Biomedical subjects

J Z Chen

Publications and source records attributed to J Z Chen.

At least 19 recordsLinked to original sources

PubMed2004

A study of mixing in thermocapillary flows on micropatterned surfaces.

The recent introduction of actuation mechanisms for microfluidic transport based on free surface flows raises a number of interesting questions involving efficient mixing configurations, especially in systems with small aspect ratios. This work investigates the characteristics of convective and diffusive mixing in continuous-mode streaming of thermocapillary microflows on chemically micropatterned surfaces. Mixing times and mixing lengths relevant to chemical microreactors or gas sensors are investigated for various geometries and parameter ranges. Scaling arguments and full numerical solutions are presented to extract optimal operating conditions. Confocal fluorescence microscopy measurements of the interfacial diffusive broadening in adjacent flowing streams confirm numerical predictions. Three important mixing regimes, based on analogues of purely diffusive dynamics, Rhines-Young shear-augmented diffusion and Taylor-Aris dispersion are identified and investigated for use in free surface flows with large surface-to-volume ratios.

Capillary Action↗

PubMed2004

Simplified intensity-modulated arc therapy for dose escalated prostate cancer radiotherapy.

Simplified intensity-modulated arc therapy (SIMAT) employs forward planned, conformal, and avoidance arc combinations with dynamic multileaf collimation (MLC) as a simpler alternative to other forms of intensity-modulated radiotherapy (IMRT). In this work, we compare SIMAT with 4-field (4F) and 6-field (6F) 3D conformal radiation therapy (CRT) for prostate cancer treatment. Prostate, seminal vesicle, bladder, and rectum were contoured on the CT images of 10 patients being planned for radiotherapy. Two planning target volumes (PTV) were defined: PTV1 (prostate + seminal vesicles + 1.0-cm margin) and PTV2 (prostate + 1.0-cm margin). SIMAT, 4F, and 6F plans were generated with a prescription dose of 78 Gy to prostate and 54 Gy to the seminal vesicles. Differences in the 3 techniques in terms of target and rectal coverage were compared. In addition, dose distributions of the SIMAT plans were verified with measurements in a phantom. Mean dose to PTV2 (4F, 76 Gy; 6F, 78 Gy; SIMAT, 76 Gy) and the dose delivered to 95% of the target volume (D(95)) were similar between the 3-techniques. Target conformity was better with SIMAT. Mean dose and calculated NTCP for the rectum were lower for SIMAT than those for 4F and 6F plans (4F 55.6 Gy vs. 6F 49.0 Gy vs. SIMAT 42.7 Gy). Mean dose to femoral heads was lower for the 4F technique vs. 6F and SIMAT techniques (4F 44.5 Gy vs. 6F 48.9 Gy vs. SIMAT 49.5 Gy). In-phantom measurement demonstrated good agreement between the plans and SIMAT treatments delivered in phantom. We concluded that SIMAT demonstrates advantages over 4F and 6F in terms of target conformity mean rectal dose and NTCP with good reproducibility in phantom. On the basis of this analysis, we have commenced a clinical pilot study of SIMAT for prostate cancer radiotherapy.

Film Dosimetry↗

PubMed2004

Effects of homocysteine on number and activity of endothelial progenitor cells from peripheral blood.

The aim of this study is to investigate whether homocysteine (Hcy) has influences on endothelial progenitor cells (EPCs) number and activity. Total mononuclear cells (MNCs) were isolated from peripheral blood by Ficoll density gradient centrifugation, and then the cells were plated on fibronectin-coated culture dishes. After 7 d cultured, attached cells were stimulated with Hcy (to make a series of final concentrations: 10, 50, 100 and 200 micromol/l) or vehicle control for the respective time points (6, 12, 24 and 48 h). EPCs were characterized as adherent cells double positive for DiLDL uptake and lectin binding by direct fluorescent staining under a laser scanning confocal microscope. EPCs proliferation, migration and in vitro vasculogenesis activity were assayed with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, modified Boyden chamber assay and in vitro vasculogenesis kit, respectively. EPCs adhesion assay was performed by replating those on fibronectin-coated dishes, and then adherent cells were counted. Incubation of isolated human MNCs with Hcy dose and time dependently decreased the number of EPCs, maximum at 200 micromol/l, 24 h (approximately 50% reduction, P < 0.01). In addition, Hcy dose and time dependently impaired EPC proliferative, migratory, adhesive and in vitro vasculogenesis capacity. In conclusion, hyperHcy may induce the reduction of EPCs with decreased functional activity.

Cell Division↗

PubMed2003

Influence of interleukin-2 on Ca2+ handling in rat ventricular myocytes.

