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Ying Xu

Publications and source records attributed to Ying Xu.

At least 181 records · Page 10Linked to original sources
PubMed2003

Metabolic enzymes from psychrophilic bacteria: challenge of adaptation to low temperatures in ornithine carbamoyltransferase from Moritella abyssi.

The enzyme ornithine carbamoyltransferase (OTCase) of Moritella abyssi (OTCase(Mab)), a new, strictly psychrophilic and piezophilic bacterial species, was purified. OTCase(Mab) displays maximal activity at rather low temperatures (23 to 25 degrees C) compared to other cold-active enzymes and is much less thermoresistant than its homologues from Escherichia coli or thermophilic procaryotes. In vitro the enzyme is in equilibrium between a trimeric state and a dodecameric, more stable state. The melting point and denaturation enthalpy changes for the two forms are considerably lower than the corresponding values for the dodecameric Pyrococcus furiosus OTCase and for a thermolabile trimeric mutant thereof. OTCase(Mab) displays higher K(m) values for ornithine and carbamoyl phosphate than mesophilic and thermophilic OTCases and is only weakly inhibited by the bisubstrate analogue delta-N-phosphonoacetyl-L-ornithine (PALO). OTCase(Mab) differs from other, nonpsychrophilic OTCases by substitutions in the most conserved motifs, which probably contribute to the comparatively high K(m) values and the lower sensitivity to PALO. The K(m) for ornithine, however, is substantially lower at low temperatures. A survey of the catalytic efficiencies (k(cat)/K(m)) of OTCases adapted to different temperatures showed that OTCase(Mab) activity remains suboptimal at low temperature despite the 4.5-fold decrease in the K(m) value for ornithine observed when the temperature is brought from 20 to 5 degrees C. OTCase(Mab) adaptation to cold indicates a trade-off between affinity and catalytic velocity, suggesting that optimization of key metabolic enzymes at low temperatures may be constrained by natural limits.

Adaptation, Biological↗
PubMed2003

Computational assignment of protein backbone NMR peaks by efficient bounding and filtering.

NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on the combination of a suite of algorithms for automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques using two recently introduced approximation algorithms. We also devise a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm. Our result demonstrates that integrating different algorithms can achieve a good tradeoff between backbone assignment accuracy and computation time.

Algorithms↗
PubMed2003

CUBIC: identification of regulatory binding sites through data clustering.

Transcription factor binding sites are short fragments in the upstream regions of genes, to which transcription factors bind to regulate the transcription of genes into mRNA. Computational identification of transcription factor binding sites remains an unsolved challenging problem though a great amount of effort has been put into the study of this problem. We have recently developed a novel technique for identification of binding sites from a set of upstream regions of genes, that could possibly be transcriptionally co-regulated and hence might share similar transcription factor binding sites. By utilizing two key features of such binding sites (i.e. their high sequence similarities and their relatively high frequencies compared to other sequence fragments), we have formulated this problem as a cluster identification problem. That is to identify and extract data clusters from a noisy background. While the classical data clustering problem (partitioning a data set into clusters sharing common or similar features) has been extensively studied, there is no general algorithm for solving the problem of identifying data clusters from a noisy background. In this paper, we present a novel algorithm for solving such a problem. We have proved that a cluster identification problem, under our definition, can be rigorously and efficiently solved through searching for substrings with special properties in a linear sequence. We have also developed a method for assessing the statistical significance of each identified cluster, which can be used to rule out accidental data clusters. We have implemented the cluster identification algorithm and the statistical significance analysis method as a computer software CUBIC. Extensive testing on CUBIC has been carried out. We present here a few applications of CUBIC on challenging cases of binding site identification.

Algorithms↗
PubMed2003

RAPTOR: optimal protein threading by linear programming.

