Biomedical subjects

Ying Xue

Publications and source records attributed to Ying Xue.

At least 19 recordsLinked to original sources

PubMed2006

Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags.

BACKGROUND: Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T. rubrum is a recognized pathogen for humans, little is known about how its transcriptional pattern is related to development of the fungus and establishment of disease. It is therefore necessary to identify genes whose expression is relevant to growth, metabolism and virulence of T. rubrum. RESULTS: We generated 10 cDNA libraries covering nearly the entire growth phase and used them to isolate 11,085 unique expressed sequence tags (ESTs), including 3,816 contigs and 7,269 singletons. Comparisons with the GenBank non-redundant (NR) protein database revealed putative functions or matched homologs from other organisms for 7,764 (70%) of the ESTs. The remaining 3,321 (30%) of ESTs were only weakly similar or not similar to known sequences, suggesting that these ESTs represent novel genes. CONCLUSION: The present data provide a comprehensive view of fungal physiological processes including metabolism, sexual and asexual growth cycles, signal transduction and pathogenic mechanisms.

Arthrodermataceae↗

PubMed2006

Ab initio potential energy surface and predicted microwave spectra for Ar--OCS dimer and structures of Arn--OCS (n = 2-14) clusters.

An ab initio potential energy surface for the Ar--OCS dimer was calculated using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)] with a large basis set containing bond functions. The interaction energies were obtained by the supermolecular approach with the full counterpoise correction for the basis set superposition error. The CCSD(T) potential was found to have two minima corresponding to the T-shaped and the collinear Ar--SCO structures. The two-dimensional discrete variable representation method was employed to calculate the rovibrational energy levels for five isotopomers Ar--OCS, Ar--OC34S, Ar--O13CS, Ar--18OCS, and Ar--17OCS. The calculated pure rotational transition frequencies for the vibrational ground state of the five isotopomers are in good agreement with the observed values. The corresponding microwave spectra show that the b-type transitions (Delta Ka = +/-1) are significantly stronger than the a-type transitions (Delta Ka = 0). Minimum-energy structures of the Ar2--OCS trimer were been determined with MP2 optimization, whereas the minimum-energy structures of the Arn--OCS clusters with n = 3-14 were obtained with the pairwise additive potentials. It was found that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The 14 nearest neighbor Ar atoms form the first solvation shell around the OCS molecule.

Journal Article↗

PubMed2006

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a.

BACKGROUND: Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been sequenced, revealing dynamic and diverse features. To investigate the intra-species diversity of S. flexneri genomes further, we have sequenced the complete genome of S. flexneri 5b strain 8401 (abbreviated Sf8401) and compared it with S. flexneri 2a (Sf301). RESULTS: The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of Sf301, mainly because the former lacks the SHI-1 pathogenicity island (PAI). Compared with Sf301, there are 6 inversions and one translocation in Sf8401, which are probably mediated by insertion sequences (IS). There are clear differences in the known PAIs between these two genomes. The bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from Sf8401 but a specific related protein is found next to the pheV locus. SHI-2 is involved in one intra-replichore inversion near the origin of replication, which may change the expression of iut/iuc genes. Moreover, genes related to the glycine-betaine biosynthesis pathway are present only in Sf8401 among the known Shigella genomes. CONCLUSION: Our data show that the two S. flexneri genomes are very similar, which suggests a high level of structural and functional conservation between the two serotypes. The differences reflect different selection pressures during evolution. The ancestor of S. flexneri probably acquired SHI-1 and SHI-2 before SHI-O was integrated and the serotypes diverged. SHI-1 was subsequently deleted from the S. flexneri 5b genome by recombination, but stabilized in the S. flexneri 2a genome. These events may have contributed to the differences in pathogenicity and epidemicity between the two serotypes of S. flexneri.

Chromosome Aberrations↗

PubMed2006

Modeling of hydrogen bonds in monohydrated 2,4-dithiothymine: an ab initio and AIM study.

