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Biomedical subjects

Tao Jiang

Publications and source records attributed to Tao Jiang.

At least 37 records · Page 2Linked to original sources
PubMed2006

In vitro evaluation of chitosan/poly(lactic acid-glycolic acid) sintered microsphere scaffolds for bone tissue engineering.

A three-dimensional (3-D) scaffold is one of the major components in many tissue engineering approaches. We developed novel 3-D chitosan/poly(lactic acid-glycolic acid) (PLAGA) composite porous scaffolds by sintering together composite chitosan/PLAGA microspheres for bone tissue engineering applications. Pore sizes, pore volume, and mechanical properties of the scaffolds can be manipulated by controlling fabrication parameters, including sintering temperature and sintering time. The sintered microsphere scaffolds had a total pore volume between 28% and 37% with median pore size in the range 170-200microm. The compressive modulus and compressive strength of the scaffolds are in the range of trabecular bone making them suitable as scaffolds for load-bearing bone tissue engineering. In addition, MC3T3-E1 osteoblast-like cells proliferated well on the composite scaffolds as compared to PLAGA scaffolds. It was also shown that the presence of chitosan on microsphere surfaces increased the alkaline phosphatase activity of the cells cultured on the composite scaffolds and up-regulated gene expression of alkaline phosphatase, osteopontin, and bone sialoprotein.

3T3 Cells↗
PubMed2006

Development of a 9600-clone procedure for oligonucleotide fingerprinting of rRNA genes: utilization to identify soil bacterial rRNA genes that correlate in abundance with the development of avocado root rot.

Oligonucleotide fingerprinting of rRNA genes (OFRG) is an array-based method that generates microbial community profiles through analysis of rRNA gene clone libraries. The original OFRG method allowed 1536 clones to be analyzed per experiment. This report describes a procedure for analyzing 9600 clones per experiment, including a new probe set for bacterial analysis, and improved data processing and statistical analysis tools. The software tools are available at the OFRG website (). Use of the 9600-clone procedure was demonstrated by examining the bacterial rRNA gene compositions of soils subjected to various temperature treatments. These treatments produced a series of soils with a range of abilities to suppress avocado root rot, enabling the identification of bacterial rRNA genes that correlate in abundance with root rot suppressiveness. OFRG analysis of these soils produced 8876 bacterial rRNA gene fingerprints grouped into 5123 clusters, or operational taxonomic units (OTUs). Eleven OTUs exhibited a positive correlation between the number of clones and the percentage of healthy roots. An in silico analysis was performed to examine the relationship between the number of rRNA genes analyzed and the number of correlates (rRNA gene-avocado root rot symptoms) identified. As the number of clones decreased, fewer correlates were identified. To further increase the throughput of the OFRG method, use of a glass slide-fluorescent probe microarray format was also explored.

DNA Fingerprinting↗
PubMed2006

A hybrid method for predicting the microstructure of polymers with complex architecture: combination of single-chain simulation with density functional theory.

A hybrid method is proposed to investigate the microstructure of various polymeric fluids confined between two parallel surfaces. The hybrid method combines a single-chain Monte Carlo (MC) simulation for the ideal-gas part of the Helmholtz energy and a density functional theory (DFT) for the excess part that arises from nonbonded intersegment interactions. The latter consists of a modified fundamental measure theory for excluded-volume effect, the first-order thermodynamics perturbation theory for chain connectivity, and a mean-field approximation for the van der Waals attraction. In comparison with a conventional DFT, the hybrid method avoids calculation of the time-consuming recursive functions and is directly applicable to polymers with arbitrary molecular architecture. Its numerical performance has been validated by extensive comparisons with MC data for the density distributions of totally flexible, semiflexible, or rigid polymers and those with starlike architecture. Special attention is also given to the formation of a nematic monolayer by rigid molecules laying perpendicular to a planar surface. The hybrid method predicts the surface pressure versus surface coverage in good agreement with experiment.

Journal Article↗
PubMed2006

Crystal structure of human pyridoxal kinase.

