Biomedical subjects

Feng Liu

Publications and source records attributed to Feng Liu.

At least 37 records · Page 2Linked to original sources

PubMed2006

Uncovering conserved patterns in bioactive peptides in Metazoa.

Bioactive (neuro)peptides play critical roles in regulating most biological processes in animals. Peptides belonging to the same family are characterized by a typical sequence pattern that is conserved among the family's peptide members. Such a conserved pattern or motif usually corresponds to the functionally important part of the biologically active peptide. In this paper, all known bioactive (neuro)peptides annotated in Swiss-Prot and TrEMBL protein databases are collected, and the pattern searching program Pratt is used to search these unaligned peptide sequences for conserved patterns. The obtained patterns are then refined by combining the information on amino acids at important functional sites collected from the literature. All the identified patterns are further tested by scanning them against Swiss-Prot and TrEMBL protein databases. The diagnostic power of each pattern is validated by the fact that any annotated protein from Swiss-Prot and TrEMBL that contains one of the established patterns, is indeed a known (neuro)peptide precursor. We discovered 155 novel peptide patterns in addition to the 56 established ones in the PROSITE database. All the patterns cover 110 peptide families. Fifty-five of these families are not characterized by the PROSITE signatures, and 12 are also not identified by other existing motif databases, such as Pfam and SMART. Using the newly identified peptide signatures as a search tool, we predicted 95 hypothetical proteins as putative peptide precursors.

Amino Acid Motifs↗

PubMed2006

Nature of reactive O2 and slow CO2 evolution kinetics in CO oxidation by TiO2 supported Au cluster.

Recent experiments on CO oxidation reaction using seven-atom Au clusters deposited on TiO2 surface correlate CO2 formation with oxygen associated with Au clusters. We perform first principles calculations using a seven-atom Au cluster supported on a reduced TiO2 surface to explore potential candidates for the form of reactive oxygen. These calculations suggest a thermodynamically favorable path for O2 diffusion along the surface Ti row, resulting in its dissociated state bound to Au cluster and TiO2 surface. CO can approach along the same path and react with the O2 so dissociated to form CO2. The origin of the slow kinetic evolution of products observed in experiments is also investigated and is attributed to the strong binding of CO2 simultaneously to the Au cluster and the surface.

Journal Article↗

PubMed2006

Application of molecularly imprinted polymers to solid-phase extraction of analytes from real samples.

A review is presented of recent developments in the use of molecularly imprinted polymers (MIPs) as selective materials for solid-phase extraction. Compared with traditional sorbents, MIPs can not only concentrate but also selectively separate the target analytes from real samples, which is crucial for the quantitatively determination of analytes in complex samples. Consequently, as one of the most effective sorbents, MIPs have been successfully applied to the pretreatment of analytes in foods, drugs, and biological and environmental samples in the past five years.

Biocompatible Materials↗

PubMed2006

Simulation of Brugada syndrome using cellular and three-dimensional whole-heart modeling approaches.

Brugada syndrome (BS) is a genetic disease identified by an abnormal electrocardiogram (ECG) (mainly abnormal ECGs associated with right bundle branch block and ST-elevation in right precordial leads). BS can lead to increased risk of sudden cardiac death. Experimental studies on human ventricular myocardium with BS have been limited due to difficulties in obtaining data. Thus, the use of computer simulation is an important alternative. Most previous BS simulations were based on animal heart cell models. However, due to species differences, the use of human heart cell models, especially a model with three-dimensional whole-heart anatomical structure, is needed. In this study, we developed a model of the human ventricular action potential (AP) based on refining the ten Tusscher et al (2004 Am. J. Physiol. Heart Circ. Physiol. 286 H1573-89) model to incorporate newly available experimental data of some major ionic currents of human ventricular myocytes. These modified channels include the L-type calcium current (I(CaL)), fast sodium current (I(Na)), transient outward potassium current (I(to)), rapidly and slowly delayed rectifier potassium currents (I(Kr) and I(Ks)) and inward rectifier potassium current (I(Ki)). Transmural heterogeneity of APs for epicardial, endocardial and mid-myocardial (M) cells was simulated by varying the maximum conductance of I(Ks) and I(to). The modified AP models were then used to simulate the effects of BS on cellular AP and body surface potentials using a three-dimensional dynamic heart-torso model. Our main findings are as follows. (1) BS has little effect on the AP of endocardial or mid-myocardial cells, but has a large impact on the AP of epicardial cells. (2) A likely region of BS with abnormal cell AP is near the right ventricular outflow track, and the resulting ST-segment elevation is located in the median precordium area. These simulation results are consistent with experimental findings reported in the literature. The model can reproduce a variety of electrophysiological behaviors and provides a good basis for understanding the genesis of abnormal ECG under the condition of BS disease.

