Biomedical subjects

Y Xue

Publications and source records attributed to Y Xue.

At least 19 recordsLinked to original sources

PubMed2004

MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids.

Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.

Computational Biology↗

PubMed2004

Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines.

A better understanding of the genetics of seedling characteristics in rice could be helpful in improving rice varieties. Zhenshan 97 and Minghui 63, the parents of Shanyou 63, an elite hybrid developed during the last decade in China, vary greatly with respect to their physiological and morphological traits at the seedling growth stage. In this study, we used a population of 240 recombinant inbred lines derived from a cross between Zhenshan 97 and Minghui 63 to identify quantitative trait loci (QTL) for seedling characteristics. All plant material was grown in hydroponic culture. Data for the following characters were collected at 30 days and 40 days post-sowing: plant height, shoot dry matter weight (SDW), maximum root length, root dry weight (RDW), total dry weight, and root-shoot ratio (the ratio of SDW to RDW). Analysis using composite interval mapping detected 16 QTL for the six traits in 30-day-old seedlings. Of these 16 QTL, Minghui 63 alleles increased trait values at only two of them. The QTL in the vicinity of R3166 on chromosome 5 simultaneously influenced PH, SDW, MRL, RDW, and TDW in the same direction. Twenty QTL were detected for the same traits in the 40-day-old seedlings. However, at this stage Minghui 63 alleles increased trait values at eight QTL. The QTL linked to R3166 also affected PH, SDW, MRL, RDW, and TDW. Only four QTL were common to the two stages. These results clearly indicate that different genes (QTL) control the same traits during different time intervals. Zhenshan 97 alleles had positive effects during the first 30 days of seedling growth, but thereafter the positive effects of Minghui 63 alleles on seedling growth gradually became more pronounced.

Biomass↗

PubMed2004

Rat intralaminar thalamic nuclei projections to the globus pallidus: a biotinylated dextran amine anterograde tracing study.

The topographical organization and ultrastructural features of the intralaminar thalamic nuclei (ITN) projections to the globus pallidus (GP) were studied using the biotinylated dextran amine (BDA) anterograde tracing method in the rat. To assess the functional association of BDA injection sites in the ITN, the known topographical organization of the ITN-neostriatal (Str) projections and calcium binding protein (CaBP) immunostaining patterns of the Str and GP were used. BDA injection in the lateral part of the lateral parafascicular nucleus and the caudal part of the central lateral nucleus labeled fibers and boutons mainly in the dorsolateral sensorimotor territory of the Str and the middle territories of the GP. BDA injection in the medial part of the lateral parafascicular nucleus and the central lateral nucleus labeled mainly the middle association territory of the Str and the border and the caudomedial territories of the GP. BDA injection in the medial parafascicular nucleus and the central medial nucleus labeled mainly the medial limbic territory of the Str. The medial parafascicular nucleus projected to the medial-most region of the GP, while the central medial nucleus projection to the GP was very sparse. Electron microscopic observations indicated that BDA-labeled boutons form asymmetric synapses mainly on 0.5-2.0 microm diameter dendritic shafts in the GP. The boutons were small but had a relatively long active zone. The present observations together with the known topographical organization of striatopallidal projections indicated that the ITN-GP projections were topographically organized in parallel to the ITN-Str projections. Thus, each part of the ITN projecting to the sensorimotor, the association, and the limbic territories of the Str also projects to the corresponding functional territories of the GP.

Animals↗

PubMed2004

Prediction of torsade-causing potential of drugs by support vector machine approach.

In an effort to facilitate drug discovery, computational methods for facilitating the prediction of various adverse drug reactions (ADRs) have been developed. So far, attention has not been sufficiently paid to the development of methods for the prediction of serious ADRs that occur less frequently. Some of these ADRs, such as torsade de pointes (TdP), are important issues in the approval of drugs for certain diseases. Thus there is a need to develop tools for facilitating the prediction of these ADRs. This work explores the use of a statistical learning method, support vector machine (SVM), for TdP prediction. TdP involves multiple mechanisms and SVM is a method suitable for such a problem. Our SVM classification system used a set of linear solvation energy relationship (LSER) descriptors and was optimized by leave-one-out cross validation procedure. Its prediction accuracy was evaluated by using an independent set of agents and by comparison with results obtained from other commonly used classification methods using the same dataset and optimization procedure. The accuracies for the SVM prediction of TdP-causing agents and non-TdP-causing agents are 97.4 and 84.6% respectively; one is substantially improved against and the other is comparable to the results obtained by other classification methods useful for multiple-mechanism prediction problems. This indicates the potential of SVM in facilitating the prediction of TdP-causing risk of small molecules and perhaps other ADRs that involve multiple mechanisms.

