Biomedical subjects

Yan Zhao

Publications and source records attributed to Yan Zhao.

At least 109 records · Page 6Linked to original sources

PubMed2005

Two modes of microsatellite instability in human cancer: differential connection of defective DNA mismatch repair to dinucleotide repeat instability.

Microsatellite instability (MSI) is associated with defective DNA mismatch repair in various human malignancies. Using a unique fluorescent technique, we have observed two distinct modes of dinucleotide microsatellite alterations in human colorectal cancer. Type A alterations are defined as length changes of < or =6 bp. Type B changes are more drastic and involve modifications of > or =8 bp. We show here that defective mismatch repair is necessary and sufficient for Type A changes. These changes were observed in cell lines and in tumours from mismatch repair gene-knockout mice. No Type B instability was seen in these cells or tumours. In a panel of human colorectal tumours, both Type A MSI and Type B instability were observed. Both types of MSI were associated with hMSH2 or hMLH1 mismatch repair gene alterations. Intriguingly, p53 mutations, which are generally regarded as uncommon in human tumours of the MSI+ phenotype, were frequently associated with Type A instability, whereas none was found in tumours with Type B instability, reflecting the prevailing viewpoint. Inspection of published data reveals that the microsatellite instability that has been observed in various malignancies, including those associated with Hereditary Non-Polyposis Colorectal Cancer (HNPCC), is predominantly Type B. Our findings indicate that Type B instability is not a simple reflection of a repair defect. We suggest that there are at least two qualitatively distinct modes of dinucleotide MSI in human colorectal cancer, and that different molecular mechanisms may underlie these modes of MSI. The relationship between MSI and defective mismatch repair may be more complex than hitherto suspected.

Adaptor Proteins, Signal Transducing↗

PubMed2005

Efficient synthesis of water-soluble calixarenes using click chemistry.

[reaction: see text] Several water-soluble calix[4]arenes were synthesized via Huisgen 1,3-dipolar cycloaddition between azides and alkynes. Cationic, anionic, and nonionic calixarenes were prepared from a common azidocalixarene intermediate. Azidocalixarenes performed better than alkynylcalixarenes as precursors. The aggregation behavior of the water-soluble calixarenes was studied by (1)H NMR spectroscopy.

Calixarenes↗

PubMed2005

Benchmark database of barrier heights for heavy atom transfer, nucleophilic substitution, association, and unimolecular reactions and its use to test theoretical methods.

A benchmark database of forward and reverse barrier heights for 19 non-hydrogen-transfer reactions has been developed by using Weizmann 1 calculations, and 29 DFT methods and 6 ab initio wave-function theory (WFT) methods have been tested against the new database as well as against an older database for hydrogen atom transfer reactions. Among the tested hybrid DFT methods without kinetic energy density, MPW1K is the most accurate model for calculations of barrier heights. Among the tested hybrid meta DFT methods, BB1K and MPWB1K are the two most accurate models for the calculations of barrier heights. Overall, the results show that BB1K and MPWB1K are the two best DFT methods for calculating barrier heights, followed in order by MPW1K, MPWKCIS1K, B1B95, MPW1B95, BH and HLYP, B97-2, mPW1PW91, and B98. The popular B3LYP method has a mean unsigned error four times larger than that of BB1K. Of the methods tested, QCISD(T) is the best ab initio WFT method for barrier height calculations, and QCISD is second best, but QCISD is outperformed by the BB1K, MPWB1K, MPWKCIS1K, and MPW1K methods.

Journal Article↗

PubMed2005

Temperature dependence of carbon-13 kinetic isotope effects of importance to global climate change.

We report here a theoretical study of the 13C kinetic isotope effect (KIE) and its temperature dependence for the reaction OH + CH4 --> H2O + CH3, the major sink of atmospheric methane in the troposphere. The KIE values at various atmospherically significant temperatures were determined by direct dynamics using variational transition state theory with multidimensional tunneling contributions (VTST/MT). The potential energy surfaces (PESs) were generated by hybrid density functional theory as well as by recently developed doubly hybrid density functional theory methods. Comparisons of our calculated KIEs with experimental data and theoretical values in the literature reveal the critical contributions due to multidimensional tunneling and torsion anharmonicity as well as the critical issue of the choice of internal rotational axis.

