Biomedical subjects
Publications and source records attributed to Bin Ma.
UNLABELLED: New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx. AVAILABILITY: The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/ CONTACT: bma@csd.uwo.ca.
A bioanalytical method using liquid chromatography-tandem mass spectrometry was developed for the analysis of fluconazole in Candida albicans after incubation with phenolic compounds, which have been proved possessing antifungal properties and have synergetic activity against C. albicans when in combination with fluconazole. Samples of C. albicans thallus obtained by centrifuging the mixed culture after 24 h incubation were saponified and centrifuged. The supernatant was evaporated to dryness, reconstituted, and injected on a C18 column using an organic-aqueous mobile phase. The chromatographic run time was 3.5 min per injection, with retention times of 2.4 min for fluconazole. The detection was by monitoring fluconazole at m/z 305-->191. The standard curve range was 1.0-100.0 ng ml(-1) with a mean correlation coefficient 0.9992. The precision and accuracy of the quality control (QC) samples were R.S.D < 5.5%, R.E. <3% for intra-day and R.S.D. <6.2%, R.E. <4% for inter-day. The concentration of fluconazole in C. albicans was found to be increased with the increment of the tested compounds concentration when they were in combination.
Separation of the water-soluble fraction of peanut skins led to the isolation of five proanthocyanidins. Based on the spectroscopic investigation and partial acid catalyzed degradation, their structures were determined to be epicatechin-(2beta-->O -->7, 4beta -->6)-[epicatechin-(4beta-->8)]-catechin (1), epicatechin-(2beta-->O -->7, 4beta-->8) epicatechin-(4beta-->8)-catechin-(4alpha-->8)-epicatechin (2), and procyanidins B2 (3), B3 (4) and B4 (5). The absolute configuration of the new compounds was determined from their circular dichroism curves and the (1)H NMR spectra of analysis of flavan-3-ols formed by thiolytic degradation of 1 and 2 in the presence of a chiral dirhodium complex (dirhodium tetra-(R)-(trifluoromethyl) phenyl acetate).
From Peucedanum praeruptorum, one new khellactone ester (3'R)-O-acetyl-(4'S)-O-angeloylkhellactone (3), as well as four known angular dihydropyranocoumarins (1, 2, 4, 5) have been isolated. On the basis of NMR spectra and X-ray crystallography, their structures were determined. We have elucidated their absolute configuration by either chiral separation of their alkaline hydrolysis products with Rp-18 HPLC eluted with 5% hydroxypropyl-beta-cyclodextrin (beta-HCD) or by measurement of their CD spectra. A general rule relating the position and absolute streochemistry of the khellactone esters to the sign of their Cotton effects in CD curves is proposed.
For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software.
Extending the single optimized spaced seed of PatternHunter(20) to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search methodology research back to a full circle.
We review recent results on local alignment. We begin with a review of classical methods and early heuristic methods, and then focus on more recent work on the seeding of local alignment. We show that these techniques give a vast improvement in both sensitivity and specificity over previous methods, and can achieve sensitivity at the level of classical algorithms while requiring orders of magnitude less runtime.
OBJECTIVE: To prevent or reduce such postoperative complications of pneumonectomy as bronchopleural fistula and promote the curative effect of the surgery by improving the technique for handling the bronchial stumps. METHODS: In 107 patients, bronchial stapler was adopted for closure of the bronchial stump and pneumonectomy was subsequently performed on the side of the staples. A 1-0 polyester suture was used to for suture in the shape of "U" deep in the mechanical suture on the bronchial stump. The postoperative complications were observed. RESULTS: The operations were performed easily and the bronchial stumps were short and sutured firmly. No fluid retention or granuloma occurred in the stumps after the operation, nor were the complications such as intractable cough and infection of thoracic cavity observed. No bronchopleural fistula was found in these patients. CONCLUSION: This new method is safe and effective for treatment of the bronchial stumps.
OBJECTIVE: To develop a method for determination of luteolin-7-O-glycoside in the roots, stems, leafs, flowers and aerial parts of Dracocephalum rupestra sampled in different seasons. METHOD: The samples were analyzed on an phenomenex C18 column, with mobile phase of methanol-acetonitrile-0.4% phosphoric acid (30:8:62) at flow rate 1.0 mL x min(-1) and detection at wavelength of 350 nm. RESULT: The content of luteolin-7-O-glycoside in different parts of D. rupestra was different maximum in leaves, while minimum in stems. Luteolin-7-O-glycoside in D. rupestra sampled before blossoming was the highest. CONCLUSION: The method simple, accurate and suitable for the quality evaluation of this plant medicine.
MOTIVATION: Genome analysis suggests that tandem duplication is an important mode of evolutionary novelty by permitting one copy of each gene to drift and potentially to acquire a new function. With more and more genomic sequences available, reconstructing duplication history has received extensive attention recently. RESULTS: An efficient method is presented for inferring the duplication history of tandemly repeated sequences based on the model proposed by Fitch (1977). We validate the method by using simulation results and real data sets of mucin genes, ZNF genes, and olfactory receptors genes. The agreement with conclusions drawn by other biological researchers strongly indicates that our method is efficient and robust. AVAILABILITY: The program is available by request.
A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.
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Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.
[reaction: see text] A new, high-yielding route to functionalized bicyclo[4.2.1]nonanes has been achieved utilizing homo Diels-Alder chemistry with subsequent Zeise's dimer-catalyzed opening of the cycloadduct.
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Arc-annotated sequences are useful in representing the structural information of RNA sequences. In general, RNA secondary and tertiary structures can be represented as a set of nested arcs and a set of crossing arcs, respectively. Since RNA functions are largely determined by molecular confirmation and therefore secondary and tertiary structures, the comparison between RNA secondary and tertiary structures has received much attention recently. In this paper, we propose the notion of edit distance to measure the similarity between two RNA secondary and tertiary structures, by incorporating various edit operations performed on both bases and arcs (i.e., base-pairs). Several algorithms are presented to compute the edit distance between two RNA sequences with various arc structures and under various score schemes, either exactly or approximately, with provably good performance. Preliminary experimental tests confirm that our definition of edit distance and the computation model are among the most reasonable ones ever studied in the literature.
While achieving the best compression ratios for DNA sequences, our new DNACompress program significantly improves the running time of all previous DNA compression programs.
MOTIVATION: Genomics and proteomics studies routinely depend on homology searches based on the strategy of finding short seed matches which are then extended. The exploding genomic data growth presents a dilemma for DNA homology search techniques: increasing seed size decreases sensitivity whereas decreasing seed size slows down computation. RESULTS: We present a new homology search algorithm 'PatternHunter' that uses a novel seed model for increased sensitivity and new hit-processing techniques for significantly increased speed. At Blast levels of sensitivity, PatternHunter is able to find homologies between sequences as large as human chromosomes, in mere hours on a desktop. AVAILABILITY: PatternHunter is available at http://www.bioinformaticssolutions.com, as a commercial package. It runs on all platforms that support Java. PatternHunter technology is being patented; commercial use requires a license from BSI, while non-commercial use will be free.