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Biomedical subjects

Z Wen

Publications and source records attributed to Z Wen.

At least 19 recordsLinked to original sources
PubMed2006

Classifying G protein-coupled receptors and nuclear receptors on the basis of protein power spectrum from fast Fourier transform.

As the potential drug targets, G-protein coupled receptors (GPCRs) and nuclear receptors (NRs) are the focuses in pharmaceutical research. It is of great practical significance to develop an automated and reliable method to facilitate the identification of novel receptors. In this study, a method of fast Fourier transform-based support vector machine was proposed to classify GPCRs and NRs from the hydrophobicity of proteins. The models for all the GPCR families and NR subfamilies were trained and validated using jackknife test and the results thus obtained are quite promising. Meanwhile, the performance of the method was evaluated on GPCR and NR independent datasets with good performance. The good results indicate the applicability of the method. Two web servers implementing the prediction are available at http://chem.scu.edu.cn/blast/Pred-GPCR and http://chem.scu.edu.cn/blast/Pred-NR.

Computer Simulation↗
PubMed2006

Delaunay triangulation with partial least squares projection to latent structures: a model for G-protein coupled receptors classification and fast structure recognition.

As an important transmembrane protein family in eukaryon, G-protein coupled receptors (GPCRs) play a significant role in cellular signal transduction and are important targets for drug design. However, it is very difficult to resolve their tertiary structure by X-ray crystallography. In this study, we have developed a Delaunay model, which constructs a series of simplexes with latent variables to classify the families of GPCRs and projects unknown sequences to principle component space (PC-space) to predict their topology. Computational results show that, for the classification of GPCRs, the method achieves the accuracy of 91.0 and 87.6% for Class A, more than 80% for the other three classes in differentiating GPCRs from non-GPCRs and 70% for discriminating between four major classes of GPCR, respectively. When recognizing the structure of GPCRs, all the N-terminals of sequences can be determined correctly. The maximum accuracy of predicting transmembrane segments is achieved in the 7th transmembrane segment of Rhodopsin, which is 99.4%, and the average error is 2.1 amino acids, which is the lowest in all of the segments prediction. This method could provide structural information of a novel GPCR as a tool for experiments and other algorithms of structure prediction of GPCRs. Academic users should send their request for the MATLAB program for classifying GPCRs and predicting the topology of them at liml@scu.edu.cn .

Algorithms↗
PubMed2005

137Cs budget during the period of 1960s in a small drainage basin on the Loess Plateau of China.

A sediment profile with a thickness of 28.12 m in a failed reservoir in a small catchment of the Yuntaishan Gully in the Loess Plateau of China consisted of 44 flood couplets deposited during the period from 1960 to 1970 with total volume of 2.36 x 10(6)m(3). Specific sediment yields for a flood event varied from 300 t km(-2) to 14,400 t km(-2) and annual sediment yields varied from 2500 t km(-2) in 1966 to 40,000 t km(-2) in 1964 with a mean value of 12,700 t km(-2)a(-1) for the period. Average annual (137)Cs concentrations of the sediments increased from 0.92 Bq kg(-1) in 1960 to 4.82 Bq kg(-1) in 1963, then decreased to 1.53 Bq kg(-1) in 1970. The total (137)Cs activity in the reservoir sediments was 9.22 x 10(9) Bq, which accounted for 31.9% of the total (137)Cs fallout precipitation of 2.89 x 10(10) Bq within the catchment during the period. The proportion of the (137)Cs loss from the catchment to the (137)Cs fallout precipitation within the catchment in a year varied between 8.01% and 66.8%, and it was 20.9% for the peak (137)Cs deposition year of 1963 and 52.0% in 1964. By analysis of the (137)Cs budget in the catchment for the (137)Cs peak precipitation period from 1962 to 1964, the (137)Cs surface enrichment coefficient Gamma should be much less than 0.23. And for calculation of soil losses on the cultivated land in the inter-gully area by using the Mass Balance Model II, the value of Gamma should be 0.05-0.1.

Cesium Radioisotopes↗
PubMed2005

Performance of a static-anode/flat-panel x-ray fluoroscopy system in a diagnostic strength magnetic field: a truly hybrid x-ray/MR imaging system.

