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Hao Xu

Publications and source records attributed to Hao Xu.

At least 55 records · Page 3Linked to original sources
PubMed2005

Away from the edge II: in-house Se-SAS phasing with chromium radiation.

Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray radiation opens a new possibility for phasing a protein with data collected in-house and has led to several successful examples of de novo structure solution using only weak anomalous scatterers such as sulfur. To further reduce data-collection time and make SAS phasing more robust, it is natural to combine selenomethionine-derivatized protein (SeMet protein) with Cr Kalpha radiation to take advantage of the larger anomalous scattering signal from selenium (f'' = 2.28 e(-)) compared with sulfur (f'' = 1.14 e(-)). As reported herein, the crystal structure of a putative chorismate mutase from Clostridium thermocellum was determined using Se-SAS with Cr Kalpha radiation. Each protein molecule contains eight selenomethionine residues in 148 amino-acid residues, providing a calculated Bijvoet ratio of about 3.5% at the Cr Kalpha wavelength. A single data set to 2.2 A resolution with approximately ninefold redundancy was collected using an imaging-plate detector coupled with a Cr source. Structure solution, refinement and deposition to the Protein Data Bank were performed within 9 h of the availability of the scaled diffraction data. The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography.

Chorismate Mutase↗
PubMed2005

Model systems for flavoenzyme activity: site-isolated redox behavior in flavin-functionalized random polystyrene copolymers.

[reaction: see text] A model system has been developed to study the redox behaviors of flavin derivatives appended onto random polystyrene copolymers through "click" chemistry strategies. The results demonstrate that flavin units attached onto polymers exhibit site-isolated redox behaviors, yielding new materials with electrochemically tunable associations (K(a)(ox) = 450 M(-)(1), K(a)(red) = 18,200 M(-)(1)) to complementary diamidopyridine (DAP) functionality.

Electrochemistry↗
PubMed2005

The high-throughput protein-to-structure pipeline at SECSG.

Using a high degree of automation, the crystallography core at the Southeast Collaboratory for Structural Genomics (SECSG) has developed a high-throughput protein-to-structure pipeline. Various robots and automation procedures have been adopted and integrated into a pipeline that is capable of screening 40 proteins for crystallization and solving four protein structures per week. This pipeline is composed of three major units: crystallization, structure determination/validation and crystallomics. Coupled with the protein-production cores at SECSG, the protein-to-structure pipeline provides a two-tiered approach for protein production at SECSG. In tier 1, all protein samples supplied by the protein-production cores pass through the pipeline using standard crystallization screening and optimization procedures. The protein targets that failed to yield diffraction-quality crystals (resolution better than 3.0 A) become tier 2 or salvaging targets. The goal of tier 2 target salvaging, carried out by the crystallomics core, is to produce the target proteins with increased purity and homogeneity, which would render them more likely to yield well diffracting crystals. This is performed by alternative purification procedures and/or the introduction of chemical modifications to the proteins (such as tag removal, methylation, surface mutagenesis, selenomethionine labelling etc.). Details of the various procedures in the pipeline for protein crystallization, target salvaging, data collection/processing and high-throughput structure determination/validation, as well as some examples, are described.

Crystallization↗
PubMed2005

The Genomes of Oryza sativa: a history of duplications.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

Base Sequence↗
PubMed2005

Protein production and crystallization at SECSG -- an overview.

Using a high degree of automation, the Southeast Collaboratory for Structural Genomics (SECSG) has developed high throughput pipelines for protein production, and crystallization using a two-tiered approach. Primary, or tier-1, protein production focuses on producing proteins for members of large Pfam families that lack a representative structure in the Protein Data Bank. Target genomes are Pyrococcus furiosus and Caenorhabditis elegans. Selected human proteins are also under study. Tier-2 protein production, or target rescue, focuses on those tier-1 proteins, which either fail to crystallize or give poorly diffracting crystals. This two tier approach is more efficient since it allows the primary protein production groups to focus on the production of new targets while the tier-2 efforts focus on providing additional sample for further studies and modified protein for structure determination. Both efforts feed the SECSG high throughput crystallization pipeline, which is capable of screening over 40 proteins per week. Details of the various pipelines in use by the SECSG for protein production and crystallization, as well as some examples of target rescue are described.

Animals↗
PubMed2005

Salvaging Pyrococcus furiosus protein targets at SECSG.

