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Y Huang

Publications and source records attributed to Y Huang.

At least 55 records · Page 3Linked to original sources
PubMed2005

Using pseudo amino acid composition to predict protein subcellular location: approached with Lyapunov index, Bessel function, and Chebyshev filter.

With the avalanche of new protein sequences we are facing in the post-genomic era, it is vitally important to develop an automated method for fast and accurately determining the subcellular location of uncharacterized proteins. In this article, based on the concept of pseudo amino acid composition (Chou, K.C. Proteins: Structure, Function, and Genetics, 2001, 43: 246-255), three pseudo amino acid components are introduced via Lyapunov index, Bessel function, Chebyshev filter that can be more efficiently used to deal with the chaos and complexity in protein sequences, leading to a higher success rate in predicting protein subcellular location.

Amino Acid Sequence↗
PubMed2005

Glutamate uptake is attenuated in spinal deep dorsal and ventral horn in the rat spinal nerve ligation model.

Alteration of glutamatergic (GLU) neurotransmission within the spinal cord contributes to hyperalgesic and allodynic responses following nerve injury. In particular, changes in expression and efficacy of glutamate transporters have been reported. Excitatory, pain transmitting primary afferent neurons utilizing glutamate as an excitatory neurotransmitter project to both superficial (I-II) and deep (III-V) laminae of the dorsal horn. These experiments were designed to examine changes in glutamate uptake occurring concomitantly within the spinal deep dorsal and ventral horn in situ after experimentally induced neuropathic pain. In vivo voltammetry, using microelectrode arrays configured for enzyme-based detection of GLU were employed. Sprague-Dawley rats had either sham surgery or tight ligation of L5 and L6 spinal nerves (SNL). Four to six weeks later, the L4-L6 spinal cord of chloral hydrate-anesthetized animals was exposed, and ceramic-based glutamate microelectrodes equipped with glass micropipettes 50 microm from the recording surfaces were placed stereotaxically at sites within the spinal cord. Pressure ejection of GLU into the ipsilateral L5-L6 spinal cord resulted in a 72% reduction of GLU uptake in SNL rats compared to sham controls in the ipsilateral L5-L6 deep dorsal horn and a 96% reduction in the ventral horn. In contrast, in the same animals, the contralateral L5-L6 or the ipsilateral L4 spinal cord showed no change in glutamate uptake. The data suggest that spinal nerve ligation produced attenuated glutamate uptake activity extending into the deep dorsal and ventral horn. The study suggests that plasticity related to spinal nerve injury produces widespread alteration in glutamate transporter function that may contribute to the pathophysiology of neuropathic pain.

Amino Acid Transport System X-AG↗
PubMed2005

Alpha B-crystallin is a major component of glial cytoplasmic inclusions in multiple system atrophy.

Multiple system atrophy (MSA) is characterized by the formation of oligodendroglial cytoplasmic inclusions (GCIs) consisting of alpha-synuclein filaments. AlphaB-crystallin, a small chaperone protein that binds to unfolded proteins and inhibits aggregation, has been documented in GCIs. We investigated the relative abundance and speciation of alphaB-crystallin in GCIs in MSA brains. We also examined the influence of alphaB-crystallin on the formation of cytoplasmic inclusions in cultured glial cells. Immunohistochemistry and confocal microscopy revealed alphaB-crystallin is a prominent component of GCIs, more abundant than in Lewy bodies in Lewy body dementia. One- and two-dimensional gel electrophoresis and mass spectrometric analysis of GCIs immunopurified from MSA brains indicated that alphaB-crystallin is a major protein component with multiple post-translationally modified species. In cultured C6 glioma cells treated with the proteasomal inhibitor, lactacystin, to induce accumulation of ubiquitinated proteins, a subset of cells showed increased cytoplasmic staining for alphaB-crystallin. Proteasome-inhibited cells transfected with GFP-tagged alpha-synuclein resulted in ubiquitin- and alphaB-crystallin-positive aggregates resembling GCIs in MSA brains. Our results indicate that alphaB-crystallin is a major chaperone in MSA, and suggest a role of the protein in the formation of inclusion bodies in glial cells.

Amino Acid Sequence↗
PubMed2005

The signaling and apoptotic effects of TNF-related apoptosis-inducing ligand in HIV-1 associated dementia.

