Biomedical subjects

Ying Xu

Publications and source records attributed to Ying Xu.

At least 55 records · Page 3Linked to original sources

PubMed2006

Olfactory cell-based biosensor: a first step towards a neurochip of bioelectronic nose.

Human olfactory system can distinguish thousands of odors. In order to realize the biomimetic design of electronic nose on the principle of mammalian olfactory system, this article reports an olfactory cell-based biosensor as a real bionic technique for odorants detection. Effective cultures of olfactory receptor neurons and olfactory bulb cells have been achieved on the semiconductor chip. Using light-addressable potentiometric sensor (LAPS) as sensing chip to monitor extracellular potential of the neurons, the response under stimulations of the odorants or neurotransmitters, such as acetic acid and glutamic acid, was tested. The results demonstrate that this kind of hybrid system of LAPS and olfactory neurons, which is sensitive to odorous changes, has great potential and is promising to be used as a novel neurochip of bioelectronic nose for detecting odors.

Animals↗

PubMed2006

[Infection pathogen analysis of 2388 patients in an open hematology ward from 1993 to 2004].

OBJECTIVE: To investigate the incidence of infection and pathogens in hematology ward. METHODS: The data of incidence, pathogen, and outcome of infection of 2388 hospitalized patients in an open hematology ward of Peking Union Medical College Hospital from 1993 to 2004 were analyzed retrospectively. RESULTS: The overall incidence of infection was 34.3% according to the person-times of hospitalization, 24.4% for nosocomial infection and 9.9% for community-acquired infection. Most of the pathogenic bacteria of the nosocomial infection were Gram negative. The most common bacteria in the sputum samples included Enterobacter (27%), Pseudomonas aeruginosa (16%) and coagulase negative Staphylococcus (MRSCoN, 12%), the most common bacteria in the blood samples included Escherichia coli (43%), Enterobacter cloacae (11%), and Klebsiella (11%). Whereas in the community-acquired infection the most common bacteria in the sputum samples were Haemophilus parainfluenzae (15%), MRSCoN (28%), and Staphylococcus epidermidis (10%), and the most common bacteria in the blood samples were MRSCoN (28%), E. coli (28%), and Klebsiella (9.4%). Fungi were more often found in nosocomial infection, especially in the sputum samples. 12-year follow up showed that in nosocomial infection Pseudomonas aeruginosa remained the most common bacteria in the sputum samples, whereas E. coli and Enterobacter cloacae became the major bacteria in the blood samples. In community-acquired infection, the proportion of Staphylococcus aureus, that of Klebsiella in blood samples, and that of E. coli in throat swab samples increased in recent years. The incidence of fungi infection had increased in both nosocomial infection and community acquired infection. The mortality of nosocomial infection was 6.1%, higher than that of the community-acquired infection, however, not statistically significant (P = 0.17). There was a trend of decrease in the mortality of community-acquired infection but did not in the nosocomial infection. CONCLUSION: The patients in hematology ward are susceptible to infection, especially nosocomial infection that has a higher mortality rate in comparison with the community-acquired infection, however, not statistically significant. The pathogens of nosocomial infection are most likely G- bacteria, fungi and other bacteria resistant to most antibiotics. The mortality rate of nosocomial infection remains almost unchanged in the 12-year follow up.

Adolescent↗

PubMed2006

CD69 acts downstream of interferon-alpha/beta to inhibit S1P1 and lymphocyte egress from lymphoid organs.