Proteins derived from the coding regions of Pyrococcus furiosus are targets for three-dimensional X-ray and NMR structure determination by the Southeast Collaboratory for Structural Genomics (SECSG). Of the 2,200 open reading frames (ORFs) in this organism, 220 protein targets were cloned and expressed in a high-throughput (HT) recombinant system for crystallographic studies. However, only 96 of the expressed proteins could be crystallized and, of these, only 15 have led to structures. To address this issue, SECSG has recently developed a two-tier approach to protein production and crystallization. In this approach, tier-1 efforts are focused on producing protein for new Pfu(italics?) targets using a high-throughput approach. Tier-2 protein production efforts support tier-1 activities by (1) producing additional protein for further crystallization trials, (2) producing modified protein (further purification, methylation, tag removal, selenium labeling, etc) as required and (3) serving as a salvaging pathway for failed tier-1 proteins. In a recent study using this two-tiered approach, nine structures were determined from a set of 50 Pfu proteins, which failed to produce crystals suitable for X-ray diffraction analysis. These results validate this approach and suggest that it has application to other HT crystal structure determination applications.

Archaeal Proteins↗
PubMed2005

Analysis of ESTs and gene expression patterns of the posterior silkgland in the fifth instar larvae of silkworm, Bombyx mori L.

The fibroin gene expression pattern and regulation of the posterior silkgland were studied by means of expressed sequence tags (ESTs) using the first and fifth day larvae of the fifth instar of silkworm, Bombyx mori L (strain: C 108). The results showed that there were 911 repetitive ESTs and 1950 single sequences (Singlets) among total 2861 consentient sequences, which were spliced. 1335 sequences were identified and the other 1526 were unknown. 5560 sequences (55.89%) in the posterior silkgland cell of the silkworm were new ESTs without homology with EST data published by Mita et al. The number of repetitive ESTs and single sequences from the first day larvae of the fifth instar was double more than that of the fifth day of the same instar in the silkworms. The unigenes which were more than 50 in repetitive EST size (contig size) came to only about 0.5% in total consentient sequences. There were significant differences between gene expression frequencies, and expressed genes were related to fibroin synthesis and its secretion and fibroin composition. Comparing the fifth day with the first day of the fifth instar, the genes-expressed quantity of fibroin heavy-chain gene was 18 fold higher, fibroin light-chain gene 9 fold and fibroin P52 gene 8 fold. 508 genes functioned for cellular component and 315 for enzyme after function tracing. These results implied that the gene expression of the first day was mainly for preparation for fibroin synthesis except for the growth of silkgland cells, and the gene expression of the fifth day of the fifth instar was mainly for synthesizing and excreting fibroin. Because the ratio of heavy chain, light chain and p25 of fibroin was not 6:6:1 as theoretically expected, or its special H-chain structure, the H-chain gene was not easy to detect through EST technique. Most of genes among total 2861 consentient sequences functioned for fibroin synthesis and secretion. This suggested the fibroin synthesis and secretion procedure of the posterior silkgland was more complex than the knowledge we have.

Animals↗
PubMed2005

[Effect of drugs for promoting blood circulation on blood lipids and inflammatory reaction of atherosclerotic plaques in ApoE gene deficiency mice].

OBJECTIVE: To observe the effect of six common Chinese medicinal herbs for promoting blood circulation, including Radix Paeoniae rubra (I), Radix Salviae miltiorrhizae (II), Rhizoma Chuanxiong (III), Radix Notoginseng (IV), Semen Persicae (V) and wine steamed Radix et Rhizoma Rhei (VI), on blood lipids and inflammatory reaction of atherosclerotic plaques in ApoE gene deficiency mice. METHODS: Ninety mice, 6 - 8 weeks old, were divided into 8 groups, the model group, the control group (treated with simvastatin) and the six treated groups treated with the above-mentioned 6 Chinese medicinal herbs respectively. All the mice were fed with the diet of western kind for 13 weeks until the mature atherosclerotic plaques formed in them. Then they were treated with respective drugs for another 13 weeks except those in the model group. All the mice were sacrificed at the end of experiment, their blood was collected for lipids determination, heart and aorta were taken out for determining the level of CD68 in root of aorta, as well as the expressions of monocyte chemotactic protein-1 (MCP-1) and tumor necrosis factor-a (TNF-a) by immunohistochemistry staining. RESULTS: All the 6 Chinese herbs showed regulatory action on blood lipids. The positive expression of CD68 in the model group displayed the highest activity. As compared with the model group, the CD68 positive expressed cells in the control group and the groups treated with Chinese herbs II, III, and IV were lesser (P < 0.05), and the expression of inflammatory factors (MCP-1 and TNF-alpha) in atherosclerotic plaques was significantly lower in the control group and the group treated with Chinese herb VI (P < 0.05). CONCLUSION: Chinese medicinal herbs tested in this study can interfere the maturing progress of atherosclerotic plaques and stabilize the plaques in ApoE deficiency mice, the mechanisms may relate to its actions in regulating lipids metabolism and inhibiting inflammatory reaction. Different Chinese medicinal herbs for activating blood circulation of conventional dosage might show difference in potency and acting links.