This paper presents a novel linear programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based on the contact map graph of the protein 3D structure template, the protein threading problem is formulated as a large scale integer programming (IP) problem. The IP formulation is then relaxed to a linear programming (LP) problem, and then solved by the canonical branch-and-bound method. The final solution is globally optimal with respect to energy functions. In particular, our energy function includes pairwise interaction preferences and allowing variable gaps which are two key factors in making the protein threading problem NP-hard. A surprising result is that, most of the time, the relaxed linear programs generate integral solutions directly. Our algorithm has been implemented as a software package RAPTOR-RApid Protein Threading by Operation Research technique. Large scale benchmark test for fold recognition shows that RAPTOR significantly outperforms other programs at the fold similarity level. The CAFASP3 evaluation, a blind and public test by the protein structure prediction community, ranks RAPTOR as top 1, among individual prediction servers, in terms of the recognition capability and alignment accuracy for Fold Recognition (FR) family targets. RAPTOR also performs very well in recognizing the hard Homology Modeling (HM) targets. RAPTOR was implemented at the University of Waterloo and it can be accessed at http://www.cs.uwaterloo.ca/~j3xu/RAPTOR_form.htm.

Algorithms↗
PubMed2003

Insurance expenditures on bipolar disorder: clinical and parity implications.

OBJECTIVE: This study assessed treatment rates and expenditures for behavioral health care by employers and behavioral health care patients in a large national database of employer-sponsored health insurance claims. METHOD: Insurance claims from 1996 from approximately 1.66 million individuals were examined. Average annual charges per person and payments for behavioral health care were calculated along with patient out-of-pocket expenses and inpatient hospital admission rates. Behavioral health care expenditures for bipolar disorder were compared to expenditures for other behavioral health care diagnoses in these same insurance plans. RESULTS: A total of 7.5% of all covered individuals filed a behavioral health care claim. Of those, 3.0% were identified as having bipolar disorder, but they accounted for 12.4% of total plan expenditures. Patients with bipolar disorder incurred annual out-of-pocket expenses of $568, more than double the $232 out-of-pocket expenses incurred by all claimants. The inpatient hospital admission rate for patients with bipolar disorder was also higher (39.1%) compared to 4.5% for all other behavioral health care claimants. Furthermore, annual insurance payments were higher for covered medical services for individuals with bipolar disorder than for patients with other behavioral health care diagnoses. CONCLUSIONS: Bipolar disorder is the most expensive behavioral health care diagnosis, both for patients with bipolar disorder and for their insurance plans. For every behavioral health care dollar spent on outpatient care for patients with bipolar disorder, $1.80 is spent on inpatient care, suggesting that better prevention management could decrease the financial burden of bipolar disorder.

Adult↗
PubMed2003

Protein threading by linear programming.

Protein three-dimensional structure prediction through threading approach has been extensively studied and various models and algorithms have been proposed. In order to further explore ways to improve accuracy and efficiency of the threading process, this paper investigates the effectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D structure, we formulate the protein threading problem as a large scale integer programming problem, then relax to a linear programming problem, and finally solve the integer program by a branch-and-bound method. The final solution is optimal with respect to energy functions incorporating pairwise interaction and allowing variable gaps. The algorithm has been implemented as software package RAPTOR--RApid Protein Threading predictOR. Experimental results for fold recognition show that RAPTOR significantly outperforms other programs at the fold similarity level. The RAPTOR webserver is at http://www.cs.uwaterloo.ca/-j3xu/RAPTOR_form.htm.

Algorithms↗
PubMed2003

Identification of regulatory binding sites using minimum spanning trees.

Recognition of protein-binding sites from the upstream regions of genes is a highly important and unsolved problem. In this paper, we present a new approach for studying this challenging issue. We formulate the binding-site recognition problem as a cluster identification problem, i.e., to identify clusters in a data set that exhibit significantly different features (e.g., density) than the overall background of the data set. We have developed a general framework for solving such a cluster identification problem. The foundation of the framework is a rigorous relationship between data clusters and subtrees of a minimum spanning tree (MST) representation of a data set. We have proposed a formal and general definition of clusters, and have demonstrated that a cluster is always represented as a connected component of the MST, and further it corresponds to a substring of a linear representation of the MST. Hence a cluster identification problem is reduced to a problem of finding substrings with certain features, for which algorithms have been developed. We have applied this MST-based cluster identification algorithm to a number of binding site identification problems. The results are highly encouraging.

Algorithms↗
PubMed2003

[The application of ultrasonography in the diagnosis of deep electric injury].