Twelve tautomers of 2,4-dithiothymine are calculated at the MP2/6-31+G(d) level, and the most stable one is referred to the di-keto form (P12). Then four H-bonded complexes between P12 and water are optimized at the MP2/6-31+G(d) level of theory. The calculation of vibrational frequencies and natural bond orbital analysis are also carried out at the same level to investigate the hydrogen bonds involved in all the systems. Within all the four complexes, three types of hydrogen bonds are formed, in which the O-H...S and N-H...O bonds are the normal bonds with the X-H bond elongation and red shift of the corresponding stretch frequencies, while the C-H...O interaction is an improper, blue-shifting hydrogen bond accompanied with the contraction of the C-H bond and a blue shift of the C-H stretch frequency. The topological properties are investigated with the atoms-in-molecules (AIM) theory. The NMR chemical shielding for the isolated and the four monohydrated 2,4-dithiothymine are calculated using the "gauge-including atomic orbital" (GIAO) method. The 1H chemical shifts are influenced by the formation of hydrogen bonds.

Hydrogen Bonding↗

PubMed2006

Comparison of the virulence plasmid genomes of two strains of Shigella which lost the ability to bind Congo red.

We determined and analyzed the Shigella flexneri serotype 5 (pSF5) and S. dysenteriae serotype 1 (pSD1) virulence plasmid genomes. The total length of pSF5 is 136513 bp, including 165 open reading frames (ORFs). Of these ORFs, 133 were identified and 32 of those had no significant homology to proteins with known functions. The length of pSD1 is 182545 bp, including 224 ORFs, of which we identified 181. The remaining 43 ORFs were not significantly homologous to proteins with known functions. The insertion sequence (IS) elements are 53787 bp in pSF5, and 49616 bp in pSD1, which represents 39.4% and 27.1% of the genome, respectively. There are 22 IS element types in pSF5 and pSD1, among which we report ISEc8 and ISSbo6 for the first time in the Shigella virulence plasmid. Compared to pCP301, there are a large number of deleted genes and gene inversions in both pSF5 and pSD1. The ipa-mxi-spa locus in pSF5 is completely absent, and the genes related to the O-antigen biosynthesis are partially missing. In contrast, the above genes in pSD1 are integral, with the exception of virF. The whole genome analysis of the two plasmids shows that the loss of genes related to gene invasion or regulation also obliterates the ability of pPF5 and pSD1 to bind Congo red (Crb). Whether these genes determine the Crb function requires continued investigation.

Acyltransferases↗

PubMed2006

Comprehensive proteomic analysis of Shigella flexneri 2a membrane proteins.

Shigella flexneri is the causative agent of most shigellosis cases in developing countries. We used different proteolytic enzymes to selectively shave the protruding proteins on the surface of purified bacterial membrane sheets or vesicles, and recovered peptides were subsequently identified using 2-D LC-MS/MS. As a result, a total of 666 proteins were unambiguously assigned, including 159 integral membrane proteins, 35 outer membrane proteins and 114 proteins previously annotated as hypothetical. The former had an average grand average hydrophobicity score of 0.362 and were predicted to separate within a pH range of 4.1-10.6 with molecular mass 8-148 kDa, which represents the largest validated set of integral membrane proteins in this organism to date. A functional classification revealed that a large proportion of the identified proteins were involved in cell envelope biogenesis and energy production and conversion. For the first time, this work provides a global view of the S. flexneri 2a membrane subproteome.

Bacterial Outer Membrane Proteins↗

PubMed2006

[Immune response and protective efficacy induced by fusion protein ESAT6-CFP10 of M.tuberculosis in mice].

