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Biomedical subjects

X L Xu

Publications and source records attributed to X L Xu.

At least 19 recordsLinked to original sources
PubMed2005

Repairing of goat tibial bone defects with BMP-2 gene-modified tissue-engineered bone.

Bone defects larger than a critical size are major challenges in orthopedic medicine. We combined tissue-engineered bone and gene therapy to provide osteoprogenitor cells, osteoinductive factors, and osteo-conductive carrier for ideal bone regeneration in critical-sized bone defects. Goat diaphyseal bone defects were repaired with tissue and genetically engineered bone implants, composed of biphasic calcined bone (BCB) and autologous bone marrow derived mesenchymal stem cells (BMSC) transduced with human bone morphogenetic protein-2 (hBMP-2). Twenty six goats with tibial bone defects were divided into groups receiving implants by using a combination of BCB and BMSCs with or without the hBMP-2 gene. In eight goats that were treated with BCB that contained hBMP-2 transduced BMSC, five had complete healing and three showed partial healing. Goats in other experimental groups had only slight or no healing. Furthermore, the area and biochemical strength of the callus in the bone defects were significantly better in animals treated with genetically engineered implants. We concluded that the combination of genetic and tissue engineering provides an innovative way for treating critical-sized bone defects.

Animals↗
PubMed2004

Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone.

The transcriptome provides the database from which a cell assembles its collection of proteins. Translation of individual mRNA species into their encoded proteins is regulated, producing discrepancies between mRNA and protein levels. Using a new modeling approach to data analysis, a striking diversity is revealed in association of the transcriptome with the translational machinery. Each mRNA has its own pattern of ribosome loading, a circumstance that provides an extraordinary dynamic range of regulation, above and beyond actual transcript levels. Using this approach together with quantitative proteomics, we explored the immediate changes in gene expression in response to activation of a mitogen-activated protein kinase pathway in yeast by mating pheromone. Interestingly, in 26% of those transcripts where the predicted protein synthesis rate changed by at least 3-fold, more than half of these changes resulted from altered translational efficiencies. These observations underscore that analysis of transcript level, albeit extremely important, is insufficient by itself to describe completely the phenotypes of cells under different conditions.

Computational Biology↗
PubMed2001

Inactivation of human SRBC, located within the 11p15.5-p15.4 tumor suppressor region, in breast and lung cancers.

A cDNA clone encoding human SRBC [serum deprivation response factor (sdr)-related gene product that binds to c-kinase] was isolated in a yeast two-hybrid screening, with amino acids 1-304 of BRCA1 as the probe. The human SRBC gene (hSRBC) was mapped to chromosome region 11p15.5-p15.4, close to marker D11S1323, at which frequent loss of heterozygosity (LOH) has been observed in sporadic breast, lung, ovarian, and other types of adult cancers as well as childhood tumors. hSRBC-coding region mutations including frame shift and truncation mutations were detected in a few ovarian and lung cancer cell lines. More significantly, the expression of hSRBC protein was down-regulated in a large fraction [30 (70%) of 43] of breast, lung, and ovarian cancer cell lines, whereas strong expression of hSRBC protein was detected in normal mammary and lung epithelial cells. The down-regulation of hSRBC expression in cancer cells was associated with hypermethylation of CpG dinucleotides in its promoter region, and 3 (60%) of 5 primary breast tumors and 11 (79%) of 14 primary lung tumors were also found to be hypermethylated. Treatment of breast cancer MCF7 cells with 5'azacytidine and Trichostatin A resulted in expression of hSRBC, confirming DNA methylation as the mode of inactivation. Our results suggest that epigenetic or mutational inactivation of hSRBC may contribute to the pathogenesis of several types of human cancers, marking hSRBC as a candidate tumor suppressor gene.

Amino Acid Sequence↗
PubMed2001

Searching for microsatellite mutations in coding regions in lung, breast, ovarian and colorectal cancers.

RepX represents a new informatics approach to probe the UniGene database for potentially polymorphic repeat sequences in the open reading frame (ORF) of genes, 56% of which were found to be actually polymorphic. We now have performed mutational analysis of 17 such sites in genes not found to be polymorphic (<0.03 frequency) in a large panel of human cancer genomic DNAs derived from 31 lung, 21 breast, seven ovarian, 21 (13 microsatellite instability (MSI)+ and eight MSI-) colorectal cancer cell lines. In the lung, breast and ovarian tumor DNAs we found no mutations (<0.03-0.04 rate of tumor associated open reading frame mutations) in these sequences. By contrast, 18 MSI+ colorectal cancers (13 cancer cell lines and five primary tumors) with mismatch repair defects exhibited six mutations in three of the 17 genes (SREBP-2, TAN-1, GR6) (P<0.000003 compared to all other cancers tested). We conclude that coding region microsatellite alterations are rare in lung, breast, ovarian carcinomas and MSI (-) colorectal cancers, but are relatively frequent in MSI (+) colorectal cancers with mismatch repair deficits.