Naive lymphocytes continually enter and exit lymphoid organs in a recirculation process that is essential for immune surveillance. During immune responses, the egress process can be shut down transiently. When this occurs locally it increases lymphocyte numbers in the responding lymphoid organ; when it occurs systemically it can lead to immunosuppression as a result of the depletion of recirculating lymphocytes. Several mediators of the innate immune system are known to cause shutdown, including interferon alpha/beta (IFN-alpha/beta) and tumour necrosis factor, but the mechanism has been unclear. Here we show that treatment with the IFN-alpha/beta inducer polyinosine polycytidylic acid (hereafter 'poly(I:C)') inhibited egress by a mechanism that was partly lymphocyte-intrinsic. The transmembrane C-type lectin CD69 was rapidly induced and CD69-/- cells were poorly retained in lymphoid tissues after treatment with poly(I:C) or infection with lymphocytic choriomeningitis virus. Lymphocyte egress requires sphingosine 1-phosphate receptor-1 (S1P1), and IFN-alpha/beta was found to inhibit lymphocyte responsiveness to S1P. By contrast, CD69-/- cells retained S1P1 function after exposure to IFN-alpha/beta. In coexpression experiments, CD69 inhibited S1P1 chemotactic function and led to downmodulation of S1P1. In a reporter assay, S1P1 crosslinking led to co-crosslinking and activation of a CD69-CD3zeta chimaera. CD69 co-immunoprecipitated with S1P1 but not the related receptor, S1P3. These observations indicate that CD69 forms a complex with and negatively regulates S1P1 and that it functions downstream of IFN-alpha/beta, and possibly other activating stimuli, to promote lymphocyte retention in lymphoid organs.

Animals↗

PubMed2006

An enzyme-linked immunosorbent assay for rare minnow (Gobiocypris rarus) vitellogenin and comparison of vitellogenin responses in rare minnow and zebrafish (Danio rerio).

A competitive enzyme-linked immunosorbent assay (ELISA) was developed to determine vitellogenin (Vtg) in rare minnow (Gobiocypris rarus) based on the separation and purification of rare minnow Vtg (r-Vtg) as well as the production of polyclonal antibody against r-Vtg in rabbits. Three different ELISAs for measuring r-Vtg were then compared: (1) indirect ELISA with the antibody against carp (Cyprinus carpio) Vtg (c-Vtg) (IC-ELISA); (2) competitive ELISA with the antibody against c-Vtg, and using r-Vtg for coating the plates and preparing standard curve (CC-ELISA); (3) competitive ELISA with the antibody against r-Vtg, and using r-Vtg for coating the plates and preparing standard curve (CR-ELISA). The result showed that the homologous CR-ELISA was the most sensitive among the three assays for quantifying r-Vtg. The sensitivities to 17alpha-ethinylestradiol (EE(2)) of rare minnow and zebrafish (Danio rerio) were compared upon the establishment of homologous competitive ELISA. The lowest observed effect concentrations (LOECs) to induce Vtg were found to be 0.8 ng EE(2) l(-1) for rare minnow and 4 ng EE(2) l(-1) for zebrafish respectively. Afterwards, CR-ELISA was applied to measure Vtg concentration in whole body homogenate (WBH) of juvenile rare minnow fed by three diets (tubifex from wastewater treatment plant, Artemia nauplii and commercial pellet food), and the agreements between bioassay and GC-MS analysis demonstrated that rare minnow was a sensitive fish model for assessing estrogenic effects of endocrine disrupting compounds in aquatic environment.

Animal Feed↗

PubMed2006

A solid-phase microextraction fiber coated with diglycidyloxycalix[4]arene yields very high extraction selectivity and sensitivity during the analysis of chlorobenzenes in soil.