Minimally invasive procedures are increasing in variety and frequency, facilitated by advances in imaging technology. Our hybrid imaging system (GE Apollo flat panel, custom Brand x-ray static anode x-ray tube, GE Lunar high-frequency power supply and 0.5 T Signa SP) provides both x-ray and MR imaging capability to guide complex procedures without requiring motion of the patient between two distant gantries. The performance of the x-ray tube in this closely integrated system was evaluated by modeling and measuring both the response of the filament to an externally applied field and the behavior of the electron beam for field strengths and geometries of interest. The performance of the detector was assessed by measuring the slanted-edge modulation transfer function (MTF) and when placed at zero field and at 0.5 T. Measured resonant frequencies of filaments can be approximated using a modified vibrating beam model, and were at frequencies well below the 25 kHz frequency of our generator for our filament geometry. The amplitude of vibration was not sufficient to cause shorting of the filament during operation within the magnetic field. A simple model of electrons in uniform electric and magnetic fields can be used to estimate the deflection of the electron beam on the anode for the fields of interest between 0.2 and 0.5 T. The MTF measured at the detector and the DQE showed no significant difference inside and outside of the magnetic field. With the proper modifications, an x-ray system can be fully integrated with a MR system, with minimal loss of image quality. Any x-ray tube can be assessed for compatibility when placed at a particular location within the field using the models. We have also concluded that a-Si electronics are robust against magnetic fields. Detailed knowledge of the x-ray system installation is required to provide estimates of system operation.

Electromagnetic Fields↗
PubMed2005

Studies into using manure in a biorefinery concept.

Animal manure is an underutilized biomass resource containing a large amount of organic carbon that is often wasted with the existing manure disposal practices. A research project funded by the US Department of Energy explored the feasibility of using manure via the sugar platform in a biorefinery, converting the carbon from fiber to biochemicals. The results showed that (1) fiber was the major component of manure dry material making up approx 50%, 40%, and 36% of the dry dairy, swine, and poultry manure material, respectively; within dairy manure, more than 56% of the dry matter was in particles larger than 1.680 mm; (2) in addition to being a carbon source, manure could provide a variety of nutrient for fungi T. reesei and A. phoenicis to produce cellulase; (3) the hemicellulose component in the manure fiber could be readily converted to sugar through acid hydrolysis; while concentrated acid decrystallization treatment was most effective in manure cellulose hydrolysis; (4) purification and separation was necessary for further chemical conversion of the manure hydrolysate to polyols through hydrogenation; and (5) the manure utilization strategy studied in this work is currently not profitable.

Agriculture↗
PubMed2003

First use of a truly-hybrid X-ray/MR imaging system for guidance of brain biopsy.

The use of a new hybrid imaging system for guidance of a brain biopsy is described. The system combines the strengths of MRI (soft-tissue contrast, arbitrary plane selection) with those of x-ray fluoroscopy (high-resolution real-time projection images, clear portrayal of bony structures) and allows switching between the imaging modalities without moving the patient. The biopsy was carried out using x-ray guidance for direction of the needle through the foramen ovale and MR guidance to target the soft-tissue lesion. Appropriate samples were acquired. The system could be particularly effective for guidance of those cases where motion, swelling, resection and other intra-operative anatomical changes cannot be accounted for using traditional stereotactic-based imaging approaches.

Adult↗
PubMed2002

Morphologic transformation of the thymus in developing zebrafish.

The morphologic transformation of the developing zebrafish thymus from 1 week postfertilization (wpf) to 15 wpf is described. The thymus overall morphology changed from a small pouch-like shape at 1 wpf to a conical shape between 2 and 3 wpf before acquiring a more complex shape from 4 wpf onward. Rapid growth rate along the lateral axis at the region near the pharyngeal epithelium occurred between 1 and 2 wpf, whereas rapid growth rate along the dorsal-ventral axis occurred between 3 and 6 wpf. Expansion of thymocyte population beginning from 1 wpf became more evident by 2 to 3 wpf, as indicated by the apparent increase of different sizes of lymphocytes, recombination activating gene-1 (rag-1), and T-cell antigen receptor alpha chain constant region (TCRAC) -positive cells. Tissue section in situ hybridization (ISH) analysis with rag-1 probe reveals that cortex-medullary regionalization has begun between 1 and 2 wpf as rag-1 expression clearly demarcated the cortex, whereas the medulla was rag-1 negative. The presence of TCRAC-positive cells in the medulla by 2-3 wpf, suggests that the thymic selection processes had begun. The zebrafish thymus is morphologically mature by 3 wpf. Early signs of thymic involution were observed in zebrafish aged 15 wpf.

Animals↗
PubMed2002

China's water environment at the beginning of the 21st century: challenges and countermeasures.

