PubMed Health⌕ Search

Biomedical subjects

Ying Xu

Publications and source records attributed to Ying Xu.

At least 109 records · Page 6Linked to original sources
PubMed2005

Structural characterization of fatty acids cationized with copper by electrospray ionization mass spectrometry under low-energy collision-induced dissociation.

Fatty acids have for many years been characterized by mass spectrometry using electron ionization after chemical derivatization. When fatty acids are ionized using desorption/ionization methods such as electrospray ionization or fast atom bombardment, structural information is usually obtained through high-energy collision-induced dissociation (CID) using sector instruments. It has been shown that copper displays very interesting properties in the gas phase during CID. In this study, the reactivity of saturated and unsaturated fatty acid-copper [M-H+Cu(II)]+ complex and the role of the copper ion in promoting fragmentations were investigated under low-energy collisional activation conditions. The decomposition of these species in an ion trap instrument led to diagnostic ion series that reflect C--C bond cleavage, which involves Cu(II) reduction followed by the release of an alkyl radical. It was demonstrated that in this way the localization of one or two homoconjugated double bonds is possible using low-energy CID. Moreover, the distinction of cis and trans isomers is possible through characteristic product ions related to a specific loss of CO2. When these experiments are repeated using a triple-quadrupole instrument with argon as collision gas, a different behavior is observed as in this case, in addition to the product ion distributions observed in the ion trap, other distributions are observed that reflect the influence of the different kinetic shifts and the occurrence of consecutive decompositions. Different examples are presented with various saturated and unsaturated fatty acid chains. Mechanisms are proposed in order to rationalize the experimental observations.

Cations↗
PubMed2005

Genetic diversity and genetic structure of an endangered species, Trillium tschonoskii.

The genetic diversity and genetic structure of Trillium tschonoskii (Maxim) were investigated using amplified fragment length polymorphism markers. Eight primer combinations were carried out on 105 different individuals sampled from seven populations. Of the 619 discernible DNA fragments generated, 169 (27.3%) were polymorphic. The percentage of polymorphic bands within populations ranged from 4.52 to 10.50. Genetic diversity (H(E)) within populations ranged from 0.0130 to 0.0379, averaging 0.0536 at the species level. Genetic differentiation among populations was detected based on Nei's genetic diversity analysis (53.03%) and analysis of molecular variance (AMOVA) (52.43%). AMOVA indicated significant genetic differentiation among populations (52.43% of the variance) and within populations (47.57% of the variance) (p < 0.0002). Gene flow was low (0.4429) among populations. Species breeding system and limited gene flow among populations are plausible reasons for the high genetic differentiation observed for this species. We propose an appropriate strategy for conserving the genetic resources of T. tschonoskii in China.

China↗
PubMed2005

Solubility and rheological behavior of silk fibroin (Bombyx mori) in N-methyl morpholine N-oxide.

As an important direct solvent for cellulose, N-methyl morpholine N-oxide (NMMO) is environmentally friendly, and potentially very economical. Silk fibroin (SF) (Bombyx mori) can also be dissolved directly in NMMO.H2O. However, it is unexpectedly difficult to obtain a silk fibroin solution with a concentration higher than 10wt.% in this way, and extensive degradation of silk fibroin occurs if the dissolution temperature is higher than 110 degrees C. On the other hand, it is found that regenerated silk fibroin (RSF) film is much easier to dissolve in NMMO.H2O than ordinary SF. The RSF in NMMO.H2O can be easily concentrated to a range from 10 to 25wt.%. The structural differences between the degummed silk fiber and the RSF film lead to this different solubility in NMMO.H2O. The rheological behavior of concentrated RSF/NMMO.H2O solutions were also investigated. Regenerated silk fiber was spun from this type of solution, and its strength can reach up to 3.07 cN/dtex.

Animals↗
PubMed2005

Antidepressant effects of curcumin in the forced swim test and olfactory bulbectomy models of depression in rats.

Curcuma longa is a major constituent of Xiaoyao-san, the traditional Chinese medicinal formula, which has been used to effectively manage stress and depression-related disorders in China. Curcumin is the active component of curcuma longa, and we hypothesized that curcumin would have an influence on depressive-like behaviors. The purpose of the present study was to confirm the putative antidepressant effect of chronic administrations of curcumin (1.25, 2.5, 5 and 10 mg/kg, p.o.) in the forced swimming test and bilateral olfactory bulbectomy (OB) models of depression in rats. In the first study, chronic treatment with curcumin (14 days) reduced the immobility time in the forced swimming test. In the second experiment, curcumin reversed the OB-induced behavioral abnormalities such as hyperactivity in the open field, as well as deficits in step-down passive avoidance. In addition, OB-induced low levels of serotonin (5-HT), noradrenaline (NA), high 5-hydroxyindoleacetic acid (5-HIAA) and 4-dihydroxyphenylacetic acid (DOPAC) in the hippocampus were observed, and were completely reversed by curcumin administration. A slight decrease in 5-HT, NA and dopamine (DA) levels was found in the frontal cortex of OB rats which was also reversed by curcumin treatment. These results confirm the antidepressant effects of curcumin in the forced swim and the OB models of depression in rats, and suggest that these antidepressant effects may be mediated by actions in the central monoaminergic neurotransmitter systems.

