WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations

BACKGROUND: Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies including population genetics, molecular genetics and pharmacogenomics. Using known AS primer design tools to create primers leads to cumbersome process to inexperience users since information about SNP/mutation must be acquired from public databases prior to the design. Furthermore, most of these tools do not offer the mismatch enhancement to designed primers. The available web applications do not provide user-friendly graphical input interface and intuitive visualization of their primer results. RESULTS: This work presents a web-based AS primer design application called WASP. This tool can efficiently design AS primers for human SNPs as well as mutations. To assist scientists with collecting necessary information about target polymorphisms, this tool provides a local SNP database containing over 10 million SNPs of various populations from public domain databases, namely NCBI dbSNP, HapMap and JSNP respectively. This database is tightly integrated with the tool so that users can perform the design for existing SNPs without going off the site. To guarantee specificity of AS primers, the proposed system incorporates a primer specificity enhancement technique widely used in experiment protocol. In particular, WASP makes use of different destabilizing effects by introducing one deliberate 'mismatch' at the penultimate (second to last of the 3'-end) base of AS primers to improve the resulting AS primers. Furthermore, WASP offers graphical user interface through scalable vector graphic (SVG) draw that allow users to select SNPs and graphically visualize designed primers and their conditions. CONCLUSION: WASP offers a tool for designing AS primers for both SNPs and mutations. By integrating the database for known SNPs (using gene ID or rs number), this tool facilitates the awkward process of getting flanking sequences and other related information from public SNP databases. It takes into account the underlying destabilizing effect to ensure the effectiveness of designed primers. With user-friendly SVG interface, WASP intuitively presents resulting designed primers, which assist users to export or to make further adjustment to the design. This software can be freely accessed at http://bioinfo.biotec.or.th/WASP

Indian genetic disease database

Indians, representing about one-sixth of the world population, consist of several thousands of endogamous groups with strong potential for excess of recessive diseases. However, no database is available on Indian population with comprehensive information on the diseases common in the country. To address this issue, we present Indian Genetic Disease Database (IGDD) release 1.0 (http://www.igdd.iicb.res.in)—an integrated and curated repository of growing number of mutation data on common genetic diseases afflicting the Indian populations. Currently the database covers 52 diseases with information on 5760 individuals carrying the mutant alleles of causal genes. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database is currently designed to work best with Internet Explorer 8 (optimal resolution 1440 × 900) and it can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers. Provisions have been made for deposition of new data and logistics for regular updation of the database. The IGDD web portal, planned to be made freely available, contains user-friendly interfaces and is expected to be highly useful to the geneticists, clinicians, biologists and patient support groups of various genetic diseases

Gaining competitive advantage through developing social network (Guanxi) : empirical study in SME in Thailand

In the Thailand market, many business practices and social life are closely interlinked through a complex network of social networks and relations, especially Small and Medium enterprises (SMEs) where the business owner hold the decision-making role and has the authority to control the company, deals with others based not just on cost- benefit economic considerations alone but also intertwined with social relationships, personal and business contacts. With the ever-changing market conditions and high competitive nature of Small and Medium enterprises (SMEs) in Thailand, where there is approximately 2.28 million SMEs in year 2006 or comprising of 99.4 percent of enterprise in Thailand (Office of Small and Medium Enterprise Promotion OSMEP, 2006), this number is increasing every each year, resulting in a highly competitive business environment. Thus, this results in the need for a more elaborate and active network management and connection which play an important role in the promotion of the competitive advantage of the firm. The knowledge of network and the competitive advantage it brings is well recognised in the literature of business network. To a certain extent, the business networking in Thailand market, as with most other countries in Asia-Pacific region where there exist a Chinese-influenced society, is influenced from a Chinese business network called `Guanxi', but major questions have not been addressed by the literatures about the nature and the parallel to the Chinese form of `Guanxi', its effectiveness, practice and operations for gaining competitive advantage in specific business segments of the Thailand market. The original perspective of the research aimed to extend the knowledge in the area of `Guanxi' and business network for practical contribution to the particular instance of SMEs in Thailand context. This perspective generated on adopting the key principles of Guanxi knowledge into local practice of Thai SMEs for gaining business competitive advantage, and achieved by identifying, examining and developing the framework for particular SMEs business in Thailand. The author's research methodological approach focuses on examining the existing `Guanxi' framework of the process of `Guanxi' development (initiating, building and using of `Guanxi') and the `Guanxi' building framework of Trust (Xin) and Feeling (Qing), as a starting point to further extend its implication in the context of the particular SME in Thailand. The author employed the `Interactionism' perspective as a philosophical stance for the research with the research strategy of 'case study research'

Developing the Conflicts Management Model for School Administrators of Secondary School under the Office of Secondary Educational Service Area 20

This study aimed to 1) investigate the cause of conflict which in the secondary schools under the Secondary School under the Office of Secondary Educational Service Area 20, 2) study the conflict management method which administrators applied in Secondary School under the Office of Secondary Educational Service Area 20, and 3) develop conflict management model for Secondary School under the Office of Secondary Educational Service Area 20. The participants were 115 school administrators (44 school directors and 71 deputy directors) which were selected by random sampling technique. The research instruments included a questionnaire, which reliability value was 0.97, and an interview schedule that were administered to the respondents. The data were analyzed by frequency, percentage, mean, and standard deviation. The result of the study showed that: 1. the causes of conflict in Secondary School under the Office of Secondary Educational Service Area 20 in overall was at the high level with the mean of 4.21, the internal conflict was at the high level with the mean of 4.22, and the external conflict was at the high level with the mean of 4.19. 2. Overall, conflict management method used by administrators in Secondary School under the Office of Secondary Educational Service Area 20was at a high level. Considering each aspect, the compromising method was the highest level at 4.48. 3. Developing conflict management model in Secondary School under the Office of Secondary Educational Service Area 20 were the collaboration and making understand method. These should be used for conflict management to achieve the success and to reach the standard which including responsibility, accountability, equality, teamwork, and communication competence