Journal Article↗

PubMed2005

Effect of Sinai san decoction on the development of non-alcoholic steatohepatitis in rats.

AIM: To explore the effect of Sinai san decoction on the development of non-alcoholic steatohepatitis induced by CCL4 combined with a fat-rich diet in rats. METHODS: Twenty-seven Sprague-Dawley rats were divided into three groups randomly: control group (n = 9), model group (n = 9) and treatment group (n = 9). The rats of model group and treatment group were given small dosage of CCL4 combined with a fat-rich diet, and those of control group were given normal diet. After four weeks of fat-rich diet feeding, the rats of treatment group were given Sinai san decoction. The serum levels of aminotransferase and lipid were measured, and the pathology of livers was observed by HE staining after the rats were sacrificed at eight weeks. RESULTS: The rats' livers presented the pathology of steatosis and inflammation with higher serum levels of ALT and AST in the model group. In the treatment group the serum ALT and AST levels decreased significantly and were close to the control group. The hepatic inflammation scores also decreased markedly, but were still higher than those of control group. And the degree of hepatocyte steatosis was similar to that of model group. CONCLUSION: Sinai san decoction may ameliorate the hepatic inflammation of rats with steatohepatitis induced by small dosage of CCL4 combined with a fat-rich diet, but does not prevent the development of hepatocyte steatosis.

Alanine Transaminase↗

PubMed2005

The 6-31B(d) basis set and the BMC-QCISD and BMC-CCSD multicoefficient correlation methods.

Three new multicoefficient correlation methods (MCCMs) called BMC-QCISD, BMC-CCSD, and BMC-CCSD-C are optimized against 274 data that include atomization energies, electron affinities, ionization potentials, and reaction barrier heights. A new basis set called 6-31B(d) is developed and used as part of the new methods. BMC-QCISD has mean unsigned errors in calculating atomization energies per bond and barrier heights of 0.49 and 0.80 kcal/mol, respectively. BMC-CCSD has mean unsigned errors of 0.42 and 0.71 kcal/mol for the same two quantities. BMC-CCSD-C is an equally effective variant of BMC-CCSD that employs Cartesian rather than spherical harmonic basis sets. The mean unsigned error of BMC-CCSD or BMC-CCSD-C for atomization energies, barrier heights, ionization potentials, and electron affinities is 22% lower than G3SX(MP2) at an order of magnitude less cost for gradients for molecules with 9-13 atoms, and it scales better (N6 vs N,7 where N is the number of atoms) when the size of the molecule is increased.

Journal Article↗

PubMed2005

Pivotal study of iodine-131-labeled chimeric tumor necrosis treatment radioimmunotherapy in patients with advanced lung cancer.

PURPOSE: Tumor necrosis treatment (TNT) uses degenerating tumor cells and necrotic regions of tumors as targets for radioimmunotherapy. Previous studies in animal tumor models and clinical trials have demonstrated that when linked to the therapeutic radionuclide iodine-131, recombinant chimeric TNT antibody ((131)I-chTNT) can deliver therapeutic doses to tumors regardless of the location or type of malignancy. Therapeutic efficacy and toxicity of (131)I-chTNT in advanced lung cancer patients were studied in this pivotal registration trial. PATIENTS AND METHODS: Patients with advanced lung cancer were treated with systemic or intratumoral injection of (131)I-chTNT in eight oncology centers in China. The objective response rate (ORR) was assessed as the primary end point. RESULTS: All 107 patients who were entered onto the study and completed therapy had experienced treatment failure after prior radiotherapy or chemotherapy a mean of three times. The results showed an ORR of 34.6% (complete response, 3.7%; partial response, 30.8%; no change, 55.1%; and progressive disease, 10.3%) in all patients and 33% in 97 non-small-cell lung cancer patients. A biodistribution study demonstrated excellent localization of the radioactivity in tumors in both systemically and intratumorally injected patients. The most obvious adverse side effect was mild and reversible bone marrow suppression. CONCLUSION: Radioimmunotherapy with (131)I-chTNT was well tolerated and can be used systemically or locally to treat refractory tumors of the lung.

