Biomedical subjects

Ting Chen

Publications and source records attributed to Ting Chen.

At least 55 records · Page 3Linked to original sources

PubMed2005

Effects of microcystin-LR on patterns of iNOS and cytokine mRNA expression in macrophages in vitro.

The presence of cyanobacterial toxins in drinking and recreational waters represent a potential health hazard to the public. Microcystin-LR (MC-LR) is the most commonly encountered toxin and is a potent cyclic heptapeptide hepatotoxin produced by cyanobacteria. In this study, the immunomodulation by MC-LR of BALB/c mice peritoneal macrophages was investigated in vitro on mRNA levels of induced nitric oxide synthase and multiple cytokines by reverse-transcription polymerase chain reaction (RT-PCR). Lavaged peritoneal macrophages were incubated for 6 h with lipopolysaccharide (LPS) at a concentration of 100 microg/L and MC-LR at doses of 1, 10, 100, and 1000 nmol/L. Total RNA was extracted from the incubated macrophages, and then the levels of mRNA for induced nitric oxide synthase (iNOS), IL-1beta, TNF-alpha, GM-CSF, and IFN-gamma were detected. The results showed that expression of mRNA for iNOS, IL-1beta, TNF-alpha, GM-CSF, and IFN-gamma decreased significantly compared to the positive control (LPS only). These results have led us to propose the need for the establishment of a survey of the immunotoxicity of microcystins.

Animals↗

PubMed2005

Novel polyethylene glycol derivative suitable for the preparation of mono-PEGylated protein.

A novel methoxypolyethylene glycol (mPEG) derivative, containing a reactive group of 1-methyl pyridinium toluene-4-sulfonate, was synthesized and characterized. The mPEG derivative was successfully conjugated with two proteins: recombinant human granulocyte-colony stimulating factor (rhG-CSF) and consensus interferon (C-IFN). Homogeneous mono-PEGylated proteins were obtained which were identified by high performance size-exclusion chromatography and MALDI-TOF mass spectrometry. The biological activities of the mono-PEGylated rhG-CSF and the mono-PEGylated C-IFN were maintained at 90% and 88%, respectively.

Chromatography, Gel↗

PubMed2005

A hybrid framework for 3D medical image segmentation.

In this paper we propose a novel hybrid 3D segmentation framework which combines Gibbs models, marching cubes and deformable models. In the framework, first we construct a new Gibbs model whose energy function is defined on a high order clique system. The new model includes both region and boundary information during segmentation. Next we improve the original marching cubes method to construct 3D meshes from Gibbs models' output. The 3D mesh serves as the initial geometry of the deformable model. Then we deform the deformable model using external image forces so that the model converges to the object surface. We run the Gibbs model and the deformable model recursively by updating the Gibbs model's parameters using the region and boundary information in the deformable model segmentation result. In our approach, the hybrid combination of region-based methods and boundary-based methods results in improved segmentations of complex structures. The benefit of the methodology is that it produces high quality segmentations of 3D structures using little prior information and minimal user intervention. The modules in this segmentation methodology are developed within the context of the Insight ToolKit (ITK). We present experimental segmentation results of brain tumors and evaluate our method by comparing experimental results with expert manual segmentations. The evaluation results show that the methodology achieves high quality segmentation results with computational efficiency. We also present segmentation results of other clinical objects to illustrate the strength of the methodology as a generic segmentation framework.

Algorithms↗

PubMed2005

Electrochemical studies on polysorbate-20 (Tween 20)-entrapped haemoglobin and its application in a hydrogen peroxide biosensor.

Haemoglobin (Hb) was entrapped in polysorbate 20 and then modified on a pyrolytic graphite electrode. Electrochemical studies revealed that a pair of stable and well-defined redox peaks attributed to the direct redox reaction of Hb could be observed in a phosphate buffer solution (pH 6.0). The anodic and cathodic peaks were located at -236 and -316 mV (versus a saturated calomel reference electrode) separately. The formal potential, E0', was linearly varied with pH in the range from 3.0 to 10.0 with a slope of -48.0 mV.pH-1. Moreover, the protein was capable of catalysing the reduction of H2O2. Accordingly, an unmediated biosensor for H2O2 was prepared with a linear range from 8.0x10(-7) to 1.0x10(-3) M. This biosensor exhibited good stability, sensitivity and reproducibility.