AIM: To study murine humoral and cellular immune response induced by fusion protein ESAT6-CFP10 and to examine its protective efficacy against M. tuberculosis (MTB) in mice. METHODS: BALB/c mice were immunized subcutaneously on the back with fusion protein ESAT6-CFP10 that was transferred to nitro cellulose (NC) membrane beforehand. Stimulation index (SI) of the spleen lymphocytes of the immunized mice was measured by MTT colorimetry. The level of IFN-gamma and IL-2 and CTL upon antigen-specific stimulation were detected. The vaccinated BALB/c mice were intravenously infected with MTB H37Rv (10(5) CFU/mouse). Four weeks later the number of CFU in spleens was determined. RESULTS: The titer of serum specific antibody in BALB/c mice immunized with fusion protein ESAT6-CFP10 was 1:6,400. The SI of fusion protein immunized group (1.90+/-0.15) was significantly higher than that of saline-immunized group (0.9+/-0.15). The level of IFN-gamma and IL-2 induced by the fusion protein was 1.792+/-19 ng/L and 0.211+/-11 ng/L respectively, which was significantly higher than that of saline-immunized group and lower than that of BCG-immunized group. The specific killing activity of splenocytes was 36%. Compared with the saline-immunized mice (bacterial load was 6.51+/-0.13), MTB number (bacterial load was 5.24+/-0.15) was reduced dramatically in the spleens of BALB/c mice immunized with the fusion protein, but the protective efficacy of the mice immunized with BCG was higher than that of ESAT6-CFP10 vaccinated group. CONCLUSION: Fusion protein ESAT6-CFP10 can be used as a candidate for novel vaccines.

Animals↗

PubMed2006

[A study of the determination of H2O2 in solid food by enzyme-oxygen electrode].

OBJECTIVE: A oxygen-electrode method is developed for the determination of H2O2 residues in solid food. METHODS: The hydrogen peroxide can be decomposed specifically into water and oxygen by catalase. The oxygen-electrode has high selectivity with the dissolved oxygen (DO). After H2O2 in the samples is extracted by PBS and the system is deoxidized by nitrogen, the DO can be detected by oxygen meter and then the content of H2O2 in samples will be calculated according to the result. RESULTS: The linear range is from 0.5 microg/ml to 7.5 microg/ml r > 0.999. The detection limit is 0.13 microg/ml. The recoveries are between 90.59%-93.88%. BSD is below 10%. CONCLUSION: The method has been used for the detection of H2O2 in health-preservation products of calcium, dried small shrimps, bean curd et al, it proved to be a simple rapid method.

Catalase↗

PubMed2005

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.

The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.

DNA Transposable Elements↗

PubMed2005

DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water.

Density functional theory (DFT) and Monte Carlo (MC) simulation with free energy perturbation (FEP) techniques have been used to study the tautomeric proton transfer reaction of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water. Two reaction pathways were considered: the direct and water-assisted transfers. The optimized structures and thermodynamic properties of stationary points for the title reaction system in the gas phase were calculated at the B3LYP/6-311+G(d, p) level of theory. The potential energy profiles along the minimum energy path in the gas phase and in water were obtained. The study of the solvent effect of water on the proton transfer of 2-amino-2-oxozoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline indicates that water as a solvent is favorable for the water-assisted process and slows down the rate of the direct transfer pathway.

Journal Article↗

PubMed2005

A computational study on the mechanism for the chemical fixation of nitric oxide leading to 1,2,3-oxadiazole 3-oxide.

The chemical fixation of nitric oxide (NO) reacting with alkynyllithium to produce 5-methyl-3-oxide-1,2,3-oxadiazole has been investigated by using ab initio (U)MP2 and DFT/(U)B3LYP methods. The solvent effect was assessed using the combination of microsolvation model with explicit THF ligands on lithium and continuum solvent model based on the SCRF/CPCM method at the (U)B3LYP/6-31G* level. Our results reveal that the overall reaction is stepwise and considered to include two processes. In process 1, the nitrogen atom in nitric oxide at first attacks the C(1) atom in alkynyllithium to afford the intermediate 5. In process 2, after another nitric oxide reacted with the intermediate 5 to produce 8a, we found that two pathways are involved. For path 1, the O(2) atom at first attacks the C(2) atom to form a five-membered ring geometry, and then lithium can rotate around the N(1)-O(1) bond, leading to the product 5-methyl-3-oxide-1,2,3-oxadiazole followed addition of water. However, for path 2, lithium atom rotates first around the N(1)-O(1) bond, and then the product 5-methyl-3-oxide-1,2,3-oxadiazole is also generated by addition of water. Our calculations indicate that path 1 is more favorable than path 2 in the gas phase, while both of them exist possibly in THF solvent. The overall reaction is exothermic.

Journal Article↗

PubMed2005

The complete sequence and analysis of the large virulence plasmid pSS of Shigella sonnei.

