Biomedical subjects

Mengsu Yang

Publications and source records attributed to Mengsu Yang.

36 records · Page 2Linked to original sources

PubMed2004

Cluster analysis of gene expression data based on self-splitting and merging competitive learning.

Cluster analysis of gene expression data from a cDNA microarray is useful for identifying biologically relevant groups of genes. However, finding the natural clusters in the data and estimating the correct number of clusters are still two largely unsolved problems. In this paper, we propose a new clustering framework that is able to address both these problems. By using the one-prototype-take-one-cluster (OPTOC) competitive learning paradigm, the proposed algorithm can find natural clusters in the input data, and the clustering solution is not sensitive to initialization. In order to estimate the number of distinct clusters in the data, we propose a cluster splitting and merging strategy. We have applied the new algorithm to simulated gene expression data for which the correct distribution of genes over clusters is known a priori. The results show that the proposed algorithm can find natural clusters and give the correct number of clusters. The algorithm has also been tested on real gene expression changes during yeast cell cycle, for which the fundamental patterns of gene expression and assignment of genes to clusters are well understood from numerous previous studies. Comparative studies with several clustering algorithms illustrate the effectiveness of our method.

Algorithms↗

PubMed2003

Hydrodynamic simulation of cell docking in microfluidic channels with different dam structures.

The immobilization of biological cells in micro-devices requires high efficiency and easy control while maintaining cell viability. One approach for cell immobilization is to utilize constriction structures such as dams to trap cells in microfluidics. In this paper, we present a comprehensive hydrodynamic analysis of two different types of constriction structures for cell immobilization: dams either in perpendicular or in parallel to the main flow route. Various structural models and experimental conditions were compared for cell docking and alignment, and the pressure and velocity profiles of the flow in the micro-channels and the hydrodynamic force and shear stress on the docked cells were calculated based on fluid dynamic theory and numerical simulation. The effects of the dam structures and cell docking on the flow properties, the transportation efficiency, and the induced stress on the docked cells were analyzed. Improved hydraulic pressure profiles in the auxiliary inlets were discussed for the modulation of the flow characteristics and attenuation of hydrodynamic forces exerted on the cells. Furthermore, a new design combining the advantages of perpendicular and parallel dam structures was proposed for cell-based microfluidics.

Cell Physiological Phenomena↗

PubMed2003

Bis-intercalative dinuclear platinum(II) 6-phenyl-2,2'-bipyridine complexes exhibit enhanced DNA affinity but similar cytotoxicity compared to the mononuclear unit.

The interactions between a series of platinum complexes, including (pyridyl)(6-phenyl-2,2'-bipyridine)platinum(II) hexafluorophosphate (1), three dinuclear bis[(6-phenyl-2,2'-bipyridine)platinum(II)] complexes (2-4), and (4-aminopyridine)(4,6-diphenyl-2,2'-bipyridine)platinum(II) perchlorate (5) with DNA have been investigated. All Pt(II) complexes, except 5, were demonstrated to be DNA intercalators, based on viscosity measurements. Absorption and fluorescence titration results indicated that the addition of a phenyl ring to the 6-phenyl-2,2'-bipyridine ligand dramatically reduced the DNA binding of the Pt(II) complex 5. The dinuclear complexes 2-4 exhibited multiple binding modes of mono/bisintercalation and groove binding, as revealed by viscosity and fluorescence titration measurements. While complexes 2-4 bound to DNA with significantly enhanced affinities as compared to 1, compounds 1 and 2-4 showed similar IC(50) values against a panel of cancer cell lines. In addition, these complexes showed similar cellular uptakes. The results indicated that the cytotoxicity of these (6-phenyl-2,2'-bipyridine)platinum compounds may not be mediated through DNA binding but may involve interacting mechanisms with cellular components other than DNA.

Antineoplastic Agents↗

PubMed2003

Inhibitory actions of genistein in human breast cancer (MCF-7) cells.

