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Ying Xu

Publications and source records attributed to Ying Xu.

At least 91 records · Page 5Linked to original sources
PubMed2005

Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis.

We have developed a new method for prediction of cis-regulatory binding sites and applied it to predicting NtcA regulated genes in cyanobacteria. The algorithm rigorously utilizes concurrence information of multiple binding sites in the upstream region of a gene and that in the upstream regions of its orthologues in related genomes. A probabilistic model was developed for the evaluation of prediction reliability so that the prediction false positive rate could be well controlled. Using this method, we have predicted multiple new members of the NtcA regulons in nine sequenced cyanobacterial genomes, and showed that the false positive rates of the predictions have been reduced on an average of 40-fold compared to the conventional methods. A detailed analysis of the predictions in each genome showed that a significant portion of our predictions are consistent with previously published results about individual genes. Intriguingly, NtcA promoters are found for many genes involved in various stages of photosynthesis. Although photosynthesis is known to be tightly coordinated with nitrogen assimilation, very little is known about the underlying mechanism. We postulate for the fist time that these genes serve as the regulatory points to orchestrate these two important processes in a cyanobacterial cell.

Algorithms↗
PubMed2005

Lymphocyte sequestration through S1P lyase inhibition and disruption of S1P gradients.

Lymphocyte egress from the thymus and from peripheral lymphoid organs depends on sphingosine 1-phosphate (S1P) receptor-1 and is thought to occur in response to circulatory S1P. However, the existence of an S1P gradient between lymphoid organs and blood or lymph has not been established. To further define egress requirements, we addressed why treatment with the food colorant 2-acetyl-4-tetrahydroxybutylimidazole (THI) induces lymphopenia. We found that S1P abundance in lymphoid tissues of mice is normally low but increases more than 100-fold after THI treatment and that this treatment inhibits the S1P-degrading enzyme S1P lyase. We conclude that lymphocyte egress is mediated by S1P gradients that are established by S1P lyase activity and that the lyase may represent a novel immunosuppressant drug target.

Aldehyde-Lyases↗
PubMed2005

Effect of chronic unpredictable mild stress on brain-pancreas relative protein in rat brain and pancreas.

Brain-pancreas relative protein (BPRP) is a novel protein whose biological function remains unknown. Here, we report a possible role of BPRP in male rats exposed to chronic unpredictable mild stress (CUMS) to induce depression for 3 weeks. Compared to unstressed rats, those exposed to CUMS showed significantly less weight gain with age, decreased consumption of (and preference for) sucrose without a change in total fluid consumption. Exposure to CUMS significantly reduced open-field exploration, rearing and grooming indicative of lethargy, apathy and bodily neglect, respectively. Brain MAO-A and MAO-B activity were both significantly increased in the stressed rats. These results verified induction of depressive symptoms by CUMS. The stressed animals showed a significant reduction in pancreatic BPRP, which was accompanied by an increase in levels of blood sugar and a decrease of insulin. But they showed no apparent alteration in levels or distribution of BPRP in the hippocampal formation, which nevertheless displayed a thinner dentate granule cell layer perhaps related to elevated MAO-B activity. These findings suggest that stress-induced reduction of pancreatic BPRP may cause diabetic symptoms. Whether those symptoms in turn contribute to the onset of depression requires further study.

Analysis of Variance↗
PubMed2005

Seasonal variations of phenolic compounds in Australia-grown tea (Camellia sinensis).