Action Potentials↗

PubMed2006

Cytosolic NADPH metabolism in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum.

This study addresses the relation between NADPH supply and penicillin synthesis, by comparing the flux through the oxidative branch of the pentose phosphate pathway (PPP; the main source of cytosolic NADPH) in penicillin-G producing and non-producing chemostat cultures of Penicillium chrysogenum. The fluxes through the oxidative part of the PPP were determined using the recently introduced gluconate-tracer method. Significantly higher oxidative PPP fluxes were observed in penicillin-G producing chemostat cultures, indicating that penicillin production puts a major burden on the supply of cytosolic NADPH. To our knowledge this is the first time direct experimental proof is presented for the causal relationship between penicillin production and NADPH supply. Additional insight in the metabolism of P. chrysogenum was obtained by comparing the PPP fluxes from the gluconate-tracer experiment to oxidative PPP fluxes derived via metabolic flux analysis, using different assumptions for the stoichiometry of NADPH consumption and production.

Anti-Bacterial Agents↗

PubMed2006

Facile synthesis of complicated 9,9-diarylfluorenes based on BF3.Et2O-mediated Friedel-Crafts reaction.

[reaction: see text] BF3.OEt2-mediated Friedel-Crafts reaction of 9-phenyl-fluoren-9-ol with electron-rich aromatic substrates to prepare a new family of complicated 9,9-diarylfluorenes is described. The 9,9-diarylfluorenes tethered with various functional substituents, e.g., bulky spiro units, hole-transporting moieties, and fluorescent dyes, will be promising building blocks for the construction of optoelectronic materials.

Journal Article↗

PubMed2006

Pressure-induced transition in magnetoresistance of single-walled carbon nanotubes.

We applied hydrostatic pressure (up to 10 GPa) to single-walled carbon nanotube bundles at low temperature (down to 2 K) to measure their magnetoresistance (MR) in a field up to 12 T. We found a pressure-induced transition in MR from positive to negative in the high-field regime. The onset of the transition occurs at approximately 1.5 GPa, which correlates closely with the tube shape transitions. The characteristics of the high-pressure MR are consistent with a model of pressure-induced two-dimensional weak localization.

Journal Article↗

PubMed2006

Effect of bearing geometry and structure support on transient elastohydrodynamic lubrication of metal-on-metal hip implants.

An effective lubrication can significantly reduce wear of metal-on-metal artificial hip joints. The improvement of the lubrication can be achieved through the optimisation of the bearing geometry in terms of a small clearance and/or the structural support such as a polyethylene backing underneath a metallic bearing in a sandwich acetabular cup form. The separate effects of these two factors on fluid film lubrication of 28 mm diameter metal-on-metal total hip joints under walking conditions were numerically investigated in this paper. The results show that a larger lubricant film due to the polyethylene backing can be significantly enhanced by the transient squeeze-film action, particularly during the stance phase, and a similar lubricant film can be developed for both the monolithic cup relying on the smaller clearance and the sandwich cup benefiting from the polyethylene backing. Both cup systems can function in a wide range of lubrication regimes, covering both mixed and fluid film, under the current design and manufacture conditions.

Computer Simulation↗

PubMed2006

Effect of cardiac motion on body surface electrocardiographic potentials: an MRI-based simulation study.