OBJECTIVE: To explore the application of ultrasonography in the diagnosis of deep electric injury. METHODS: HP-IPHX high resolution color and pulse doppler ultrasonography was employed in the study. The hemodynamic indices were determined in the burn wound area and tissues 5 - 15 cm proximal to the wound in 12 patients with deep electric injury. At the same time, injuries to subcutaneous and muscular tissue and blood vessels (fifty-six blood vessels detected) were detected. RESULTS: 1. It was found by two-dimentional ultrasonography that the injury degree in different tissue after deep electric injury was different, i.e. blood vessels were most liable to injury followed by muscles and subcutaneous tissue. In the burn wound area, endothelium was not visualized in 7 blood vessels and endothelial swelling was identified in 12 blood vessels. Furthermore, vascular occlusion was found in 4 blood vessels and thrombosis found in 5 vessels. 2. It was also demonstrated by color ultrasonography that change in course of blood vessel and tortuesity were observed in 12 blood vessels, stenosis of lumen in 21 vessels and widened intravascular space in 11 vessels, All these findings were confirmed in the subsequent operations. 3. It was revealed by pulse Doppler that the top blood flow speed increased during vascular contraction period in narrowed blood vessels with decreased blood flow per minute. CONCLUSION: Being an non-invasive examination, ultrasonography could directly demonstrate the morphological changes in subcutaneous tissue, muscle and blood vessels after a deep electric injury, which might help determine the injury degree and the hemodynamic changes in the injured site.

Adolescent↗
PubMed2003

The effects of different donor cells and passages on development of reconstructed embryos.

In order to study the effects of different donor cells and passages on development of nuclear transfer embryos, we constructed embryos by electrofusing several kinds of donor cells into enucleated M II oocytes from Kun Ming (KM) mouse. These cells include 2-cell embryonic blastomeres, KMW embryonic stem (ES) cells, fetal fibroblast, ear fibroblast, tail tip fibroblast, sertoil cells and spermatogonia. Meanwhile, we compared the effects of passage numbers of fetal fibroblast cells on developmental competency after nuclear transfer. We found that 7.4% of reconstructed embryos from 2-cell embryonic blastomeres and 0.7% from ES cell could develop to blastocyst in vitro; embryos from fetal fibroblast could only develop to morula stage with the rate of 0.2%; embryos from spermatogonia could only develop to 8-cell stage and the rate was 0.3%; embryos respectively from ear fibroblast, sertoli cell and tail tip fibroblast could only develop to 4-cell stage. Although 2-cell development rate of embryos reconstructed from fetal fibroblast in first passage was significantly lower than those from the 2nd, the 3rd and the 4th passage, embryos from different passages could develop to 8-cell stage except the 3rd passage. The result indicated that it is more difficult for terminally differentiated cell nuclei to be reprogrammed in enucleated M II oocytes than for low differentiated cell nuclei. The reason of low development rate from ES cells maybe that most of ES cells was at S stage of the cell cycle, which out of coordination with M II oocytes. We could conclude that culture and passage of donor cells might be benefit to nucleus reprogramming.

Animals↗
PubMed2003

[Effects of 6-dimethylaminopurine and passages of embryonic stem cells on the development in vitro of interspecific reconstructed oocytes].

The development of reconstructed oocytes and the survival rate of cloned animal were affected by many factors during nuclear transfer. The genetic constitution and the genetic state of donor nucleus were proposed to be primary factors, which affected the survival rate of cloned animal. In addition, the survival rate of cloned animal might be influenced by nuclear transfer technique itself and passages of donor cells as well as the activation methods of oocytes. We reconstructed oocytes with outbreeding Kunming albino mouse ES cells and enucleated rabbit oocytes, and analyzed the effects of the passages of ES cells and 6-DMAP on the development of interspecific reconstructed oocytes. The interspecific reconstructed ES-rabbit oocytes were activated either by combined two set electric pulses and 6-DMAP or by two set electric pulses alone. The rate of cleavage was significantly higher for the group (86.2%) treated with 6-DMAP than the group (64.2%, P < 0.05) treated with electric pulses only, and the rate of blastocysts was 17.0% and 13.4% respectively, which were not significantly different between two groups. When ES cells that had been passed for 24 and 14 generations were used as donors, the cleavage rates of the reconstructed oocytes were 88.5% and 82.1%, respectively (P > 0.05), and the rates of blastolation were 16.7% and 15.4%, respectively (P > 0.05). The results show that 6-DMAP increases the cleavage rate of reconstructed oocytes derived from ES cells, and affects slightly the developmental rate of blastocysts. There are no differences when high passage and low passage ES cells are used as nuclear donors.