In the present study, we examined the effect of interleukin-2 (IL-2) on cardiomyocyte Ca(2+) handling. The effects of steady-state and transient changes in stimulation frequency on the intracellular Ca(2+) transient were investigated in isolated ventricular myocytes by spectrofluorometry. In the steady state (0.2 Hz) IL-2 (200 U/ml) decreased the amplitude of Ca(2+) transients induced by electrical stimulation and caffeine. At 1.25 mM extracellular Ca(2+) concentration ([Ca(2+)](o)), when the stimulation frequency increased from 0.2 to 1.0 Hz, diastolic Ca(2+) level and peak intracellular Ca(2+) concentration ([Ca(2+)](i)), as well as the amplitude of the transient, increased. The positive frequency relationships of the peak and amplitude of [Ca(2+)](i) transients were blunted in the IL-2-treated myocytes. The effect of IL-2 on the electrically induced [Ca(2+)](i) transient was not normalized by increasing [Ca(2+)](o) to 2.5 mM. IL-2 inhibited the frequency relationship of caffeine-induced Ca(2+) release. Blockade of sarcoplasmic reticulum (SR) Ca(2+)-ATPase with thapsigargin resulted in a significant reduction of the amplitude-frequency relationship of the transient similar to that induced by IL-2. The restitutions were not different between control and IL-2 groups at 1.25 mM [Ca(2+)](o), which was slowed in IL-2-treated myocytes when [Ca(2+)](o) was increased to 2.5 mM. There was no difference in the recirculation fraction (RF) between control and IL-2-treated myocytes at both 1.25 and 2.5 mM [Ca(2+)](o). The effects of IL-2 on frequency relationship, restitution, and RF may be due to depressed SR functions and an increased Na(+)-Ca(2+) exchange activity, but not to any change in L-type Ca(2+) channels.

Adenosine Triphosphatases↗

PubMed2001

Significance of local electrostatic interactions in staphylococcal nuclease studied by site-directed mutagenesis.

In this paper, we show that amino acids Glu(73) and Asp(77) of staphylococcal nuclease cooperate unequally with Glu(75) to stabilize its structure located between the C-terminal helix and beta-barrel of the protein. Amino acid substitutions E73G and D77G cause losses of the catalytic efficiency of 24 and 16% and cause thermal stability losses of 22 and 26%, respectively, in comparison with the wild type (WT) protein. However, these changes do not significantly change global and local secondary structures, based on measurements of fluorescence and CD(222 nm). Furthermore, x-ray diffraction analysis of the E75G protein shows that the overall structure of mutant and WT proteins is similar. However, this mutation does cause a loss of essential hydrogen bonding and charge interactions between Glu(75) and Lys(9), Tyr(93), and His(121). In experiments using double point mutations, E73G/D77G, E73G/E75G, and E75G/D77G, significant changes are seen in all mutants in comparison with WT protein as measured by fluorescence and CD spectroscopy. The losses of thermal stability are 47, 59, and 58%, for E73G/D77G, E73G/E75G, and E75G/D77G, respectively. The triple mutant, E73G/E75G/D77G, results in fluorescence intensity and CD(222 nm) close to those of the denatured state and in a thermal stability loss of 65% relative to the WT protein. Based on these results, we propose a model in which significant electrostatic interactions result in the formation of a locally stable structure in staphylococcal nuclease.

Calorimetry, Differential Scanning↗

PubMed2001

C2 domains from different Ca2+ signaling pathways display functional and mechanistic diversity.

The ubiquitous C2 domain is a conserved Ca2+ triggered membrane-docking module that targets numerous signaling proteins to membrane surfaces where they regulate diverse processes critical for cell signaling. In this study, we quantitatively compared the equilibrium and kinetic parameters of C2 domains isolated from three functionally distinct signaling proteins: cytosolic phospholipase A2-alpha (cPLA2-alpha), protein kinase C-beta (PKC-beta), and synaptotagmin-IA (Syt-IA). The results show that equilibrium C2 domain docking to mixed phosphatidylcholine and phosphatidylserine membranes occurs at micromolar Ca2+ concentrations for the cPLA2-alpha C2 domain, but requires 3- and 10-fold higher Ca2+ concentrations for the PKC-beta and Syt-IA C2 domains ([Ca2+](1/2) = 4.7, 16, 48 microM, respectively). The Ca2+ triggered membrane docking reaction proceeds in at least two steps: rapid Ca2+ binding followed by slow membrane association. The greater Ca2+ sensitivity of the cPLA2-alpha domain results from its higher intrinsic Ca2+ affinity in the first step compared to the other domains. Assembly and disassembly of the ternary complex in response to rapid Ca2+ addition and removal, respectively, require greater than 400 ms for the cPLA2-alpha domain, compared to 13 ms for the PKC-beta domain and only 6 ms for the Syt-IA domain. Docking of the cPLA2-alpha domain to zwitterionic lipids is triggered by the binding of two Ca2+ ions and is stabilized via hydrophobic interactions, whereas docking of either the PKC-beta or the Syt-IA domain to anionic lipids is triggered by at least three Ca2+ ions and is maintained by electrostatic interactions. Thus, despite their sequence and architectural similarity, C2 domains are functionally specialized modules exhibiting equilibrium and kinetic parameters optimized for distinct Ca2+ signaling applications. This specialization is provided by the carefully tuned structural and electrostatic parameters of their Ca2+ and membrane-binding loops, which yield distinct patterns of Ca2+ coordination and contrasting mechanisms of membrane docking.