Genistein, a natural isoflavanoid phytoestrogen, is thought to be the active ingredient in soy that possesses breast cancer preventive properties. The molecular mechanisms that are involved in its cancer preventive properties have not been completely understood. The present study is designed to investigate the mechanism involved in the inhibitory action of genistein in MCF-7 cells. Genistein at 50 and 100 microM significantly arrested the growth of MCF-7 cells at G2/M phase (P<0.05) and decreased at the proliferative S phase (P<0.05). Using cDNA microarray technology, genes differentially regulated by genistein were identified. In particular, as confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR), genistein up-regulated heat shock protein 105 (HSP) mRNA and down-regulated mRNA expression of serum response factor (SRF), estrogen receptor (ER) alpha, disabled homolog 2 (DOC 2) and recombination activation gene 1 (RAG-1). Using real time RT-PCR, we have shown that HSP and SRF mRNA were both regulated by genistein in a time- and dose-dependent manner; however, it appears that only the effect of genistein on SRF mRNA, but not HSP mRNA expression, can be partially abolished by cotreatment with estrogen antagonist ICI 182,780. Western blotting analysis showed that the expressions of the ERalpha and SRF protein decreased significantly with genistein treatment (P<0.05). These results suggest that the inhibitory action of genistein on human breast cancer cells appears to be complex and is only partially mediated by the alteration of estrogen receptor-dependent pathways.

Antineoplastic Agents↗

PubMed2003

Classification of short human exons and introns based on statistical features.

The classification of human gene sequences into exons and introns is a difficult problem in DNA sequence analysis. In this paper, we define a set of features, called the simple Z (SZ) features, which is derived from the Z-curve features for the recognition of human exons and introns. The classification results show that SZ features, while fewer in numbers (three in total), can preserve the high recognition rate of the original nine Z-curve features. Since the size of SZ features is one-third of the Z-curve features, the dimensionality of the feature space is much smaller, and better recognition efficiency is achieved. If the stop codon feature is used together with the three SZ features, a recognition rate of up to 92% for short sequences of length <140 bp can be obtained.

Algorithms↗

PubMed2003

Synthesis and biological activity of a platinum(II) 6-phenyl-2,2'-bipyridine complex and its dimeric analogue.

We have synthesized (pyridyl)-(6-phenyl-2,2'-bipyridine)platinum(II) hexafluorophosphate (1) and its corresponding dimer, micro-N,N'-bis(isonicotinyl)-1,6-hexanediamino bis-[6-phenyl-2,2'-bipyridine-platinum(II)] dichloride (2). The DNA binding constants of 1 and 2 at 20 degrees C were determined by absorption titration to be 2.25 x 10(4) M(-1) and 3.07 x 10(6) M(-1), respectively. Compound 1 showed an AT preference, while 2 had no base preference. The binding site sizes of 2 for [poly(dA-dT)](2), calf thymus DNA (ctDNA), and [poly(dG-dC)](2), as determined by fluorescence titration, were 6.6, 4.0, and 2.8 bp, respectively. Compound 2 probably bound to [poly(dA-dT)](2) through bisintercalation, and to [poly(dG-dC)](2) by monointercalation. Binding of DNA by both complexes is favorable, since the binding free energies of 1 and 2 were estimated to be -5.8 and -8.7 kcal mol(-1), respectively. The results of viscosity measurements and gel mobility shift assay demonstrated that binding of 1 and 2 caused DNA lengthening. The cytotoxicities of the complexes in various human cancer cell lines were determined by MTT assay. Complex 2 exhibited cytotoxicity comparable to that of cisplatin, and was more toxic than 1 by an order of magnitude.

Algorithms↗

PubMed2003

Electrochemical properties of DNA-intercalating doxorubicin and methylene blue on n-hexadecyl mercaptan-doped 5'-thiol-labeled DNA-modified gold electrodes.