Algorithms↗

PubMed2001

Generation of three selenium-containing catalytic antibodies with high catalytic efficiency using a novel hapten design method.

A novel strategy for design of haptens that were used to produce catalytic antibodies was developed and three monoclonal antibodies, 3G5, 2F3, and 5C9, were generated using this strategy. These monoclonal antibodies were converted into selenium-containing abzymes by chemically modifying the hydroxyl group of serines followed by sodium hydrogen selenide displacement. These selenium-containing abzymes exhibited remarkable glutathione peroxidase activity, which surpasses the activity of some native glutathione peroxidases. The activities of the selenium-containing abzymes Se-3G5, Se-2F3, and Se-5C9 which catalyzed reduction of hydroperoxides by glutathione were 2.23, 4.20, and 3.79 times that of rabbit liver glutathione peroxidase, respectively. Detailed steady-state kinetics study on Se-2F3 was carried out and the value of k(cat)/K(m) (H(2)O(2)) was found to be 2.11 x 10(7) M(-1) min(-1) which was supposed to be one of the highest among the known catalytic antibodies. The data of association constants and glutathione peroxidase activities of these catalytic antibodies and the steady-state kinetics of Se-2F3 showed that the method might be a remarkably efficient one for generating catalytic antibodies with glutathione peroxidase activity.

Amino Acid Sequence↗

PubMed2001

A novel dicyclodextrinyl ditelluride compound with antioxidant activity.

Reactive oxygen species (ROS) primarily arise from products of normal metabolic activities and are thought to be the etiology of many diseases. A novel dicyclodextrinyl ditelluride (2-TeCD) compound was designed to be a functional mimic of the glutathione peroxidase that normally removes ROS. 2-TeCD exhibited highly catalytic efficiency and good water solubility. Antioxidant activity was studied by using ferrous sulfate/ascorbate-induced mitochondria damage model system. 2-TeCD protected the mitochondria against oxidative damage in a dose-dependent manner and exhibited also great antioxidant ability in comparison with 2-phenyl-1,2-benziososelenazol-3(2H)-one. The mimic may result in better clinical therapies for the treatment of ROS-mediated diseases.

Animals↗

PubMed2001

Proliferative activity and branching morphogenesis in the human prostate: a closer look at pre- and postnatal prostate growth.

BACKGROUND: To gain further insight into the molecular cell biologic features of prostate development, we investigated the proliferative activity of prostate epithelial and stromal cells and their topographic relationship with neuroendocrine (NE) cell distribution and regional heterogeneity. METHODS: Consecutive sections from 43 prostates taken during autopsy representing fetuses (12-38 weeks of gestation), infants, prepubertal males and adults were double stained for chromogranin A and MIB-1. MIB-1 labeling index (LI) was calculated in the budding tips, forming acini, major collecting ducts, adjacent and non-adjacent stromal compartments. Furthermore, the topographic relationship between proliferating cells and NE cells was evaluated. RESULTS: In the first half of gestation, cell proliferation as revealed by MIB-1 LI was significantly higher in epithelial structures and stroma than in older fetuses and other age groups. MIB-1 LI was higher in budding tips than in other epithelial regions. MIB-1 LI in stroma adjacent to budding tips was not higher than that adjacent to other epithelial branching segments. Co-expression of chromogranin A and MIB-1 staining was not observed. MIB-1 LI was lower in cells in the direct vicinity of chromogranin A positive NE cells than at a distance from NE cells. CONCLUSIONS: Prostate development in the first half of gestation is explosive. Thereafter, the prostate basically is a slow-growing organ. Budding tips are the major growth foci during early prostate development, while stromal growth is evenly distributed throughout the prostate, probably indicating that stromal-epithelial interactions do not manifest in enhanced proliferation at their interface. NE cells may have an inhibitory effect on proliferation of exocrine epithelial cells and are probably only associated with differentiation of prostate exocrine cells in the prostate.

Adult↗

PubMed2001

Overexpression of manganese superoxide dismutase suppresses tumor formation by modulation of activator protein-1 signaling in a multistage skin carcinogenesis model.