Binding Sites↗

PubMed2001

Fluorescence-based directed termination PCR: direct mutation characterization without sequencing.

We describe a fluorescence-based directed termination PCR (fluorescent DT-PCR) that allows accurate determination of actual sequence changes without dideoxy DNA sequencing. This is achieved using near infrared dye-labeled primers and performing two PCR reactions under low and unbalanced dNTP concentrations. Visualization of resulting termination fragments is accomplished with a dual dye Li-cor DNA sequencer. As each DT-PCR reaction generates two sets of terminating fragments, a pair of complementary reactions with limiting dATP and dCTP collectively provide information on the entire sequence of a target DNA, allowing an accurate determination of any base change. Blind analysis of 78 mutants of the supF reporter gene using fluorescent DT-PCR not only correctly determined the nature and position of all types of substitution mutations in the supF gene, but also allowed rapid scanning of the signature sequences among identical mutations. The method provides simplicity in the generation of terminating fragments and 100% accuracy in mutation characterization. Fluorescent DT-PCR was successfully used to generate a UV-induced spectrum of mutations in the supF gene following replication on a single plate of human DNA repair-deficient cells. We anticipate that the automated DT-PCR method will serve as a cost-effective alternative to dideoxy sequencing in studies involving large-scale analysis for nucleotide sequence changes.

Automation↗

PubMed2001

Helical structures in proteins.

We examine a minimal model for helix-forming polymers. The monomer-monomer potential energy is based on the anisotropic potentials seen in proteins and is used in conjunction with a wormlike backbone. We show that the coil-helix transition involves four states. As the temperature is lowered, the first observed state is a coil state, the second a collapsed globular, the third a highly flexible helical state, and the fourth a crystalline helical state. We discuss in detail what effect the potential energy form has on these various states by systematically varying the potential from strongly anisotropic to isotropic. The data demonstrate that the foldability of a helix is strongly related to anisotropic nature of the potential. In the isotropic case, we show that the transition following a globular collapse is not first order as postulated for these systems. In the strongly anisotropic case the globular-helix transition is consistent with cooperative first-order-like behavior.

Algorithms↗

PubMed2001

The effects of sensitization and hypersensitivity reaction on transepithelial antigen transport of rat nasal mucosa.

METHODS: The prevalence of airway allergy is very high. The ways that antigen passes across the airway tract epithelial barrier are not well understood. This study uses a model antigen, horseradish peroxidase (HRP), to sensitize and challenge the respiratory tract in the rat model. RESULTS: The results showed increases in HRP endosomes in nasal epithelial cells 5 minutes after HRP challenge in the sensitized rats compared with controls, which were further increased 30 minutes after HRP challenge, as well as with the paracellular region filled with HRP products. Meanwhile, mast cells were activated as shown by degranulation. Analysis of cell type showed that there were many more HRP endosomes in the nonciliated cells and there were many more nonciliated cells in the nasal mucosa of the sensitized rats. CONCLUSION: The results demonstrate that sensitization promotes airway mucosal epithelial cells' uptake and transport of specific antigen and that mast cells may play certain roles in this process.

Animals↗

PubMed2001

A two-source model for electron beams: calculation of relative output factors.

A two-source model for the calculation of relative output factors (ROF) for clinical applications of electron beams has been developed. The model consists of (1) an effective extended source above the final field-defining aperture (cutout) plane and (2) a source due to scattering from the aperture. Calculations are based on Fermi-Eyges theory and a pencil beam algorithm with parameters determined independently for each major scattering component. The model predicts a modified inverse square law for determining the dose rate for the electron beams. It also generalizes the "square-root method" and "one-dimensional method" that are often used clinically for ROF calculations. A computer program based on the model has been developed to calculate ROF for irregular fields. The predictions of ROF values have been compared with measurements on a Varian CLINAC 2100C/D accelerator for different cutout size, energies, applicators, and SSDs for square fields, rectangular fields, circular fields, and irregular fields. The agreement between prediction and measurement of the ROF for these wide range of conditions is generally within 1% for energies from 6 to 20 MeV. This two-source model can be used for clinical applications and it requires a minimal set of measured input data.