Biosensing Techniques↗

PubMed2005

An approximation algorithm for haplotype inference by maximum parsimony.

This paper studies haplotype inference by maximum parsimony using population data. We define the optimal haplotype inference (OHI) problem as given a set of genotypes and a set of related haplotypes, find a minimum subset of haplotypes that can resolve all the genotypes. We prove that OHI is NP-hard and can be formulated as an integer quadratic programming (IQP) problem. To solve the IQP problem, we propose an iterative semidefinite programming-based approximation algorithm, (called SDPHapInfer). We show that this algorithm finds a solution within a factor of O(log n) of the optimal solution, where n is the number of genotypes. This algorithm has been implemented and tested on a variety of simulated and biological data. In comparison with three other methods, (1) HAPAR, which was implemented based on the branching and bound algorithm, (2) HAPLOTYPER, which was implemented based on the expectation-maximization algorithm, and (3) PHASE, which combined the Gibbs sampling algorithm with an approximate coalescent prior, the experimental results indicate that SDPHapInfer and HAPLOTYPER have similar error rates. In addition, the results generated by PHASE have lower error rates on some data but higher error rates on others. The error rates of HAPAR are higher than the others on biological data. In terms of efficiency, SDPHapInfer, HAPLOTYPER, and PHASE output a solution in a stable and consistent way, and they run much faster than HAPAR when the number of genotypes becomes large.

Algorithms↗

PubMed2005

Using proteomics and network analysis to elucidate the consequences of synaptic protein oxidation in a PS1 + AbetaPP mouse model of Alzheimer's disease.

Increasing evidence suggests that oxidative injury is involved in the pathogenesis of many age-related neurodegenerative disorders, including Alzheimer's disease (AD). Identifying the protein targets of oxidative stress is critical to determine which proteins may be responsible for the neuronal impairments and subsequent cell death that occurs in AD. In this study, we have applied a high-throughput shotgun proteomic approach to identify the targets of protein carbonylation in both aged and PS1 + AbetaPP transgenic mice. However, because of the inherent difficulties associated with proteomic database searching algorithms, several newly developed bioinformatic tools were implemented to ascertain a probability-based discernment between correct protein assignments and false identifications to improve the accuracy of protein identification. Assigning a probability to each identified peptide/protein allows one to objectively monitor the expression and relative abundance of particular proteins from diverse samples, including tissue from transgenic mice of mixed genetic backgrounds. This robust bioinformatic approach also permits the comparison of proteomic data generated by different laboratories since it is instrument- and database-independent. Applying these statistical models to our initial studies, we detected a total of 117 oxidatively modified (carbonylated) proteins, 59 of which were specifically associated with PS1 + AbetaPP mice. Pathways and network component analyses suggest that there are three major protein networks that could be potentially altered in PS1 + AbetaPP mice as a result of oxidative modifications. These pathways are 1) iNOS-integrin signaling pathway, 2) CRE/CBP transcription regulation and 3) rab-lyst vesicular trafficking. We believe the results of these studies will help establish an initial AD database of oxidatively modified proteins and provide a foundation for the design of future hypothesis driven research in the areas of aging and neurodegeneration.

Activating Transcription Factor 2↗

PubMed2005

Src inhibition enhances paclitaxel cytotoxicity in ovarian cancer cells by caspase-9-independent activation of caspase-3.

Src tyrosine kinase has been found to be overexpressed and activated in a high proportion of ovarian cancers and ovarian cancer cell lines. Furthermore, Src activation is associated with activation of growth and survival signaling pathways. The present study was conducted in order to determine the effects of Src inhibition on ovarian cancer cell survival in response to chemotherapeutic agents. Inhibition of Src, either pharmacologically or through expression of a Src dominant-negative fusion construct, enhanced the cytotoxicity of two different classes of chemotherapeutics: paclitaxel and cisplatinum, in both mouse and human ovarian cancer cells. Interestingly, Src inhibition also restored sensitivity to drug-resistant ovarian cancer cells. The increased cytotoxicity in response to Src inhibition was associated with a large increase in processing and activation of caspase-3. The activation of caspase-3 seems to be independent of cytochrome c release and caspase-9 activation. The present study indicates that Src tyrosine kinase may provide an important target for small molecule inhibition in ovarian cancer.