Manganese superoxide dismutase (MnSOD) is a nuclear encoded primary antioxidant enzyme localized in mitochondria. Because expression of MnSOD plays a major role in maintaining cellular redox status and reactive oxygen species are known to play a role in signal transduction and carcinogenesis, we investigated the role of MnSOD in the development of cancer using a two-stage [7,12-dimethylbenz(a)-anthracene plus 12-O-tetradecanoylphorbol-13-acetate (TPA)] skin carcinogenesis model. Female transgenic mice expressing the human MnSOD gene in the skin and their nontransgenic counterparts were used in this study. Pathological examination demonstrated significant reduction of papilloma formation in transgenic mice. Quantitative analysis of 4-hydroxy-2-nonenal-modified proteins showed greater accumulation of oxidative damage products in nontransgenic compared with transgenic mice, and this oxidative damage was demonstrated to be present in both mitochondria and nucleus. TPA increased activator protein-1 (AP-1) binding activity within 6 h in nontransgenic mice, but increased AP-1 binding activity was delayed in the transgenic mice. Electrophoretic mobility shift assay, transcription of the target genes, and Western analysis studies indicated that the increased AP-1 binding activity was attributable to induction of the Jun but not the Fos protein families. Overexpression of MnSOD selectively inhibited the TPA-induced activation of protein kinase Cepsilon and prevented subsequent activation of c-Jun NH(2)-terminal kinase in response to TPA. Overall, these results indicate that MnSOD regulates both cellular redox status and selectively modulates PKCepsilon signaling, thereby delaying AP-1 activation and inhibiting tumor promotion, resulting in reduction of tumors in MnSOD transgenic mice.

9,10-Dimethyl-1,2-benzanthracene↗

PubMed2001

Kinetics study of a selenium-containing ScFv catalytic antibody that mimics glutathione peroxidase.

The steady-state kinetics study and some enzymatic characterization of a selenium-containing scFv catalytic antibody (Se-scFv2F3) were carried out. A novel reaction formula of this abzyme-catalyzed reaction was proposed and a rate equation was obtained according to the formula. The constants in the equation were compared with Dalziel's parameters and the exact meanings of these constants were analyzed. The obtained kinetics parameters from the kinetics study of Se-scFv2F3 were analyzed and compared with those of native glutathione peroxidase.

Antibodies, Catalytic↗

PubMed2001

Kinetics study of a selenium-containing ScFv catalytic antibody that mimics glutathione peroxidase.

The steady state kinetic study and some enzymic characterization of a selenium-containing scFv catalytic antibody (Se-scFv2F3) was carried out. A novel reaction formula of this abzyme-catalyzed reaction was proposed and a rate equation was gotten according to the formula. The constants in the equation were compared with Dalziel's parameters and the exact meanings of these constants were analyzed. The gotten kinetics parameters from the kinetics study of Se-scFv2F3 were analyzed and compared with that of native glutathione peroxidase.

Antibodies, Catalytic↗

PubMed2001

Sperm protein 17 is a novel cancer-testis antigen in multiple myeloma.

Various studies have demonstrated the aberrant expression of normal testicular proteins in neoplastic cells. These proteins collectively form the new class of tumor antigens called cancer-testis (CT) antigens. Their selective normal tissue expression makes them ideal antigens for immune targeting of the malignant disease. In this study, the expression of a spermatozoa protein, Sp17, in multiple myeloma was investigated. It was found that Sp17 is detectable in tumor cells from 12 of 47 (26%) myeloma patients. Reverse transcription polymerase chain reaction (RT-PCR) and Western blot analysis detected Sp17 transcripts and proteins, respectively. Northern blot analysis and RT-PCR demonstrated that Sp17 transcripts were detected only in normal testis, supporting its tissue specificity. Since a high proportion of normal individuals develop antibodies against Sp17 following vasectomy, Sp17 is likely to be a highly immunogenic protein in vivo. Sp17 is therefore a novel member of the CT antigen family and should be an ideal target for immunotherapy of multiple myeloma.

Antigens, Neoplasm↗

PubMed2001

The Streptomyces venezuelae pikAV gene contains a transcription unit essential for expression of enzymes involved in glycosylation of narbonolide and 10-deoxymethynolide.