Pyridoxal kinase, a member of the ribokinase superfamily, catalyzes the ATP-dependent phosphorylation reaction of vitamin B6 and is an essential enzyme in the formation of pyridoxal-5'-phosphate, a key cofactor for over 100 enzymes. Pyridoxal kinase is thus regarded as a potential target for pharmacological agents. In this paper, we report the 2.8 angstroms crystal structure of human pyridoxal kinase (HPLK) expressed in Escherichia coli. The diffraction data revealed unexpected merohedral perfect twinning along the crystallographic c axis. Taking perfect twinning into account, the structure in dimeric form was well refined according to the CNS program. Structure comparison reveals that the key 12-residue peptide over the active site in HPLK is a beta-strand/loop/beta-strand flap, while the corresponding peptide in sheep brain enzyme adopts a loop conformation. Moreover, HPLK possesses a more hydrophobic ATP-binding pocket. This structure will facilitate further biochemical studies and structure-based design of drugs related to pyridoxal kinase.

Adenosine Triphosphate↗
PubMed2006

Design and synthesis of 7H-pyrrolo[2,3-d]pyrimidines as focal adhesion kinase inhibitors. Part 2.

A series of 2-amino-9-aryl-7H-pyrrolo[2,3-d]pyrimidines were designed and synthesized as focal adhesion kinase (FAK) inhibitors using molecular modeling in conjunction with a co-crystal structure. Chemistry was developed to introduce functionality onto the 9-aryl ring, which resulted in the identification of potent FAK inhibitors. In particular, compound 32 possessed single-digit nanomolar IC(50) and represents one of the most potent FAK inhibitors discovered to date.

Enzyme Inhibitors↗
PubMed2006

Studies on induction of L-aspartic acid modified chitosan to crystal growth of the calcium phosphate in supersaturated calcification solution by quartz crystal microbalance.

Acidic amino acids, such as aspartic acid (L-Asp) and glutamic acid, are the primary bioactive molecules of the glycoprotein on the organic/inorganic interface of biomineralized tissues. In this study, the induction of chitosan film modified with L-Asp on the crystal growth of hydroxyapatite (HAP) was investigated by a novel in situ analysis approach, quartz crystal microbalance (QCM), associated with the dynamically structural and morphological characterization of precipitation products on various phases by X-ray diffraction (XRD), Fourier-transformed infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM). The natural chitosan exhibited no inducing ability on the crystal growth of HAP. However, the growth rate of induced HAP was dramatically accelerated by the L-Asp modification of chitosan film and increased with the increase of the concentration of L-Asp in the chitosan substrate. It was shown that the chelation of calcium ion with L-Asp provided a nucleation centre and the cluster nuclei was formed by adsorbing further PO(4)(3-), Ca(2+), and then HAP deposited on the original HAP coating in the supersaturated calcification solution (SCS). The developed method allows a kinetic evaluation of the induction of organic film on crystal nucleation and the growth of HAP in vitro.

Aspartic Acid↗
PubMed2006

Design, synthesis and biological evaluations of novel oxindoles as HIV-1 non-nucleoside reverse transcriptase inhibitors. Part I.

A novel oxindole was discovered as an HIV non-nucleoside reverse transcriptase inhibitor via HTS using a cell-based assay. Systematic structural modifications were carried out to establish its SAR. These modifications led to the identification of oxindoles with low nanomolar potency for inhibiting HIV replication. These novel and potent oxindoles could serve as advanced leads for further optimizations.

Anti-HIV Agents↗
PubMed2006

Design and synthesis of 7H-pyrrolo[2,3-d]pyrimidines as focal adhesion kinase inhibitors. Part 1.

A series of 2-amino-9-aryl-7H-pyrrolo[2,3-d]pyrimidines were designed and synthesized to target focal adhesion kinase (FAK). A number of these pyrrolopyrimides exhibited low micromolar inhibitory activities against focal adhesion kinase, and their preliminary SAR was established via systematic chemical modifications. The 2-amino-9-aryl-7H-pyrrolo[2,3-d]pyrimidines represent a new class of kinase inhibitors.

Antineoplastic Agents↗
PubMed2006

Does modification of olfacto-gustatory stimulation diminish sensory-specific satiety in humans?

