Biomedical subjects

M Wei

Publications and source records attributed to M Wei.

At least 19 recordsLinked to original sources

PubMed2005

Unbalanced placental expression of imprinted genes in human intrauterine growth restriction.

Imprinted genes control fetal and placental growth in mice and in rare human syndromes, but the role of these genes in sporadic intrauterine growth restriction (IUGR) is less well-studied. We measured the ratio of mRNA from a maternally expressed imprinted gene, PHLDA2, to that from a paternally expressed imprinted gene, MEST, by Northern blotting in 38 IUGR-associated placentae and 75 non-IUGR placentae and found an increase in the PHLDA2/MEST mRNA ratio in IUGR (p=0.0001). Altered expression of PHLDA2 and MEST was not accompanied by changes in DNA methylation within their imprinting centers, and immunohistochemistry showed PHLDA2 protein appropriately restricted to villous and intermediate cytotrophoblast in the IUGR placentae. We next did a genome-wide survey of mRNA expression in 14 IUGR placentae with maternal vascular under-perfusion compared to 15 non-IUGR placentae using Affymetrix U133A microarrays. In this series six imprinted genes were differentially expressed by ANOVA with a Benjamini-Hochberg false discovery rate of 0.05, with increased expression of PHLDA2 and decreased expression of MEST, MEG3, GATM, GNAS and PLAGL1 in IUGR placentae. At lower significance, we found IGF2 mRNA decreased and CDKN1C mRNA increased in the IUGR cases. We confirmed the significant reduction in MEG3 non-translated RNA in IUGR placentae by Northern blotting. In addition to imprinted genes, the microarray data highlighted non-imprinted genes acting in endocrine signaling (LEP, CRH, HPGD, INHBA), tissue growth (IGF1), immune modulation (INDO, PSG-family genes), oxidative metabolism (GLRX), vascular function (AGTR1, DSCR1) and metabolite transport (SLC-family solute carriers) as differentially expressed in IUGR vs. non-IUGR placentae.

Adult↗

PubMed2005

Precipitation of hydroxyapatite nanoparticles: effects of precipitation method on electrophoretic deposition.

Electrophoretic deposition is a low-cost, simple, and flexible coating method for producing hydroxyapatite (HA) coatings on metal implants with a broad range of thicknesses, from < 1 microm to > 500 microm. As for many other HA coating techniques, densification of electrophoretically deposited coatings involves heating the coated metal to temperatures above 1000 degrees C. Metal substrates tend to react with HA coatings at such temperatures inducing decomposition at temperatures below 1050 degrees C (decomposition for pure HA normally occurs above 1300 degrees C). Therefore, densification of these coatings needs to be conducted at temperatures lower than 1050 degrees C, and this necessitates the use of high-surface-area HA nano-precipitates, rather than commercially available pre-calcined powders, which densify at temperatures typically higher than 1200 degrees C. HA nano-precipitates were prepared by three methods and deposited on metal substrates by electrophoresis: (1) the acid base method, which produced plate-like nano-particles with a 2.5:1 aspect ratio, and severely cracked coatings; (2) the calcium acetate method, which produced needle-like nano-particles with a 10:1 aspect ratio, and slightly cracked coatings; (3) the metathesis method, which produced rounded nano-particles with a 2:1 aspect ratio, and high-quality crack-free coatings. The results suggested that the less equiaxed the nano-particles, the more cracked the coatings obtained by the electrophoretic deposition technique.

Acetates↗

PubMed2005

Synthesis and characterization of fluorine-containing hydroxyapatite by a pH-cycling method.

Different fluorine-containing hydroxyapatite (FHA) powders were synthesized through a pH-cycling method by varying sodium fluoride (NaF) concentration in hydroxyapatite (HA) suspensions. The powders were then calcined at 1200 ( composite function)C for 1 h. Both uncalcined and calcined powders were characterized using X-ray diffraction (XRD), Fourier transform infra-red (FTIR), and F-electrode. It was discovered that fluorine incorporation increased with the fluorine content in the initial solution and the number of pH cycles employed. A relatively low fluorine incorporation efficiency, approximately 60%, was attained for most of the FHA samples, and it did not vary significantly after calcination. It was also revealed that the FHA particles produced by the pH-cycling method were inhomogeneous. They were a mixture of hydroxyapatite and F-rich apatite (or FA) particles. After calcination, however, these FHA particles were homogenized and became single phased FHA.

Bone Substitutes↗

PubMed2005

Hydroxyapatite-coated metals: interfacial reactions during sintering.

