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Ning Xu

Publications and source records attributed to Ning Xu.

At least 37 records · Page 2Linked to original sources
PubMed2005

Stabilization of nonlinear velocity profiles in athermal systems undergoing planar shear flow.

We perform molecular dynamics simulations of model frictionless granular systems undergoing boundary-driven planar shear flow in two spatial dimensions with the goal of developing a more complete understanding of how dense particulate systems respond to applied shear. In particular, we are interested in determining when these systems will possess linear velocity profiles and when they will develop highly localized velocity profiles in response to shear. In previous work on similar systems we showed that nonlinear velocity profiles form when the speed of the shearing boundary exceeds the speed of shear waves in the material. However, we find that nonlinear velocity profiles in these systems are unstable at very long times. The degree of nonlinearity slowly decreases in time; the velocity profiles become linear when the granular temperature and density profiles are uniform across the system at long times. We measure the time t(l) required for the velocity profiles to become linear and find that t(l) increases as a power law with the speed of the shearing boundary and increases rapidly as the packing fraction approaches random close packing. We also performed simulations in which differences in the granular temperature across the system were maintained by vertically vibrating one of the boundaries during shear flow. We find that nonlinear velocity profiles form and are stable at long times if the difference in the granular temperature across the system exceeds a threshold value that is comparable to the glass transition temperature in an equilibrium system at the same average density. Finally, the sheared and vibrated systems form stable shear bands, or highly localized velocity profiles, when the applied shear stress is lowered below the yield stress of the static part of the system.

Journal Article↗
PubMed2005

AICAR stimulates IL-6 production via p38 MAPK in cardiac fibroblasts in adult mice: a possible role for AMPK.

Though known as a sensor of energy balance, AMP-activated protein kinase (AMPK) was recently shown to limit damage and apoptotic activity and contribute to the late preconditioning in heart. Interleukin-6 was also reported to involve in anti-apoptosis and cardio-protection in myocardium. Interestingly, both AMPK activity and IL-6 level were increased in response to ischemia, hypertrophy and oxidative stress. To determine whether AMPK activation will promote IL-6 production, cardiac fibroblasts (CFs) from mice were incubated with AMPK activator, 5-aminoimidazole-4-carboxamide-1-4-ribofuranoside (AICAR). The results demonstrated that AICAR time and dose-dependently stimulated IL-6 production by ELISA and immunofluorescence. Pretreatment with p38 mitogen-activated protein kinase (MAPK) inhibitor blocked AICAR-induced IL-6 production; furthermore, AICAR-activated p38 MAPK phosphorylation by Western blot. To confirm that the increase in IL-6 production is ascribed to AMPK activation, we used another known AMPK activator, metformin. It also dose-dependently potentiated IL-6 production in CFs, and this potentiation could be reversed by p38 MAPK inhibitor. In conclusion, AMPK activation promoted IL-6 production in CFs via p38 MAPK-dependent pathway.

AMP-Activated Protein Kinases↗
PubMed2005

Targeted disruption of Smad4 in cardiomyocytes results in cardiac hypertrophy and heart failure.

Transforming growth factor-betas (TGF-betas) are pleiotropic cytokines involved in many physiological and pathological processes, including heart development and heart disease. Smad4 is the central intracellular mediator of TGF-beta signaling. To investigate the function of Smad4 in heart development further, we generated a strain of cardiomyocyte-specific Smad4 knockout mice using the Cre-loxP system. Unexpectedly, the deletion of Smad4 in cardiomyocytes resulted in cardiac hypertrophy characterized by an increase in the size of cardiac myocytes, age-associated fibrosis, and reexpression of certain fetal genes. Approximately 70% of the Smad4 mutant mice died spontaneously between 5 and 12 months of age. Echocardiography and an invasive hemodynamic study of the left ventricle revealed markedly decreased cardiac contractility in Smad4 mutant mice compared with littermate controls. Moreover, phosphorylated extracellular signal-regulated kinase (ERK) 1/2 and mitogen-activated protein kinase-ERK (MEK) 1 were increased in the Smad4 mutants, suggesting that an upregulation of MEK1-ERK1/2 signaling as a consequence of deletion of Smad4 underlies the impaired cardiac function. These results reveal an important function of Smad4 in cardiac remodeling and suggest that an altered cellular response to TGF-beta could be a mechanism by which cardiac myocytes undergo hypertrophy.