Animals↗
PubMed2005

Cloning, expression, and refolding of a secretory protein ESAT-6 of Mycobacterium tuberculosis.

A DNA encoding the 6-kDa early secretory antigenic target (ESAT-6) of Mycobacterium tuberculosis was inserted into a bacterial expression vector of pQE30 resulting in a 6x His-esat-6 fusion gene construction. This plasmid was transformed into Escherichia coli strain M15 and effectively expressed. The expressed fusion protein was found almost entirely in the insoluble form (inclusion bodies) in cell lysate. The inclusion bodies were solubilized with 8M urea or 6M guanidine-hydrochloride at pH 7.4, and the recombinant protein was purified by Ni-NTA column. The purified fusion protein was refolded by dialysis with a gradient of decreasing concentration of urea or guanidine hydrochloride or by the size exclusion protein refolding system. The yield of refolded protein obtained from urea dialysis was 20 times higher than that from guanidine-hydrochloride. Sixty-six percent of recombinant ESAT-6 was successfully refolded as monomer protein by urea gradient dialysis, while 69% of recombinant ESAT-6 was successfully refolded as monomer protein by using Sephadex G-200 size exclusion column. These results indicate that urea is more suitable than guanidine-hydrochloride in extracting and refolding the protein. Between the urea gradient dialysis and the size exclusion protein refolding system, the yield of the monomer protein was almost the same, but the size exclusion protein refolding system needs less time and reagents.

Antigens, Bacterial↗
PubMed2005

More reliable protein NMR peak assignment via improved 2-interval scheduling.

Protein NMR peak assignment refers to the process of assigning a group of "spin systems" obtained experimentally to a protein sequence of amino acids. The automation of this process is still an unsolved and challenging problem in NMR protein structure determination. Recently, protein NMR peak assignment has been formulated as an interval scheduling problem (ISP), where a protein sequence P of amino acids is viewed as a discrete time interval I (the amino acids on P one-to-one correspond to the time units of I), each subset S of spin systems that are known to originate from consecutive amino acids from P is viewed as a "job" j(s), the preference of assigning S to a subsequence P of consecutive amino acids on P is viewed as the profit of executing job j(s) in the subinterval of I corresponding to P, and the goal is to maximize the total profit of executing the jobs (on a single machine) during I. The interval scheduling problem is max SNP-hard in general; but in the real practice of protein NMR peak assignment, each job j(s) usually requires at most 10 consecutive time units, and typically the jobs that require one or two consecutive time units are the most difficult to assign/schedule. In order to solve these most difficult assignments, we present an efficient 13/7-approximation algorithm for the special case of the interval scheduling problem where each job takes one or two consecutive time units. Combining this algorithm with a greedy filtering strategy for handling long jobs (i.e., jobs that need more than two consecutive time units), we obtain a new efficient heuristic for protein NMR peak assignment. Our experimental study shows that the new heuristic produces the best peak assignment in most of the cases, compared with the NMR peak assignment algorithms in the recent literature. The above algorithm is also the first approximation algorithm for a nontrivial case of the well-known interval scheduling problem that breaks the ratio 2 barrier.

Algorithms↗
PubMed2005

Accurate prediction of orthologous gene groups in microbes.

We present a new computational method for the prediction of orthologous gene groups for microbial genomes based on the prediction of co-occurrences of homologous genes. The method is inspired by the observation that homologous genes are highly likely to be orthologous if their neighboring genes are also homologous. Based on co-occurrences of homologous genes, we have grouped the (predicted) operons of 77 selected sequenced microbial genomes so that operons of the same group are highly likely to be functionally similar or related. We then cluster the homologous genes in the same operon group so that genes of the same cluster are highly likely to be similar in terms of their sequences and functions, i.e., they are predicted to be orthologous genes. By comparing our predicted orthologous gene groups with the COG assignments and NCBI annotations, we conclude that our method is promising to provide more accurate and specific predictions than the existing methods.