Electrophoretic deposition (EPD) is a low cost flexible process for producing HA coatings on metal implants. Its main limitation is that it requires heating the coated implant in order to densify the HA. HA typically sinters at a temperature below 1150 degrees C, but metal implants are degraded above 1000 degrees C. Further, the metal induces the decomposition of the HA coating upon sintering. Recent developments have enabled EPD of metathesis-synthesised uncalcined HA which sinters at approximately 1000 degrees C. The effects of temperature on HA-coated Ti, Ti6Al4V, and 316L stainless steel were investigated for dual coatings of metathesis HA sintered at 1000 degrees C. The use of dual HA coatings (coat, sinter, coat, sinter) enabled decomposition to be confined to the "undercoat" (HA layer 1), with the surface coating decomposition free. The tensile strength of the three metals was not significantly affected by the high sintering temperatures (925 degrees C < T < 1000 degrees C). XRD/SEM/EDS analyses of the interfacial zones revealed that 316L had a negligible HA:metal interfacial zone (approximately 1 microm) while HA:Ti and HA:Ti6Al4V had large interfacial zones (>10 microm) comprising a TiO2 oxidation zone and a CaTiO2 reaction zone.

Alloys↗

PubMed2005

Influence of temperature and aging time on HA synthesized by the hydrothermal method.

The influence of temperature and aging time on the morphology and mechanical properties of nano-sized hydroxyapatite (HA) synthesized by a hydrothermal method is reported here. The pre-mixed reactants were poured into a stirred autoclave and reacted at temperatures between 25-250 degrees C for 2-10 h. HA powders thus obtained were examined using X-ray diffraction (XRD), high-resolution field emission scanning electron microscopy (FESEM) and a particle size analyzer. It was found that the aspect ratio of the particles increased with the reaction temperature. The length of the HA particles increased with the reaction temperature below 170 degrees C, but it decreased when the temperature was raised above 170 degrees C. The agglomerates of HA particles were formed during synthesis, and their sizes were strongly dependent on reaction temperatures. As the reaction temperature increased, the agglomerate size decreased (p = 0.008). The density of the discs pressed from these samples reached 85-90% of the theoretical density after sintering at 1200 degrees C for 1 h. No decomposition to other calcium phosphates was detected at this sintering temperature. A correlation existed (p = 0.05) between the agglomerate sizes of HA particles synthesized at various conditions and their sintered densities. With the increase of the agglomerate size, the sintered density of the HA compact decreased. It was found that both the sintered density and flexural strength increased with increasing aging time and reaction temperature. A maximum flexural strength of 78 MPa was observed for the samples synthesized at 170 degrees C for 5 h with the predicted average at these conditions being 65 MPa. These samples attained an average sintered density of 88%.

Crystallization↗

PubMed2005

Incorporation of fluorine ions into hydroxyapatite by a pH cycling method.

Fluorine ions were incorporated into hydroxyapatite (HA) using a pH cycling method and the resulting materials were studied using transmission electron microscopy (TEM), X-ray diffraction (XRD), and electrochemical analysis. TEM observations showed that fluoridated hydroxyapatite (FHA) nanoparticles with a narrow particle size distribution were obtained at several different levels of fluorine incorporation. Significant particle growth was observed following calcining at 1200 degrees C. The TEM data revealed that, instead of forming laminated structures, a mixture of HA and FA was obtained, and that this mixture transformed into a single homogeneous FHA phase upon heating. It was found that the efficiency of fluorine incorporation did not vary significantly with the initial HA particle size, but increased as the fluorine content of the initial solution was increased. A relatively low fluorine incorporation efficiency, approximately 60%, was attained for most of the FHA samples and this was attributed to the short holding time at each pH cycle and the limited number of pH cycles employed in the current study.

Biocompatible Materials↗

PubMed2003

Synthesis and characterization of hydroxyapatite, fluoride-substituted hydroxyapatite and fluorapatite.