Seasonal variations of phenolic compounds in fresh tea shoots grown in Australia were studied using an HPLC method. Three principal tea flavanols [epigallocatechin gallate (EGCG), epicatechin gallate (ECG), and epigallocatechin (EGC)] and four grouped phenolics [total catechins (Cs), total catechin gallates (CGs), total flavanols (Fla), and total polyphenols (PPs)] in fresh tea shoots were analyzed and compared during the commercial harvest seasons from April 2000 to May 2001. The levels of EGCG, ECG, and CGs in the fresh tea shoots were higher in the warm months of April 2000 (120.52, 34.50, and 163.75 mg/g, respectively) and May 2000 (128.63, 44.26, and 183.83 mg/g, respectively) and lower during the cool months of July 2000 (91.39, 35.16, and 132.30 mg/g, respectively), August 2000 (91.31, 31.56, and 128.64 mg/g, respectively), and September 2000 (96.12, 33.51, and 136.90 mg/g, respectively). Thereafter, the levels increased throughout the warmer months from October to December 2000 and remained high until May 2001. In the warmer months, the levels of EGCG, ECG, and CGs were in most cases significantly higher (P < 0.05) than those in the samples harvested in the cooler months. In contrast, the levels of EGC and Cs were high and consistent in the cooler months and low in the warmer months. The seasonal variations of the individual and grouped catechins were significant (P < 0.05) between the cooler and warmer months. This study revealed that EGCG and ECG could be used as quality descriptors for monitoring the seasonal variations of phenolics in Australia-grown tea leaves, and the ratio (EGCG + ECG)/EGC has been suggested as a quality index for measuring the differences in flavanol levels in fresh tea shoots across the growing seasons. Mechanisms that induce seasonal variations in tea shoots may include one or all three of the following environmental conditions: day length, sunlight, and/or temperature, which vary markedly across seasons. Therefore, further studies under controlled conditions such as in a greenhouse may be required to direct correlate flavonoid profiles of green tea leaves with their yields and also to with conditions such as rainfall and humidity.

Australia↗
PubMed2005

Hybrid embryos produced by transferring panda or cat somatic nuclei into rabbit MII oocytes can develop to blastocyst in vitro.

The developmental potential of hybrid embryos produced by transferring panda or cat fibroblasts into nucleated rabbit oocytes was assessed. Both the panda-rabbit and the cat-rabbit hybrid embryos were able to form blastocysts in vitro. However, the rates of attaining the two-cell, four-cell, eight-cell, morula, or blastocyst stages for panda-rabbit hybrids were significantly greater than those of cat-rabbit hybrids (P<0.05). Transferring the rabbit fibroblasts into nucleated rabbit oocytes, 31.0% of the blastocyst rate was obtained, which was significantly higher than that of both the panda-rabbit and the cat-rabbit hybrid embryos (P<0.05). Whether or not the second polar body (PB2) was extruded from the one-cell hybrid embryos (both panda-rabbit and cat-rabbit hybrids) significantly affected their developmental capacity. Embryos without an extruded PB2 showed a higher capacity to develop into blastocysts (panda-rabbit: 19.2%; cat-rabbit: 4.3%), while embryos with extruded PB2 could only develop to the morula stage. The hybrid embryos formed pronucleus-like structures (PN) in 2-4 hr after activation, and the number of PN in one-cell embryos varied from one to five. Tracking of the nucleus in the egg after fusion revealed that the somatic nucleus could approach and aggregate with the oocyte nucleus spontaneously. Chromosome analysis of the panda-rabbit blastocysts showed that the karyotype of the hybrid embryos (2n=86) consisted of chromosomes from both the panda (2n=42) and the rabbit (2n=44). The results demonstrate that (1) it is possible to produce genetic hybrid embryos by interspecies nuclear transfer; (2) the developmental potential of the hybrid embryos is highly correlated to the donor nucleus species; and (3) the hybrid genome is able to support the complete preimplantation embryonic development of the hybrids.

Animals↗
PubMed2005

The presence of a haloarchaeal type tyrosyl-tRNA synthetase marks the opisthokonts as monophyletic.

Lateral gene transfer plays an important role in the evolution of life. Events of ancient gene transfer can transmit genetic novelties to descendent lineages and subsequently shape their genetic systems. We here present the analyses of the gene encoding tyrosyl-tRNA synthetase (tyrRS), which reveal two eukaryotic tyrRS lineages, one including the opisthokonts and the other the remaining eukaryotes. The different origins of tyrRS lineages between the opisthokonts and the remaining eukaryotes indicate a likely case of ancient lateral gene transfer of tyrRS from an archaeon to the opisthokonts, which lends further support for the monophyly of the latter group. Ancient paralogy followed by differential gene loss is an alternative, albeit less parsimonious explanation for the distribution of the two eukaryotic tyrRS types. In either case, the presence of a haloarchaeal tyrRS type in the opisthokonts marks this group as monophyletic. This finding also points to the potential utility of ancient gene transfer events as molecular markers for major organismal lineages.

Amino Acid Sequence↗
PubMed2005

The effects of curcumin on depressive-like behaviors in mice.