This paper describes an electrical model of cardiac ventricles incorporating real geometry and motion. The heart anatomy and its motion through the cardiac cycle are obtained from segmentations of multiple-slice MRI time sequences; the special conduction system is constructed using an automated mapping procedure from an existing static heart model. The heart model is mounted in an anatomically realistic voxel model of the human body. The cardiac electrical source and surface potentials are determined numerically using both a finite-difference scheme and a boundary-element method with the incorporation of the motion of the heart. The electrocardiograms (ECG) and body surface potential maps are calculated and compared to the static simulation in the resting heart. The simulations demonstrate that introducing motion into the cardiac model modifies the ECG signals, with the most obvious change occurring during the T-wave at peak contraction of the ventricles. Body surface potential maps differ in some local positions during the T-wave, which may be of importance to a number of cardiac models, including those incorporating inverse methods.

Algorithms↗

PubMed2006

Unexpected one-pot method to synthesize spiro[fluorene-9,9'-xanthene] building blocks for blue-light-emitting materials.

[reaction: see text] An unexpected one-pot synthetic approach toward spiro[fluorene-9,9'-xanthene] (SFX) under excessive MeSO(3)H conditions has been developed. The key step involves a thermodynamically controlled cyclization reaction. Blue-light-emitting materials based on SFX building blocks that exhibit high thermal stability have also been synthesized.

Journal Article↗

PubMed2006

A morphogenetic wave of p27Kip1 transcription directs cell cycle exit during organ of Corti development.

The molecular mechanisms coordinating cell cycle exit with cell differentiation and organogenesis are a crucial, yet poorly understood, aspect of normal development. The mammalian cyclin-dependent kinase inhibitor p27(Kip1) is required for the correct timing of cell cycle exit in developing tissues, and thus plays a crucial role in this process. Although studies of p27(Kip1) regulation have revealed important posttranscriptional mechanisms regulating p27(Kip1) abundance, little is known about how developmental patterns of p27(Kip1) expression, and thus cell cycle exit, are achieved. Here, we show that during inner ear development transcriptional regulation of p27(Kip1) is the primary determinant of a wave of cell cycle exit that dictates the number of postmitotic progenitors destined to give rise to the hair cells and supporting cells of the organ of Corti. Interestingly, transcriptional induction from the p27(Kip1) gene occurs normally in p27(Kip1)-null mice, indicating that developmental regulation of p27(Kip1) transcription is independent of the timing of cell cycle exit. In addition, cell-type-specific patterns of p27(Kip1) transcriptional regulation are observed in the mature organ of Corti and retina, suggesting that this mechanism is important in differential regulation of the postmitotic state. This report establishes a link between the spatial and temporal pattern of p27(Kip1) transcription and the control of cell number during sensory organ morphogenesis.

Animals↗

PubMed2006

Ultraviolet wave plates based on monolithic integration of two fully filled and planarized nanograting layers.

We successfully fabricated a high-performance half-wave plate for the 405 nm wavelength based on monolithic integration of two nanograting layers. Each of the nanograting layers functions as a quarter-wave plate. Both of the nanograting layers were fully filled and planarized to achieve the monolithic integration. UV-nanoimprint lithography, along with thin-film deposition, high-aspect-ratio reactive ion etching, and trench-filling technologies, was used in fabrication and integration of the individual nanograting layers. High-aspect-ratio nanogratings with sub-50 nm linewidths and 100 nm spacing were fabricated to achieve good optical performance at the near-UV wavelength. The ability to integrate multiple nanostructure-based optical layers opens a path for integrated multifunction devices, as well as a new strategy for driving both miniaturization and cost.

Journal Article↗

PubMed2006

Fine tuning PDK1 activity by phosphorylation at Ser163.