Powders of hydroxyapatite (HA), partially fluoride-substituted hydroxyapatite (fHA), and fluorapatite (FA) were synthesized in house using optimum methods to achieve relatively pure powders. These powders were assessed by the commonly used bulk techniques of X-ray diffraction (XRD), Fourier transform infra-red (FTIR) and FT-Raman spectroscopies, inductively coupled plasma atomic emission spectroscopy (ICP-AES), and F-selective electrode. In addition, the current study has employed transmission electron microscopy (TEM), involving morphological observation, electron diffraction and energy-dispersive X-ray spectrometry (EDX), as an effective analytical technique to evaluate the powders at a microscopic level. The HA and fHA particles were elongated platelets about 20 x 60 nm in size, while FA particles were over twice this size. Calcination of the HA and fHA powders at 1000 degrees C for 1 h resulted in increased grain size and crystallinity. The calcined fHA material appeared to possess a crystal structure intermediate between HA and FA, as evidenced by the (3 0 0) peak shift in XRD, as well as by the position of the hydroxyl bands in the FTIR spectra. This result was consistent with electron diffraction of individual particles. Small levels of impurities in some of the powders were identified by EDX and electron diffraction, and the carbonate content was detected by FTIR. The use of TEM in conjunction with the bulk techniques has allowed a more thorough assessment of the apatites, and has enabled the constituents in these closely related apatite powders to be identified.

Journal Article↗

PubMed2003

Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China.

Severe acute respiratory syndrome (SARS), now known to be caused by a coronavirus, probably originated in Guangdong province in southern China in late 2002. The first major outbreak occurred in Guangzhou, the capital of Guangdong, between January and March 2003. This study reviews the clinical presentation, laboratory findings and response to four different treatment protocols. Case notes and laboratory findings were analysed and outcome measures were collected prospectively. The SARS outbreak in Guangdong province and the outbreak in Guangzhou associated with hospitals in the city are described, documenting clinical and laboratory features in a cohort of 190 patients randomly allocated to four treatment regimens. Patients were infected by close contact in either family or health-care settings, particularly following procedures likely to generate aerosols of respiratory secretions (e.g. administration of nebulized drugs and bronchoscopy). The earliest symptom was a high fever followed, in most patients, by dyspnoea, cough and myalgia, with 24 % of patients complaining of diarrhoea. The most frequent chest X-ray changes were patchy consolidation with progression to bilateral bronchopneumonia over 5-10 days. Thirty-six cases developed adult respiratory distress syndrome (ARDS), of whom 11 died. There was no response to antibiotics. The best response (no deaths) was seen in the group of 60 patients receiving early high-dose steroids and nasal CPAP (continuous airway positive pressure) ventilation; the other three treatment groups had significant mortality. Cross-infection to medical and nursing staff was completely prevented in one hospital by rigid adherence to barrier precautions during contact with infected patients. The use of rapid case identification and quarantine has controlled the outbreak in Guangzhou, in which more than 350 patients have been infected. Early administration of high-dose steroids and CPAP ventilation appears to offer the best supportive treatment with a reduced mortality compared with other treatment regimens.

Adult↗

PubMed2001

Investigation of the role of the domain linkers in separate site catalysis by Clostridium symbiosum pyruvate phosphate dikinase.

Pyruvate phosphate dikinase (PPDK) catalyzes the reversible reaction: ATP + P(i) + pyruvate <--> AMP + PP(i) + PEP using Mg2+ and NH4+ ions as cofactors. The reaction takes place in three steps, each mediated by a carrier histidine residue located on the surface of the central domain of this three-domain enzyme: (1) E-His + ATP <--> E-His-PP.AMP, (2) E-His-PP.AMP + P(i) <--> E-His-P + AMP + PP(i), (3) E-His-P + pyruvate <--> E-His + PEP. The first two partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain travels from one terminal domain to the other. The goal of this work is to determine whether the two connecting linkers direct the movement of the central domain between active sites during catalytic turnover. The X-ray crystal structure of the enzyme suggests interaction between the two linkers that may result in their coordinated movement. Mutations were made at the linkers for the purpose of disrupting the linker-linker interaction and, hence, synchronized linker movement. Five linker mutants were analyzed. Two of these contain 4-Ala insertions within the solvated region of the linker, and three have 3-residue deletions in this region. The efficiencies of the mutants for catalysis of the complete reaction as well as the E-His + ATP <--> E-His-PP.AMP partial reaction at the N-terminal domain and the E-His + PEP <--> E-His-P + pyruvate reaction at the C-terminal domain were measured to assess linker function. Three linker mutants are highly active catalysts at both active sites, and the fourth is highly active at one site but not the other. These results are interpreted as evidence against coordinated linker movement, and suggest instead that the linkers move independently as the central domain travels between active sites. It is hypothesized that while the linkers play a passive role in central domain-terminal domain docking, their structural design minimizes the conformational space searched in the diffusion process.

Adenosine Monophosphate↗

PubMed2001

Inflammatory cytokines and soluble receptors after coronary artery bypass grafting.