Animals↗

PubMed2005

[Construction of fused osmoregulation proBA gene from a salt-tolerant mutant of Bacillus subtilis and its influence on the osmotolerance of Escherichia coli].

The osmoregulation proB and proA genes from Bacillus subtilis 93151 are overlapping genes, which encode two proteins ProB and ProA. A restriction enzyme site was inserted in the overlapping region of proB and proA genes from a salt-tolerant mutant of B. subtilis 93151, and a fusion gene was constructed by cloning proB and proA genes respectively. SDS-PAGE analysis showed that a novel protein with molecular mass of 85 kD was observed. When expressed in E. coli, enhanced intracellular concentrations of free proline and osmotolerance of the strain carrying the fusion gene were observed, compared with the control host cell harbouring a plasmid encoding the separate ProB and ProA.

Adaptation, Physiological↗

PubMed2005

[Separation and purification of PEGylated rhG-CSF by two-step ion-exchange chromatography].

In order to separate and purify the PEGylated recombinant human granulocyte stimulating factor (rhG-CSF) at large laboratory-scale level, a two-step ion-exchange chromatographic separation procedure was designed. Cation-exchange chromatography was applied first to separate PEGylated rhG-CSF from un-reacted rhG-CSF, followed by anion-exchange chromatography to dissolve individual PEG-rhG-CSF species (mono-, di- and tri-PEGylated rhG-CSF) and remove the free PEG. The molecular weight of individual PEGylated rhG-CSF was determined by MALDI-TOF and SDS-PAGE. MALDI-TOF mass spectrometry revealed that the molecular weights of mono-, di- and tri-PEGylated rhG-CSF are 23.8 kD, 28.6kD and 33.8kD, respectively. Cell proliferation activity was detected by MTT assay using NFS-60 cell. The in vitro residual bioactivity of mono-, di- and tri-PEGylated rhG-CSF were 90%, 75% and 43% respectively, comparing with the un-conjugated rhG-CSF. These results indicated that the un-conjugated rhG-CSF and excess free PEG can be removed completely and the three conjugate species can be purified into homogeneity by the two consecutive ion-exchange chromatographic steps. The purification procedure is easy to scale-up, high in performance and recovery.

Chromatography, Ion Exchange↗

PubMed2005

[Genioglossus advancement and hyoid suspension plus uvulopalatopharyngoplasty for severe OSAHS].

OBJECTIVE: To explore a comprehensive surgical approach of genioglossus advancement and hyoid suspension plus uvulopalatopharyngoplasty on the treatment of severe obstructive sleep apnea hypopnea syndrome. METHOD: Eighteen patients with severe OSAHS (RDI > 40)diagnosed by polysomnography. The obstruction in both the oropharynx and the hypopharynx were determined by preoperative physical examination, fiberoptic pharyngolaryngoscopy, cephalometry, and computed tomography of the upper airway. All the cases were given continuous airway pressure via nose,five to seven days before operation and then were performed genioglossus advancement and hyoid suspension plus uvulopalatopharyngoplasty. The follow up was at least 6 months postoperatively. The Wilcoxon Signed Rank test was used to compare the preoperative and postoperative results by SPSS11.0 for windows. RESULT: Postoperative 6-24 months, there were statistically significance in all but BMI between preoperative and postoperative measurement. Mean RDI was reduced from preoperative (63.83 +/- 16.34) to postoperative (21.43 +/- 20. 34), lowest mean oxygen saturation increased from (72.44 +/- 7.07)% to (81.33 +/- 13.32)%. According to criterion at home, the 6-month rate of responder is 83.33%. The severe complications such as fracture of the mandible and injure of apex of inferior anterior teeth did not occurred. CONCLUSION: GAHM plus UPPP is effective surgical approach for patients with severe OSAHS who suffer from oropharyngeal and hypopharyngeal obstruction.

Adult↗

PubMed2004

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms.