Algorithms↗
PubMed2005

Multi-scale hierarchical structure prediction of helical transmembrane proteins.

As the first step toward a multi-scale, hierarchical computational approach for membrane protein structure prediction, the packing of transmembrane helices was modeled at the residual and atomistic levels, respectively. For predictions at the residual level, the helix-helix and helix-lipid interactions were described by a set of knowledge-based energy functions. For predictions at the atomistic level, CHARMM19 force field was employed. To facilitate the system to overcome energy barriers, Wang-Landau sampling was carried out by performing a random walk in the energy and conformational spaces. Native-like structures were predicted at both levels for 2- and 7-helix systems. Interestingly, consistent results were obtained from simulations at residual and atomistic levels for the same system, strongly suggesting the feasibility of a hierarchical approach for membrane structure prediction.

Algorithms↗
PubMed2005

The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry.

Proteomic techniques are fast becoming the main method for qualitative and quantitative determination of the protein content in biological systems. Despite notable advances, efficient and accurate analysis of high throughput proteomic data generated by mass spectrometers remains one of the major stumbling blocks in the protein identification problem. We present a model for the number of random matches between an experimental MS-MS spectrum and a theoretical spectrum of a peptide. The shape of the probability distribution is a function of the experimental accuracy, the number of peaks in the experimental spectrum, the length of the interval over which the peaks are distributed, and the number of theoretical spectral peaks in this interval. Based on this probability distribution, a goodness-of-fit tool can be used to yield fast and accurate scoring schemes for peptide identification through database search. In this paper, we describe one possible implementation of such a method and compare the performance of the resulting scoring function with that of SEQUEST. In terms of speed, our algorithm is roughly two orders of magnitude faster than the SEQUEST program, and its accuracy of peptide identification compares favorably to that of SEQUEST. Moreover, our algorithm does not use information related to the intensities of the peaks.

Algorithms↗
PubMed2005

Clustering gene expression data with kernel principal components.

Kernel principal component analysis (KPCA) has been applied to data clustering and graphic cut in the last couple of years. This paper discusses the application of KPCA to microarray data clustering. A new algorithm based on KPCA and fuzzy C-means is proposed. Experiments with microarray data show that the proposed algorithms is in general superior to traditional algorithms.

Algorithms↗
PubMed2005

Optimization of angiotensin I-converting enzyme (ACE) inhibition by rice dregs hydrolysates using response surface methodology.

Angiotensin I-converting enzyme (ACE) inhibitory peptides have been shown to have antihypertensive effects and have been utilized for physiologically functional foods and pharmaceuticals. The ACE inhibitory ability of a hydrolysate is determined by its peptide composition. However, the peptide composition of a hydrolysate depends on proteolytic enzyme and the hydrolysis conditions. In this study, the effect of process conditions on the ACE inhibitory activity of rice dregs hydrolyzed with a trypsin was investigated systematically using response surface methodology. It was shown that the ACE inhibitory activity of rice dregs hydrolysates could be controlled by regulation of five process conditions. Hydrolysis conditions for optimal ACE inhibition were defined using the response surface model of fractional factorial design (FFD), steepest ascent design, and central composite design (CCD).

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2005

Effective extraction of elastase from Bacillus sp. fermentation broth using aqueous two-phase system.

This paper presents the evaluation of an aqueous two-phase system (ATPS) for extracting elastase produced by Bacillus sp. EL31410. The elastase and cell partition behavior in polyethylene glycol (PEG)/salt systems was investigated. The suitable system for elastase extraction was PEG/KH(2)PO(4)-K(2)HPO(4), in which elastase is mainly partitioned into the PEG-rich phase, while the cells remained in the other phase. The influence of defined system parameters (e.g. PEG molecular mass, pH, NaCl addition) on the partitioning behavior of elastase is described. The concentration of phase forming components, PEG and KH(2)PO(4)-K(2)HPO(4), was optimized for elastase recovery by means of response surface methodology, and it was found that they greatly influenced extraction recovery. The optimal ATPS was 23.1% (w/w) PEG 2 000 and 11.7% (w/w) KH(2)PO(4)-K(2)HPO(4). The predicted recovery was about 89.5%, so this process is suggested to be a rapid and convenient method for elastase extraction.

Bacillus↗
PubMed2005

[Role of procalcitonin in the differentiation and surveillance of systemic inflammatory response syndrome].