Base Pair Mismatch↗
PubMed2001

Amino acid residue mutations uncouple cooperative effects in Escherichia coli D-3-phosphoglycerate dehydrogenase.

d-3-Phosphoglycerate dehydrogenase from Escherichia coli contains two Gly-Gly sequences that occur at junctions between domains. A previous study (Grant, G. A., Xu, X. L., and Hu, Z. (2000) Biochemistry 39, 7316-7319) determined that the Gly-Gly sequence at the junction between the regulatory and substrate binding domain functions as a hinge between the domains. Mutations in this area significantly decrease the ability of serine to inhibit activity but have little effect on the K(m) and k(cat). Conversely, the present study shows that mutations to the Gly-Gly sequence at the junction of the substrate and nucleotide binding domains, which form the active site cleft, have a significant effect on the k(cat) of the enzyme without substantially altering the enzyme's sensitivity to serine. In addition, mutation of Gly-294, but not Gly-295, has a profound effect on the cooperativity of serine inhibition. Interestingly, even though cooperativity of inhibition can be reduced significantly, there is little apparent effect on the cooperativity of serine binding itself. An additional mutant, G336V,G337V, also reduces the cooperativity of inhibition, but in this case serine binding also is reduced to the point at which it cannot be measured by equilibrium dialysis. The double mutant G294V,G336V demonstrates that strain imposed by mutation at one hinge can be relieved partially by mutation at the other hinge, demonstrating linkage between the two hinge regions. These data show that the two cooperative processes, serine binding and catalytic inhibition, can be uncoupled. Consideration of the allowable torsional angles for the side chains introduced by the mutations yields a range of values for these angles that the glycine residues likely occupy in the native enzyme. A comparison of these values with the torsional angles found for the inhibited enzyme from crystal coordinates provides potential beginning and ending orientations for the transition from active to inhibited enzyme, which will allow modeling of the dynamics of domain movement.

Carbohydrate Dehydrogenases↗
PubMed2001

Specific interactions at the regulatory domain-substrate binding domain interface influence the cooperativity of inhibition and effector binding in Escherichia coli D-3-phosphoglycerate dehydrogenase.

The crystal structure of d-3-phosphoglycerate dehydrogenase reveals a limited number of contacts between the regulatory and substrate binding domains of each subunit in the tetrameric enzyme. These occur between the side chains of Arg-339, Arg-405, and Arg-407 in the regulatory domain and main chain carbonyls in the substrate binding domain. In addition, Arg-339 participates in a hydrogen bonding network within the regulatory domain involving Arg-338 and Tyr-410, the C-terminal residue of the enzyme subunit. Mutagenic analysis of these residues produce profound effects on the enzyme's sensitivity to serine, the cooperativity of serine inhibition, and in some cases, the apparent overall conformation of the enzyme. Mutations of Arg-405 and Arg-407, which span the interface where the two domains come together, reduce the cooperativity of inhibition and increase the sensitivity of the enzyme to serine concentration. Serine binding studies with Arg-407 converted to Ala demonstrate that cooperativity of serine binding is also significantly reduced in a manner similar to the reduction in the cooperativity of inhibition. Mutations of Tyr-410 and Arg-338 decrease the sensitivity to serine without an appreciable effect on the cooperativity of inhibition. In the case of Tyr-410, a deletion mutant demonstrates that this effect is due to the loss of the C-terminal carboxyl group rather than the tyrosine side chain. All mutations of Arg-339, with the exception of its conversion to Lys, had profound effects on the stability of the enzyme. In general, those mutants that decrease sensitivity to serine are those that participate mainly in intradomain interactions and may also directly affect the serine binding sites themselves. Those mutants that decrease cooperativity are those that participate in interdomain interaction within the subunit. The observation that the mutants that decrease cooperativity also increase sensitivity to serine suggests a potential separation of pathways between how the simple act of serine binding results in noncooperative active site inhibition in the first place and how serine binding also leads to cooperativity between sites in the native enzyme.

Amino Acid Substitution↗
PubMed2001

Actinopolymorpha singaporensis gen. nov., sp. nov., a novel actinomycete from the tropical rainforest of Singapore.

