Biomedical subjects

Tao Jiang

Publications and source records attributed to Tao Jiang.

At least 145 records · Page 8Linked to original sources

PubMed2003

Complete genome sequences of the SARS-CoV: the BJ Group (Isolates BJ01-BJ04).

Beijing has been one of the epicenters attacked most severely by the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) since the first patient was diagnosed in one of the city's hospitals. We now report complete genome sequences of the BJ Group, including four isolates (Isolates BJ01, BJ02, BJ03, and BJ04) of the SARS-CoV. It is remarkable that all members of the BJ Group share a common haplotype, consisting of seven loci that differentiate the group from other isolates published to date. Among 42 substitutions uniquely identified from the BJ group, 32 are non-synonymous changes at the amino acid level. Rooted phylogenetic trees, proposed on the basis of haplotypes and other sequence variations of SARS-CoV isolates from Canada, USA, Singapore, and China, gave rise to different paradigms but positioned the BJ Group, together with the newly discovered GD01 (GD-Ins29) in the same clade, followed by the H-U Group (from Hong Kong to USA) and the H-T Group (from Hong Kong to Toronto), leaving the SP Group (Singapore) more distant. This result appears to suggest a possible transmission path from Guangdong to Beijing/Hong Kong, then to other countries and regions.

Genome, Viral↗

PubMed2003

Excess non-synonymous substitutions suggest that positive selection episodes occurred during the evolution of DNA-binding domains in the Arabidopsis R2R3-MYB gene family.

It has been suggested that evolutionary changes in regulatory genes may be the predominant molecular mechanism governing both physiological and morphological evolution. R2R3-AtMYB is one of the largest transcription factor gene families in Arabidopsis. Using inferred ancestral sequences we show that several lineages in the R2R3-AtMYB phylogeny experienced excess non-synonymous nucleotide substitution upon gene duplication, indicating episodes of positive selection driving adaptive shifts early in the evolution of this gene family. A noise reduction technique was then used to determine individual sites in DNA-binding domains (R2 domain and R3 domain) of R2R3-AtMYB protein sequence that were favored by frequent non-synonymous substitutions. The analyses reveal that the first helix (helix1) and the second helix (helix2) in both R2 and R3 domains are characterized by more frequent non-synonymous substitutions, and thus experienced significantly higher positive selection pressure than the third helix (helix3) in both domains. Previous MYB protein structure studies have suggested that helix1 and helix2 in both R2 and R3 domains are involved in the characteristic packing of R2R3-AtMYB DNA-binding domains. This suggests that excess non-synonymous substitutions in these helices could have resulted in MYB recognition of novel gene target sites.

Amino Acid Sequence↗

PubMed2003

MAVG: locating non-overlapping maximum average segments in a given sequence.

SUMMARY: MAVG is a software tool for finding k non-overlapping maximum-average segments that are sufficiently long in a given sequence of real numbers, for any k > 0. It has applications in several areas of biomolecular sequence analysis including locating GC-rich regions and CpG islands in a genomic sequence, and annotating multiple sequence alignments. AVAILABILITY: http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/.

Algorithms↗

PubMed2003

Self-contained in-the-ear device to deliver altered auditory feedback: applications for stuttering.

The design and operating characteristics of the first self-contained in-the-ear device to deliver altered auditory feedback is described for applications with those who stutter. The device incorporates a microdigital signal processor core that reproduces the high fidelity of unaided listening and auditory self-monitoring while at the same time delivering altered auditory feedback. Delayed auditory feedback and frequency-altered feedback signals in combination or isolation can be generated to the user in a cosmetically appealing custom in-the-canal and completely-in-the-canal design. Programming of the device is achieved through a personal computer, interface, and fitting software. Researchers and clinicians interested in evaluating persons who stutter outside laboratory settings in a natural environment and persons who stutter looking for an alternative or adjunct to traditional therapy options are ideal candidates for this technology. In both instances an inconspicuous ear level alternative to traditional body worn devices with external microphones and earphones is offered.

Amplifiers, Electronic↗

PubMed2003

Computational assignment of protein backbone NMR peaks by efficient bounding and filtering.

NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on the combination of a suite of algorithms for automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques using two recently introduced approximation algorithms. We also devise a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm. Our result demonstrates that integrating different algorithms can achieve a good tradeoff between backbone assignment accuracy and computation time.

Algorithms↗

PubMed2003

Efficient inference of haplotypes from genotypes on a pedigree.