Interactions between DNA-intercalating molecules, methylene blue (MB) and doxorubicin (DOX), and gold surface modified by various DNA species and n-hexadecyl mercaptan (HDM) were investigated by cyclic voltammetry (CV). Hydrophilic DOX was completely blocked by the HDM film from contacting the gold electrode whereas hydrophobic MB could readily partition into the film. Unlabeled single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) underwent non-specific adsorption on gold surface but the adsorbed DNA can be partially displaced by HDM. Thiol-labeled ssDNA and dsDNA adsorbed on gold surface via both thiol-gold linkage and non-specific interactions between DNA strands and gold. The non-specific interactions could be interrupted by the addition of HDM, forming a mixed monolayer containing both HDM and DNA attached to the gold surface at 5'-thiol termini. The presence of ssDNA and dsDNA in the monolayer facilitated the redox reaction of MB and DOX on the modified electrode. Both MB and DOX diffuse along the ssDNA in the ssDNA-containing monolayers, and they additionally intercalate into the dsDNA in the dsDNA-containing monolayers. No sufficient evidence is shown to indicate that an organized monolayer is formed by the thiol-labeled dsDNA on gold surface, and that the redox reactions of MB and DOX were carried out by electron transfer through DNA helix.

Adsorption↗

PubMed2003

PDMS-based microfluidic device with multi-height structures fabricated by single-step photolithography using printed circuit board as masters.

We have developed a method for fabricating microfluidic devices with multi-height structures using single step photolithography. The whole fabrication process is executed by conventional printed circuit board (PCB) technology without the need of having access to clean room facilities. Specifically designed "windows" and "rims" architectures were printed on films that were used as photomasks. Different levels of protruding features on the PCB master were produced by exposing a photomask followed by chemical wet etching. Poly(dimethylsiloxane) (PDMS) was then moulded against the positive relief master to generate microfluidic structures. In this report, we described the fabrication of a microfluidic device featured with a multi-height "sandbag" structure for particle entrapment and peripheral microchannels. Controlled immobilization of biological cells and immunocytochemcial staining assays were performed to demonstrate the applicability of the microfluidic device for cellular analysis. The integrity of the microdevice remained stable under applied pressure, indicating the robustness of the elastic PDMS structures for analytical operation. The simple microfabrication process requires only low-cost materials and minimal specialized equipment and can reproducibly produce mask lines of about 20 microm in width, which is sufficient for most microfluidic applications.

Journal Article↗

PubMed2003

Effects of DNA mismatches on binding affinity and kinetics of polymerase-DNA complexes as revealed by surface plasmon resonance biosensor.

In this study, surface plasmon resonance (SPR) biosensor techniques were used to obtain quantitative information on the kinetics of the DNA and polymerase I (Klenow fragment) interaction. DNA duplexes containing different base compositions at the binding site were immobilized on the SPR sensor surface via biotin-streptavidin chemistry and the subsequent binding of the polymerase was measured in real time. Various kinetic models were tested and a translocation model was shown to provide the best fit for the binding and dissociation profiles. The results revealed that the enzyme binds to DNA at both the polymerase and the exonuclease domains with different association and dissociation rates as well as affinity constants, depending on the presence of mismatches near the primer 3'-end. Introduction of unpaired bases increases the DNA binding affinity towards the exonuclease domain and promotes the translocation of DNA from the polymerase site to the exonuclease site. The results also demonstrated that SPR biosensors may be used as a sensitive technique for studying molecular recognition events such as single-base discrimination involved in protein-DNA interaction.

Animals↗

PubMed2003

cDNA microarray analysis of gene expression profiles in human fibroblast cells irradiated with red light.