Much interest has been focused on the overexpression of proinflammatory cytokines, but studies on their soluble receptors are rare. For a comprehensive picture of cytokine activation in cardiac surgery, a combination of cytokines and the corresponding soluble receptor concentration should be determined. Blood samples were collected from the radial artery and coronary sinus perioperatively in ten patients undergoing coronary artery bypass grafting with cardiopulmonary bypass. TNF-alpha, IL-6, sTNFRI, sTNFRII, and sIL-6R levels in the plasma were determined. Systemic TNFRI, TNFRII and IL-6 increased significantly after reperfusion to the myocardium, while perioperative systemic sIL-6r levels were similar. Arterial and sinus levels of TNFRI, TNFRII and sIL-6r were similar before cardiopulmonary bypass. Five minutes after reperfusion to the myocardium, higher sinus TNFRI and TNFRII and lower sinus sIL-6R levels were observed as compared to the arterial levels. The myocardium release of sTNFRI (r=0.57, P=0.089) and sTNFRII (r=0.64, P=0.047) positively correlated with the change of cardiac index after cardiopulmonary bypass. Myocardium releases sTNFRI and sTNFRII after ischaemic-reperfusion injury, and this may be of benefit to cardiac performance. sIL-6R is constantly being produced in areas other than the myocardium, while sIL-6R levels are reduced by consumption in the myocardium after ischaemic-reperfusion injury.

Aged↗

PubMed2001

Effects of spectator ligands on the specific recognition of intrastrand platinum-DNA cross-links by high mobility group box and TATA-binding proteins.

The results presented describe the effects of various spectator ligands, attached to a platinum 1,2-intrastand d(GpG) cross-link in duplex DNA, on the binding of high mobility group box (HMGB) domains and the TATA-binding protein (TBP). In addition to cisplatin-modified DNA, 15-base pair DNA probes modified by [Pt(1R,2R-diaminocyclohexane)](2+), cis-[Pt(NH(3))(cyclohexylamine)](2+), [Pt(ethylenediamine)](2+), cis-[Pt(NH(3))(cyclobutylamine)](2+), and cis-[Pt(NH(3))(2-picoline)](2+) were examined. Electrophoretic mobility shift assays show that both the A and B domains of HMGB1 as well as TBP discriminate between different platinum-DNA adducts. HMGB1 domain A is the most sensitive to the nature of the spectator ligands on platinum. The effect of the spectator ligands on protein binding also depends highly on the base pairs flanking the platinated d(GpG) site. Double-stranded oligonucleotides containing the AG*G*C sequence, where the asterisks denote the sites of platination, with different spectator ligands are only moderately discriminated by the HMGB proteins and TBP, but the recognition of dsTG*G*A is highly dependent on the ligands. The effects of HMGB1 overexpression in a BG-1 ovarian cancer cell line, induced by steroid hormones, on the sensitivity of cells treated with [Pt(1R,2R-diaminocyclohexane)Cl(2)] and cis-[Pt(NH(3))(cyclohexylamine)Cl(2)] were also examined. The results suggest that HMGB1 protein levels influence the cellular processing of cis-[Pt(NH(3))- (cyclohexylamine)](2+), but not [Pt((1R,2R)-diaminocyclohexane)](2+), DNA lesions. This result is consistent with the observed binding of HMGB1a to platinum-modified dsTG*G*A probes but not with the binding affinity of HMGB1a and HMGB1 to platinum-damaged dsAG*G*C oligonucleotides. These experiments reinforce the importance of sequence context in platinum-DNA lesion recognition by cellular proteins.

Cisplatin↗

PubMed2001

Investigation of the catalytic site within the ATP-grasp domain of Clostridium symbiosum pyruvate phosphate dikinase.