A novel actinomycete was isolated from soil in the tropical rainforest of Singapore. The cells of this actinomycete are highly pleomorphic. In the early stages of growth, most cells are of irregular squarish shape and varied sizes. Cells remain attached after cell division, often forming chains or aggregates of a few cells. Cells at the end of a chain tend to elongate. With prolonged cultivation, cells show different degrees of elongation and enlargement, producing branched hyphae of uneven thickness. At the periphery of the colony, long hyphae form, which are divided into alternating segments of elongated cells and chains of squarish cells. This actinomycete is considerably salt-tolerant, able to grow in the presence of 15% NaCl. Chemotaxonomically, it contains LL-diaminopimelic acid (DAP) in the cell wall, type PI phospholipids and MK-9(H6) as the predominant menaquinone. 16S rDNA sequence analysis assigned this actinomycete to the family Nocardioidaceae, but its 16S rDNA shared no more than 91.2% sequence similarity with other members of the family. Based on phenotypic, chemotaxonomic and phylogenetic evidence, it is proposed that this actinomycete be classified as a new species in a new genus, Actinopolymorpha singaporensis gen. nov., sp. nov.

Actinomycetales↗
PubMed2001

[Experimental study on effect of xinkang oral liquid on coxsackie B3 viral myocarditis in mice].

OBJECTIVE: To study the therapeutic effect of Xinkang Oral Liquid (XKOL) in treating acute Coxsackie B3 viral myocarditis in mice. METHODS: Viral myocarditis model was established by intraperitoneal inoculation with Coxsackie B3 virus. Mice were randomly divided into 4 groups randomly, the model group, the positive control group (treated with Ribavilin), the XKOL group and the normal control group. Body weight of mice was weighed at the 5th, 10th and 20th day. Weight, macro- and histopathologic changes of heart were observed by microscope and measured by morphometric quantification, and the data were treated statistically. RESULTS: In the XKOL group, the body weight of mice increased, the degree of myocardial necrosis mild and small in size, which has been repaired more completely, the antiviral effect was found in XKOL group. CONCLUSION: XKOL has definite therapeutic effect on viral myocarditis, its effect is better than Ribavilin in protecting myocardium and anti-virus.

Animals↗
PubMed2001

[The software design for the molecular biological image processing system].

With the use of Visual Basic 6.0 language and molecular biological technology, we have developed a new molecular biological information processing system to detect the characteristic parameter of molecular biological electrophoresis image. The software can determine the molecular weight of the restriction endonuclease hydrolytic DNA fragment and protein or other macromolecules. The application indicates that the system with its accuracy reliability high efficiency and a large capacity of data to be stored, It is very useful to gene diagnosis and molecular biological researches.

Computer Systems↗
PubMed2000

Role of an interdomain Gly-Gly sequence at the regulatory-substrate domain interface in the regulation of Escherichia coli. D-3-phosphoglycerate dehydrogenase.

The regulatory and substrate binding domains of D-3-phosphoglycerate dehydrogenase (PGDH, EC 1.1.1.95) from Escherichia coli are connected by a single polypeptide strand that contains a Gly-Gly sequence approximately midway between the domains. The potential flexibility of this sequence and its strategic location between major domain structures suggests that it may function in the conformational change leading from effector binding to inhibition of the active site. Site-directed mutagenesis of this region (Gly-336-Gly-337) supports this hypothesis. When bulky side chains were substituted for the glycines at these positions, substantial changes in the ability of serine to inhibit the enzyme were seen with little effect on the activity of the enzyme. The effect of these substitutions could be alleviated by placing a new glycine residue at position 335, immediately flanking the original glycine pair. On the other hand, substituting a glycine at position 338 revealed a critical role for the side chain of Arg-338. This residue may function in stabilizing the conformation about the Gly-Gly turn, resulting in a specific orientation of the adjacent domains relative to each other. Rotation about the phi or psi bonds of either Gly-336 or Gly-337 would have a profound effect on this orientation. The data are consistent with this as a role for the Gly-Gly sequence between the regulatory and substrate binding domains of PGDH.

Binding Sites↗
PubMed2000

Removal of the tryptophan 139 side chain in Escherichia coli D-3-phosphoglycerate dehydrogenase produces a dimeric enzyme without cooperative effects.