UNLABELLED: Alimentary sensory pleasure is an important factor in ingestive behavior. Renewal of olfacto-gustatory pleasure by introducing new foods or through seasoning of previously consumed food might increase intake. OBJECTIVES: To explore whether sensory-specific satiety (SSS) for a food could be modulated, either by introducing a novel food or by a modification of sensory stimulation via seasoning the food just eaten. METHODS: 180 out of 242 subjects were distributed over 3 experiments involving ad libitum intake of one of 6 fresh foods (cucumber, tomato, pineapple, banana, peanut, pistachio). Blindfolded subjects reported their sensations for the foods on 3 parameters before and after intake of an olfactorily chosen food: Olfactory pleasure (OP), Specific appetite (SA) and Stimulus-Induced Salivation (SIS). EXP. 1: One chosen food was repeatedly presented orthonasally and rated before and after it was eaten. EXP. 2: A second food was olfactorily chosen and ingested after the first one. EXP. 3: The same food was offered again after seasoning. RESULTS: 2 min after ingestion, food intake was limited by SSS. OP, SA, SIS correlated with each other for eaten and non-eaten foods. OP for non-eaten foods increased (p<0.01) after ingestion of the chosen food to specific satiety. When the food just eaten was seasoned, OP increased (p<0.01) and led to additional intake (80% of first intake). CONCLUSION: A reduction in SSS after introduction of a new flavor or after seasoning an ingested food was observed. Such a reduction has not previously been reported. This could hint at how food sensory variation leads to over-consumption.

Adolescent↗
PubMed2006

Controlled synthesis of Ag/TiO2 core-shell nanowires with smooth and bristled surfaces via a one-step solution route.

Ag/TiO2 core-shell nanowires were synthesized via a one-step solution method without using a template. Interestingly, the shell morphologies can be controlled to be smooth or bristled by altering the reaction temperature. Moreover, the TiO2 shell thickness and bristle length can be tuned by changing the AgNO3 concentration. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), selected-area electron diffraction (SAED), energy-dispersive X-ray analysis (EDS), X-ray powder diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) were used to characterize the resultant Ag/TiO2 core-shell nanowires. Moreover, the absorption peaks of our samples are significantly red-shifted compared with those of the uncoated pure silver nanowires, indicating that interaction between the core and shell occurred. On the basis of the experimental results, we proposed a template-induced Oswald ripening mechanism to explain the formation of the Ag/TiO2 core-shell nanowires.

Journal Article↗
PubMed2006

OligoSpawn: a software tool for the design of overgo probes from large unigene datasets.

BACKGROUND: Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets. RESULTS: OLIGOSPAWN is a suite of software tools that offers two complementary services, namely (1) the selection of "unique" oligos each of which appears in one unigene but does not occur (exactly or approximately) in any other and (2) the selection of "popular" oligos each of which occurs (exactly or approximately) in as many unigenes as possible. In this paper, we describe the functionalities of OLIGOSPAWN and the computational methods it employs, and we report on experimental results for the overgo probes designed with it. CONCLUSION: The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of several tens of Mb in a few hours on a regular PC. The software has been used to design overgo probes employed to screen a barley BAC library (Hordeum vulgare). OLIGOSPAWN is freely available at http://oligospawn.ucr.edu/.

Base Sequence↗
PubMed2006

Efficient and robust feature extraction by maximum margin criterion.

In pattern recognition, feature extraction techniques are widely employed to reduce the dimensionality of data and to enhance the discriminatory information. Principal component analysis (PCA) and linear discriminant analysis (LDA) are the two most popular linear dimensionality reduction methods. However, PCA is not very effective for the extraction of the most discriminant features, and LDA is not stable due to the small sample size problem. In this paper, we propose some new (linear and nonlinear) feature extractors based on maximum margin criterion (MMC). Geometrically, feature extractors based on MMC maximize the (average) margin between classes after dimensionality reduction. It is shown that MMC can represent class separability better than PCA. As a connection to LDA, we may also derive LDA from MMC by incorporating some constraints. By using some other constraints, we establish a new linear feature extractor that does not suffer from the small sample size problem, which is known to cause serious stability problems for LDA. The kernelized (nonlinear) counterpart of this linear feature extractor is also established in the paper. Our extensive experiments demonstrate that the new feature extractors are effective, stable, and efficient.

Algorithms↗
PubMed2006

Aldose reductase regulates TGF-beta1-induced production of fibronectin and type IV collagen in cultured rat mesangial cells.