In Streptomyces venezuelae, four polyketide synthase (PKS) polypeptides encoded by pikAI-pikAIV are used to generate 10 and 12-membered macrocyclic structures, narbonolide and 10-deoxymethynolide. Sequence analysis suggests these genes are translationally coupled with downstream genes, pikAV (encoding a type II thioesterase), desVIII-desVI (encoding enzymes responsible for production of the final glycosylated products pikromycin, narbomycin, methymycin and neomethymycin) and desR (a resistance gene). Type II thioesterases have been suggested to have an editing function in polyketide biosynthesis and deletion of the corresponding genes often leads to decreased levels of polyketide production. Surprisingly an in-frame deletion of 687 bp of the 843 bp pikAV ORF led to a strain SC1022 that produced normal yields of polyketide products, but only in the aglycone form. Plasmid-based expression of the desVIII-VI and desR in the SC1022 strain completely restored production of glycosylated products, despite the absence of a functional pikAV gene product. Under these conditions the PikAV TEII therefore does not play an important role in polyketide biosynthesis, and its function remains an enigma. These observations also demonstrate that the region of pikAV DNA deleted in strain SC1022 contains a transcription unit essential for expression of the des genes. A sequence alignment of PikAV with members of the highly conserved type II thioesterases revealed a short divergent region at the carboxy terminus, suggesting a region of pikAV that might contain such a transcription unit. DNA containing this region of pikAV was shown to be able to increase plasmid-based expression of both crotonyl CoA reductase gene (ccr) and the erythromycin resistance gene (ermE) in S. venezuelae.

Acyl-CoA Dehydrogenases↗

PubMed2001

alpha-lactalbumin mutant acting as lysozyme.

A mutant of alpha-lactalbumin was expressed and purified, in which His32, Thr33, Glu49, Ile59, Val99, and Tyr103 were substituted by Leu32, Glu33, Asp49, Trp59, Asn99, and Ala103, respectively, to create a catalytic site of lysozyme in alpha-lactalbumin. The mutant catalyzed hydrolysis of the synthetic substrate, pNP-(NAcGlc)(3), with a K(M) and k(cat) of 0.160 +/- 0.00986 mmol/L and 3.39 +/- 0. 0456 x10(-5) min(-1), respectively, which was comparable with those of chicken lysozyme of 0.137 +/- 0.0153 mmol/L and 5.25 +/- 0.115 x10(-4) min(-1). By using the Isothermal Titration Calorimetre (ITC), the average binding enthalpy of the mutant or chicken lysozyme with the substrate (chitopentaose) was measured, which was 49.22 KJ/mol for the mutant and 105.47 KJ/mol for chicken lysozyme. In conclusion, the six point mutations occurring in alpha-lactalbumin could be converted into an enzyme that was 17.5-fold less efficient than chicken lysozyme but nevertheless capable of hydrolyzing the glycosidic bond.

Amino Acid Sequence↗

PubMed2001

Sperm protein 17 (Sp17) in multiple myeloma: opportunity for myeloma-specific donor T cell infusion to enhance graft-versus-myeloma effect without increasing graft-versus-host disease risk.

We recently found that sperm protein 17 (Sp17), a spermatozoa-restricted protein, is aberrantly expressed on the tumor cells in patients with multiple myeloma (MM). It may therefore be possible to generate donor-derived Sp17-specific CTL for administration following allogeneic stem cell transplant to augment graft-versus-myeloma (GVM) effect without inducing a global GVHD. To assess this approach, we have produced recombinant Sp17 protein and used Sp17 protein-pulsed dendritic cells to generate HLA class I-restricted Sp17-specific CTL from a previously unimmunized healthy donor. These CTL were able to lyse autologous Epstein-Barr virus-transformed lymphoblastoid cells in a Sp17-dependent manner. Target lysis was HLA-A1 and HLA-B27 restricted. Cytotoxicity could be blocked by antibodies against monomorphic HLA class I, HLA-A1 and HLA-B27 molecules but not HLA class II molecules. Most importantly, the CTL lysed HLA class I-matched Sp17-positive tumor cells, suggesting that Sp17 is processed and presented in association with the HLA class I molecules in Sp17-positive tumor cells in a concentration and configuration that could be recognized by recombinant protein-primed CTL. Analysis by flow cytometry of the CTL indicated that they were predominantly CD8 in phenotype and they produced IFN-gamma and very little IL-4. Our results suggest the potential for the generation and administration of donor-derived Sp17-specific CTL to augment GVM without inducing GVHD following allogeneic stem cell transplant for MM.

Antigen Presentation↗

PubMed2001

Biosynthesis and combinatorial biosynthesis of pikromycin-related macrolides in Streptomyces venezuelae.