Curcuma longa is a major constituent of Xiaoyao-san, the traditional Chinese medicinal formula, which has been used effectively to treat depression-related diseases in China. There is no information available about the antidepressant activity of curcumin, the active component of curcuma longa. In the present study, we analyzed the effects of curcumin on depressive-like behaviors in mice, using two animal models of depression. Our results showed that curcumin treatment at 5 and 10 mg/kg (p.o.) significantly reduced the duration of immobility in both the tail suspension and forced swimming tests. These doses that affected the immobile response did not affect locomotor activity. In addition, the neurochemical assays showed that curcumin produced a marked increase of serotonin and noradrenaline levels at 10 mg/kg in both the frontal cortex and hippocampus. Dopamine levels were also increased in the frontal cortex and the striatum. Moreover, curcumin was found to inhibit monoamine oxidase activity in the mouse brain. These findings suggest that the antidepressant-like effects of curcumin may involve the central monoaminergic neurotransmitter systems.

3,4-Dihydroxyphenylacetic Acid↗
PubMed2005

Prediction of functional modules based on comparative genome analysis and Gene Ontology application.

We present a computational method for the prediction of functional modules encoded in microbial genomes. In this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. We first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and Gene Ontology assignments. We then combine the three different sources of information in the framework of Bayesian inference, and we use the combined information to measure the strength of gene functional relationship. Finally, we apply a threshold-based method to predict functional modules. By applying this method to Escherichia coli K12, we have predicted 185 functional modules. Our predictions are highly consistent with the previously known functional modules in E.coli. The application results have demonstrated that our approach is highly promising for the prediction of functional modules encoded in a microbial genome.

Bayes Theorem↗
PubMed2005

Photochemical surface mapping of C14S-Sml1p for constrained computational modeling of protein structure.

Photochemically generated hydroxyl radicals were used to map solvent-exposed regions in the C14S mutant of the protein Sml1p, a regulator of the ribonuclease reductase enzyme Rnr1p in Saccharomyces cerevisiae. By using high-performance mass spectrometry to characterize the oxidized peptides created by the hydroxyl radical reactions, amino acid solvent-accessibility data for native and denatured C14S Sml1p that revealed a solvent-excluding tertiary structure in the native state were obtained. The data on solvent accessibilities of various amino acids within the protein were then utilized to evaluate the de novo computational models generated by the HMMSTR/Rosetta server. The top five models initially generated by the server all disagreed with both published nuclear magnetic resonance (NMR) data and the solvent-accessibility data obtained in this study. A structural model adjusted to fit the previously reported NMR data satisfied most of the solvent-accessibility constraints. Through minor adjustment of the rotamers of two amino acid side chains for this latter structure, a model that not only provided a lower energy conformation but also completely satisfied previously reported data from NMR and tryptophan fluorescence measurements, in addition to the solvent-accessibility data presented here, was generated.

Amino Acid Sequence↗
PubMed2005

Functional consequences of a CKIdelta mutation causing familial advanced sleep phase syndrome.

Familial advanced sleep phase syndrome (FASPS) is a human behavioural phenotype characterized by early sleep times and early-morning awakening. It was the first human, mendelian circadian rhythm variant to be well-characterized, and was shown to result from a mutation in a phosphorylation site within the casein kinase I (CKI)-binding domain of the human PER2 gene. To gain a deeper understanding of the mechanisms of circadian rhythm regulation in humans, we set out to identify mutations in human subjects leading to FASPS. We report here the identification of a missense mutation (T44A) in the human CKIdelta gene, which results in FASPS. This mutant kinase has decreased enzymatic activity in vitro. Transgenic Drosophila carrying the human CKIdelta-T44A gene showed a phenotype with lengthened circadian period. In contrast, transgenic mice carrying the same mutation have a shorter circadian period, a phenotype mimicking human FASPS. These results show that CKIdelta is a central component in the mammalian clock, and suggest that mammalian and fly clocks might have different regulatory mechanisms despite the highly conserved nature of their individual components.

Amino Acid Sequence↗
PubMed2005

Cell-based biosensors based on light-addressable potentiometric sensors for single cell monitoring.