UNLABELLED: Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed with regions of low LD. Such LD patterns make it possible to select a set of single nucleotide polymorphism (SNPs; tag SNPs) for genome-wide association studies. We have developed a suite of computer programs to analyze the block-like LD patterns and to select the corresponding tag SNPs. Compared to other programs for haplotype block partitioning and tag SNP selection, our program has several notable features. First, the dynamic programming algorithms implemented are guaranteed to find the block partition with minimum number of tag SNPs for the given criteria of blocks and tag SNPs. Second, both haplotype data and genotype data from unrelated individuals and/or from general pedigrees can be analyzed. Third, several existing measures/criteria for haplotype block partitioning and tag SNP selection have been implemented in the program. Finally, the programs provide flexibility to include specific SNPs (e.g. non-synonymous SNPs) as tag SNPs. AVAILABILITY: The HapBlock program and its supplemental documents can be downloaded from the website http://www.cmb.usc.edu/~msms/HapBlock.

Algorithms↗

PubMed2004

Biomolecule-directed assembly of nanoscale building blocks studied via lattice Monte Carlo simulation.

We perform lattice Monte Carlo simulations to study the self-assembly of functionalized inorganic nanoscale building blocks using recognitive biomolecule linkers. We develop a minimal coarse-grained lattice model for the nanoscale building block (NBB) and the recognitive linkers. Using this model, we explore the influence of the size ratio of linker length to NBB diameter on the assembly process and the structural properties of the resulting aggregates, including the spatial distribution of NBBs and aggregate topology. We find the constant-kernel Smoluchowski theory of diffusion-limited cluster-cluster aggregation describes the aggregation kinetics for certain size ratios.

Algorithms↗

PubMed2004

Quantitative determination of astilbin in rabbit plasma by liquid chromatography.

A simple method for determining the concentration of astilbin, a flavanone, in rabbit plasma has been developed. After liquid-liquid extraction, the flavanone was detected by HPLC on a 4.6-microm octadecylsilica column (Nova-Pak C-18) at 291 nm. Linear calibration graphs for astilbin were constructed from 0.44 to 22.17 microM. The limit of quantitation was 0.44 microM in plasma. The method has been applied to pharmacokinetic studies after a single i.v. and an oral administration of the compound to rabbits.

Animals↗

PubMed2004

Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies.

Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed by regions of low LD. A small fraction of SNPs (tag SNPs) is sufficient to capture most of the haplotype structure of the human genome. In this paper, we develop a method to partition haplotypes into blocks and to identify tag SNPs based on genotype data by combining a dynamic programming algorithm for haplotype block partitioning and tag SNP selection based on haplotype data with a variation of the expectation maximization (EM) algorithm for haplotype inference. We assess the effects of using either haplotype or genotype data in haplotype block identification and tag SNP selection as a function of several factors, including sample size, density or number of SNPs studied, allele frequencies, fraction of missing data, and genotyping error rate, using extensive simulations. We find that a modest number of haplotype or genotype samples will result in consistent block partitions and tag SNP selection. The power of association studies based on tag SNPs using genotype data is similar to that using haplotype data.

Algorithms↗

PubMed2004

Analysis of immunomodulating nitric oxide, iNOS and cytokines mRNA in mouse macrophages induced by microcystin-LR.

Microcystins (MCs) are the toxic molecules produced by common cyanobacterium in freshwater blooms. Their toxicities have brought severe health issues to livestock and human being. Microcystin-LR (MC-LR) is one of the most toxic MCs. This paper presents the profile of the immunomodulation of MC-LR to BALB/c mice peritoneal macrophages. Macrophages were stimulated with 100microg/l lipopolysaccharide (LPS) and MC-LR at dose of 1, 10, 100, 1000nmol/l, respectively, for 24h. Nitric oxide (NO) production in cell culture supernatants was quantified by using Griess reagent method. Total RNA was extracted from incubated macrophages then the mRNA abundance of induced nitric oxide synthase (iNOS), IL-1beta, TNF-alpha, GM-CSF, IFN-gamma was monitored by using reverse-transcriptional polymerase chain reaction (RT-PCR). The results demonstrated that NO production, mRNA levels of iNOS, IL-1beta, TNF-alpha were down regulated by MC-LR dose-dependently and mRNA levels of GM-CSF and IFN-gamma were also decreased but in dose-independent manner. Our results illustrated the involvement of NO production, iNOS and some cytokines in mice immune system in microcystin shock.