Pikromycin-related macrolides have recently attracted significant research interest because they are structurally related to the semisynthetic ketolide antibiotics that have demonstrated promising potential in combating multi-drug-resistant respiratory pathogens. Cloning and in-depth studies of the pikromycin biosynthetic gene cluster from Streptomyces venezuelae have led to new avenues in modular polyketide synthases, deoxysugar biosynthesis, cytochrome P450 hydroxylase, secondary metabolite gene regulation, and antibiotic resistance. Moreover, the knowledge and tools used for these studies are proving to be valuable in the development of advanced technologies for combinatorial biosynthesis of new macrolide antibiotics. This review summarizes these new developments and introduces S. venezuelae as a powerful new system for secondary metabolite pathway engineering from bench-top genetic manipulation to product fermentation.

Anti-Bacterial Agents↗

PubMed2001

Expressional profiling of genes related to pollination and fertilization in rice.

Pollination and fertilization are key steps leading to seed and fruit formation. To obtain genes involved in pollination and fertilization in rice, an RNA fingerprinting technique, cDNA-AFLP (amplified fragment length polymorphism), was used to generate transcript profiles related to pollination. Of 15,000 cDNA fragments inspected, 2,100 showed altered expression in the pollinated pistil, of which about 1/5 were up-regulated (URP) and the rest down-regulated (DRP), suggesting that gene repression is a predominant mode of gene regulation in the pollinated pistil. Over 200 URP genes were sequenced and databank searches revealed that 70% of them represented previously unnoticed rice genes. DNA blot analysis of 20 URP genes detected no restriction fragment length polymorphisms (RFLP) between two relatively distant rice varieties, suggesting that the URP genes are highly conserved and likely play important roles in pollination and fertilization. Furthermore, two genes, URP47 and URP63, probably encoding an ADP-ribosylation factor and a membrane transporter, respectively, in relation to pollination were discussed.

DNA, Plant↗

PubMed2001

Microencapsulated bovine chromaffin cell xenografts into hemiparkinsonian rats: a drug-induced rotational behavior and histological changes analysis.

Bovine chromaffin cells were microencapsulated within alginate-polylysine-alginate (APA) membranes. Microencapsulated bovine chromaffin cells as well as unencapsulated cells and empty microcapsules were grafted into the brain of hemiparkinsonian rats with 6-hydroxydopamine (6-OHDA) lesions. Apomorphine-induced rotational behavior of the host animals and the survival of the grafted chromaffin cells were examined after transplantation. The animals receiving microencapsulated bovine chromaffin cells showed a significant decrease (17.6--35.6%) in apomorphine-induced rotation 1 week postimplantation that remained stable for the 10 month test period. Fluorescent histochemistry further revealed that microencapsulation increased the chromaffin cell survival with only a minimum host reaction for up to 10 months posttransplantation while the survival of free, unencapsulated chromaffin cells was only modest and was accompanied by a large inflammatory response. The reduction of apomorphine-induced rotations was correlated with the survival of bovine chromaffin cells in the host brain. The data indicate that encapsulation of bovine chromaffin cells in APA membranes reduces the host immune response to the xenograft and prolongs the viability of the grafted cells.

Animals↗

PubMed2001

Treponema parvum sp. nov., a small, glucoronic or galacturonic acid-dependent oral spirochaete from lesions of human periodontitis and acute necrotizing ulcerative gingivitis.

Small oral spirochaetes with a strict dependence on either glucuronic acid (GluA) or galacturonic acid (GalA) were isolated from European patients with periodontitis and from Chinese patients with either gingivitis or acute necrotizing ulcerative gingivitis (ANUG). Thirteen such isolates were similar phenotypically to Treponema pectinovorum ATCC 33768T and this classification was confirmed by 16S rRNA sequencing. However, four isolates differed from T. pectinovorum by their small cell size, by a prominent beta-glucuronidase activity, by a distinct protein and antigen profile, by an inability to grow on pectin as sole source of carbohydrate and by a markedly enhanced growth rate when supplied with a second carbohydrate (L-arabinose, D-galactose, D-glucose, D-fructose, D-mannitol, D-mannose, pectin, D-ribose or D-xylose) in addition to the essential GluA/GalA. By 16S rRNA sequencing these four isolates clustered in the recently described phylotype 'Smibert-2'. T. pectinovorum (14 strains) and 'Smibert-2' (four isolates with beta-glucuronidase activity) could each be subdivided into two serotypes based on immunoblot reactivity with two mAbs. Representatives of the two groups, including T. pectinovorum ATCC 33768T, showed a 1:2:1-type periplasmic flagellar arrangement. 'Smibert-2' is described as a novel species, Treponema parvum sp. nov., with isolate OMZ 833T (= ATCC 700770T) proposed as the type strain and OMZ 842 (= ATCC 700773) as reference strain for a second serotype.

Acute Disease↗