Cell-based biosensors incorporate cells as sensing elements that convert changes in immediate environment to signals for processing. This paper reports an investigation on light-addressable potentiometric sensor (LAPS) to be used as a possible cell-base biosensor that will enable us to monitor extracellular action potential of single living cell under stimulant. In order to modify chip surface and immobilize cells, we coat a layer of poly-L-ornithine and laminin on surface of LAPS chip on which rat cortical cells are grown well. When 10 microg/ml acetylcholine solution is administrated, the light pointer is focused on a single neuronal cell and the extracellular action potential of the targeted cell is recorded with cell-based biosensor based on LAPS. The results demonstrate that this kind of biosensor has potential to monitor electrophysiology of living cell non-invasive for a long term, and to evaluate drugs primarily.

Acetylcholine↗
PubMed2005

MPSS: an integrated database system for surveying a set of proteins.

SUMMARY: We design and implement an integrated database system called 'multi-protein survey system' (MPSS), which provides a platform to retrieve information about many proteins at a time. This system integrates several important and widely used databases including SwissProt, TrEMBL, PDB and InterPro, plus useful references such as GO and KEGG to other databases. Users may submit a group of protein IDs, entry names, SwissProt/TrEMBL accession numbers or GenBank GIs through MPSS' web interface, and obtain protein annotation information from public databases and pre-computed molecular properties speedily. MPSS can also supply comprehensive information about query proteins, including 3D structures, domains, pathway, gene ontology and visual presentation of mapping to the GO tree and KEGG pathway, to provide an up-to-date view of available knowledge with regard to the structures and molecular functions of proteins under study. AVAILABILITY: MPSS is freely accessible at http://www.scbit.org/mpss/

Database Management Systems↗
PubMed2005

Synthesis and characterization of iron oxide-coated silica and its effect on metal adsorption.

To accurately model metal mobility and bioavailability in soils and sediments, systematic adsorption studies are needed in considering heterogeneous, well characterized minerals. Two important surfaces are iron oxide and silica, which are ubiquitous and associated with one another in the environment playing important roles in metal distribution. This study focuses on the synthesis and characterization of such a system, iron oxide-coated silica. A three-level fractional factorial study was used to determine the optimum conditions for producing goethite-coated silica. The amount of coating achieved was between 0.59 and 21.36 mg Fe g(-1) solid. The most significant factor in coating using either adsorption or precipitation was the particle size of silica, where Fe increased from an average of 0.85 to 9.6 mg Fe g(-1) solid as silica size decreased from 1.5 to 0.2 mm. Other factors investigated, including coating temperature, initial iron concentration, and contact time, were of less importance. The iron oxide coatings were observed to be non-uniform, concentrated in rough concave areas. FTIR revealed a band shift as well as a new band indicating changes in the chemical environment of FeO and SiO bonds; these results along with abrasion studies suggest that the interaction between the oxide coating and silica surface potentially involves chemical forces. Because the nano-sized iron oxide coatings increased surface area, introduced small pores, and changed the surface charge distribution of silica, the coated system demonstrates a greater affinity for Ni compared to that of uncoated silica.

Adsorption↗
PubMed2005

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

Computational evaluation of protein-DNA interaction is important for the identification of DNA-binding sites and genome annotation. It could validate the predicted binding motifs by sequence-based approaches through the calculation of the binding affinity between a protein and DNA. Such an evaluation should take into account structural information to deal with the complicated effects from DNA structural deformation, distance-dependent multi-body interactions and solvation contributions. In this paper, we present a knowledge-based potential built on interactions between protein residues and DNA tri-nucleotides. The potential, which explicitly considers the distance-dependent two-body, three-body and four-body interactions between protein residues and DNA nucleotides, has been optimized in terms of a Z-score. We have applied this knowledge-based potential to evaluate the binding affinities of zinc-finger protein-DNA complexes. The predicted binding affinities are in good agreement with the experimental data (with a correlation coefficient of 0.950). On a larger test set containing 48 protein-DNA complexes with known experimental binding free energies, our potential has achieved a high correlation coefficient of 0.800, when compared with the experimental data. We have also used this potential to identify binding motifs in DNA sequences of transcription factors (TF). The TFs in 79.4% of the known TF-DNA complexes have accurately found their native binding sequences from a large pool of DNA sequences. When tested in a genome-scale search for TF-binding motifs of the cyclic AMP regulatory protein (CRP) of Escherichia coli, this potential ranks all known binding motifs of CRP in the top 15% of all candidate sequences.