Animals↗
PubMed2005

Random close packing revisited: ways to pack frictionless disks.

We create collectively jammed (CJ) packings of 50-50 bidisperse mixtures of smooth disks in two dimensions (2D) using an algorithm in which we successively compress or expand soft particles and minimize the total energy at each step until the particles are just at contact. We focus on small systems in 2D and thus are able to find nearly all of the collectively jammed states at each system size. We decompose the probability P(phi) for obtaining a collectively jammed state at a particular packing fraction phi into two composite functions: (1) the density of CJ packing fractions rho(phi), which only depends on geometry, and (2) the frequency distribution beta(phi), which depends on the particular algorithm used to create them. We find that the function rho(phi) is sharply peaked and that beta(phi) depends exponentially on phi. We predict that in the infinite-system-size limit the behavior of P(phi) in these systems is controlled by the density of CJ packing fractions--not the frequency distribution. These results suggest that the location of the peak in P(phi) when N --> infinity can be used as a protocol-independent definition of random close packing.

Journal Article↗
PubMed2005

Optical detection of single molecules in living cells.

Single molecule detection is a technology of studying biomolecules with high spatial and temporal resolution. By exploiting recent technical advances, we are able to observe, detect, even manipulate individual molecules and study their conformational changes and dynamic behaviors. New information can be obtained from the single molecule research, which is otherwise hidden or averaged out. In recent years, the development of single molecule detection techniques has opened up a new era of life science. In this review, we introduce the advances of the techniques for detecting single molecules in cell biology and review the development of single molecule detection in living cells.

Animals↗
PubMed2005

Tetrahydrobiopterin prevents cyclosporine-induced vasomotor dysfunction.

BACKGROUND: Cyclosporine A (CsA) is associated with negative side effects such as endothelial injury, which may lead to transplant vasculopathy. CsA can impair nitric oxide (NO) homeostasis. Therefore, tetrahydrobiopterin (BH4), a NO synthase cofactor, may limit endothelial injury by improving NO production. Our study examines the effect of CsA and BH4 exposure on endothelial function. METHODS: Lewis rats were injected with CsA, BH4, CsA+BH4, or saline intraperitoneally daily for 2 weeks. With use of a small vessel myograph, thoracic aortic segments were assessed for endothelial-dependent (Edep) and independent relaxation after exposure to acetylcholine and sodium nitroprusside. Sensitivity to vasospasm was evaluated after exposure to endothelin (ET)-1. RESULTS: CsA exposure resulted in impaired Edep vasorelaxation compared with control (P=0.01). BH4 attenuated the deleterious effects of CsA. Compared with control, all treatment groups demonstrated significantly increased sensitivity to ET-1. Furthermore, endothelial nitric oxide synthase expression in the thoracic aorta was reduced after CsA treatment, and this reduction was attenuated by BH4 therapy (P<0.01). ETA receptor expression in the aorta was increased after CsA treatment, but BH4 treatment prevented CsA-induced ETA over-expression (P=0.004). However, ETB receptor expression was increased by BH4 treatment compared with CsA and control (P=0.02). CONCLUSION: Our findings suggest that CsA-induced vasomotor dysfunction is a result of alterations in both NO and ET-1 regulation and that BH4 may prevent the deleterious effects of CsA. However, the beneficial effects of BH4 are associated with increased sensitivity to ET-1. Therefore, a combination of BH4 and ET-1 blockade may prove to be an ideal combination for preservation of endothelial function.

Animals↗
PubMed2005

Leptin inhibits apolipoprotein M transcription and secretion in human hepatoma cell line, HepG2 cells.