In this paper, the cDNA microarray technique was used to investigate the gene expression profiles of human fibroblasts irradiated by low-intensity red light. Proliferation assays showed that the fibroblast HS27 cells responded with a curve effect to different doses of low-intensity red light irradiation at a wavelength of 628 nm. An optimal dose of 0.88 J per cm2 was chosen for subsequent cDNA microarray experiments. The gene expression profiles revealed that 111 genes were regulated by the red light irradiation and can be grouped into 10 functional categories. Most of these genes directly or indirectly play roles in the enhancement of cell proliferation and the suppression of apoptosis. Two signaling pathways, the p38 mitogen-activated protein kinase signaling pathway and the platelet-derived growth factor signaling pathway, were found to be involved in cell growth induced by irradiation of low-intensity red light. Several genes related to antioxidation and mitochondria energy metabolism were also found to express differentially upon irradiation. This study provides insight into the molecular mechanisms associated with the beneficial effects of red light irradiation in accelerating wound healing.

Antioxidants↗

PubMed2003

Pyranocoumarins isolated from Peucedanum praeruptorum as differentiation inducers in human leukemic HL-60 cells.

Differentiation therapy for myeloid leukemia offers great potential as a supplement to the current treatment modalities. In the present report, we investigated if the pyranocoumarins, (+/-)-4'- O-acetyl-3'- O-angeloyl- cis-khellactone (or angular pyranocoumarin, APC) isolated from the medicinal plant Peucedanum praeruptorum Dunn, could induce human acute myeloid leukemic HL-60 cells to differentiate and elucidated the molecular mechanism(s) involved. The ability of HL-60 cells to reduce nitroblue tetrazolium (NBT) was significantly increased after APC treatment for 72 h. In these differentiating HL-60 cells, cell surface differentiation markers CD11b (for myeloid cells) and CD14 (for monocytic cells) were detected in 90.3 % and 70.1 % of the cells, respectively. The differentiation inducing effect of APC was time- and dose-dependent. Treatment with 20 microg/mL APC for 72 h inhibited cell growth by 90 % and cell cycle analysis revealed an increase in the proportion of G1 phase cells. In these growth-inhibited cells the expression of the cyclin-dependent kinase inhibitor p27 kip1, but not p21 WAF1, was up-regulated as shown by Western blotting. Differentiation inducing signal pathways were investigated and it was shown that phospho-MEK and phospho-ERK were elevated shortly after the addition of APC. Pre-incubation of the cells with MEK1 inhibitor PD98059 blocked this APC-induced differentiation. Our results suggest that APC are potent inducers of HL-60 cell differentiation along both the myelocytic and monocytic lineages and are potential agents for differentiation-treatment of leukemia.

Antineoplastic Agents, Phytogenic↗

PubMed2003

Interaction between pyridoxal kinase and pyridoxal-5-phosphate-dependent enzymes.

The interactions of two pyridoxal-5-phosphate (PLP)-dependent enzymes, alanine aminotransferase (ALT) and glutamate decarboxylase (GAD), with pyridoxal kinase (PK) were studied by fluorescence polarization as well as surface plasmon resonance techniques. The results demonstrated that PK can specifically bind to ALT and GAD. Moreover, binding profiles of both enzymes to immobilized PK were altered by excess amount of PLP. The equilibrium affinity constants for ALT in the absence and presence of PLP are 20.4 x 10(4) M(-1)and 6.7 x 10(4) M(-1), and for GAD are 37 x 10(4) M(-1)and 20.8 x 10(4) M(-1), respectively. It appears that specific interactions occur between PK and PLP-dependent enzymes, and the binding affinities of PK for PLP-dependent enzymes decrease in the presence of PLP. The results support our hypothesis that PLP transfer from PK to PLP-dependent enzymes requires a specific interaction between PK and the enzyme.

Alanine Transaminase↗

PubMed2002

Cell docking and on-chip monitoring of cellular reactions with a controlled concentration gradient on a microfluidic device.