Water environment crisis is a common challenge throughout the world, and the situation is becoming worse. This paper analyzes the development trend of water environment worldwide, and then evaluates the status of China's water environment and the progress in the work of protection of the water environment. According to the future development of economy and society in China, the paper discusses the severe challenges in water environment that China faces at the beginning of the 21st century and proposes related countermeasures.

China↗
PubMed2001

Two-component molecular crystals from N-heteroaromatics and nitrobenzoic acids.

Five two-component molecular crystals, benzimidazolium 3-nitrobenzoate, C(7)H(7)N(2)(+).C(7)H(4)NO(4)(-), (I), benzimidazolium 4-nitrobenzoate, C(7)H(7)N(2)(+).C(7)H(4)NO(4)(-), (II), 1H-benzotriazole-3-nitrobenzoic acid (1/1), C(6)H(5)N(3).C(7)H(5)NO(4), (III), imidazolium 3-nitrobenzoate, C(3)H(5)N(2)(+).C(7)H(4)NO(4)(-), (IV), and imidazolium 4-nitrobenzoate, C(3)H(5)N(2)(+).C(7)H(4)NO(4)(-), (V), were prepared with the aim of making chiral crystals. Only (I) crystallizes in a chiral space group. The molecules of (I) and (II) are linked by hydrogen bonds to form 2(1) spiral chains. In (III), (IV) and (V), macrocyclic structures are formed from two acid and two base components, by an alternate arrangement of the acid and base moieties.

Journal Article↗
PubMed2001

Fluorophore-labeled S-nitrosothiols.

A series of fluorophore-labeled S-nitrosothiols were synthesized, and their fluorescence enhancements upon removal of the nitroso (NO) group were evaluated either by transnitrosation or by photolysis. It was shown that, with a suitable alkyl linker, the fluorescence intensity of dansyl-labeled S-nitrosothiols could be enhanced up to 30-fold. The observed fluorescence enhancement was attributed to the intramolecular energy transfer from fluorophore to the SNO moiety. Ab initio density functional theory (DFT) calculations indicated that the "overlap" between the SNO moiety and the dansyl ring is favored because of their stabilizing interaction, which was in turn affected by both the length of the alkyl linker and the rigidity of the sulfonamide unit. In addition, one of the dansyl-labeled S-nitrosothiols was used to explore the kinetics of S-nitrosothiol/thiol transnitrosation and was evaluated as a fluorescence probe of S-nitrosothiol-bound NO transfer in human umbilical vein endothelial cells.

Cell Membrane↗
PubMed2001

CYP9E2, CYP4C21 and related pseudogenes from German cockroaches, Blattella germanica: implications for molecular evolution, expression studies and nomenclature of P450s.

The cDNAs of two novel P450s (CYP9E2 and CYP4C21) were isolated from German cockroaches, Blattella germanica. Both CYP9E2 and CYP4C21 are typical microsomal P450s and their deduced amino acid sequences share a number of common characteristics with other members of the P450 superfamily. Northern blot analyses using a CYP9E2 or CYP4C21 probe showed that 'CYP9E2' and 'CYP4C21' were expressed at all life stages. Two pseudogenes related to CYP9E2 and three pseudogenes related to CYP4C21 were also isolated. These represent the first P450 pseudogenes from an insect other than Drosophila melanogaster. The relative number of P450 pseudogenes in B. germanica is apparently higher than in D. melanogaster. The implications of these results for the molecular evolution, expression studies and nomenclature of P450s are discussed.

Base Sequence↗
PubMed2001

Effects of olfactory bulbectomy on NMDA receptor density in the rat brain:.

Olfactory bulbectomy (OBX) transects the glutamatergic efferents from the olfactory bulbs, and the changes of glutamatergic N-methyl-D-aspartate (NMDA) receptor-mediated function are though to be involved in the behavioral deficits seen in OBX rats. In the present study, irritability scores in OBX male Wistar rats were correlated with discrete regional effects on NMDA receptor function measured using a [3H] MK-801 binding assay. Irritability scores, measured before and for 2 weeks after OBX, showed a gradual increase in irritability after OBX. A reduction of the NMDA receptor density was observed in the cerebral cortex and amygdala 16 days after OBX, but not in the striatum, olfactory tubercle, entorhinal cortex, and hippocampus. These results demonstrate that OBX causes changes in the NMDA receptor system in certain brain regions and suggest that these changes may be responsible for the behavioral deficits of OBX rats.

Animals↗
PubMed2001

On the direction and magnitude of radical substituent effects: the role of polar interaction on thermodynamic stabilities of benzylic C-H bonds and related carbon radicals.