HIV-1 Associated Dementia (HAD) develops during progressive HIV-1 infection and is characterized by cognitive impairments, behavioral disorders and potential progressive motor abnormality. Abnormal inflammation within the central nervous system (CNS), activation of macrophage/microglia and involvement of proinflammatory cytokines have been suggested as primary factors in the pathogenesis of HAD. Impairment of neuronal function and neuronal cell death are believed to be the end pathophysiological result of HAD. TNF-related apoptosis-inducing ligand (TRAIL), a member of the TNF family of cytokines, was suggested to participate in apoptotic cell death during HAD. As a death ligand, TRAIL was originally thought to target only tumor cells. TRAIL is not typically present in CNS; however, emerging data show that TRAIL can be induced by immune stimuli on macrophage and microglia, major disease effector cells during HAD. Upregulated TRAIL may then cause neuronal apoptosis through direct interaction with TRAIL receptors on neurons or through macrophage death-mediated release of neurotoxins. In this review, we summarize the pivotal role of TRAIL in HAD and TRAIL-initiated intracellular death cascades that culminate in neuronal apoptosis as observed in HAD.

AIDS Dementia Complex↗
PubMed2005

Transcriptional upregulation of PUMA modulates endoplasmic reticulum calcium pool depletion-induced apoptosis via Bax activation.

PUMA, a key mediator of p53-induced apoptosis, is a BH3-only domain proapoptotic protein that localizes to mitochondria and interacts with antiapoptotic Bcl-2 and Bcl-X(L). Recent evidence implicates Bax to be an important mediator of PUMA-activated apoptotic signals. We have previously demonstrated that Bax deficiency significantly affects thapsigargin (TG)-mediated endoplasmic reticulum calcium pool depletion-induced apoptosis. We now present evidence that TG upregulates PUMA expression and that although Bax-deficient cells exhibit resistance to TG, Bax deficiency does not attenuate TG upregulation of PUMA expression. Furthermore, TG transcriptionally upregulates PUMA expression in a p53-independent manner and that PUMA-deficient cells are more resistant to undergo TG-induced apoptosis than the PUMA-proficient counterparts. Thus, our results demonstrate that TG engages PUMA and Bax for full transduction of apoptotic signals and both PUMA and Bax appear to exist in the same TG-activated apoptotic pathway in which PUMA may reside upstream of Bax.

Apoptosis↗
PubMed2005

Desferrioxamine induces leukemic cell differentiation potentially by hypoxia-inducible factor-1 alpha that augments transcriptional activity of CCAAT/enhancer-binding protein-alpha.

We reported recently that cobalt chloride-simulated hypoxia and mild hypoxia modified the differentiation of human acute myeloid leukemic (AML) cells, probably acting via a hypoxia-inducible factor-1 alpha (HIF-1 alpha)-dependent mechanism. In this study, we investigated the effect of desferrioxamine (DFO), an iron chelator with 'hypoxia-mimetic' activity, on the differentiation of AML cells. The results showed that DFO at nontoxic concentrations induced the differentiation of AML cell lines NB4 and U937, as assessed by morphological criteria and differentiation-associated antigens. DFO-induced differentiation parallel to the rapid accumulation of HIF-1 alpha protein in these two cell lines. Of importance, the transient transfection of HIF-1 alpha cDNA induced U937 cells to develop the differentiation-related alterations such as growth arrest and increased CD11b expression. Furthermore, the inducible expression of chromosome translocation t(8;21)-generated leukemogenic AML1-ETO fusion gene attenuated DFO-induced differentiation of U937 cells with the decrease of CCAAT/enhancer-binding protein alpha (C/EBP alpha), a critical factor for granulocytic differentiation. Using immunoprecipitation and luciferase reporter assay, HIF-1 alpha was also shown to interact physically with and to increase the transcriptional activity of C/EBP alpha. Taken together, these results provided novel evidence for a role of HIF-1 alpha in AML cell differentiation, and suggested that C/EBP alpha might be a downstream effector for HIF-1 alpha-mediated differentiation.

Acute Disease↗
PubMed2005

Correlating gene expression with chemical scaffolds of cytotoxic agents: ellipticines as substrates and inhibitors of MDR1.