Algorithms↗

PubMed2001

Abnormal gastric slow waves in patients with functional dyspepsia assessed by multichannel electrogastrography.

The aim of this study was to utilize multichannel electrogastrography to investigate whether patients with functional dyspepsia had impaired propagation or coordination of gastric slow waves in the fasting state compared with healthy controls. The study was performed in 10 patients with functional dyspepsia and 11 healthy subjects. Gastric myoelectrical activity was measured by using surface electrogastrography with a specially designed four-channel device. The study was performed for 30 min or more in the fasting state. Special computer programs were developed for the computation of the propagation and coupling of the gastric slow wave. It was found that, compared with the healthy controls, the patients showed a significantly lower percentage of slow wave propagation (58.0 +/- 8.9 vs. 89.9 +/- 2.6%, P < 0.002) and a significantly lower percentage of slow wave coupling (46.9 +/- 4.4 vs. 61.5 +/- 6.9%, P < 0.04). In addition, the patients showed inconsistencies in the frequency and regularity of the gastric slow wave among the four-channel electrogastrograms (EGGs). It was concluded that patients with functional dyspepsia have impaired slow wave propagation and coupling. Multichannel EGG has more information than single-channel EGG for the detection of gastric myoelectrical abnormalities.

Adult↗

PubMed2001

[Probe into the virtual medical instruments].

With the use of 3DSMAX and AUTO CAD 2000, we have practiced the dynamic simulation of the virtual medical instrument, which is very useful in design. The engineer and doctor can watch a product and change it before making so as to save the time of design and to improve the quality.

Computer Simulation↗

PubMed2001

[Study of the reproducibility and sensitivity of laser microspectral analysis in argon atmosphere at reduced pressure].

In argon atmosphere at reduced pressure, the spectral analysis reproducibility and sensitivity are experimentally studied with the laser microprobe emission spectral analysis(LMESA) system for the metal alloy standard samples. For the atomic spectral analysis line, the relative standard deviation(RSD) in argon atmosphere at reduced pressure is better than that in air atmosphere. For the ionic spectral analysis line, the RSD is almost the same in both cases. The RSD is strongly affected by the composition of the sample and the concentration of elements. The measured slope of calibration curves for the determination of Cu, Zn and Mg in an aluminum alloy in argon atmosphere is about 1.5-2 times of that in the air atmosphere, which indicates an obvious improvement of the sensitivity and is helpful to expand the dynamic range of the spectral analysis.

Alloys↗

PubMed2000

Mutational spectrum analysis of RNase H(35) deficient Saccharomyces cerevisiae using fluorescence-based directed termination PCR.

Mutational spectrum analysis has become an informative genetic tool to understand those protein functions involved in mutation avoidance pathways since specific types of mutations are often associated with particular protein defects involved in DNA replication and repair. In this study, we describe a novel, fluorescence-based procedure for direct determination of deletions and insertions with 100% accuracy. We performed two complementary directed termination PCR with near infrared dye-labeled primers, followed by visualization of termination fragments using an automated Li-cor DNA sequencer. This method is used for rapid analysis of mutational spectra generated in nuclease-defective strains of Saccharomyces cerevisiae to elucidate the role of RNase H(35) in RNA primer removal during DNA replication and in mutation avoidance. Strains deficient in RNH35 displayed a distinct spontaneous mutation spectrum of deletions characterized by a unique 4 bp deletion in a lys2-Bgl allele. This was in sharp contrast to strains deficient in rad27 that displayed duplication mutations. Further analysis of mutations in a rnh35/rad27 double mutant revealed a mixed spectrum. These results indicate that RNase H(35) may participate in a redundant pathway in Okazaki fragment processing and that mutational spectra caused by protein deficiencies may be more intermediate-specific than pathway-specific.

DNA Mutational Analysis↗

PubMed1999

High-resolution NMR and computer modeling studies of the cannabimimetic aminoalkylindole prototype WIN-55212-2.