The complete sequence of pSS, which is the large virulence plasmid of Shigella sonnei, was determined. The 214-kb plasmid is composed of segments of virulence-associated genes, the O-antigen gene clusters, a range of replication and maintenance genes, and large numbers of insertion sequence (IS) elements. Two hundred and forty-one open reading frames (ORFs) were identified, of which 117 are highly homologous to IS elements or transposases, 57 are homologous to known pathogenesis-associated proteins, and 30 are related to replication, plasmid maintenance, or other metabolic functions. Thirty-seven ORFs have no similarity to proteins with a known function, including two with no significant similarity to any hypothetical proteins. Interestingly, 10 ORFs encoding O-antigen gene clusters were identified on the plasmid and this is markedly different from most other Shigella spp. virulent plasmids. A novel toxin-antitoxin system, a series of stbDE homologs, was found on the plasmid immediately downstream of the replication region; the sole segregation stability system may be responsible for the instability of pSS. The pSS plasmid is a mixture of genes with different origins and functions. The sequence suggests a remarkable history of IS-mediated recombination and acquisition of DNA across a range of bacterial species.

Bacterial Proteins↗

PubMed2005

Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant.

In order to overcome the defects of difficult gene operations in low-copy suicide plasmid pCVD442, Gateway technology was applied in the construction process of recombinant plasmid for gene knockout in this study. With this improved knockout system, we inactivated sitC gene, which is associated with iron transport in Shigella flexneri 2a strain 301, to yield the mutant, MTS. The functional detection of the mutant was performed at the level of culture medium, cell and animal experiment, respectively. The gene expression profiles were compared with DNA microarray between the mutant and the wild type under iron-restricted conditions. The results showed that MTS grew obviously less well than the wild-type strains in L broth containing 150 micromol/L iron chelator DIP (2,2'-dipyridyl). Addition of iron or manganese to the cultures stimulated the growth of MTS to wild-type levels in rich culture medium. In either the experiment on the ability of intracellular multiplication and cell-to-cell spread in HeLa and U937 cell lines, or the experiment on keratoconjunctivitis in guinea pigs, MTS showed no obvious changes in virulence compared with the parental strain Sf301. When 65 micromol/L DIP was added to the cultured HeLa cells, the ability of intracellular multiplication of MTS reduced about 51.6% as compared with that of Sf301. The analysis of expression profiles under iron-limited condition showed that MTS was more sensitive for the change of iron deficiency than Sf301. There are 106 more up-regulated genes in MTS than in wild-type strains, which are involved in membrane transportation, amino acid metabolism and uncategorized function genes, while down-regulated genes are mainly involved in energy and carbohydrate metabolism. Under low iron conditions, the expression levels of known iron-transport associated genes generally increased. Additionally, the number of these genes and their increase amplitude in MTS are more than those in Sf301. Together, these results confirmed that Sit iron-transport system is important for the growth of Shigella.

ATP-Binding Cassette Transporters↗

PubMed2005

Structural and functional analysis of denitrification genes in Pseudomonas stutzeri A1501.

Four gene clusters associated with denitrification were identified in the genome of A1501 strain, nar, nir, nor and nos, including 40 genes totally, which encode proteins for substance transportation, gene regulation and reductases. The three gene clusters, nir, nor and nos are adjacent on chromosome and are far from nar gene cluster. Compared with other denitrifying bacteria, the 40 denitrification genes in A1501 strain compose a complete denitrification catalysis system. In A1501 strain, this system has the following characteristics: (i) only one copy of narK gene is found in nar gene cluster; (ii) a narM gene is present between narK and narG; (iii) two genes, dnarE and orfl are identified at downstream of narX and narL genes, of which dnrE perhaps is a transcriptional factor belonging to FNR family; (iv) there are 16 nir genes in A1501, the most in the known denitrifying bacteria; (v) it is for the first time that norR gene has been found in A1501 and also in Pseudomonas; (vi) nos gene cluster is relatively conservative, with a completely identical composition and arrangement of genome to the reference bacteria strain.

Escherichia coli↗

PubMed2005

[Screening and construction of recombinant BCG strains expressing the Ag85B-ESAT6 fusion protein].