Apolipoprotein M (apoM) is a novel apolipoprotein presented mostly in high-density lipoprotein (HDL) in human plasma. Previously we have reported that both leptin and leptin receptor are essential for apoM expression in vivo. The expression of apoM is lower in the leptin deficient (ob/ob) mouse and leptin receptor deficient (db/db) mouse than in the normal mouse. In the present study, however, we demonstrated that supra-physiological concentrations of recombinant leptin significantly inhibited apoM transcription and secretion in the human hepatoma cell line, HepG2 cells. Both Northern blotting and real-time RT-PCR were applied into the analyses of apoM mRNA levels, and compatible data were obtained. The inhibitory effect of leptin on apoM mRNA levels in HepG2 cells is dose dependent, i.e. 100 ng/mL of leptin decreased apoM mRNA levels by 30%, and 500 ng/mL of leptin decreased apoM mRNA levels about 50%. Even at a physiological concentration of leptin (10 ng/mL), apoM expression was decreased, and in parallel, the secretion of apoM into the medium was also decreased. Furthermore, we examined apoAI, apoB and apoE by Northern blotting analyses. The results demonstrated that leptin does not significantly influence the expressions of apoAI, apoB and apoE in HepC2 cells, suggesting that leptin has a specific regulatory effect on hepatic apoM transcription and secretion in vitro. The mechanism on the contradictory effects of leptin on apoM expression in vivo and in vitro needs further investigation.

Animals↗
PubMed2005

Effective temperature in athermal systems sheared at fixed normal load.

We perform molecular dynamics simulations of repulsive athermal systems sheared at fixed normal load to study the effective temperature TL defined from time-dependent fluctuation-dissipation relations for density. We show that these systems possess two distinct regimes as a function of the ratio TS/V of the granular temperature to the potential energy per particle. At small TS/V, these systems are pressure controlled and TL is set by the normal load. In contrast, they behave as quasiequilibrium systems with TL approximately TS that increases with the shear rate at large TS/V. These results point out several problems with using TL in thermodynamic descriptions of slowly sheared athermal systems.

Journal Article↗
PubMed2005

Inhibition of hepatitis B virus surface antigen expression by small hairpin RNA in vitro.

AIM: To explore the anti-hepatitis B virus effect of RNA interference (RNAi) using small hairpin RNA (shRNA) expression vector. METHODS: Hepatitis B virus surface antigen green fluorescent protein (HBs-GFP) fusion vector and shRNA expression vectors were constructed and cotransfected transiently into HepG2 cells. mRNAs extracted from HepG2 cells were detected by real-time PCR. Fluorescence of HBs-GFP protein was detected by fluorescence-activated cell sorting (FACS). The effective shRNA expression vector was transfected into HepG2.2.15 cells. HBsAg and HBeAg in HepG2.2.15 cells were analyzed by radioimmunoassay (RIA) method. RESULTS: FACS revealed that shRNA targeting at HBsAg reduced the GFP signal by 56% compared to the control. Real-time PCR showed that HBs-GFP mRNA extracted from HepG2 cells cotransfected with pAVU6+27 and HBs-GFP expression plasmids decreased by 90% compared to the empty vector control. The expressions of HBsAg and HBeAg were also inhibited by 43% and 64%, respectively. CONCLUSION: RNAi using shRNA expression vector can inhibit the expression of HBsAg, providing a fresh approach to screening the efficient small interfering RNAs (siRNAs).

Carcinoma, Hepatocellular↗
PubMed2005

Velocity profiles in repulsive athermal systems under shear.

We conduct molecular dynamics simulations of athermal systems undergoing boundary-driven planar shear flow in two and three spatial dimensions. We find that these systems possess nonlinear mean velocity profiles when the velocity u of the shearing wall exceeds a critical value u(c). Above u(c), we also show that the packing fraction and mean-square velocity profiles become spatially dependent with dilation and enhanced velocity fluctuations near the moving boundary. In systems with overdamped dynamics, u(c) is only weakly dependent on packing fraction phi. However, in systems with underdamped dynamics, u(c) is set by the speed of shear waves in the material and tends to zero as phi approaches phi(c), which is near random close packing at small damping. For underdamped systems with phi<phi(c), u(c) is zero; thus they possess nonlinear velocity profiles at any nonzero u.