A novel fiber coated with novel sol-gel (5,11,17,23-tetra-tert-butyl-25,27-dihydroxy-26,28-diglycidyloxycalix[4]arene/hydroxy-terminated silicone oil; diglycidyloxy-C[4]/OH-TSO) was prepared for use with headspace solid-phase microextraction (HS-SPME) combined with gas chromatography (GC) and electron capture detection (ECD), which was applied in order to determine nine chlorobenzenes in soil matrices. Due to the improved fiber preparation, which increases the percentage of calixarene in the coating, the new calixarene fiber exhibits very high extraction selectivity and sensitivity to chlorine-substituted compounds. Various parameters affecting the extraction efficiency were optimized in order to maximize the sensitivity during the chlorobenzene analysis. Interferences from different soil matrices with different characteristics were investigated, and the amount extracted was strongly influenced by the matrix. Therefore, a standard addition protocol was performed on the real soil samples. The linear ranges of detection for the chlorobenzenes tested covered three orders of magnitude, and correlation coefficients >0.9976 and relative standard deviations (RSD) <8% were observed. The detection limits were found at sub-ng/g of soil levels, which were about an order of magnitude lower than those given by the commercial poly(dimethylsiloxane) (PDMS) coating for most of the compounds. The recoveries ranged from 64 to 109.6% for each analyte in the real kaleyard soil matrix when different concentration levels were determined over the linear range, which confirmed the reliability and feasibility of the HS-SPME/GC-ECD approach using the fiber coated with diglycidyloxy-C[4]/OH-TSO for the ultratrace analysis of chlorobenzenes in complex matrices.

Journal Article↗

PubMed2006

Surface complexation of Pb(II) on amorphous iron oxide and manganese oxide: spectroscopic and time studies.

Hydrous Fe and Mn oxides (HFO and HMO) are important sinks for heavy metals and Pb(II) is one of the more prevalent metal contaminants in the environment. In this work, Pb(II) sorption to HFO (Fe(2)O(3) x nH(2)O, n=1-3) and HMO (MnO(2)) surfaces has been studied with EXAFS: mononuclear bidentate surface complexes were observed on FeO(6) (MnO(6)) octahedra with PbO distance of 2.25-2.35 Angstrom and PbFe(Mn) distances of 3.29-3.36 (3.65-3.76) Angstrom. These surface complexes were invariant of pH 5 and 6, ionic strength 2.8 x 10(-3) to 1.5 x 10(-2), loading 2.03 x 10(-4) to 9.1 x 10(-3) mol Pb/g, and reaction time up to 21 months. EXAFS data at the Fe K-edge revealed that freshly precipitated HFO exhibits short-range order; the sorbed Pb(II) ions do not substitute for Fe but may inhibit crystallization of HFO. Pb(II) sorbed to HFO through a rapid initial uptake ( approximately 77%) followed by a slow intraparticle diffusion step ( approximately 23%) resulting in a surface diffusivity of 2.5 x 10(-15) cm(2)/s. Results from this study suggest that mechanistic investigations provide a solid basis for successful adsorption modeling and that inclusion of intraparticle surface diffusion may lead to improved geochemical transport depiction.

Journal Article↗

PubMed2006

Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102.

Deciphering the regulatory networks encoded in the genome of an organism represents one of the most interesting and challenging tasks in the post-genome sequencing era. As an example of this problem, we have predicted a detailed model for the nitrogen assimilation network in cyanobacterium Synechococcus sp. WH 8102 (WH8102) using a computational protocol based on comparative genomics analysis and mining experimental data from related organisms that are relatively well studied. This computational model is in excellent agreement with the microarray gene expression data collected under ammonium-rich versus nitrate-rich growth conditions, suggesting that our computational protocol is capable of predicting biological pathways/networks with high accuracy. We then refined the computational model using the microarray data, and proposed a new model for the nitrogen assimilation network in WH8102. An intriguing discovery from this study is that nitrogen assimilation affects the expression of many genes involved in photosynthesis, suggesting a tight coordination between nitrogen assimilation and photosynthesis processes. Moreover, for some of these genes, this coordination is probably mediated by NtcA through the canonical NtcA promoters in their regulatory regions.

Bacterial Proteins↗

PubMed2006

The impact of Mn oxide coatings on Zn distribution.

