world. Effective polysaccharide and polysaccharide-protein conjugate vaccines that offer protection against infection with meningococcal serogroups A, C, Y and W-135 have been licensed and are available worldwide. Serogroup B remains the most prevalent cause of meningococcal disease responsible for 32% of all meningococcal disease in the United States, 45 to 80% of the cases in Europe, and for the majority of cases in the rest of the world. The development of a vaccine against serogroup B poses the biggest problem due to the similarity between the B capsular polysaccharide structure and a polysialic acid containing glycopeptides that are a part of human brain tissue. Prevention of meningococcal disease will require the development of an effective vaccine to combat serogroup B, which is the cause of most meningococcal cases in developed countries. The availability of the complete sequence information of Neisseria meningitides serogroup B proteome has made it possible to carry out the in silico analysis of its genome for identification of potential vaccine and drug targets. Our study revealed 1413 proteins which are non-homologous to human genome. Screening these proteins using the Database of Essential Genes (DEG) resulted in the identification of 362 proteins as essential proteins of the bacterium. Analysis of the identified essential proteins, using the KEGG Automated Annotation Server (KAAS) housed at Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways database, revealed 35 enzymes of N. Meningitides that may be used as potential drug targets, as they belongs to pathways present only in the bacterium and not present in humans. Subcelluler localization prediction of these essential proteins revealed that 9 proteins lie on the outer membrane of the pathogen which could be potential vaccine targets. Screening of the functional inhibitors against these novel targets may result in discovery of novel therapeutic compounds that can be effective against Neisseria meningitides Serogroup B.