Pyruvate phosphate dikinase (PPDK) catalyzes the interconversion of ATP, P(i), and pyruvate with AMP, PP(i), and phosphoenolpyruvate (PEP) in three partial reactions as follows: 1) E-His + ATP --> E-His-PP.AMP; 2) E-His-PP.AMP + P(i) --> E-His-P.AMP.PP(i); and 3) E-His-P + pyruvate --> E.PEP using His-455 as the carrier of the transferred phosphoryl groups. The crystal structure of the Clostridium symbiosum PPDK (in the unbound state) reveals a three-domain structure consisting of consecutive N-terminal, central His-455, and C-terminal domains. The N-terminal and central His-455 domains catalyze partial reactions 1 and 2, whereas the C-terminal and central His-455 domains catalyze partial reaction 3. Attempts to obtain a crystal structure of the enzyme with substrate ligands bound at the nucleotide binding domain have been unsuccessful. The object of the present study is to demonstrate Mg(II) activation of catalysis at the ATP/P(i) active site, to identify the residues at the ATP/P(i) active site that contribute to catalysis, and to identify roles for these residues based on their positions within the active site scaffold. First, Mg(II) activation studies of catalysis of E + ATP + P(i) --> E-P + AMP + PP(i) partial reaction were carried out using a truncation mutant (Tem533) in which the C-terminal domain is absent. The kinetics show that a minimum of 2 Mg(II) per active site is required for the reaction. The active site residues used for substrate/cofactor binding/activation were identified by site-directed mutagenesis. Lys-22, Arg-92, Asp-321, Glu-323, and Gln-335 mutants were found to be inactive; Arg-337, Glu-279, Asp-280, and Arg-135 mutants were partially active; and Thr-253 and Gln-240 mutants were almost fully active. The participation of the nucleotide ribose 2'-OH and alpha-P in enzyme binding is indicated by the loss of productive binding seen with substrate analogs modified at these positions. The ATP, P(i), and Mg(II) ions were docked into the PPDK N-terminal domain crevice, in an orientation consistent with substrate/cofactor binding modes observed for other members of the ATP-Grasp fold enzyme superfamily and consistent with the structure-function data. On the basis of this docking model, the ATP polyphosphate moiety is oriented/activated for pyrophosphoryl transfer through interaction with Lys-22 (gamma-P), Arg-92 (alpha-P), and the Gly-101 to Met-103 loop (gamma-P) as well as with the Mg(II) cofactors. The P(i) is oriented/activated for partial reaction 2 through interaction with Arg-337 and a Mg(II) cofactor. The Mg(II) ions are bound through interaction with Asp-321, Glu-323, and Gln-335 and substrate. Residues Glu-279, Asp-280, and Arg-135 are suggested to function in the closure of an active site loop, over the nucleotide ribose-binding site.

Adenosine Triphosphate↗

PubMed2001

Autoxidation of substituted phenols catalyzed by cobalt Schiff base complexes in supercritical carbon dioxide.

This first study of O(2) oxidation (autoxidation) of substituted phenols catalyzed by a dioxygen carrier in supercritical carbon dioxide (scCO(2)) provides additional insights into the established mechanism of reactions that have been much studied in conventional solvents. As has been long believed, the cobalt(II) dioxygen carriers of the class represented by [[N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexanediaminato(2-)]cobalt(II)], Co(salen), show both oxidase and oxygenase activities during oxygenation of substituted phenols in scCO(2). The catalytic autoxidation of 2,6-di-tert-butylphenol (DTBP) and 3,5-di-tert-butylphenol (35-DTBP) in scCO(2) was studied by analysis of products in batch reactions with carefully controlled variables, in the presence of a large excess of O(2), at 207 bar of total pressure and a reaction temperature of 70 degrees C. The oxidation of 35-DTBP yielded only traces of products under the same experimental conditions that converted DTBP totally to a mixture of the oxygenation product 2,6-di-tert-butyl-1,4-benzoquinone (DTBQ) and the related product of radical coupling 3,5,3',5'-tetra-tert-butyl-4,4'-diphenoquinone (TTDBQ). The effects on conversion of DTBP to products and on selectivity between the two products were studied for variations in temperature and the concentrations of catalyst, oxygen, and methylimidazole. Selectivity in favor of the O-transfer product DTBQ over the self-coupling of the phenoxy radical was observed upon changing the oxygen concentration. In contrast, selectivity remained unaffected over a wide range of temperatures and catalyst concentrations. The oxygen dependence of both the conversion and selectivity showed saturation effects identifying the dioxygen complex as the effective oxidant in both the initial radical formation step and the oxygenation of that radical. No direct reaction is observed between the electrophilic phenoxy radical and O(2).

Journal Article↗

PubMed2001

Epigenetic heterogeneity at imprinted loci in normal populations.