Zinc sorption to hydrous manganese oxide (HMO)-coated clay was investigated macroscopically, kinetically, and spectroscopically. Adsorption edges and isotherms revealed that the affinity and capacity of the HMO-coated montmorillonite was greater than that of montmorillonite, and when normalized to the oxide present, the coatings behaved similarly to the discrete Mn oxide. Over two pH conditions, 5 and 6, a linear relationship was observed for the isotherms; further analysis with X-ray absorption spectroscopy (XAS) resulted in one type of sorption configuration as a function of loading and ionic strength at pH 5. However, at a surface loading of 10(-3) mol(Zn) g(HMO-coatedclay)(-1) when the pH increased from 5 to 7, the first shell distance decreased slightly, while the atoms and coordination numbers remained the same; this change may be attributed to an increase in electrostatic interactions. After a contact time of 4 months where an additional 60% of the sites become occupied, the slower sorption process was modeled as intraparticle surface diffusion. Best fit diffusivities ranged from 10(-18) to 10(-17) cm2/s, where a slower process was observed for the coated surface as compared to the discrete oxide. Interestingly, the porosity of the Mn oxide coating appears to be influenced by the substrate during its growth, as its increase and shift to a smaller pore size distribution resulted in a diffusivity between that observed for discrete HMO and montmorillonite.

Journal Article↗

PubMed2006

Energetics and stability of transmembrane helix packing: a replica-exchange simulation with a knowledge-based membrane potential.

The energetics and stability of the packing of transmembrane helices were investigated by Monte Carlo simulations with the replica-exchange method. The helices were modeled with a united atom representation, and the CHARMM19 force field was employed. Based on known experimental structures of membrane proteins, an implicit knowledge-based potential was developed to describe the helix-membrane interactions at the residue level, whose validity was tested through prediction of the orientations when single helices were inserted into a membrane. Two systems were studied in this article, namely the glycophorin A dimer, and helices A and B of Bacteriorhodopsin. For the glycophorin A dimer, the most stable structure (0.5 A away from the experimental structure) is mainly stabilized by the favorable helix-helix interactions, and has the most population regardless of the helix-membrane interaction. However, for helices A and B of Bacteriorhodopsin, it was found that the packing determined by helix-helix interactions is nonspecific, and a native-like structure (0.2 A from the experimental one) can be identified from several structural analogs as the most stable one only after applying the membrane potential. Our results suggest that the contribution from the helix-membrane interaction could be critical in the correct packing of transmembrane helices in the membrane.

Computer Simulation↗

PubMed2006

CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).

UNLABELLED: Palmitoylation is an important post-translational lipid modification of proteins. Unlike prenylation and myristoylation, palmitoylation is a reversible covalent modification, allowing for dynamic regulation of multiple complex cellular systems. However, in vivo or in vitro identification of palmitoylation sites is usually time-consuming and labor-intensive. So in silico predictions could help to narrow down the possible palmitoylation sites, which can be used to guide further experimental design. Previous studies suggested that there is no unique canonical motif for palmitoylation sites, so we hypothesize that the bona fide pattern might be compromised by heterogeneity of multiple structural determinants with different features. Based on this hypothesis, we partition the known palmitoylation sites into three clusters and score the similarity between the query peptide and the training ones based on BLOSUM62 matrix. We have implemented a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction (CSS-Palm) system, and found that the program's prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% and specificity 83.17% for cut-off score 2.6). Our analyses indicate that CSS-Palm could provide a powerful and effective tool to studies of palmitoylation sites. AVAILABILITY: CSS-Palm is implemented in PHP/PERL+MySQL and can be freely accessed at http://bioinformatics.lcd-ustc.org/css_palm/ CONTACT: yaoxb@ustc.edu.cn; xuyn@bmb.uga.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bionformatics online.

Algorithms↗

PubMed2006

Predicting emissions of SVOCs from polymeric materials and their interaction with airborne particles.