We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principle on pedigree data. We prove that the problem of finding a minimum-recombinant haplotype configuration (MRHC) is in general NP-hard. This is the first complexity result concerning the problem to our knowledge. An iterative algorithm based on blocks of consecutive resolved marker loci (called block-extension) is proposed. It is very efficient and can be used for large pedigrees with a large number of markers, especially for those data sets requiring few recombinants (or recombination events). A polynomial-time exact algorithm for haplotype reconstruction without recombinants is also presented. This algorithm first identifies all the necessary constraints based on the Mendelian law and the zero recombinant assumption, and represents them using a system of linear equations over the cyclic group Z2. By using a simple method based on Gaussian elimination, we could obtain all possible feasible haplotype configurations. A C++ implementation of the block-extension algorithm, called PedPhase, has been tested on both simulated data and real data. The results show that the program performs very well on both types of data and will be useful for large scale haplotype inference projects.

Algorithms↗

PubMed2003

Animal study on expression of laminin and fibronectin in cornea during wound healing following alkali burn.

OBJECTIVE: To observe the expression of laminin and fibronectin in alkali-burned corneas in rats. METHODS: A total of 18 normal Wistar rats were randomly divided into 6 groups (n = 3 in each group). For each rat, one eye was injured by alkali burn, the other one was taken as the normal control. Then all the corneas were surgically removed and the expression of laminin and fibronectin was observed with immunohistochemistry respectively at 7 hours, 1 day, 3 days, 7 days, 14 days and 28 days after alkali burn. RESULTS: Compared with that of the normal controls, the expression of laminin and fibronectin of the burned eyes was dramatically higher at 7 hours, reached peak at 14 days and decreased to the normal level at 28 days after alkali burn. CONCLUSIONS: In the process of wound healing after alkali burn, the expression of laminin and fibronectin increases dramatically, which suggests that laminin and fibronectin may participate in the process of corneal wound healing.

Animals↗

PubMed2003

Study on retinal ganglion cell apoptosis after explosive injury of eyeballs in rabbits.

PURPOSE: To explore the pathological changes of retinal ganglion cell apoptosis and its relation to the value of glutamate concentration in vitreous body after explosive injury of eyeballs in the rabbits. METHOD: Similar explosive injury models of eyeballs in 10 adult grey rabbits were made. The rabbits were killed on scheduled time. The retinal tissues of studied eyes and control eyes were obtained for the pathological examination with TUNEL method respectively. The value of glutamate in vitreum of injured eyes was measured and was compared with that of contralateral eyes. Statistical comparison analysis on the experiment data was performed. RESULT: The value of glutamate in vitreum of injured eyes was significantly higher than that of contralateral eyes in all rabbits in the study. A lot of TUNEL positive cells were observed in the injured eyes. It suggested that apoptosis of the retinal ganglion cells took place. CONCLUSION: We speculate that apoptosis of the retinal ganglion cells is perhaps among the causes resulting in damage of visual function after explosive injury of eyeballs and that the increasing of the value of glutamate in vitreum possibly associated with apoptosis of the retinal ganglion cells.

Animals↗

PubMed2003

[Measurement of sound pressure level at outlet of external auditory canal and eardrum].

OBJECTIVE: To evaluate the sound pressure level at outlet of external auditory canal and eardrum, and to observe the range of maximum frequency of sound effect of outlet ear canal, so as to provide exact data for designing personal noise rating instrument and studying the effect of environmental noise on human body, and to provide basis for calibration of noise sound pressure level. METHOD: Sound pressure level at eardrum and outlet of external auditory canal in 30 young people (60 ears) were measured by Audio Scan RM500 at 50 dB SPL narrow band noise with different frequencies (0.25 - 8.00 kHz). RESULTS: At the same frequency, sound pressure levels at eardrum were less than (0.6 +/- 2.6) dB SPL, at outlet of outlet ear canal less than (0.2 +/- 1.8) dB SPL, there were no significant differences between both sound pressure levels (P > 0.05). There were significant differences in sound pressure levels between both places at 1.50 - 8.00 kHz (P < 0.01). The maximum difference was (10.5 +/- 3.4) dB SPL at 2.00 kHz, and the minimum was (0.5 +/- 6.2) dB SPL at 0.50 kHz. CONCLUSION: The effects of increased sound pressure should be considered in the evaluation of environmental noise and the design for individual noise rating meter when the noise frequency was >or= 1.50 kHz.

Adult↗

PubMed2003

[Cell behavior of periodontal ligament cells cultured on commercially pure titanium].

OBJECTIVE: To study the cell behavior of periodontal ligament cells (PDLCs) cultured on commercially pure titanium (cpTi) by cell morphology, cell counting and osteoclin (OC) immunofluorescent staining. METHODS: 1 x 10(5)/ml PDLCs in 2 ml culture medium were seeded on cpTi discs fixed in 24-well culture plates. Morphological study of cell attachment was observed by scanning electron microscope (SEM) and fluorescence microscopy. Cell adhesion was analyzed by MTT at 0.5, 1, 2, 4 hours respectively. OC was directly observed by immunofluorescent staining. RESULTS: PDLCs could attach and spread on cpTi discs. SEM showed that PDLCs had pseudopod-like protuberance. PDLCs showed different attaching phase and reached saturation in cell number at the early stage. The cells and ECM could express OC 7 days later. CONCLUSION: PDLCs show a regular, dynamic pattern in early stage and they can keep proliferating and differentiating on CpTi in vitro. It was indicated that the biological function of PDLCs around dental implant should be reconsidered.