OBJECTIVE: To evaluate the discrimination of serum procalcitonin (PCT) and interleukin-6 (IL-6) between patients with sepsis and non-infectious inflammatory response syndrome (SIRS) and the prediction power of clinical outcome. METHODS: A perspective study was performed in 27 patients with sepsis and 30 patients with non-infectious SIRS. The serum concentrations of PCT, IL-6, C-reactive protein (CRP), white blood cell count, percentage of neutrophil, absolute neutrophil count, and maximal body temperature were obtained less than 24 hours after clinical onset of sepsis or SIRS. RESULTS: The serum levels of PCT and IL-6 and percentage of neutrophil were significantly higher in patients with sepsis than in those with non-infectious SIRS (PCT: 5.54 [1.20, 32.74] microg/L vs 0.77 [0.22, 3.90] microg/L, P=0.001; IL-6: 163.66 [33.60, 505.26] ng/L vs 37.72 [22.52, 110.78] ng/L, P=0.004; CRP [15.28 +/- 8.41] g/L vs [9.51 +/- 7.65] g/L, P=0.010; and percentage of neutrophil: 0.91 +/- 0.04 vs 0.88 +/- 0.04, P=0.010). Receiver operating characteristic curve showed that the power of PCT and IL-6 were the best of all above. There was significant correlation between serum PCT or IL-6 and the acute physiology and chronic health evaluation (APACHE II) or sepsis-related organ failure assessment (SOFA) scores, so was between serum PCT and the intensive care unit (ICU) length of stay. CONCLUSIONS: PCT and IL-6 are more reliable indicators to differentiate sepsis and non-infectious SIRS than the conventional inflammatory markers, and correlate with the disease severity. PCT levels are significantly correlated with ICU length of stay.

APACHE↗
PubMed2005

[One-step purification of monoclonal antibody against gp130 by cation exchange liquid chromatography].

AIM: To develop a one-step purification method of anti-gp130 monoclonal antibody (mAb) B-S12 from mouse ascites. METHODS: After filtrated by centrifugation, the ascites sample was loaded on a cation exchange column and purified by using ion-strength gradient elution buffer. The effects of pH of the loading buffer and ion strength gradients of the elution buffer on the purity of antibody obtained were investigated. The antibody's biological activity was tested by MTT colorimetry. RESULTS: It was shown that the mAb B-S12 with a purity of over 90% could be achieved by using 20 mmol/L HEPES buffer (pH 4.0) as loading buffer and 0-1.0 mol/L NaCl as elution buffer. The total recovery rate of the mAb was 52%. The purified antibody could stimulate the proliferation of XG-2 cell line. CONCLUSION: The established one-step purification method was simple and suitable for purification of mAb B-S12.

Animals↗
PubMed2005

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

OBJECTIVE: To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. METHODS: Gpat, which is based on SPLASH algorithm, was developed by using open source software. RESULTS: GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. CONCLUSION: Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

Algorithms↗
PubMed2005

B7-H3: another molecule marker for Mo-DCs?

Using a newly generated monoclonal antibody (2E6) against human B7-H3, we explored the expression of the molecule on dendritic cells derived from monocytes (Mo-DCs). Its expression was examined by means of immunostaining and flow cytometric (FCM) analysis. The results showed that B7-H3 was expressed in the course of Mo-DC maturation induced with interleukin 4 (IL-4) and granulocyte/macrophage colony-stimulating factor (GM-CSF). The expression could be detected at all the stages of Mo-DC differentiation, and remained at a quite stable level. Interestingly, B7-H3 was not expressed by T cells and B cells, even these cells were activated respectively by PHA or PWM. A weak expression could be detected on resting monocytes. These data showed that constitutive expression of B7-H3 at a high level was found on imDCs and mDCs derived from monocytes. Due to no expression on T cells and B cells, we speculate that B7-H3 might be another valuable molecule marker for Mo-DCs.

Animals↗
PubMed2005

A clinical study on the treatment of urinary infection with Zishen Tongli Jiaonang.

OBJECTIVE: To observe the therapeutic effects of Zishen Tongli Jiaonang (capsules for nourishing the kidney and promoting urination) for treatment of urinary infection. METHOD: The treatment group with a control group were randomly set up. 120 patients in the control group were given antibiotics according to drug sensitive tests for orally taking or intravenous drip, while 136 patients in the treatment group were additionally given the capsules on the basis of the above-mentioned treatment. One course of treatment lasted 2 weeks. Statistical analysis on the therapeutic effects was conducted after a two-course treatment. The recurrence rates of the two groups were compared one year later. RESULTS: The total remission rates were respectively 96.3% in the treatment group and 81.7% in the control group (P<0.05). The recurrence rates one year later were respectively 4.4% in the treatment group and 30.0% in the control group (P<0.01). CONCLUSION: The capsules show good effects for urinary infection, especially in the long-term effect.

Adolescent↗