To facilitate a systematic study of chemoresistance across diverse classes of anticancer drug candidates, we performed correlation analyses between cytotoxic drug potency and gene expression in 60 tumor cell lines (NCI-60; NCI-National Cancer Institute). Ellipticine analogs displayed a range of correlation coefficients (r) with MDR1 (ABCB1, encoding multidrug resistance (MDR) protein MDR1 or P-glycoprotein). To determine MDR1 interactions of five ellipticines with diverse MDR1-r values, we employed MDR1-transport and cytotoxicity assays, using MDR1 inhibitors and siRNA-mediated MDR1 downregulation, in MDR1-overexpressing cells. Ellipticines with negative correlations-indicative of MDR1-mediated resistance-were shown to be MDR1 substrates, whereas those with neutral or positive correlations served as MDR1 inhibitors, which escape MDR1-mediated chemoresistance. Correlation with additional genes in the NCI-60 confirmed topoisomerases as ellipticine targets, but suggested distinct mechanisms of action and chemoresistance among them, providing a guide for selecting optimal drug candidates.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2005

Immunization with a bovine herpesvirus 1 glycoprotein B DNA vaccine induces cytotoxic T-lymphocyte responses in mice and cattle.

Virus-specific cytotoxic T lymphocytes (CTLs) are considered to be important in protection against and recovery from viral infections. In this study, several approaches to induce cytotoxicity against bovine herpesvirus 1 (BHV-1) were evaluated. Vaccination of C57BL/6 mice with BHV-1 induced a strong humoral, but no CTL, response, which may be due to downregulation of major histocompatibility complex class I molecules. In contrast, vaccinia virus expressing glycoprotein B (gB) elicited a weaker antibody response, but strong cytotoxicity, in mice. As an approach to inducing both strong humoral and cellular immune responses, a plasmid vector was then used to express gB. Both antibody and CTL responses were induced by the plasmid encoding gB in C57BL/6 and C3H mice, regardless of the type of vector backbone. This demonstrated that DNA immunization induces a broad-based immune response to BHV-1 gB. Interestingly, removal of the membrane anchor, which resulted in secretion of gB from transfected cells, did not result in reduced cytotoxicity. Here, it is shown that, compared with the cell-associated counterpart, plasmid-encoded secreted protein may induce enhanced immune responses in cattle. Therefore, calves were immunized intradermally with pMASIAtgB, a plasmid encoding the secreted form of gB (tgB), using a needle-free injection system. This demonstrated that pMASIAtgB elicited both humoral responses and activated gamma interferon-secreting CD8+ CTLs, suggesting that a DNA vaccine expressing tgB induces a CTL response in the natural host of BHV-1.

Animals↗
PubMed2005

Radiation-induced changes in gene expression in the silkworm revealed by serial analysis of gene expression (SAGE).

Serial analysis of gene expression (SAGE) was used to examine the profile of expressed genes during embryonic development in the domesticated silkworm, Bombyx mori, after irradiation with Cobalt-60. A comparison of the SAGE sequence tags derived from irradiated embryos with those from normal embryos revealed 673 differentially expressed genes (P < 0.01 and at least three folds change). Of these, 292 genes were highly expressed in normal embryos and 381 genes were highly expressed in irradiated embryos. These results provide valuable information for understanding the mechanisms of radiation-induced changes in gene expression. In addition, it was noted that the generation of longer cDNA fragments from SAGE tags is an efficient way to identify genes, thereby facilitating the analysis of large numbers of unknown genes.

Animals↗
PubMed2005

An interaction between the TaqIB polymorphism of cholesterol ester transfer protein and smoking is associated with changes in plasma high-density lipoprotein cholesterol levels in Turks.

Low levels of high-density lipoprotein cholesterol (HDL-C) are an independent risk factor for atherosclerosis. We investigated the effects of the TaqIB polymorphism of cholesterol ester transfer protein (CETP) on CETP activity and plasma HDL-C levels in random nondiabetic and self-reported diabetic subjects in a population with very low HDL-C levels. The rare B2B2 genotype was associated with significantly higher HDL-C levels and lower CETP activity in random subjects and with higher HDL-C in diabetic subjects. After stratification of random subjects by smoking status, the common B1B1 genotype was associated with lower HDL-C levels than the B2B2 genotype. Although smoking was associated with lower HDL-C, especially in men, HDL-C levels between smokers and nonsmokers were not different in subjects with the B1B2 or B2B2 genotypes. However, smoking (20+ cigarettes/day) was associated with a marked reduction in HDL-C in the B1B1 subjects. The B1B1/smoking interaction was not reflected in a difference in CETP activity. High triglycerides and elevated body mass index (BMI) lower HDL-C. The B2B2 genotype was associated with the highest HDL-C levels, and these levels were significantly lower in the hypertriglyceridemic subjects (>or=50th percentile). The lowest HDL-C levels were seen in hypertriglyceridemic subjects with the B1B1 genotype. Although BMI (>or=50th vs<50th percentile) did not affect HDL-C in B2B2 subjects, a high BMI was associated with markedly lower HDL-C in B1B1 subjects. Thus, HDL-C levels in Turks may be modulated by an interaction between the CETP TaqIB polymorphism and smoking, as well as an interaction with hypertriglyceridemia and BMI.