Animals↗
PubMed2005

[On establishment and assessment of experimental vulnerable plaques animal models].

Vulnerable plaques is the hot spot in the researching field of cardiovascular diseases. In this paper, literature about establishment of experimental vulnerable plaques model animals published recent years were briefly reviewed and introduced concretely the conception, significance of researching, histopathologic characteristics of various types model, model assessment and current status of research.

Animals↗
PubMed2005

[Clinical observation on needle pricking for treatment of infertility due to varicocele after varicocelectomy].

OBJECTIVE: To observe clinical therapeutic effect of needle pricking therapy on infertility with varicocele after varicocelectomy. METHODS: One hundred and twenty-two cases were randomly divided into a treatment group of 62 cases and a control group of 60 cases. The treatment group were treated with needle pricking at sacral plexus nerve spots and lumbar plexus nerve spots, and the control group were treated with intramuscular injection of HCG. RESULTS: After treatment, the pregnancy rate of the patient's wife was 79.0% in the treatment group and 41.7% in the control group with a significant difference between the two groups (P < 0.01); the production hormones improved significantly in the both groups (P < 0.01); superoxide dismutase and Zn in the semen elevated significantly in the treatment group (P < 0.05). CONCLUSION: Needle pricking therapy can significantly improve and regulate endocrines in the patient of varicocele after varicocelectomy, and elevate quality of semen and sperm and the pregnancy rate of the patient's wife.

Biopsy↗
PubMed2004

Micromechanical measurement of membrane receptor binding for label-free drug discovery.

A potential novel binding assay based on binding-driven micromechanical motion is described. A membrane preparation containing 5-HT(3AS) receptors was used to modify a microcantilever. The modified microcantilever was found to bend on application of the naturally occurring agonist (5-hydroxytryptamine, which is also called serotonin) or the antagonist MDL-72222, but not to other similar molecules. Control experiments show that cantilevers modified by membrane preparations that do not contain 5-HT(3AS) receptors do not respond to serotonin or MDL-72222. K(d) values obtained for serotonin and MDL-72222 are identical to those obtained from radio-ligand binding assays. These results suggest that the microcantilever system has potential for use in label-free, drug screening applications.

Cell Membrane↗
PubMed2004

Biomimetically inspired total synthesis and structure activity relationships of 1-O-methyllateriflorone. 6 pi electrocyclizations in organic synthesis.

The total synthesis of 1-O-methyllateriflorone (2) is described. The construction of the cage-like domain of the molecule involved a biomimetic Claisen/Diels-Alder cascade, whereas the novel spiroxalactone framework was generated by an intramolecular Michael reaction within precursor 16a involving the carboxylate residue as the nucleophile. This finding might bear on the biosynthetic pathway by which nature forms lateriflorone. Described herein is also an interesting cascade sequence involving facile 6 pi electrocyclizations which leads to complex benzopyran systems. The biological evaluation of a small library of lateriflorone analogues and related systems establishing the first SAR within this class of compounds is also included. Among the most active compounds against tumor cells are 2, 16b, 56, 58, and 59.

Benzopyrans↗
PubMed2004

Shim design using a linear programming algorithm.

The advent of open magnetic resonance imaging (MRI) scanners and dedicated MRI scanners tailored to specific body parts has led to an increasing number of noncylindrical MRI scanner geometries, for which noncylindrical gradients and shims are needed. These new scanner geometries are driving the need for fast, flexible shim design methods that can design shim coils for any geometry. A linear programming (LP) algorithm was developed to design minimum-power resistive shim coils on an arbitrary surface. These coils can be designed to produce any order shim field over an arbitrarily shaped target region, which can be placed anywhere within the coil. The resulting designs are relatively sparse and can be readily constructed. This algorithm was used to design and construct a seven-coil cylindrical shim set for a knee imaging magnet with a cylindrical homogeneous region. The algorithm was then used to design shim coils for a biradial head imager with an asymmetrically located spherical target region for brain imaging.

Algorithms↗
PubMed2004

Optochemical nanosensor PEBBLEs: photonic explorers for bioanalysis with biologically localized embedding.

