Inference of hidden structures in complex physical systems by multi-scale clustering

We survey the application of a relatively new branch of statistical physics--"community detection"-- to data mining. In particular, we focus on the diagnosis of materials and automated image segmentation. Community detection describes the quest of partitioning a complex system involving many elements into optimally decoupled subsets or communities of such elements. We review a multiresolution variant which is used to ascertain structures at different spatial and temporal scales. Significant patterns are obtained by examining the correlations between different independent solvers. Similar to other combinatorial optimization problems in the NP complexity class, community detection exhibits several phases. Typically, illuminating orders are revealed by choosing parameters that lead to extremal information theory correlations.Comment: 25 pages, 16 Figures; a review of earlier work

Expression of Recombinant Protein B Subunit Pili from Vibrio Cholera

Abstract: Background & Aims: Vibrio cholerae is a gram-negative bacterial pathogen that causes cholera disease. Following ingestion by a host and entry into the upper intestine, V. cholera colonizes and begins to emit enterotoxin. One of the most pathogenic factors of Vibrio cholera is toxin-coregulated pili (TCP). Toxin-Coregulated pili is as the primary factor requiered for the colonization and insistence of bacteria in the small intestine. The toxin-coregulated pili are bundle-forming pili that are coordinately regulated with cholerae toxin (CT). The CT operon is part of the genome of the cholera toxin bacteriophage (CTXQ) which utilizes TCP as its receptor. The aim of this study is to produce a recombinant vaccine for V. cholerae in the future. Methods: The tcpB gene was amplified by Polymerase chain reaction (PCR) method and subcloned into pET32a expression vector. Escherichia coli BL21 (DE3) plysS competent cells were transformed by pET32a - tcpB recombinant plasmid. In different media with changing the parameters of nutrient content like glucose as carbon source and yeast extract as nitrogen source, protein expression was induced by using IPTG. Recombinant protein were purified by affinity chromatography (Ni-NTA). The concentration of Recombinant proteins measured according to Bradford assay. Results: The sequencing results by Sanger method showed a similar sequence as tcpB gene. Escherichia coli BL21 plysS was transformed with TCPB-pET32a and gene expression was induced by IPTG. The expressed protein was purified by affinity chromatography and Ni-NTA kit. Conclusion: Recombinant protein tcpB was produced in the cytoplasm of Escherichia coli BL21 plysS, by pET32a expression vector. Therefore, utilization of this protein in Escherichia coli BL21 plysS by expression vectors such as pET32a is possible

Recombinant toxin-coregulated pilus A (TcpA) as a candidate subunit cholera vaccine

BACKGROUND AND OBJECTIVES: The toxin co-regulated pilus A (TcpA) has been described as a critical pathogenicity factor of Vibrio cholerae. TcpA is a candidate for making subunit vaccine against cholera. The aim of this study was to produce a candidate vaccine by expressing recombinant TcpA in E. coli. MATERIALS AND METHODS: In this study, the toxin co-regulated pilus A gene from EL-Tor, V. cholerae subspecies, was amplified by PCR and sub-cloned into prokaryotic expression vector pGEX4T1. E. coli BL21 (DE3) was transformed with pGEX4T1- TcpA and gene expression was induced by IPTG and purified by GST resin. The integrity of the product was confirmed by Western blot analysis using a standard rabbit anti-V. cholerae antibody. Sera reactivity of infected individuals was further analyzed against the recombinant TcpA protein. RESULTS: The concentration of purified recombinant protein was calculated to be 8 mg/L of initial culture. The integrity of product was confirmed by Western blot analysis using a standard rabbit anti V. cholerae antibody. Sera reactivity of infected individual was further analyzed against the recombinant TcpA protein. The obtained data indicated that recombinant TcpA protein from V. cholerae was recognized by patient serum and animal sera. CONCLUSION: These results show that the recombinant TcpA is antigenic and could be used in a carrier host as an oral vaccine against cholera