Journal Article↗
PubMed2005

Screening candidate genes for mutations in patients with hypogonadotropic hypogonadism using custom genome resequencing microarrays.

OBJECTIVE: The purpose of this study was to determine the consistency of calling single nucleotide polymorphisms (SNPs) by custom genome resequencing microarrays compared with capillary DNA sequencing. STUDY DESIGN: Amplified genomic DNA from 23 patients with hypogonadotropic hypogonadism was hybridized to microarrays containing 30 kilobases of sequence from 6 different candidate genes. Capillary DNA sequencing was performed in 10 patients. RESULTS: For 10 patients with > or =90% of bases called, 49 SNPs in 5 of 6 genes were identified. Of the 490 bases, 75 were ambiguous (read as "N"), and 415 were able to be called an A, C, G, or T. Of 415 called, 401 (96.6%) sequences were confirmed by DNA sequencing. All homozygotes (285/285) were called identically, while sequence from 89.2% (116/130) of heterozygotes agreed by both methods. The level of agreement between microarray calls and capillary DNA sequencing demonstrated substantial accuracy. CONCLUSION: Custom genome resequencing microarrays are highly consistent with capillary sequencing in calling individual bases in genomic DNA from patients with human disease.

Adolescent↗
PubMed2005

Cardiac allograft preservation using donor-shed blood supplemented with L-arginine.

BACKGROUND: Despite improved preservation techniques, myocardial and endothelial dysfunction persists after cardiac transplantation. L-arginine has been shown to decrease endothelial injury in several models of ischemia and reperfusion. We assessed the effects of L-arginine on allograft preservation in a porcine model of cardiac transplantation. METHODS: Orthotopic cardiac transplants were performed in Yorkshire pigs. Hearts were randomly arrested with high potassium cardioplegia with or without L-arginine at a dose of 2.5 mmol/liter (LARGlow) and 5.0 mmol/liter. Donor-shed blood was collected at the time of organ harvest and intermittently perfused throughout the storage period. Coronary endothelial function was assessed at baseline and after reperfusion by measuring the change in coronary blood flow after exposure to acetylcholine or nitroglycerin. Pressure-volume relationships before and after transplant were evaluated with conductance catheter measurements. Myocardial biopsy specimens were assessed for inflammatory markers of cellular injury. RESULTS: High-dose L-arginine uniformly resulted in ischemic contracture in all hearts, and there was no return of function in any hearts after storage. The low-dose L-arginine group had a greater ability to wean off cardiopulmonary bypass and displayed improved recovery of left ventricular function. Control animals had a 26% reduction in coronary flow compared with 13% for LARGlow. LARGlow resulted in decreased release of inflammatory cytokines compared with control. CONCLUSIONS: Low-dose L-arginine preserves myocardial and endothelial function and decreases endothelial injury when it is used as a supplement to intermittent donor blood perfusion. In contrast, high-dose L-arginine resulted in severe endothelial injury and an inability to recover ventricular function after 5 hours of global ischemia.

Animals↗
PubMed2005

Suppression of RNA interference by adenovirus virus-associated RNA.

We show that human adenovirus inhibits RNA interference (RNAi) at late times of infection by suppressing the activity of two key enzyme systems involved, Dicer and RNA-induced silencing complex (RISC). To define the mechanisms by which adenovirus blocks RNAi, we used a panel of mutant adenoviruses defective in virus-associated (VA) RNA expression. The results show that the virus-associated RNAs, VA RNAI and VA RNAII, function as suppressors of RNAi by interfering with the activity of Dicer. The VA RNAs bind Dicer and function as competitive substrates squelching Dicer. Further, we show that VA RNAI and VA RNAII are processed by Dicer, both in vitro and during a lytic infection, and that the resulting short interfering RNAs (siRNAs) are incorporated into active RISC. Dicer cleaves the terminal stem of both VA RNAI and VA RNAII. However, whereas both strands of the VA RNAI-specific siRNA are incorporated into RISC, the 3' strand of the VA RNAII-specific siRNA is selectively incorporated during a lytic infection. In summary, our work shows that adenovirus suppresses RNAi during a lytic infection and gives insight into the mechanisms of RNAi suppression by VA RNA.