Base Sequence↗
PubMed2005

Cyclical modulation of sphingosine-1-phosphate receptor 1 surface expression during lymphocyte recirculation and relationship to lymphoid organ transit.

Sphingosine-1-phosphate receptor 1 (S1P(1)) was recently shown to be required for lymphocyte egress from lymphoid organs. Here we have examined the relationship between S1P(1) abundance on the cell and egress efficiency. Using an integrin neutralization approach to separate the processes of entry and exit, we show that pertussis toxin treatment reduces lymphocyte egress from lymph nodes. Retrovirally mediated S1P(1) overexpression is sufficient to reduce B cell accumulation in the splenic white pulp and to promote egress of activated T cells from lymph nodes, whereas S1P(1)(+/-) cells have reduced lymph node exit efficiency. Furthermore, lymphocyte S1P(1) is down-regulated in the blood, up-regulated in lymphoid organs, and down-regulated again in the lymph. We propose that cyclical ligand-induced modulation of S1P(1) on circulating lymphocytes contributes to establishing their lymphoid organ transit time.

Animals↗
PubMed2005

Properties and structure of manganese oxide-coated clay.

In the environment, heavy metals are important contaminants that sorb to and accumulate in soils and sediments. Dominant minerals in the subsurface are oxides and clay, which occur as discrete particles and heterogeneous systems; these surfaces can significantly impact the mobility and bioavailability of metals through sorption. To better understand heterogeneous systems, amorphous (hydrous manganese oxide (HMO)) and crystalline manganese oxides (birnessite and pyrolusite) were coated on montmorillonite. However, the montmorillonite substrate potentially inhibited crystallization of the pyrolusite coating, and also resulted in a poorly crystalline birnessite. Mineralogy and morphology of the coated systems suggest an amorphous structure for HMO and uniform coverage for HMO and birnessite coatings; the presence of Si and Al indicates uncoated areas along intraplanar surfaces. The coating surface charge behaved similarly to that of discrete oxides and clay where the pH(znpc) of HMO- and birnessite-coated clay were 2.8 and 3.1, respectively. Surface area of the coated systems increased while the pore size distribution decreased as compared to the external surface area and pores of montmorillonite. X-ray absorption spectroscopy (XAS) revealed the local structural environment of Mn in the HMO- and birnessite-coated clay was consistent with the pure phase oxides: for HMO-coated clay 3.1 atoms of oxygen at 1.89 +/- 0.02 A in the first shell and 2.7 atoms of manganese at 2.85 +/- 0.02 in the second shell; and, for birnessite-coated clay 6 atoms of oxygen at 1.91 +/- 0.02 A in the first shell and 6 atoms of manganese at distance 2.99 +/- 0.02 A in the second shell. Overall, the surface properties suggest that the coating behaves like that of discrete oxides, an important sink for metal contaminants.

Journal Article↗
PubMed2005

Modeling Pb sorption to microporous amorphous oxides as discrete particles and coatings.

Hydrous amorphous Al (HAO), Fe (HFO), and Mn (HMO) oxides are ubiquitous in the subsurface as both discrete particles and coatings and exhibit a high affinity for heavy metal contaminants. To assess risks associated with heavy metals, such as Pb, to the surrounding environment and manage remedial activities requires accurate mechanistic models with well-defined transport parameters that represent sorption processes. Experiments were conducted to evaluate Pb sorption to microporous Al, Fe, and Mn oxides, as well as to montmorillonite and HAO-coated montmorillonite. Intraparticle diffusion, a natural attenuating process, was observed to be the rate-limiting mechanism in the sorption process, where best-fit surface diffusivities ranged from 10(-18) to 10(-15) cm(2) s(-1). Specifically, diffusivities of Pb sorption to discrete aluminum oxide, aluminum oxide-coated montmorillonite, and montmorillonite indicated substrate surface characteristics influence metal mobility where diffusivity increased as affinity decreased. Furthermore, the diffusivity for aluminum oxide-coated montmorillonite was consistent with the concentrations of the individual minerals present and their associated particle size distributions. These results suggest that diffusivities for other coated systems can be predicted, and that oxide coatings and montmorillonite are effective sinks for heavy metal ions.

Journal Article↗