Aminoalkylindoles (AAIs), although structurally dissimilar from the classical cannabinoids (CCs), are known to be capable of binding to cannabinoid receptors and of evoking cannabimimetic responses. However, their mode of binding remains unknown. In this communication, we have carried out further studies on the AAI prototype (R)-[2, 3-dihydro-5-methyl-3-[(4-morpholinyl)methyl]pyrrolo[1,2,3-de]-1, 4-benzoxazin-6-yl](1-naphthalenyl)methanone (WIN-55212-2, 1) by the combined use of high-resolution 2D NMR and computer modeling. Our results suggest that the minimum energy conformations of the molecule 1 have distinct pharmacophoric features: (i) The naphthyl ring is oriented off the plane of the benzoxazine ring by approximately 59 degrees with the carbonyl C=O group pointing toward the C2-CH(3) group. (ii) At the C10-position the axial morpholinomethyl conformation is preferred over the equatorial in order to relieve a steric interaction with the C2-methyl group. The preferred conformer as defined by the three key pharmacophores, naphthyl, morpholino, and 3-keto groups, shows that the morpholinyl ring of the molecule 1 deviates from the plane of the benzoxazine ring by about 32 degrees and orients in the left molecular quadrant. This model supports the hypothesis that a certain deviation of the morpholino group from the plane of the indole ring in compound 1 is essential for cannabimimetic activity. We postulate that such an alignment by the respective pharmacophores allows them to interact optimally with the receptor. The results should help us to better understand the pharmacophoric requirements of the AAIs and serve as a basis for future SAR studies and drug design.

Benzoxazines↗

PubMed1999

Intraindividual sequence diversity and a hierarchical approach to the study of mitochondrial DNA mutations.

Investigations of intraindividual sequence diversity in mtDNA are a key step in exploring the linkage between somatic mutations in mtDNA and mitochondrial genome evolution. This paper reports a directional cloning procedure enabling the isolation of multiple copies of the D-loop region of the mitochondrial genome from the fish Ameiurus nebulosus. Sequence analysis of 708 D-loop molecules revealed eight mutants, an average intraindividual mutation frequency of 1.12%. Three different types of mutations were detected but each derived from a single mutational event. By contrasting the spectrum of nucleotide variation at multiple biological levels, one can investigate the effects of spontaneous mutations on genome evolution. Such hierarchical analysis suggested shifts in the type and distribution of mtDNA (mitochondrial DNA) mutations at different biological levels, indicating the need to recognize three different rates of mtDNA sequence change from the cellular to population level.

Animals↗

PubMed1999

Terminal branch haplotype analysis: a novel approach to investigate newly arisen variants of mitochondrial DNA in natural populations.

The discrimination of recent mutational derivatives from ancestral variation is a critical antecedent to any effort which aims to identify the factors modulating the rates of origin and persistence of new mutants. We propose that newly arisen mtDNA variants, which we designate as terminal branch haplotypes (TBHs), can be recognized by joint sequencing and phylogenetic analysis. This study examined mtDNA diversity in natural populations of the brown bullhead (Ameiurus nebulosus) from four heavily contaminated sites and three relatively pristine locations. While sequence analysis of the mtDNA D-loop region revealed that TBHs were prevalent in these populations, contaminant exposure appeared to play a minor role in their generation. Instead, most TBHs likely arose due to spontaneous mutations with variation in their incidence among sites reflecting the impact of demographic factors.

Animals↗

PubMed1999

Role of lipid modifications in targeting proteins to detergent-resistant membrane rafts. Many raft proteins are acylated, while few are prenylated.

Sphingolipid and cholesterol-rich Triton X-100-insoluble membrane fragments (detergent-resistant membranes, DRMs) containing lipids in a state similar to the liquid-ordered phase can be isolated from mammalian cells, and probably exist as discrete domains or rafts in intact membranes. We postulated that proteins with a high affinity for such an ordered lipid environment might be targeted to rafts. Saturated acyl chains should prefer an extended conformation that would fit well in rafts. In contrast, prenyl groups, which are as hydrophobic as acyl chains but have a branched and bulky structure, should be excluded from rafts. Here, we showed that at least half of the proteins in Madin-Darby canine kidney cell DRMs (other than cytoskeletal contaminants) could be labeled with [3H]palmitate. Association of influenza hemagglutinin with DRMs required all three of its palmitoylated Cys residues. Prenylated proteins, detected by [3H]mevalonate labeling or by blotting for Rap1, Rab5, Gbeta, or Ras, were excluded from DRMs. Rab5 and H-Ras each contain more than one lipid group, showing that hydrophobicity alone does not target multiply lipid-modified proteins to DRMs. Partitioning of covalently linked saturated acyl chains into liquid-ordered phase domains is likely to be an important mechanism for targeting proteins to DRMs.

Acylation↗