Adult↗
PubMed2005

Effects of isoflurane on oxygen-glucose deprivation-induced changes of gene expression profiling in glial-neuronal cocultures.

BACKGROUND: Isoflurane decreases ischemia-induced neuronal injury. The mechanisms of this effect are largely unknown. We hypothesize that isoflurane induces expression of protective stress genes and decreases expression of apoptosis-related genes. METHODS: The mRNA expression of about 1300 genes related to neurobiology in rat glial-neuronal cocultures was evaluated by microarray technology. Four experimental conditions were examined: control; 2% isoflurane; oxygen-glucose deprivation (OGD, to simulate ischemia in vitro); or isoflurane (2%) plus OGD. RESULTS: There were four immediate early genes/transcription factors (early growth response 1, c-fos, nerve growth factor-induced factor A and Knox-24) whose mRNA expression was increased to more than 1.4-fold of control levels under the conditions of isoflurane, OGD or isoflurane plus OGD. Isoflurane increased the mRNA expression of heme oxygenase, a 32-kDa heat-shock protein, and decreased the mRNA expression of caspase-2, calpain 1 and the Bcl-2-associated death agonist. These isoflurane effects were still apparent under the condition of isoflurane plus OGD. The mRNA expression of Gbeta1, early growth response 1 and the death effector domain-containing protein DEFT in the samples used for microarray assay was determined by reverse transcriptase-polymerase chain reaction, and the results were consistent with the patterns of changes across the experimental conditions as revealed by microarray technology. CONCLUSION: Our data suggest that the effects of isoflurane on the mRNA expression of multiple genes in glial-neuronal cocultures are consistent with its neuroprotection against ischemia. A coordinated change in expression of many genes (increased expression of potentially protective gene and decreased expression of potentially damaging genes) after the exposure of isoflurane was revealed by this study.

Anesthetics, Inhalation↗
PubMed2005

Metal oxide coating on carbon nanotubes by a methanol-thermal method.

A methanol-thermal method has been developed to fabricate one-dimensional composite nanowires by coating multiwalled carbon nanotubes with lanthanum oxide and iron oxide, respectively. The coating structure and composition have been investigated by transmission electron microscopy and the X-ray energy dispersive spectrum. Magnetic measurement for the iron oxide coatings indicated that the coercivity has been enhanced after coating. The method reported here provides a novel procedure for the fabrication of one-dimensional composite nanostructures.

Crystallization↗
PubMed2005

The role of TNF related apoptosis-inducing ligand in neurodegenerative diseases.

A hallmark of all forms of neurodegenerative diseases is impairment of neuronal functions, and in many cases neuronal cell death. Although the etiology of neurodegenerative diseases may be distinct, different diseases display a similar pathogenesis, for example abnormal immunity within the central nervous system (CNS), activation of macrophage/microglia and the involvement of proinflammatory cytokines. Recent studies show that neurons in a neurodegenerative state undergo a highly regulated programmed cell death, also called apoptosis. TNF-related apoptosis-inducing ligand (TRAIL), a member of the TNF family, has been shown to be involved in apoptosis during many diseases. As one member of a death ligand family, TRAIL was originally thought to target only tumor cells and was not present in CNS. However, recent data showed that TRAIL was unregulated in HIV-1-infected and immune-activated macrophages, a major disease inducing cell during HIV-1-associated dementia (HAD). TRAIL is also induced on neuron by beta-amyloid protein, an important pathogen for Alzheimer's disease. In this review, we summarize the possible common aspects that TRAIL involved those neurodegenerative diseases, TRAIL induced apoptosis signaling in the CNS cells, and specific role of TRAIL in individual diseases.

AIDS Dementia Complex↗
PubMed2004

Using complexity measure factor to predict protein subcellular location.