Adenine↗
PubMed2003

Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102.

We present a computational protocol for inference of regulatory and signaling pathways in a microbial cell, through literature search, mining "high-throughput'' biological data of various types, and computer-assisted human inference. This protocol consists of four key components: (a) construction of template pathways for microbial organisms related to the target genome, which either have been extensively studied and/or have a significant amount of (relevant) experimental data, (b) inference of initial pathway models for the target genome, through combining the template pathway models and target genome-specific information, (c) refinement and expansion of the initial pathway models through applications of various data mining tools, including phylogenetic profile analysis, inference of protein-protein interactions, and prediction of transcription factor binding sites, and (d) validation and refinement of the pathway models using pathway-specific experimental data or other information. To demonstrate the effectiveness of this procedure, we have applied it to the construction of the phosphorus assimilation pathways in cyanobacterium sp. WH8102. We present, in this paper, a model of the core components of this pathway.

Bacterial Proteins↗
PubMed2002

Synergistic inhibitory effects of transplatin and beta-hydroxyisovalerylshikon on carcinoma A431 cells involve epidermal growth factor receptor.

Treatment of human epidermoid carcinoma A431 cells with transplatin (trans-DDP) and beta-hydroxyisovalerylshikon (beta-HIVS) together had a strong inhibitory effect on A431 cells. By contrast, trans-DDP and beta-HIVS by themselves, at the same respective concentrations, had practically no effect. The tyrosine kinase activities of v-Src and epidermal growth factor (EGFR) were inhibited by each of the two agents alone and strongly inhibited by combination. The observed synergistic inhibitory effect on the growth of A431 cells might have resulted from the inhibition of EGFR by trans-DDP, as well as by beta-HIVS.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2002

Role of KIFC3 motor protein in Golgi positioning and integration.

KIFC3, a microtubule (MT) minus end-directed kinesin superfamily protein, is expressed abundantly and is associated with the Golgi apparatus in adrenocortical cells. We report here that disruption of the kifC3 gene induced fragmentation of the Golgi apparatus when cholesterol was depleted. Analysis of the reassembly process of the Golgi apparatus revealed bidirectional movement of the Golgi fragments in both wild-type and kifC3-/- cells. However, we observed a markedly reduced inwardly directed motility of the Golgi fragments in cholesterol-depleted kifC3-/- cells compared with either cholesterol-depleted wild-type cells or cholesterol-replenished kifC3-/- cells. These results suggest that (a) under the cholesterol-depleted condition, reduced inwardly directed motility of the Golgi apparatus results in the observed Golgi scattering phenotype in kifC3-/- cells, and (b) cholesterol is necessary for the Golgi fragments to attain sufficient inwardly directed motility by MT minus end-directed motors other than KIFC3, such as dynein, in kifC3-/- cells. Furthermore, we showed that Golgi scattering was much more drastic in kifC3-/- cells than in wild-type cells to the exogenous dynamitin expression even in the presence of cholesterol. These results collectively demonstrate that KIFC3 plays a complementary role in Golgi positioning and integration with cytoplasmic dynein.

Animals↗
PubMed2002

Differing activities of homeostatic chemokines CCL19, CCL21, and CXCL12 in lymphocyte and dendritic cell recruitment and lymphoid neogenesis.

Despite their widespread expression, the in vivo recruitment activities of CCL19 (EBV-induced molecule 1 ligand chemokine) and CXCL12 (stromal cell-derived factor 1) have not been established. Furthermore, although CXCL13 (B lymphocyte chemoattractant) has been shown to induce lymphoid neogenesis through induction of lymphotoxin (LT)alpha1beta2, it is unclear whether other homeostatic chemokines have this property. In this work we show that ectopic expression in pancreatic islets of CCL19 leads to small infiltrates composed of lymphocytes and dendritic cells and containing high endothelial venules and stromal cells. Ectopic CXCL12 induced small infiltrates containing few T cells but enriched in dendritic cells, B cells, and plasma cells. Comparison of CCL19 transgenic mice with mice expressing CCL21 (secondary lymphoid tissue chemokine) revealed that CCL21 induced larger and more organized infiltrates. A more significant role for CCL21 is also suggested in lymphoid tissues, as CCL21 protein was found to be present in lymph nodes and spleen at much higher concentrations than CCL19. CCL19 and CCL21 but not CXCL12 induced LTalpha1beta2 expression on naive CD4 T cells, and treatment of CCL21 transgenic mice with LTbetaR-Fc antagonized development of organized lymphoid structures. LTalpha1beta2 was also induced on naive T cells by the cytokines IL-4 and IL-7. These studies establish that CCL19 and CXCL12 are sufficient to mediate cell recruitment in vivo and they indicate that LTalpha1beta2 may function downstream of CCL21, CCL19, and IL-2 family cytokines in normal and pathological lymphoid tissue development.