A model that predicts the emission rate of volatile organic compounds (VOCs) from building materials is extended and used to predict the emission rate of semivolatile organic compounds (SVOCs) from polymeric materials. Reasonable agreement between model predictions and gas-phase di-2-ethylhexyl phthalate (DEHP) concentrations is achieved using data collected in a previous experimental study that measured emissions of DEHP from vinyl flooring in two very different chambers. While emissions of highly volatile VOCs are subject to "internal" control (the material-phase diffusion coefficient), emissions of the very low volatility SVOCs are subject to "external" control (partitioning into the gas phase, the convective mass-transfer coefficient, and adsorption onto interior surfaces). The effect of SVOCs partitioning onto airborne particles is also examined. The DEHP emission rate is increased when the gas-phase concentration is high, and especially when partitioning to the airborne particles is strong. Airborne particles may play an important role in inhalation exposure as well as in transporting SVOCs well beyond the source. Although more rigorous validation is needed, the model should help elucidate the mechanisms governing emissions of phthalate plasticizers, brominated flame retardants, biocides, and other SVOCs from a wide range of building materials and consumer products.

Air Pollutants↗

PubMed2006

Bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of N-acetylated intermediates in prokaryotes.

BACKGROUND: The N-acetylation of L-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. Until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical N-acetylglutamate synthase (NAGS, gene argA) first characterized in Escherichia coli and Pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (OAT, gene argJ) present in Bacteria, Archaea and many Eukaryotes. This paper focuses on a new and surprising aspect of glutamate acetylation. We recently showed that in Moritella abyssi and M. profunda, two marine gamma proteobacteria, the gene for the last enzyme in arginine biosynthesis (argH) is fused to a short sequence that corresponds to the C-terminal, N-acetyltransferase-encoding domain of NAGS and is able to complement an argA mutant of E. coli. Very recently, other authors identified in Mycobacterium tuberculosis an independent gene corresponding to this short C-terminal domain and coding for a new type of NAGS. We have investigated the two prokaryotic Domains for patterns of gene-enzyme relationships in the first committed step of arginine biosynthesis. RESULTS: The argH-A fusion, designated argH(A), and discovered in Moritella was found to be present in (and confined to) marine gamma proteobacteria of the Alteromonas- and Vibrio-like group. Most of them have a classical NAGS with the exception of Idiomarina loihiensis and Pseudoalteromonas haloplanktis which nevertheless can grow in the absence of arginine and therefore appear to rely on the arg(A) sequence for arginine biosynthesis. Screening prokaryotic genomes for virtual argH-X 'fusions' where X stands for a homologue of arg(A), we retrieved a large number of Bacteria and several Archaea, all of them devoid of a classical NAGS. In the case of Thermus thermophilus and Deinococcus radiodurans, the arg(A)-like sequence clusters with argH in an operon-like fashion. In this group of sequences, we find the short novel NAGS of the type identified in M. tuberculosis. Among these organisms, at least Thermus, Mycobacterium and Streptomyces species appear to rely on this short NAGS version for arginine biosynthesis. CONCLUSION: The gene-enzyme relationship for the first committed step of arginine biosynthesis should now be considered in a new perspective. In addition to bifunctional OAT, nature appears to implement at least three alternatives for the acetylation of glutamate. It is possible to propose evolutionary relationships between them starting from the same ancestral N-acetyltransferase domain. In M. tuberculosis and many other bacteria, this domain evolved as an independent enzyme, whereas it fused either with a carbamate kinase fold to give the classical NAGS (as in E. coli) or with argH as in marine gamma proteobacteria. Moreover, there is an urgent need to clarify the current nomenclature since the same gene name argA has been used to designate structurally different entities. Clarifying the confusion would help to prevent erroneous genomic annotation.

Acetylation↗

PubMed2006

Amyloid fibril structure modeling using protein threading and molecular dynamics simulations.

The elucidation of the structure of amyloid fibrils is an important step toward understanding the mechanism of amyloid formation and developing new reagents that could inhibit fibril formation. Here we describe an approach to modeling amyloid fibril structures using computational techniques, including protein threading and molecular dynamics simulations. Specifically, we introduce these methods using Abeta amyloid fibril modeling as an example. First, the amyloid protein sequence is threaded against a set of structural templates. Structural models are generated on the basis of threading alignments and are then subjected to molecular dynamic simulations to assess the stabilities of the model.

Amyloid beta-Peptides↗

PubMed2006

A study of Legionella pneumophilia in Tianjin, China.