We have developed a microfluidic device for on-chip monitoring of cellular reactions. The device consists of two primary analytical functions: control of cell transport and immobilization, and dilution of an analyte solution to generate a concentration gradient. In this device, a dam structure in parallel to the fluid flow was constructed for docking and alignment of biological cells, which allows the fragile cells to move in the microfluidic channels and to be immobilized with controllable numbers in desired locations. The cells docked on the parallel dam structure are exposed to minimal stress caused by fluidic pressure. Additionally, a network of microfluidic channels was designed to generate a concentration gradient by controlled fluid distribution and diffusive mixing. An analyte solution could be diluted to different gradients as a function of distance along the dam. We used the ATP-dependent calcium uptake reaction of HL-60 cells as a model for on-chip measurement of the threshold ATP concentration that induces significant intracellular calcium signal. The results have demonstrated the feasibility of using the microchip for real-time monitoring of cellular processes upon treatment of a concentration gradient of a test solution. The integration of cell manipulation and solution manipulation on a microchip allows the measurement of concentration-dependent biological responses within a confined microscale feature.

Adenosine Triphosphate↗

PubMed2002

Syntheses of ruthenium(II) quinonediimine complexes of cyclam and characterization of their DNA-binding activities and cytotoxicity.

The synthesis and characterization of ruthenium(II) complexes, [Ru(cyclam)(bqdi)] x ZnCl(4) (1 x ZnCl(4); cyclam = 1,4,8,11-tetraazacyclotetradecane, bqdi = o-benzoquinonediimine), [Ru(cyclam)(nqdi)] x (ClO(4))(2) (2 x (ClO(4))(2); nqdi = 2,3-naphthoquinonediimine), and [Ru(cyclam)(phi)] x (ClO(4))(2) (3 x (ClO(4))(2); phi = 9,10-phenanthroquinonediimine), are described. The DNA binding properties and biological activity of the Ru(II) complexes were studied by various biophysical and cytological techniques. As expected, only 3 showed significant binding with DNA. The thermodynamic profile of the binding of 3 and DNA was constructed by analyzing the experimental data of absorption titration and UV melting studies with the McGhee equation, van't Hoff's equation, and the Gibbs-Helmholtz equation. Compound 3 binds double-stranded DNA with a binding constant of 5.0 x 10(4) M(-1) at 20 degrees C, and the binding mode of the complex to DNA was proved to be intercalative. Cytotoxicity and induced type of cell death of 1-3 were also investigated. Basically, metal complexes with ligands of molecular shape closely related to the structure of DNA are more likely to bind DNA and possess higher toxicity.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2002

Generation of concentration gradient by controlled flow distribution and diffusive mixing in a microfluidic chip.

We have developed a simple method to generate a concentration gradient in a microfluidic device. This method is based on the combination of controlled fluid distribution at each intersection of a microfluidic network by liquid pressure and subsequent diffusion between laminas in the downstream microchannel. A fluid dynamic model taking into account the diffusion coefficient was established to simulate the on-chip flow distribution and diffusion. Concentration gradients along a distance of a few hundred micrometers were generated in a series of microchannels. The gradients could be varied by carefully regulating the liquid pressure applied to the sample injection vials. The observed concentration gradients of fluorescent dyes generated on the microfluidic channel are consistent with the theoretically predicted results. The microfluidic design described in this study may provide a new tool for applications based on concentration gradients, including many biological and chemical analyses such as cellular reaction monitoring and drug screening.

Journal Article↗

PubMed2002

Study of substrate-enzyme interaction between immobilized pyridoxamine and recombinant porcine pyridoxal kinase using surface plasmon resonance biosensor.