Escherichia coli d-3-phosphoglycerate dehydrogenase (PGDH) is a homotetrameric enzyme whose activity is allosterically regulated by l-serine, the end-product of its metabolic pathway. Previous studies have shown that PGDH displays two modes of cooperative interaction. One is between the l-serine binding sites and the other is between the l-serine binding sites and the active sites. Tryptophan 139 participates in an intersubunit contact near the active site catalytic residues. Site-specific mutagenesis of tryptophan 139 to glycine results in the dissociation of the tetramer to a pair of dimers and in the loss of cooperativity in serine binding and between serine binding and inhibition. The results suggest that the magnitude of inhibition of activity at a particular active site is primarily dependent on serine binding to that subunit but that activity can be modulated in a cooperative manner by interaction with adjacent subunits. The disruption of the nucleotide domain interface in PGDH by mutating Trp-139 suggests the potential for a critical role of this interface in the cooperative allosteric processes in the native tetrameric enzyme.

Allosteric Regulation↗
PubMed2000

[Clinical significance of plasma PGE2 levels in pre- and post-operative patients with laryngeal carcinoma].

OBJECTIVE: To study the clinical significance of PGE2 Levels in patients with laryngeal carcinoma. METHOD: Radioimmunoassay was used to evaluate plasma PGE2 levels in 35 patients with laryngeal carcinoma. RESULT: The plasma PGE2 levels in patients with laryngeal carcinoma were significant higher than that of normal subjects (P < 0.05), but there was no correlation with the stage of laryngeal carcinoma (P > 0.05). The plasma PGE2 levels of postoperative patients with laryngeal carcinoma were significant lower than that of preoperative patients (P < 0.05). After operation, the plasma PGE2 levels of recurrent patients were significant higher than that in patients with no recurrence (P < 0.01). CONCLUSION: The determination of PGE2 levels in patient plasma may help the diagnosis and prognostic judgment of laryngeal carcinoma.

Carcinoma, Squamous Cell↗
PubMed1999

Phosphate ion partially relieves the cooperativity of effector binding in D-3-phosphoglycerate dehydrogenase without altering the cooperativity of inhibition.

The binding of L-serine to phosphoglycerate dehydrogenase from E. coli displays elements of both positive and negative cooperativity. In addition, the inhibition of enzymatic activity by L-serine is also cooperative with Hill coefficients greater than 1. However, phosphate buffer significantly reduces the cooperative effects in serine binding without affecting the cooperativity of inhibition of activity. The maximal degree of inhibition and fluorescence quenching in Tris buffer occurs when an average of two serine binding sites out of four are occupied. This value increases to three out of the four sites at maximal levels of inhibition and quenching in phosphate buffer. The increase from two to three sites appears to be due to the ability of phosphate to reduce the site to site cooperative effects and render each ligand binding site less dependent on each other. The correlation between the level of inhibition and the fractional site occupancy indicates that in Tris buffer, one serine is bound to each interface at maximal effect. In the presence of phosphate, the order of binding appears to change so that both sites at one interface fill before the first site at the opposite interface is occupied. In each case, there is a good correlation between serine binding, conformational change at the regulatory site interfaces, and inhibition of enzyme activity. The observation that phosphate does not appear to have a similar effect on the cooperativity of inhibition of enzymatic activity suggests that there are two distinct cooperative pathways at work: one path between the four serine binding sites, and one path between the serine binding sites and the active sites.

Binding Sites↗
PubMed1999

The contribution of adjacent subunits to the active sites of D-3-phosphoglycerate dehydrogenase.

D-3-Phosphoglycerate dehydrogenase (PGDH) from Escherichia coli is allosterically inhibited by L-serine, the end product of its metabolic pathway. Previous results have shown that inhibition by serine has a large effect on Vmax and only a small or negligible effect on Km. PGDH is thus classified as a V-type allosteric enzyme. In this study, the active site of PGDH has been studied by site-directed mutagenesis to assess the role of certain residues in substrate binding and catalysis. These consist of a group of cationic residues (Arg-240, Arg-60, Arg-62, Lys-39, and Lys-141') that potentially form an electrostatic environment for the binding of the negatively charged substrate, as well as the only tryptophan residue found in PGDH and which fits into a hydrophobic pocket immediately adjacent to the active site histidine residue. Interestingly, Trp-139' and Lys-141' are part of the polypeptide chain of the subunit that is adjacent to the active site. The results of mutating these residues show that Arg-240, Arg-60, Arg-62, and Lys-141' play distinct roles in the binding of the substrate to the active site. Mutants of Trp-139' show that this residue may play a role in stabilizing the catalytic center of the enzyme. Furthermore, these mutants appear to have a significant effect on the cooperativity of serine inhibition and suggest a possible role for Trp-139' in the cooperative interactions between subunits.