Legionella is a bacterium identified as the causative agent of Legionnaires' disease commonly found in water and soil in natural environments and human habitats. While most studies are focused on cooling tower water as the source of infection, few studies have compared Legionella from cooling-tower water and water in man-made environments. This cross-sectional study with a randomized cluster sampling design aims to provide information on Legionella found in cooling-tower water and water in man-made environments. Legionella was identified using a dual analytical approach: the serological and the 16SrRNA semi-nest PCR methods. Nine different types of Legionella were identified with the Lp7 type detected in China for the first time. Results indicated slight but insignificantly increased odds (OR = 1.64, 95%CI = 0.54-4.98) of Legionella detection in cooling tower water as compared to water obtained from fountains and parks, suggesting that the mechanism of exposure plays an important role in the causal pathway of outbreaks of Legionnaires' disease.

China↗

PubMed2006

Expression, purification and anti-tumor activity of curcin.

Curcin, purified from the seeds of Jatropha curcas, can be used as a cell-killing agent. Understanding the anti-tumor activity of the recombinant protein of curcin is important for its application in clinical medicine. The segment encoding the mature protein of curcin was inserted into Escherichia coli strain M15, and the recombinant strain was induced to express by isopropyl-beta-D-thiogalactopyranoside at a concentration of 0.5 mM. The recombinant protein was expressed in the form of inclusion bodies and purified by Ni-NTA affinity chromatography. The target protein was incubated with the tumor cells at different concentrations for different times and the results demonstrated that the target protein could inhibit the growth of tumor cells (NCL-H446, SGC-7901 and S180) at 5 microg/ml.

Animals↗

PubMed2006

Structure prediction of helical transmembrane proteins at two length scales.

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 residue and atom levels, respectively. For predictions at the residue level, the helix-helix and helix-membrane interactions were described by a set of knowledge-based energy functions. For predictions at the atom level, CHARMM19 force field was used. To facilitate the system to overcome energy barriers, the Wang-Landau method was employed, where a random walk is performed in the energy space with a uniform probability. Native-like structures were predicted at both levels for two model systems, each of which consists of two transmembrane helices. Interestingly, consistent results were obtained from simulations at the residue and atom levels for the same system, strongly suggesting the feasibility of a hierarchical approach for membrane protein structure predictions.

Amino Acid Sequence↗

PubMed2006

Gene expression data analysis in subtypes of ovarian cancer using covariance analysis.

Many studies have used microarray technology to identify the molecular signatures of human cancer, yet the critical features of these often unmanageably large set of signatures remain elusive. We have investigated co-expression pattern in four subtypes of ovarian cancer from 104 cancer patients using covariance analysis, treating each subtype of ovarian cancer as a distinct disease entity. We sought gene pairs that were transcriptionally co-expressed in one or multiple subtypes of ovarian cancer, establishing a high confidence network of 87 genes interconnected by significantly high co-expression links that were observed in at least two subtypes of ovarian cancer. We have shown that certain groups of co-expressed gene pairs are cancer subtype specific, through demonstrating significant differences in co-expression patterns of gene pairs between subtypes of ovarian cancer. In addition, we identified a set of 24 genes that classified patients into specific cancer subtypes with a misclassification error rate of less than 5%. Our findings illustrate how large public microarray gene expression datasets could be exploited for identification of cancer subtype specific molecular signatures, and how to classify cancer patients into specific subtypes of cancer using gene expression profiles.

Biomarkers, Tumor↗

PubMed2006

[The advance of research in electro-physiology and chip techniques for olfaction and gustation].

This paper introduces the new research achievement and progress of electro-physiology in olfaction and gustation. Classical implements such as patch-clamp or glass pipette are not appropriate in the dynamic detection of cellular signal transportation. In view of this, we have analyzed the feasibilities and challenges of olfactory or gustatory cell-based biosensors such as field effect transistor (FET) and light addressable potentiometric sensor (LAPS). Finally we present the research work carried our in out lab and a future prospective on the development in this field.

Biosensing Techniques↗