Identifying DNA motifs based on match and mismatch alignment information

The conventional way of identifying DNA motifs, solely based on match alignment information, is susceptible to a high number of spurious sites. A novel scoring system has been introduced by taking both match and mismatch alignment information into account. The mismatch alignment information is useful to remove spurious sites encountered in DNA motif searching. As an example, a correct TATA box site in Homo sapiens H4/g gene has successfully been identified based on match and mismatch alignment information

Fourier-based classification of protein secondary structures

The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices

Programmable DNA-mediated multitasking processor

Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices

In Vitro Antibacterial Effect of Lactobacillus plantarum Postbiotics Against Fish Bacterial Pathogens

The intensification of aquaculture farms leads to stressful conditions for fish. This causes the outbreak of bacterial diseases and lowers production in aquaculture. Probiotics and chemical treatments are effective, but it possesses a risk to the environment and human health. Postbiotics emerged to become one of the treatments for bacterial diseases. In this study, Lactobacillus plantarum GS12 and GS13 strains were used to determine the antibacterial effect of postbiotics on different pathogenic bacteria. The postbiotics were extracted and both strains show positive inhibition in the screening test. The postbiotics from both strains of L. plantarum were then used for further testing on minimum inhibitory concentration. Postbiotic from GS12 showed no inhibition activity, whereas GS13 has the lowest inhibition concentration of 8.0 µg ml⁻¹ when tested on Aeromonas hydrohila and Vibrio harveyi, and 16.7 µg ml⁻¹ when tested on A. salmonicida and V. parahaemolyticus. Postbiotic produced by L. plantarum GS13 had better capacity in terms of antibacterial effect compared to L. plantarum GS12. L. plantarum GS13 postbiotics may be useful against bacterial disease in the future. This study shows a potential alternative control measure for bacterial disease often occurring in aquaculture

Adjunctive benzodiazepine treatment of hospitalized schizophrenia patients in Asia from 2001 to 2008

10.1017/S146114571000163XThe International Journal of Neuropsychopharmacology146735-74

DNA-based computing

DNA-based computing provides an alternative to solving optimization problems in graph theory. In this research, it is shown how DNA-based computing is used to find solutions to these problems, which involve logical thinking and are often NP hard complete. These include the shortest path, shortest spanning tree, maximum flow and maximum bipartite matching problems. DNA-based computing is a suitable tool for these problems because of its massive parallelism during computation. The success of a DNA-based experiment designed around the shortest path problem, global positioning system problem, reinforced and revealed the potential of this approach.DOCTOR OF PHILOSOPHY (MAE

DNA and protein sequence analysis

The objective of this thesis is to improve the analysis of DNA and protein sequences. Sequence analysis is an important step in drug design to find the relationship among DNA sequences, protein sequences and their functions. The effectiveness of a drug is very much dependent on the correct associations of the sequences to their functions. In this thesis, three novel methods have been developed to enhance the analysis of DNA and protein sequences. Two of the methods target the alignment and prediction of motif sites in DNA sequences. Their improvements are made by introducing joint and vector weight matrix scoring scheme. The third method targets the protein secondary structures, by using new classification indices. The new results show that the structures can be classified into more categories as compared with the existing methods, which hydrophobicity factor is solely considered as a classification index.Master of Engineering (MAE

An improved scoring matrix for multiple sequence alignment

The way for performing multiple sequence alignment is based on the criterion of the maximum-scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper addresses this issue by introducing the concept of joint weight matrix to eliminate the randomness in selecting the best multiple sequence alignment. Alignments with equal scores are iteratively rescored with the joint weight matrix of increasing level (nucleotide pairs, triplets, and so on) until one single best alignment is eventually found. This method for resolving ambiguity in multiple sequence alignment can be easily implemented by use of the improved scoring matrix.Published versio

DNA-based computing of strategic assignment problems

DNA-based computing is a novel technique to tackle computationally difficult problems, in which computing time grows exponentially corresponding to problematic size. A strategic assignment problem is a typical nondeterministic polynomial problem, which is often associated with strategy applications. In this Letter, a new approach dealing with strategic assignment problems is proposed based on manipulating DNA strands, which is believed to be better than the conventional silicon-based computing in solving the same problem.Published versio