Nanosized photonic explorers for bioanalysis with biologically localized embedding (PEBBLEs) have been created for the intracellular monitoring of small analytes (e.g. H(+), Ca(2+), Mg(2+), Zn(2+), O(2), K(+), Na(+), Cl(-), OH and glucose). The probes are based on the inclusion of fluorescent analyte-sensitive indicator dyes and analyte-insensitive reference dyes in a polymer (polyacrylamide, polydecylmethacrylate) or sol-gel (silica, ormosil) nanoparticle. The probes are ratiometric, reversible and protected from interaction with the cellular environment, a quality which is of benefit to the integrity of both the cell and the sensor functionalities. Herein we describe two types of PEBBLE sensors, direct measurement sensors and ion correlation sensors, as well as the use of these PEBBLEs in intracellular sensing.

Acrylic Resins↗
PubMed2004

Exploring the characteristics of sequence elements in proximal promoters of human genes.

Central to reconstruction of cis-regulatory networks is identification and classification of naturally occurring transcription factor-binding sites according to the genes that they control. We have examined salient characteristics of 9-mers that occur in various orders and combinations in the proximal promoters of human genes. In evaluations of a dataset derived with respect to experimentally defined transcription initiation sites, in some cases we observed a clear correspondence of highly ranked 9-mers with protein-binding sites in genomic DNA. Evaluations of the larger dataset, derived with respect to the 5' end of human ESTs, revealed that a subset of the highly ranked 9-mers corresponded to sites for several known transcription factor families (including CREB, ETS, EGR-1, SP1, KLF, MAZ, HIF-1, and STATs) that play important roles in the regulation of vertebrate genes. We identified several highly ranked CpG-containing 9-mers, defining sites for interactions with the CREB and ETS families of proteins, and identified potential target genes for these proteins. The results of the studies imply that the CpG-containing transcription factor-binding sites regulate the expression of genes with important roles in pathways leading to cell-type-specific gene expression and pathways controlled by the complex networks of signaling systems.

5' Untranslated Regions↗
PubMed2004

Preparation and study on the novel solid inclusion complex of ciprofloxacin with HP-beta-cyclodextrin.

The interaction of ciprofloxacin with HP-beta-cyclodextrin (HP-beta-CD) has been studied by several analytical techniques, including 1H nuclear magnetic resonance (NMR), 13C NMR, fluorescence spectra, infrared spectroscopy, thermal analyzer and scanning electron microscope. In this paper, solid inclusion complex of ciprofloxacin with HP-beta-CD was synthesized by the coprecipitation method. In addition, the characterization of the inclusion complex has been proved by fluorimetry, infrared, differential scanning calorimetry and one-dimensional (1D), 2D NMR. The experimental results confirmed the existence of 1:1 inclusion complex of ciprofloxacin with HP-beta-CD. The formation constant of complex was determined by fluorescence method and 1H NMR. Spacial configuration of complex has been proposed on two-dimensional NMR technique.

2-Hydroxypropyl-beta-cyclodextrin↗
PubMed2004

Expression of MRP14 gene is frequently down-regulated in Chinese human esophageal cancer.

Migration inhibitory factor-related protein 14 (MRP14) is one of calcium-binding proteins, referred as S100A9. The heterodimeric molecule formed by MRP14 with its partner MRP8 (S100A8) is the major fatty acid carrier in neutrophils. The MRP8/14 complex has been also implicated in the intracellular transport of arachidonic acid and its precursors in keratinocytes. We show here the involvement of MRP14 in human esophageal cancer. In an initial study, mRNA differential display-reverse transcription polymerase chain reaction (DD-PCR) was performed with two esophageal carcinomas, one esophageal adenocarcinoma and matched normal adjacent mucosa. DD-PCR with the arbitrary primer OPA3 showed that one cDNA band was highly expressed in normal tissues, but disappeared or substantially decreased in tumor counterparts. It was later identified to be the 3'-end of migration inhibitory factor-related protein 14 (MRP14). Northern blotting, RT-PCR and Western blotting corroborated the down-regulation of MRP14 in 58/64 squamous cell carcinomas and 2/2 adenocarcinomas as compared with adjacent normal epithelia of the esophagus. MRP14 was undetectable in 3/3 esophageal-carcinoma cell lines. Immunochemistry demonstrated that expression of MRP14 was restricted to normal esophageal epithelia. No mutation was found in the genomic DNA of the MRP14 gene by PCR and directed DNA sequencing. Our finding suggested that the reduction of MRP14 expression is a frequent event in Chinese human esophageal cancer.

ATP-Binding Cassette Transporters↗