Adjuvants, Immunologic↗

PubMed2004

Mapping Gene Ontology to proteins based on protein-protein interaction data.

MOTIVATION: Gene Ontology (GO) consortium provides structural description of protein function that is used as a common language for gene annotation in many organisms. Large-scale techniques have generated many valuable protein-protein interaction datasets that are useful for the study of protein function. Combining both GO and protein-protein interaction data allows the prediction of function for unknown proteins. RESULT: We apply a Markov random field method to the prediction of yeast protein function based on multiple protein-protein interaction datasets. We assign function to unknown proteins with a probability representing the confidence of this prediction. The functions are based on three general categories of cellular component, molecular function and biological process defined in GO. The yeast proteins are defined in the Saccharomyces Genome Database (SGD). The protein-protein interaction datasets are obtained from the Munich Information Center for Protein Sequences (MIPS), including physical interactions and genetic interactions. The efficiency of our prediction is measured by applying the leave-one-out validation procedure to a functional path matching scheme, which compares the prediction with the GO description of a protein's function from the abstract level to the detailed level along the GO structure. For biological process, the leave-one-out validation procedure shows 52% precision and recall of our method, much better than that of the simple guilty-by-association methods.

Chromosome Mapping↗

PubMed2004

An integrated probabilistic model for functional prediction of proteins.

We develop an integrated probabilistic model to combine protein physical interactions, genetic interactions, highly correlated gene expression networks, protein complex data, and domain structures of individual proteins to predict protein functions. The model is an extension of our previous model for protein function prediction based on Markovian random field theory. The model is flexible in that other protein pairwise relationship information and features of individual proteins can be easily incorporated. Two features distinguish the integrated approach from other available methods for protein function prediction. One is that the integrated approach uses all available sources of information with different weights for different sources of data. It is a global approach that takes the whole network into consideration. The second feature is that the posterior probability that a protein has the function of interest is assigned. The posterior probability indicates how confident we are about assigning the function to the protein. We apply our integrated approach to predict functions of yeast proteins based upon MIPS protein function classifications and upon the interaction networks based on MIPS physical and genetic interactions, gene expression profiles, tandem affinity purification (TAP) protein complex data, and protein domain information. We study the recall and precision of the integrated approach using different sources of information by the leave-one-out approach. In contrast to using MIPS physical interactions only, the integrated approach combining all of the information increases the recall from 57% to 87% when the precision is set at 57%-an increase of 30%.

Computational Biology↗

PubMed2004

Nucleocytoplasmic shuttling of JAZ, a new cargo protein for exportin-5.

Exportin-5 is a nuclear export receptor for certain classes of double-stranded RNA (dsRNA), including pre-micro-RNAs, viral hairpin RNAs, and some tRNAs. It can also export the RNA binding proteins ILF3 and elongation factor EF1A. However, the rules that determine which RNA binding proteins are exportin-5 cargoes remain unclear. JAZ possesses an unusual dsRNA binding domain consisting of multiple C2H2 zinc fingers. We found that JAZ binds to exportin-5 in a Ran-GTP- and dsRNA-dependent manner. Exportin-5 stimulates JAZ shuttling, and gene silencing of exportin-5 reduces shuttling. Recombinant exportin-5 also stimulates nuclear export of JAZ in permeabilized cells. JAZ also binds to ILF3, and surprisingly, this interaction is RNA independent, even though it requires the dsRNA binding domains of ILF3. Exportin-5, JAZ, and ILF3 can form a heteromeric complex with Ran-GTP and dsRNA, and JAZ increases ILF3 binding to exportin-5. JAZ does not contain a classical nuclear localization signal, and in digitonin-permeabilized cells, nuclear accumulation of JAZ does not require energy or cytosol. Nonetheless, low temperatures prevent JAZ import, suggesting that nuclear entry does not occur via simple diffusion. Together, these data suggest that JAZ is exported by exportin-5 but translocates back into nuclei by a facilitated diffusion mechanism.

Active Transport, Cell Nucleus↗