Recent advances in large-scale genome sequencing have led to the rapid accumulation of amino acid sequences of proteins whose functions are unknown. Because the functions of these proteins are closely correlated with their subcellular localizations, it is vitally important to develop an automated method as a high-throughput tool to timely identify their subcellular location. Based on the concept of the pseudo amino acid composition by which a considerable amount of sequence-order effects can be incorporated into a set of discrete numbers (Chou, K. C., Proteins: Structure, Function, and Genetics, 2001, 43: 246-255), the complexity measure approach is introduced. The advantage by incorporating the complexity measure factor as one of the pseudo amino acid components for a protein is that it can more effectively reflect its overall sequence-order feature than the conventional correlation factors. With such a formulation frame to represent the samples of protein sequences, the covariant-discriminant predictor (Chou, K. C. and Elrod, D. W., Protein Engineering, 1999, 12: 107-118) was adopted to conduct prediction. High success rates were obtained by both the jackknife cross-validation test and independent dataset test, suggesting that introduction of the concept of the complexity measure into prediction of protein subcellular location is quite promising, and might also hold a great potential as a useful vehicle for the other areas of molecular biology.

Algorithms↗
PubMed2004

Postmortem mu-opioid receptor binding in suicide victims and controls.

BACKGROUND: Endogenous opiates may reinforce self-injurious behavior in animal and human subjects. Higher postmortem mu-opioid receptor binding is reported in some brain regions in young compared with older suicide victims. The present study compared opioid receptor binding kinetics in postmortem brains of young suicide victims and matched controls in two brain areas. METHODS: The density (Bmax) and affinity (K(D)) of the mu-opioid receptors were assayed postmortem using [3H] DAGO in prefrontal cortex (PFC) and pre-post central gyri (PPCG) in 9 suicide victims and 10 controls, matched for age and gender ratio. RESULTS: Binding indices did not differ between suicide victims and controls in either brain area and did not correlate with age. PFC Bmax was higher than PPCG Bmax (F=8.030; df=1,16; p=.012) for the combined sample. There was no brain region difference in K(D) between PFC and PPCG, but the interaction between K(D) and group was significant (F = 5.890; df = 1,16; p = .027). The K(D) in the suicide victims was lower than controls in the PFC and higher than controls in the PPCG. CONCLUSION: Our study demonstrated more mu-opioid receptors in PFC compared with PPCG binding regardless of suicide status. The region-dependent differences in binding affinity in suicide victims may reflect regionally different opiate transmission.

Adult↗
PubMed2004

Intrinsic energy loss mechanisms in a cantilevered carbon nanotube beam oscillator.

Classical molecular dynamics is applied to study the energy dissipation (the Q factor) of the cantilever-type beam oscillators of single wall and double-walled carbon nanotubes (CNTs). The study finds that the Q factor of the CNT beam oscillator varies with the temperature T following the 1/T(0.36) dependence. For single wall CNT, the Q factor drops from 2 x 10(5) at 0.05 K to 1.5 x 10(3) at 293 K. The study further reveals that the weak interlayer binding strength and the interlayer commensurance significantly increases the energy dissipation in the double-walled CNT oscillator.

Journal Article↗
PubMed2004

The relaxant effect of urocortin in rat pulmonary arteries.

Urocortin is a potent vasodilator, which plays physiological or pathophysiological roles in systemic circulation. However, little is known about its action on pulmonary circulation. The present study was aimed to characterize some cellular mechanisms underlying the relaxant effect of urocortin in isolated rat pulmonary arteries. Changes in isometric tension were measured on small vessel myographs. Urocortin inhibited U46619-induced contraction with reduction of the maximal response. Urocortin-induced relaxation was independent of the presence of endothelium. Inhibitors of nitric oxide (NO)-dependent dilator, NG-nitro-L-arginine methyl ester or 1H-[1,2,4]oxadizolo[4,3-a]quinoxalin-1-one, did not affect the relaxation. Astressin (100-500 nM), a corticotropin-releasing factor (CRF) receptor antagonist and KT5720, a protein kinase A (PKA) inhibitor reduced urocortin-induced relaxation. Urocortin produced less relaxant effect in 30 mM K+- than U46619-contracted arterial rings. Urocortin did not reduce CaCl2-induced contraction in 60 mM K+-containing solution. Ba2+ (100-500 microM) but not other K+ channel blockers reduced the relaxant responses to urocortin. Urocortin also relaxed the rings preconstricted by phorbol 12,13-diacetae in normal Krebs solution while this relaxation was less in a Ca2+-free solution. Our results show that urocortin relaxed rat pulmonary arteries via CRF receptor-mediated and PKA-dependent but endothelium/NO or voltage-gated Ca2+ channel-independent mechanisms. Stimulation of Ba2+-sensitive K+ channel may contribute to urocortin-induced relaxation. Finally, urocortin relaxed pulmonary arteries partly via inhibition of a PKC-dependent contractile mechanism.

Animals↗