Cells, Cultured↗

PubMed2003

Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102.

We present a computational protocol for inference of regulatory and signaling pathways in a microbial cell, through literature search, mining "high-throughput'' biological data of various types, and computer-assisted human inference. This protocol consists of four key components: (a) construction of template pathways for microbial organisms related to the target genome, which either have been extensively studied and/or have a significant amount of (relevant) experimental data, (b) inference of initial pathway models for the target genome, through combining the template pathway models and target genome-specific information, (c) refinement and expansion of the initial pathway models through applications of various data mining tools, including phylogenetic profile analysis, inference of protein-protein interactions, and prediction of transcription factor binding sites, and (d) validation and refinement of the pathway models using pathway-specific experimental data or other information. To demonstrate the effectiveness of this procedure, we have applied it to the construction of the phosphorus assimilation pathways in cyanobacterium sp. WH8102. We present, in this paper, a model of the core components of this pathway.

Bacterial Proteins↗

PubMed2003

Clustering binary fingerprint vectors with missing values for DNA array data analysis.

Oligonucleotide fingerprinting is a powerful DNA array based method to characterize cDNA and ribosomal RNA gene (rDNA) libraries and has many applications including gene expression profiling and DNA clone classification. We are especially interested in the latter application. A key step in the method is the cluster analysis of fingerprint data obtained from DNA array hybridization experiments. Most of the existing approaches to clustering use (normalized) real intensity values and thus do not treat positive and negative hybridization signals equally (positive signals are much more emphasized). In this paper, we consider a discrete approach. Fingerprint data are first normalized and binarized using control DNA clones. Because there may exist unresolved (or missing) values in this binarization process, we formulate the clustering of (binary) oligonucleotide fingerprints as a combinatorial optimization problem that attempts to identify clusters and resolve the missing values in the fingerprints simultaneously. We study the computational complexity of this clustering problem and a natural parameterized version, and present an efficient greedy algorithm based on MINIMUM CLIQUE PARTITION on graphs. The algorithm takes advantage of some unique properties of the graphs considered here, which allow us to efficiently find the maximum cliques as well as some special maximal cliques. Our experimental results on simulated and real data demonstrate that the algorithm runs faster and performs better than some popular hierarchical and graph-based clustering methods. The results on real data from DNA clone classification also suggest that this discrete approach is more accurate than clustering methods based on real intensity values, in terms of separating clones that have different characteristics with respect to the given oligonucleotide probes.

Algorithms↗

PubMed2002

Chemical reaction in binary mixtures near the critical region: thermal decomposition of 2,2'-azobis(isobutyronitrile) in CO2/ethanol.

The effects of pressure and of the composition of the CO2/ethanol mixed solvent in the critical region on the kinetics of the decomposition of 2,2'-azobis(isobutyronitrile) (AIBN) were studied at 333.15 K. The rate constants (kd) in the mixed solvent far from the critical point and in liquid n-hexane and ethanol were also determined for comparison. It was found that kd is very sensitive to pressure in the mixed solvent near the critical point. However, in the mixed solvent outside the critical region kd is nearly independent of pressure. Interestingly, kd in the mixed solvent in the critical region can be higher than that in ethanol at the same temperature, suggesting that no significant enhancement in the reaction rate by a small pressure change in the critical region of the mixed solvent can be achieved by changing the composition of the liquid solvent in the traditional way. Transition-state theory can predict kd in the mixed solvent far from the critical point and in the liquid solvents well. However, it cannot predict kd in the mixed solvent in the critical region. The special intermolecular interaction between the solvent and the reaction species may contribute to this interesting phenomenon. This work also shows that if pure CO2 or ethanol are used as solvents, the reaction cannot be carried out in the critical region of the solvents at the desired temperature, while it can be conducted in the critical region of the mixed solvent of suitable composition, where the solvent is highly compressible.

Journal Article↗

PubMed2002

Why do co-solvents enhance the solubility of solutes in supercritical fluids? New evidence and opinion.