OBJECTIVE: To screen and construct recombinant BCG strains which express the Ag85B-ESAT6 fusion protein. METHODS: The heat shock protein 60 (Hsp60) and the alpha-ss signal peptide encoding sequence were amplified by PCR from Mycobacterium tuberculosis H(37)Rv and cloned into E. coli/Mycobacteria shuttle vector-pOLYG. The resulting expression vector was named pDE22, and then ag85b and esat6 genes were cloned into pDE22 at different sites. The resulting recombinant plasmids Ag85B-ESAT6 and ESAT6-Ag85 were electroporated into BCG. Positive clones were screened by hygromycin resistance and confirmed by PCR. Recombinant BCG culture supernatants were collected and analyzed by SDS-PAGE and Western blot. RESULTS: Two recombinant BCG strains were obtained, which secreted the 37,000 fusion protein in their culture supernatant, which was confirmed by Western blot with specific immune serum against Ag85B and ESAT6. CONCLUSIONS: Recombinant BCG strains expressing Ag85B and ESAT6 fusion proteins of Mycobacterium tuberculosis were constructed. They may serve as new vaccine candidates for preventing tuberculosis.

Acyltransferases↗

PubMed2005

[Determination of estrogen-like compounds in beverages by high performance liquid chromatography].

A comprehensive analytical method based on high performance liquid chromatography-ultraviolet-fluorescence detection (HPLC-UV-FL) has been established for the determination of bisphenol A (BPA), nonylphenol (NP) and octylphenol (OP) in beverages with different samples and concentrations. Clean-up of samples was performed on an OASIS HLB solid extraction cartridges (6 mL, 200 mg). The method was successfully applied to the investigation of residual bisphenol A, nonylphenol and octylphenol in the beverages (mineral waters and soft drinks) available in commercial markets in Beijing. Recoveries for bisphenol A, nonylphenol and octylphenol at different spiked levels were ranged from 91.08% to 103.19% with relative standard deviations of 0.5% to 5.49%. The method is simple with good reproducibility and selectivity, and high sensitivity.

Beverages↗

PubMed2005

[Determination of acrylamide in heated starchy food by liquid chromatography-electrospray ionization tandem mass spectrometry].

An isotope dilution liquid chromatographic-electrospray ionization tandem mass spectrometric method has been established for the determination of acrylamide in heated starchy food with a C18 analytical column and methanol-water containing 0.1% formic acid (2:98, v/v) as mobile phases. The clean-up of samples was performed on an Oasis HLB solid phase extraction cartridge. The calibration curve of acrylamide showed good linearity in the range of 10-500 microg/L with correlation coefficient of 0.9995. The detection limit of the method was 6 microg/kg (S/N = 3), and the limit of quantification was 20 microg/kg (S/N = 10). The average recoveries at three levels ranged from 96.8% to 97.4% (n = 5), and the relative standard derivations were lower than 10%.

Acrylamide↗

PubMed2005

[Simultaneous determination of seventeen sulfonamide residues in chickens by liquid chromatography-electrospray tandem mass spectrometry].

A liquid chromatography-electrospray tandem mass spectrometry (LC-MS/MS) for the simultaneous determination of seventeen commonly used sulfonamide (SA) residues in chickens has been developed. Stable isotopic compound (13)C6-sulfamethazine was used as internal standard. Multi-reaction monitoring mode was employed for the quantitative determination. The separation was performed on a Capcell Pak C8 DD column (150 mm x 2.0 mm i.d., 5 microm) with a gradient system of water (containing 0.2% formic acid)-methanol (containing 0.2% formic acid) as mobile phase at a flow rate of 0.2 mL/min. Samples were prepared by homogenizing the chicken, extracting with acetonitrile, defatting with n-hexane and cleaning-up with Sep-Pak Silica solid-phase extraction. The detection limits of 0.02 - 1 microg/kg proved to be much better than the previously reported ones. Average recoveries of seventeen SAs ( spiked at the levels of 1, 5, 10 microg/kg) ranged from 52.3% to 124.9%, with relative standard deviations between 1.0% and 17.6%. Intra-day and inter-day variations of the method were all with in the acceptable ranges. The results demonstrated that the method is simple, accurate and suitable for the identification and quantification of these sulfonamide residues in chickens.

Animals↗