Pyridoxal kinase (PK) is an important enzyme involved in bioactivation of vitamin B(6). Binding of PK with its substrate is the prerequisite step for the subsequent catalytic phosphorylation of the substrate. In the present study, a surface plasmon resonance biosensor (BIAcore) was employed to characterize the binding interaction between wild-type porcine PK and an immobilized substrate, pyridoxamine. Pyridoxamine was modified with 11-mercaptoundecanic acid and immobilized on a sensor chip through the formation of a self-assembled monolayer. The binding of PK to the immobilized pyridoxamine was followed in real time and the kinetic parameters were derived from non-linear analysis of the sensorgram. The effects of buffer pH, monovalent cations (Na(+), K(+)) and divalent cations (Mn(2+), Zn(2+), Mg(2+)) on the binding kinetics were determined. Optimal pH for PK-pyridoxamine interaction in the absence of divalent ions is at around 7.4. While K(+) increased and Na(+) decreased the binding affinity (K(A)) of PK to immobilized pyridoxamine, all divalent cations increased the K(A) of PK for pyridoxamine. Solution phase affinity measurement based on a competitive binding assay was used to determine the affinities of PK for different vitamin B(6) analogues. The order of affinity of PK for different analogues is: pyridoxal-oxime>pyridoxine>pyridoxamine>pyridoxal>pyridoxal phosphate. This is the first study to demonstrate that buffer conditions such as pH and concentration of monovalent and/or divalent ions can directly alter the binding of PK for its substrates. The quantitative kinetic and thermodynamic parameters obtained by SPR measurement provide the insight information into the catalytic activity of this enzyme.

Animals↗

PubMed2002

Kinetic study of various binding modes between human DNA polymerase beta and different DNA substrates by surface-plasmon-resonance biosensor.

The interaction of a series of DNA substrates with human DNA polymerase beta has been studied in real time by using a surface-plasmon-resonance (SPR) biosensor technique. We have prepared the sensor surfaces comprising different DNA targets, including single-stranded DNA, blunt-end double-stranded DNA, gapped DNA and DNA template-primer duplexes containing various mismatches at different positions. The binding and dissociation of polymerase beta at the DNA-modified surfaces was measured in real time, and the kinetics profiles of polymerase-DNA interaction were analysed using various physical models. The results showed that polymerase beta binding to single-stranded DNA (K(A)=1.25 x 10(8) M(-1); where K(A) is the equilibrium affinity constant) was thermodynamically more favourable than to blunt-end DNA duplex (K(A)=7.56x10(7) M(-1)) or gapped DNA (K(A)=8.53x10(7) M(-1)), with a single binding mode on each DNA substrate. However, polymerase beta bound to DNA template-primer duplexes (15 bp with a 35 nt overhang) at two sites, presumably one at the single-strand overhang and the other at the 3'-end of the primer. When the DNA duplex was fully matched, most of the polymerase beta (83%) bound to the template-primer duplex region. The introduction of different numbers of mismatches near the 3'-end of the primer caused the binding affinity and the fraction of polymerase beta bound at the duplex region to decrease 8-58-fold and 15-40%, respectively. On the other hand, the affinity of polymerase beta for the single-strand overhang remained unchanged while the fraction bound to the single-strand region increased by 15-40%. The destabilizing effect of the mismatches was due to both a decrease in the rate of binding and an increase in the rate of dissociation for polymerase beta.

Base Sequence↗

PubMed2002

Impedance analysis of an electrode-separated piezoelectric sensor as a surface monitoring technique for surfactant adsorption on quartz surface.

This paper describes the measurement of the kinetics of adsorption of sodium dodecyl sulfate (SDS), an anionic surfactant, onto a quartz surface with a pre-adsorbed layer of Ca2+ as an ion bridge, using an electrode-separated piezoelectric sensor (ESPS). An impedance analysis method was employed to characterize the responses of the ESPS. The impedance and frequency parameters of the ESPS were examined as functions of the conductivity, permittivity, viscosity and density of the liquid. The adsorption process of SDS onto the quartz surface resulted in an increase in both the mass and energy dissipation of the oscillating quartz crystal. The adsorption densities could be estimated by the ESPS method after taking into consideration the effects of surface viscosity and roughness. The adsorption and desorption rate constants of SDS onto the quartz surface were calculated as ka = (88.1 +/- 0.26) mol(-1) L s(-1) and kd = (4.92 +/- 0.53) x 10(-3) s(-1), respectively, based on the Langmuir model. ESPS was shown to be a powerful means of examining anionic surfactant adsorption to the solid/liquid interface.

Journal Article↗