Genomic imprinting is the phenomenon by which the two alleles of certain genes are differentially expressed according to their parental origin. Extensive analysis of allelic expression at multiple imprinted loci in a normal population has not performed so far. In the present study, we examined the allelic expression pattern of three imprinted genes in a panel of 262 Japanese normal individuals. We observed differences in the extent of maintenance of allele-specific expression of the three genes. The allelic expression of small nuclear ribonucleoprotein N (SNRPN) was stringently regulated while that of multimembrane-spanning polyspecific transporter-like gene 1 (IMPT1) showed a large degree of variation. Significant biallelic expression of insulin-like growth factor II (IGF2) was observed in about 10% of normal individuals. Our findings add to the accumulating evidence for variable allelic expression at multiple loci in a normal human population. This epigenetic heterogeneity can be a stable trait and potentially influence individual phenotypes.

Alleles↗

PubMed2001

Presence of a no-observed effect level for enhancing effects of development of the alpha-isomer of benzene hexachloride (alpha-BHC) on diethylnitrosamine-initiated hepatic foci in rats.

The dose dependence of the promoting effects of the alpha-isomer of benzene hexachloride (alpha-BHC) on hepatocarcinogenesis was investigated in a medium-term rat liver bioassay (Ito test). A total of 195 F344 male rats, 6 weeks old, were given a single intraperitoneal injection of diethylnitrosamine (DEN) at the start of the experiment and subjected to two-thirds partial hepatectomy at week 3. Two weeks after the administration of DEN, alpha-BHC were fed to rats at doses of 0, 0.01, 0.1, 0.5, 1, 2, 4, 7.5, 15, 30, 60, 125 and 500 ppm in diet for 6 weeks. All surviving animals were killed at week 8, and their livers were examined immunohistochemically for detection of glutathione S-transferase placental form (GST-P)-positive foci, surrogate preneoplastic lesions. Quantitative values for numbers and areas were dose-dependently increased in rats given alpha-BHC at 0.5-500 ppm. However, those for groups treated with 0.01 and 0.1 ppm were decreased, albeit not significantly in comparison to the controls. Cytochrome P450 3A2 (CYP3A2) protein levels and activities showed a good correlation to the number and area of GST-P-positive foci. These results support evidence of hormesis and indicate a no-observed effect level for alpha-BHC promoting potentials may exist regarding rat liver carcinogenesis, which correlates with expression of CYP3A2 in the liver.

Animals↗

PubMed2001

The sequence of the human genome.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Algorithms↗

PubMed2001

Possible prevention by abieslactone of development of diethylnitrosamine-initiated GST-P positive foci in the rat liver.

Triterpenoid compounds, isolated from plants of Abies genus (Pinceae), are known to exert anti-tumor promotion activities in mouse skin carcinogenesis. In the present study, we investigated whether AVB-1 and acid and acid methyl ester derivatives have inhibitory effects on rat hepatocarcinogenesis by using a liver medium-term bioassay for carcinogens (Ito's test), immunohistochemically assessing the numbers and areas per cm(2) of preneoplastic lesions, glutathione S-transferase placental form (GST-P)-positive foci. In experiment 1, 6-week-old male Fisher 344 rats were given a single intraperitoneal injection of diethylnitrosamine (200 mg/kg b.w.) and subjected to two-thirds partial hepatectomy at week 3. From weeks 2 to 8, the compounds were given three times a week at a dose of 1 mg/kg b.w. by i.g. gavage and found to significantly decrease the number of GST-P-positive foci in the liver. In experiment 2, AVB-1 was given three times a week at doses of 3, 1, or 0.3 mg/kg b.w. by i.g. gavage from weeks 2 to 8. All doses of AVB-1 significantly decreased the numbers of GST-P-positive foci. Thus, our results suggest that AVB-1 is a chemopreventive agent for rat hepatocarcinogenesis.

Alkylating Agents↗

PubMed2001

Cephalometric image analysis and measurement for orthognathic surgery.

Automatic identification of landmarks in cephalometry is very important and useful for orthognathic surgery. A computerised automatic cephalometric analysis system (CACAS), based on image processing, is presented. For an original X-ray image, median filtering and histogram equalisation are used to improve image quality. The edge of an X-ray image is detected by a wavelet transform and Canny filter. Seventeen landmarks in cephalometry are successfully identified by knowledge-based edge tracing and changeable templates. Seventy-three measurements based on distances, angles and ratios between landmarks are computed automatically. The reliability of the landmarks and the validity of the measurements are compared for automatic and manual operation. The values of measurements obtained by CACAS are more precise and reliable: the mean error for linear measurements is less than 0.9mm; the mean error for angular measurements is less than 1.2 degrees. The rate of validity is over 80%, even if the image quality is poor. For an image with a high signal-to-noise ratio, the rate of validity of landmarking and measurements using the CACAS system is over 90%.

Cephalometry↗