3-Phosphoinositide-dependent protein kinase-1 (PDK1) mediates phosphorylation and activation of members of the AGC protein kinase family and plays an essential role in insulin signaling and action. However, whether and how PDK1 activity is regulated in cells remains largely uncharacterized. In the present study, we show that PDK1 undergoes insulin-stimulated and phosphatidylinositol 3-kinase-dependent phosphorylation at Ser244 in the activation loop and at a novel site: Ser163 in the hinge region between the two lobes of the kinase domain. Sequence alignment studies revealed that the residue corresponding to Ser163 of PDK1 in all other AGC kinases is glutamate, suggesting that a negative charge at this site may be important for PDK1 function. Replacing Ser163 with a negatively charged residue, glutamate, led to a 2-fold increase in PDK1 activity. Molecular modeling studies suggested that phosphorylated Ser163 may form additional hydrogen bonds with Tyr149 and Gln223. In support of this, mutation of Tyr149 to Ala is sufficient to reduce PDK1 activity. Taken together, our results suggest that PDK1 phosphorylation of Ser163 may provide a mechanism to fine-tune PDK1 activity and function in cells.

3-Phosphoinositide-Dependent Protein Kinases↗

PubMed2006

Identification and characterization of NYGGF4, a novel gene containing a phosphotyrosine-binding (PTB) domain that stimulates 3T3-L1 preadipocytes proliferation.

A novel gene named NYGGF4, which was expressed at a higher level in obese subjects, was isolated and characterized. It is a 1527-bp cDNA, containing 753 nucleotides of an ORF (open reading frame) predicting 250 amino acids with a molecular mass of 28.27 kDa. Amino acid sequence analysis revealed NYGGF4 has a phosphotyrosine-binding (PTB) domain. Northern blot analysis revealed NYGGF4 is expressed primarily in adipose tissue, heart, and skeletal muscle but not in any other tissue examined. Confocal imagery analyses with green fluorescent protein-tagged protein transiently expressed in 3T3-L1 preadipocytes and 293-T cells show that NYGGF4 localizes in the cytoplasm. Furthermore, ectopic expression of NYGGF4 dramatically increases the proliferation of 3T3-L1 peadipocytes without affecting adipocytic differentiation. And the NYGGF4 expression 3T3-L1 cells had a greater number of cells in S-phase. Our data suggest that NYGGF4 might be a signaling molecule and could play a role in cell growth and adipogenesis process.

3T3-L1 Cells↗

PubMed2006

PseG of pseudaminic acid biosynthesis: a UDP-sugar hydrolase as a masked glycosyltransferase.

The flagellin proteins in pathogenic bacteria such as Campylobacter jejuni and Helicobacter pylori are heavily glycosylated with the nine-carbon alpha-keto acid, pseudaminic acid. The presence of this posttranslational modification is absolutely required for assembly of functional flagella. Since motility is required for colonization, pseudaminic acid biosynthesis represents a virulence factor in these bacteria. Pseudaminic acid is generated from UDP-N-acetylglucosamine in five biosynthetic steps. The final step has been shown to involve the condensation of 2,4-diacetamido-2,4,6-trideoxy-L-altrose (6-deoxy-Altdi-NAc) with phosphoenolpyruvate as catalyzed by the enzyme pseudaminic acid synthase, NeuB3. The 6-deoxy-AltdiNAc used in this process is generated from its nucleotide-linked form, UDP-6-deoxy-AltdiNAc, by the action of a hydrolase that cleaves the glycosidic bond and releases UDP. This manuscript describes the first characterization of a UDP-6-deoxy-AltdiNAc hydrolase, namely PseG (Cj1312) from C. jejuni. The activity of this enzyme is independent of the presence of divalent metal ions, and the values of the catalytic constants were found to be k(cat) = 27 s(-1) and K(m) = 174 microm. The enzyme was shown to hydrolyze the substrate with an overall inversion of stereochemistry at C-1 and to utilize a C-O bond cleavage mechanism during catalysis. These results, coupled with homology comparisons, suggest that the closest ancestors to the hydrolase are members of the metal-independent GT-B family of glycosyltransferases that include the enzyme MurG.

Campylobacter jejuni↗

PubMed2006

Electro-osmotic flow and mixing in heterogeneous microchannels.