Adenoviruses, Human↗
PubMed2005

[Inhibition of HBV core antigen gene expression in human embryonic kidney cell line AD293 by plasmid-based RNAi].

OBJECTIVE: To inhibit HBV core antigen gene expression with plasmid-based RNAi. METHODS: The shRNA expression vector targeting HBV core antigen gene was designed and constructed. Human embryonic kidney cell line AD293 was co-transfected with HBcAg-EGFP fusion protein expression vector and shRNA expression vector transiently, and the cells without shRNA-transfection and with non-specific shRNA transfection were used as controls. Inhibitory effect of RNAi was detected by fluorescence-activated cell sorting (FACS) and real-time fluorescence quantificational RT-PCR. RESULTS: HBV core antigen gene expression in AD293 was inhibited by shRNA, with the maximal inhibition rate of 76 % measured by FACS and of 63.1 % by real-time PCR. CONCLUSION: Effective inhibition of HBV core antigen gene expression by plasmid-based RNAi provides an alternative for anti-HBV study in vitro, which has potential clinical application.

Cell Line↗
PubMed2005

Study on model of indoor air pollution forecast for decoration under natural ventilation condition.

OBJECTIVE: To establish the model of indoor air pollution forecast for decoration. METHODS: The model was based on the balance model for diffusing mass. RESULTS: The data between testing concentration and estimating concentration were compared. The maximal error was less than 30% and average error was 14.6%. CONCLUSION: The model can easily predict whether the pollution for decoration exceeds the standard and how long the room is decorated.

Air Pollution, Indoor↗
PubMed2004

Apolipoprotein M.

Apolipoprotein M (apoM) is a 26-kDa protein that is mainly associated with high-density lipoprotein (HDL) in human plasma, with a small proportion present in triglyceride-rich lipoproteins (TGRLP) and low-density lipoproteins (LDL). Human apoM gene is located in p21.31 on chromosome 6 (chromosome 17, in mouse). Human apoM cDNA (734 base pairs) encodes 188-amino acid residue-long protein. It belongs to lipocalin protein superfamily. Human tissue expression array study indicates that apoM is only expressed in liver and in kidney and small amounts are found in fetal liver and kidney. In situ apoM mRNA hybridization demonstrates that apoM is exclusively expressed in the hepatocytes and in the tubule epithelial cells in kidney. Expression of apoM could be regulated by platelet activating factor (PAF), transforming growth factors (TGF), insulin-like growth factor (IGF) and leptin in vivo and/or in vitro. It has been demonstrated that apoM expression is dramatically decreased in apoA-I deficient mouse. Hepatocyte nuclear factor-1alpha (HNF-1alpha) is an activator of apoM gene promoter. Deficiency of HNF-1alpha mouse shows lack of apoM expression. Mutations in HNF-1alpha (MODY3) have reduced serum apoM levels. Expression of apoM is significantly decreased in leptin deficient (ob/ob) mouse or leptin receptor deficient (db/db) mouse. ApoM concentration in plasma is positively correlated to leptin level in obese subjects. These may suggest that apoM is related to the initiation and progression of MODY3 and/or obesity.

Journal Article↗
PubMed2004

Both leptin and leptin-receptor are essential for apolipoprotein M expression in vivo.

It was previously shown that circulating levels of leptin and apolipoprotein M (apoM) correlate to each other. In this study, we examined whether plasma leptin and leptin-receptors are of importance for apoM expression in vivo. It was found that in both liver and kidney, expression of apoM was significantly lower in leptin deficient ob/ob mice and in leptin-receptor deficient db/db mice than in control mice. Furthermore, leptin administration (0.5 or 1.5 microg/g body weight) significantly increased plasma apoM levels and apoM mRNA levels in liver and in kidney in ob/ob mice. We conclude that both leptin and leptin-receptor are essential for the apoM expression, indicating that leptin is physiologically regulating apoM synthesis in vivo.

Animals↗