AIM: To study the effects of aldose reductase (AR) on production of fibronectin and type IV collagen in rat mesangial cells (MsC). METHODS: The vector, pcDNA3-AR, was constructed based on pET-15b-AR. Lipofect AMINE was used for stable transfection and G418 was used for selecting positive clones. Sorbinil and zopolrestat were added for suppressing the activity of AR, respectively. The production of fibronectin and type IV collagen and the activation of Smads and MAPK signal transduction pathway were analysed by western blot and AP-1 activity was analysed by electrophoretic mobility shift assays (EMSA). RESULTS: The normal MsC showed increased expression of fibronectin and type IV collagen with stimulation of TGF-beta1. Compared with the normal MsC, the MsC pre-incubated with ARI showed reduced expression (P < 0.05) and the AR-transfected MsC showed increased expression (P < 0.05). The normal MsC showed activation of ERK, JNK and p38 with stimulation of TGF-beta1, while the activation of JNK and p38 was inhibited in the MsC pre-incubated with ARI and only the activation of JNK was enhanced in the AR-transfected MsC. The normal MsC showed enhanced AP-1 activity with the stimulation of TGF-beta1, and similarly the activity was inhibited in the MsC pre-incubated with ARI and was more enhanced in the AR transfected MsC. CONCLUSION: AR can regulate the expression of fibronectin and type IV collagen with the stimulation of TGF-beta1 in MsC, which may have relations with the activation of JNK-MAPK and p38-MAPK signalling pathways and AP-1.

Aldehyde Reductase↗
PubMed2006

A general framework for biclustering gene expression data.

A large number of biclustering methods have been proposed to detect patterns in gene expression data. All these methods try to find some type of biclusters but no one can discover all the types of patterns in the data. Furthermore, researchers have to design new algorithms in order to find new types of biclusters/patterns that interest biologists. In this paper, we propose a novel approach for biclustering that, in general, can be used to discover all computable patterns in gene expression data. The method is based on the theory of Kolmogorov complexity. More precisely, we use Kolmogorov complexity to measure the randomness of submatrices as the merit of biclusters because randomness naturally consists in a lack of regularity, which is a common property of all types of patterns. On the basis of algorithmic probability measure, we develop a Markov Chain Monte Carlo algorithm to search for biclusters. Our method can also be easily extended to solve the problems of conventional clustering and checkerboard type biclustering. The preliminary experiments on simulated as well as real data show that our approach is very versatile and promising.

Algorithms↗
PubMed2006

Crystallization and preliminary x-ray diffraction analysis of three mastoparans.

Mastoparans are tetradecapeptides found to be the major component of wasp venoms. These peptides possess a variety of biological activities. Three related mastoparans, mastoparan from Polistes jadwagae (MP-PJ), mastoparanX (MP-X) and its carboxyl-free C-terminal form (MP-X-COO-), were crystallized. X-ray diffraction data for them were collected at resolutions of 1.2 A, 2.0 A and 3.3 A respectively.

Amino Acid Sequence↗
PubMed2006

Regulation of renal fatty acid and cholesterol metabolism, inflammation, and fibrosis in Akita and OVE26 mice with type 1 diabetes.

In Akita and OVE26 mice, two genetic models of type 1 diabetes, diabetic nephropathy is characterized by mesangial expansion and loss of podocytes, resulting in glomerulosclerosis and proteinuria, and is associated with increased expression of profibrotic growth factors, proinflammatory cytokines, and increased oxidative stress. We have also found significant increases in renal triglyceride and cholesterol content. The increase in renal triglyceride content is associated with 1) increased expression of sterol regulatory element-binding protein (SREBP)-1c and carbohydrate response element-binding protein (ChREBP), which collectively results in increased fatty acid synthesis, 2) decreased expression of peroxisome proliferator-activated receptor (PPAR)-alpha and -delta, which results in decreased fatty acid oxidation, and 3) decreased expression of farnesoid X receptor (FXR) and small heterodimer partner (SHP). The increase in cholesterol content is associated with 1) increased expression of SREBP-2 and 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase, which results in increased cholesterol synthesis, and 2) decreased expression of liver X receptor (LXR)-alpha, LXR-beta, and ATP-binding cassette transporter-1, which results in decreased cholesterol efflux. Our results indicate that in type 1 diabetes, there is altered renal lipid metabolism favoring net accumulation of triglycerides and cholesterol, which are driven by increases in SREBP-1, ChREBP, and SREBP-2 and decreases in FXR, LXR-alpha, and LXR-beta, which may also play a role in the increased expression of profibrotic growth hormones, proinflammatory cytokines, and oxidative stress.

Animals↗