Amino Acid Substitution↗
PubMed1999

The relationship between effector binding and inhibition of activity in D-3-phosphoglycerate dehydrogenase.

The binding of L-serine to phosphoglycerate dehydrogenase from Escherichia coli displays elements of both positive and negative cooperativity. At pH 7.5, approximately 2 mol of serine are bound per mole of tetrameric enzyme. A substantial degree of positive cooperativity is seen for the binding of the second ligand, but the binding of the third and fourth ligand display substantial negative cooperativity. The data indicate a state of approximately 50% inhibition when only one serine is bound and approximately 80-90% inhibition when two serines are bound. This is consistent with the tethered domain hypothesis that has been presented previously. Comparison of the data derived directly from binding stoichiometry to the binding constants determined from the best fit to the Adair equation, produce a close agreement, and reinforce the general validity of the derived binding constants. The data also support the conclusion that the positive cooperativity between the binding to the first and second site involves binding sites at opposite interfaces over 110 A apart. Thus, an order of binding can be envisioned where the binding of the first ligand initiates a conformational transition that allows the second ligand to bind with much higher affinity at the opposite interface. This is followed by the third ligand, which binds with lesser affinity to one of the two already occupied interfaces, and in so doing, completes a global conformational transition that produces maximum inhibition of activity and an even lower affinity for the fourth ligand, excluding it completely. Thus, maximal inhibition is accomplished with less than maximal occupancy of effector sites through a mechanism that displays strong elements of both positive and negative cooperativity.

Binding Sites↗
PubMed1999

[Direct gene transfer into rabbit peripheral nerve in vivo].

OBJECTIVE: To probe the possibility of direct transfer of exogenous gene into peripheral nerve and its following expression in vivo. METHODS: The PCMV beta plasmid containing cytomegalovirus (CMV) promoter and Escherichia Coli (E. Coli), beta-Galactosidease (beta-Gal) structural gene (lacZ gene) was constructed and injected into the rabbit sciatic nerve. The control group was injected PBS solution. The injected nerves were sampled and tested by beta-Gal enzyme activity assay of the 5-bromo-4-chloro-3-indolyl-beta-D-galactoside and beta-Gal histochemical stain. RESULTS: In the control group, no beta-Gal enzyme activity was detected in the different stages after operation, and beta-Gal histochemical stains showed positive. In the experimental group, enzyme activity could be detected from 2 days to 30 days after operation, and the histochemical stains showed negative. CONCLUSION: The exogenous gene can be transferred into peripheral nerve and expressed with bioactivity, thus the gene therapy to accelerate the recovery of nerve is practical.

Animals↗
PubMed1998

Differential roles for disulfide bonds in the structural integrity and biological activity of kappa-Bungarotoxin, a neuronal nicotinic acetylcholine receptor antagonist.

kappa-Bungarotoxin, a kappa-neurotoxin derived from the venom of the banded Krait, Bungarus multicinctus, is a homodimeric protein composed of subunits of 66 amino acid residues containing five disulfide bonds. kappa-Bungarotoxin is a potent, selective, and slowly reversible antagonist of alpha3 beta2 neuronal nicotinic acetylcholine receptors. kappa-Bungarotoxin is structurally related to the alpha-neurotoxins, such as alpha-bungarotoxin derived from the same snake, which are monomeric in solution and which effectively antagonize muscle type receptors (alpha1 beta1 gamma delta) and the homopentameric neuronal type receptors (alpha7, alpha8, and alpha9). Like the kappa-neurotoxins, the long alpha-neurotoxins contain the same five conserved disulfide bonds, while the short alpha-neurotoxins only contain four of the five. Systematic removal of single disulfide bonds in kappa-bungarotoxin by site-specific mutagenesis reveals a differential role for each of the disulfide bonds. Removal of either of the two disulfides connecting elements of the carboxy terminal loop of this toxin (Cys 46-Cys 58 and Cys 59-Cys 64) interferes with the ability of the toxin to fold. In contrast, removal of each of the other three disulfides does not interfere with the general folding of the toxin and yields molecules with biological activity. In fact, when either C3-C21 or C14-C42 are removed individually, no loss in biological activity is seen. However, removing both produces a polypeptide chain which fails to fold properly. Removal of the C27-C31 disulfide only reduces the activity of the toxin 46.6-fold. This disulfide may play a role in specific interaction of the toxin with specific neuronal receptors.

Alanine↗