The C-H bond dissociation enthalpies (BDEs) of polarized benzylic molecules, i.e., para-substituted phenylacetonitriles (PANs), and the spin variations of the radicals of the general type p-GC6H4CH*-Y were investigated using density functional theory (DFT) calculations. In contrast to the commonly observed S-type substituent effect (see text), the present work shows that there should be three (rather than one) primary patterns (i.e., S, O, and counter-O) for remote G to affect spin and radical stability, depending upon the polarity of the alpha-Y group. Correlation analyses reveal that both the direction and magnitude of spin/radical effects are quantitatively related to the intensity of polar interaction in radical system, as registered by either the calculated group charges of the phenyl ring (C(Ph)) or by the polar constant sigma(+)s (Figures 1-4). A unified platform (Scheme 1) to rationalize the apparent differences of radical substituent effect is proposed.

Journal Article↗
PubMed2001

Equilibrium and kinetics studies of transnitrosation between S-nitrosothiols and thiols.

Using UV-vis spectrometrical measurements, equilibrium constants for NO transfer between S-nitroso-N-acetyl-penicillamine (SNAP) and different thiols as well as kinetic data for NO transfer from S-nitroso bovine serum albumin (BSANO) to thiols have been obtained. NO transfer from SNAP to other primary/secondary thiols are thermodynamically favorable, whereas other S-nitrosothiols exhibit similar NO transfer potential. The obtained Gibbs free energy, enthalpy and entropy data indicated that NO transfer reactions from SNAP to four thiols are exothermic with entropy loss. The kinetic behavior of BSANO/RSH transfer can be related to both the acidity of sulfhydryl group and the electronic structure in thiol.

Kinetics↗
PubMed2001

A truly hybrid interventional MR/X-ray system: feasibility demonstration.

A system enabling both x-ray fluoroscopy and MRI in a single exam, without requiring patient repositioning, would be a powerful tool for image-guided interventions. We studied the technical issues related to acquisition of x-ray images inside an open MRI system (GE Signa SP). The system includes a flat-panel x-ray detector (GE Medical Systems) placed under the patient bed, a fixed-anode x-ray tube overhead with the anode-cathode axis aligned with the main magnetic field and a high-frequency x-ray generator (Lunar Corp.). New challenges investigated related to: 1) deflection and defocusing of the electron beam of the x-ray tube; 2) proper functioning of the flat panel; 3) effects on B0 field homogeneity; and 4) additional RF noise in the MR images. We have acquired high-quality x-ray and MR images without repositioning the object using our hybrid system, which demonstrates the feasibility of this new configuration. Further work is required to ensure that the highest possible image quality is achieved with both MR and x-ray modalities.

Brain↗
PubMed2001

Cytochromes P450 of insects: the tip of the iceberg.

The cytochrome P450-dependent monooxygenases are an extremely important metabolic system involved in the metabolism of endogenous compounds and xenobiotics. Collectively, P450 monooxygenases can metabolize numerous substrates and carry out multiple oxidative reactions. The large number of substrates metabolized is due to the plethora of P450 isoforms and to the broad substrate specificity of some isoforms. Monooxygenases of insects have several functional roles, including growth, development, feeding and protection against xenobiotics, including resistance to pesticides and tolerance to plant toxins. This review begins with background information about P450s and their evolution, followed by a discussion of the extraordinary diversity of insect P450s. Given the enormous interest in studying individual P450s, we then provide a synopsis of the different methods that have been used in their isolation and the substrates that are known to be metabolized. We conclude by summarizing the lessons we have learned from the study of individual insect P450s, including their roles in insecticide resistance, plant-insect interactions and insect physiology. However, these studies are just the 'tip of the iceberg'. Our knowledge continues to expand at a rapid pace, suggesting that the next decade will outpace the last in terms of improving our understanding of the cytochromes P450 of insects.

Animals↗
PubMed2001

Low viscosity Ektacytometry and its validation tested by flow chamber.

The flow chamber was used to observe the orientation and small deformation of red blood cells (RBCs) in a shear flow of low viscosity. With the aid of computer software, the percentage of RBCs oriented to the C=0 orbit (OI)(F) and the degree of deformation (DI)(F) of such RBCs were calculated by processing the photographs. It was found that these parameters were highly correlated, respectively, to the orientation index (OI)(E) and the small deformation index (DI)(E) obtained by our low viscosity Ektacytometry (LVE). Thus, our flow chamber research has provided direct evidence to validate the use of this low viscosity Ektacytometry. Although there are relative merits for the flow chamber method using low viscosity medium, the LVE is more likely to be applied in clinic for its simplicity and convenience.

Animals↗