The effects of two polar co-solvents, chlorodifluoromethane and acetone, on the solubility and enthalpy of a solution of 1,4-naphthoquinone in supercritical (SC) CO2 were studied. We found that the dissolution process becomes less exothermic in the presence of the co-solvents relative to that in pure CO2, although the solubility is enhanced significantly by the co-solvents. This indicates that the increase in the solubility by adding co-solvents results from the increase of the entropy of solution. On the basis of the unexpected results we propose a new mechanism for the solubility enhancement of the solute by the co-solvents in supercritical fluids (SCF); this should be applicable to cases in which the local density of the SC solvent around the solute and the co-solvent is larger, and the co-solvent associates preferentially with the solute. The results are also very important for the understanding of other fundamental questions of SCF science, such as the effect of co-solvents on the thermodynamic and kinetic properties of the reactions in SCFs.

Journal Article↗

PubMed2002

Crystallization and preliminary X-ray diffraction studies of cobra venom beta-nerve growth factor.

beta-Nerve growth factor (beta-NGF) is a 118 amino acid residue polypeptide with an important role in the survival and development of certain neuronal populations. A beta-NGF purified from cobra venom was crystallized by the hanging-drop vapor diffusion method. The crystals belong to the tetragonal space group P4(1)2(1)2 (or its enantiomorph P4(3)2(1)2) with unit-cell parameters a=b=61.75, c=154.40A. X-ray data from these crystals were collected to 3.2A resolution. Analysis of the packing density shows that the asymmetric unit probably contains two molecules. The self-rotation calculation implied that a beta-NGF dimer might exist in the asymmetric unit.

Animals↗

PubMed2002

Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily.

The three-dimensional structures of brain pyridoxal kinase and its complex with the nucleotide ATP have been elucidated in the dimeric form at 2.1 and 2.6 A, respectively. Results have shown that pyridoxal kinase, as an enzyme obeying random sequential kinetics in catalysis, does not possess a lid shape structure common to all kinases in the ribokinase superfamily. This finding has been shown to be in line with the condition that pyridoxal kinase binds substrates with variable sizes of chemical groups at position 4 of vitamin B(6) and its derivatives. In addition, the enzyme contains a 12-residue peptide loop in the active site for the prevention of premature hydrolysis of ATP. Conserved amino acid residues Asp(118) and Tyr(127) in the peptide loop could be moved to a position covering the nucleotide after its binding so that its chance to hydrolyze in the aqueous environment of the active site was reduced. With respect to the evolutionary trend of kinase enzymes, the existence of this loop in pyridoxal kinase could be classified as an independent category in the ribokinase superfamily according to the structural feature found and mechanism followed in catalysis.

Animals↗

PubMed2002

Crystal structure studies on rubrerythrin: enzymatic activity in relation to the zinc movement.

Rubrerythrin (Rr) is a non-heme iron protein isolated from anaerobic sulfate-reducing bacteria. Rr is a dimeric molecule, each monomer contains a Fe(SCys)(4) center in the C-terminal domain and a binuclear metal center in the N-terminal domain. Rr structures with different protein sources and/or preparation procedures have been studied. Two Rr crystal structures have been solved with significant differences in their binuclear metal centers. The first structure, which was obtained from expressed protein under aerobic conditions, has a diiron-oxo center. The second structure, which was obtained from native protein of Desulfovibrio vulgaris under aerobic conditions, has an Fe-Zn center with the zinc position differing from the corresponding iron position in the former structure by approximately 2 A. The crystal structures of Rr isolated from D. vulgaris (Hildenborough, NCIB 8303), the same as the second structured but prepared under anaerobic conditions, are reported in this paper. The binuclear metal center in these structures is an Fe-Zn center. When the crystal was exposed to air, the zinc atom moved gradually, approximately 2 A, accompanied by the entrance of a water molecule (or hydroxyl group) and changes in the binuclear metal center microenvironment. This finding can explain the differences between the two different structures. The results suggest that the zinc movement may be related to the enzymatic activity of Rr.

Bacterial Proteins↗

PubMed2002

Recovery of silver nanoparticles synthesized on AOT/C(12)E(4) mixed reverse micelles by antisolvent CO(2).

Silver nanoparticles were synthesized in sodium bis(2-ethylhexyl)sulfosuccinate (AOT) reverse micelles in isooctane with tetraethylene glycol dodecyl ether (C(12)E(4)) as a cosurfactant. Recovery of the Ag particles from the reverse micelles by dissolving antisolvent CO(2) in the micellar solution was investigated. All the Ag particles in the reverse micelles could be precipitated by compressed CO(2) at suitable pressures, while the surfactants remained in the isooctane continuous phase, and well-dispersed Ag nanoparticles were obtained. The effects of operating conditions on the size and size distribution of the Ag particles were investigated. The particle size decreased with decreasing molar ratio (w) of water to surfactant. A higher CO(2) pressure in the recovery process favored production of smaller particles. A decrease in the molar ratio of reductant KBH(4) to AgNO(3) resulted in larger Ag particles with higher polydispersity.

Journal Article↗