Analytical and numerical studies of secondary electro-osmotic flow (EOF) and its mixing in microchannels with heterogeneous zeta potentials are carried out in the present work. The secondary EOFs are analyzed by solving the Stokes equation with heterogeneous slip velocity boundary conditions. The analytical results obtained are compared with the direct numerical simulation of the Navier-Stokes equations. The secondary EOFs could transport scalar in larger areas and increase the scalar gradients, which significantly improve the mixing rate of scalars. It is shown that the heterogeneous zeta potentials could generate complex flow patterns and be used to enhance scalar mixing.

Journal Article↗

PubMed2006

siRNA-mediated silencing of Cockayne Cyndrome group B gene potentiates radiation-induced apoptosis and antiproliferative effect in HeLa cells.

BACKGROUND: Cockayne syndrome (CS) is a rare human genetic disorder characterized by increased UV sensitivity, developmental abnormalities and premature aging. Cells isolated from individuals with CS have a defect in transcription-coupled DNA repair. Despite the repair defect, there is no any increased risk of spontaneous or UV-induced cancer for CS individuals. The strategy of RNA interfering was used here to explore the potential radiosensitizing and anticancer activity of targeting CS group B (CSB) gene. METHODS: The vectors encoding CSB-specific siRNAs were constructed by inserting duplex siRNA encoding oligonucleotides into the plasmid P(silencer TM 3.1). The cell lines expressing the CSB-siRNA were generated from HeLa cells transfected with the above vectors. Colony-forming ability was used to assay cell survival. Cell cycle was analyzed by FACScan flow cytometry. The apoptosis was measured by detecting the accumulation of sub-G(1) population as well as by fluorescence staining assay. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to semi-quantify mRNA expression. Protein level was detected by Western blotting analysis. RESULTS: Two constructs encoding CSB-specific siRNA were generated, both of them resulted in remarkable suppression on CSB expression in HeLa cells, and led to an increased sensitivity to (gamma-ray and UV light. siRNA-mediated silencing of CSB decreased cell proliferation rate, increased spontaneous apoptosis as well as the occurrence of UV- or cisplatin-induced apoptosis by 2 to 3.5 fold. A significant S phase blockage and a remarkable reduction of G(1) population were induced in control HeLa cells at 18 hours after being exposed to 10 J/m(2) of UV light. The S phase blockage was also observed in UV-irradiated CSB-siRNA transfected HeLa cells, but the extent of increased S phase population was lower than that in the UV-irradiated control cells. No or a relative weak reduction on G(1) phase population was observed in UV-irradiated CSB-siRNA transfected HeLa cells. In addition, siRNA-mediated silencing of CSB promoted the elimination of G(2)/M phase cells after UV light radiation. CONCLUSIONS: siRNA-mediated silencing of CSB causes cells to proliferate more slowly, sensitize cells to genotoxicants, and modify UV radiation-induced cell cycle changes. siRNA-mediated inactivation of CSB could be an attractive strategy for ameliorating cancer therapy, which can be fulfilled via the combination of gene therapy and sensitization of radiotherapy or chemotherapy.

Apoptosis↗

PubMed2006

Overexpression of uncoupling protein 4 promotes proliferation and inhibits apoptosis and differentiation of preadipocytes.

Uncoupling proteins are a family of mitochondrial proteins involved in energy metabolism. We previously showed that uncoupling protein 4 (UCP4) is differentially expressed in omental adipose tissue in diet-induced obese and normal rats. However, the effect of UCP4 on adipocytes is unclear. In this work, we established a stable preadipocyte cell line overexpressing UCP4 to observe the direct effect of UCP4 on adipocytes. Cells overexpressing UCP4 showed significantly attenuated differentiation of preadipocytes into adipocytes. During differentiation, expression of adipogenesis-associated markers such as fatty acid synthetase, peroxisome proliferator-activated receptor gamma, CCAAT enhancer binding protein alpha, adipocyte lipid binding protein and lipoprotein lipase were downregulated. Preadipoctes expressing UCP4 grew faster and more of them stayed in S phase compared to control cells. In addition, UCP4 overexpression protected preadipocytes from apoptosis induced by serum deprivation. Our results demonstrate that overexpression of UCP4 can promote proliferation and inhibit apoptosis and differentiation of preadipocytes.

3T3-L1 Cells↗