Animals↗
PubMed2002

Participation of the conventional calpains in apoptosis.

The conventional calpains, m- and micro-calpain, are suggested to be involved in apoptosis triggered by many different mechanisms. However, it has not been possible to definitively associate calpain function with apoptosis, largely because of the incomplete selectivity of the cell permeable calpain inhibitors used in previous studies. In the present study, Chinese hamster ovary (CHO) cell lines overexpressing micro-calpain or the highly specific calpain inhibitor protein, calpastatin, have been utilized to explore apoptosis signals that are influenced by calpain content. This approach allows unambiguous alteration of calpain activity in cells. Serum depletion, treatment with the endoplasmic reticulum (ER) calcium ATPase inhibitor thapsigargin, and treatment with calcium ionophore A23187 produced apoptosis in CHO cells, which was increased in calpain overexpressing cells and decreased by induced expression of calpastatin. Inhibition of calpain activity protected beta-spectrin, but not alpha-spectrin, from proteolysis. The calpains seemed not to be involved in apoptosis triggered by a number of other treatments. Calpain protected against TNF-alpha induced apoptosis. In contrast to previous studies, we found no evidence that calpains proteolyze I kappa B-alpha in TNF-alpha-stimulated cells. These studies indicate that the conventional calpains participate in some, but not all, apoptotic signaling mechanisms. In most cases, they contributed to apoptosis, but in at least one case, they were protective.

Animals↗
PubMed2002

Calpain inhibition decreases the growth rate of mammalian cell colonies.

The calpains, a family of calcium-requiring intracellular proteases, are proposed regulators of cell proliferation. However, ablation of the calpain small subunit gene necessary for function of the conventional calpains did not result in decreased rate of proliferative growth of mouse stem cells under routine culture conditions. To address the reasons for this discrepancy, Chinese hamster ovary cell lines were established that overexpress the calpain inhibitor protein, calpastatin, under control of the ecdysone congener, ponasterone A. Overexpression of calpastatin in these cell lines resulted in a decreased growth of isolated colonies adhering to tissue culture plates. However, when cells were plated at higher density, calpastatin overexpression had no influence on proliferative growth rate. Growth of colonies in soft agar was not inhibited by calpastatin overexpression. Cell adhesion, cell de-adhesion, and cell motility all appeared to be normal after calpastatin overexpression. Differential display analysis was initiated to detect possible alteration of gene expression upon calpastatin overexpression. Analysis of approximately 3000 differential display PCR signals resulted in identification of one band that was underexpressed. Northern blot analysis confirmed a decreased amount of approximately 1 kb mRNA in cells overexpressing calpastatin. Sequence analysis identified a putative protein, Csr, containing a region homologous to two ubiquitin transferases and a putative cation channel protein.

Amino Acid Sequence↗
PubMed2002

Was our ancestor a hyperthermophilic procaryote?

In this paper we critically review the 'classical' model for the emergence of the three domains (Archaea, Bacteria, Eucarya), which presents hyperthermophilic procaryotes as the ancestors of all life on this planet. We come to the conclusion that our last common ancestor is likely to have been rather a non-hyperthermophilic protoeucaryote endowed with sn-1,2 glycerol ester lipids (as in modern Bacteria and Eucarya), from which Archaea emerged by streamlining under pressure for adapting to heat, a process which involved an important molecular innovation: the advent of sn-2,3 glycerol ether lipids. The nature of the primeval bacterial lines of descent is less clear; it would appear, nevertheless, that the first extreme- and hyperthermophilic Bacteria emerged by converging mechanisms; lateral gene transfer from Archaea may have played a role in this adaptation.

Animals↗