Adult↗

PubMed2005

Microsatellite instability in gastrointestinal tract cancers: a brief update.

Microsatellite instability (MSI) was initially reported in colorectal cancer and, particularly, in hereditary nonpolyposis colorectal cancer (HNPCC). Since mutations in the genes functioning in DNA mismatch repair (MMR) were found in HNPCC kindred, this phenotype has been connected to a deficiency in MMR. The MSI(+) phenotype is associated with various human malignancies. As MSI(+) tumors appear to form a unique clinicopathological and molecular entity that is clearly distinct from that of classical colorectal tumors, which are accompanied by chromosomal instability (CIN), an exclusive pathway of tumorigenesis has been proposed in colorectal cancer. However, this scheme, comprising two mutually exclusive pathways, is now being reexamined, in light of a series of evidence accumulating in the literature, which relates to (a) distinction between high-level MSI (MSI-H) and low-level MSI (MSI-L), (b) heterogeneity in MSI-H, particularly in the sporadic and hereditary settings, (c) molecular mechanisms underlying the MSI(+) phenotypes, and (d) relationships between the MSI(+) and CIN phenotypes. Several molecular mechanisms may underlie repeat instability in eukaryotic cells. The relationship between MSI and defective MMR may be more complicated than has been suspected. The role of MMR deficiency in tumorigenesis in the digestive tract appears to be diverse and is not simple, even in the colorectum.

Adaptor Proteins, Signal Transducing↗

PubMed2005

Development of a candidate vaccine for Newcastle disease virus by epitope display in the Cucumber mosaic virus capsid protein.

A peptide fusion to the capsid protein (CP) of Cucumber mosaic virus(CMV) was designed to express either a 17 amino acid (aa) neutralizing epitope of the Newcastle disease virus (NDV) fusion (F) protein or an eight aa neutralizing epitope of the NDV hemagglutinin-neuraminidase (HN) protein. Fusions of the F, HN and HN2 (duplicated HN epitope) were made in the internal betaH-betaI loop (motif 5) within the CMV CP. Recombinant RNA3 transcripts of the Ixora strain of CMV were inoculated on to Nicotiana benthamiana, together with CMV RNA1 and CMV RNA2. When the F and HN epitopes were placed in the internal motif, the modified virus was infectious and the HN NDV epitope was recognized by anti-NDV sera. However, in some plants, deletions of one to several of the inserted amino acids occurred. A duplication of the HN epitope rendered the virus non-viable.

Amino Acid Sequence↗

PubMed2005

Eicosapentaenoic acid prevents lipopolysaccharide-stimulated DNA binding of activator protein-1 and c-Jun N-terminal kinase activity.

Activator protein-1 (AP-1) is a transcription factor that plays an important role in regulating the expression of proinflammatory cytokines including tumor necrosis factor-alpha (TNF-alpha). Many studies have shown that fish oil supplementation inhibits TNF-alpha production in mice and humans; however, the mechanisms remain unclear. In this study, the effects of eicosapentaenoic acid (EPA), a major n-3 fatty acid in fish oil, on lipopolysaccharide (LPS)-stimulated activation of AP-1 were investigated in human monocytic THP-1 cells. The results demonstrated that AP-1 DNA binding activity stimulated by LPS was suppressed by preincubating cells with EPA. Lipopolysaccharide-stimulated increase of c-Jun and c-Fos protein levels was also attenuated by EPA pretreatment. In addition, EPA pretreatment decreased LPS-induced c-Jun phosphorylation and c-Jun N-terminal kinase (JNK) activation. The results suggest that suppression of TNF-alpha expression by EPA may be partly mediated by its inhibitory effect on AP-1 activation.

Cell Line↗

PubMed2005

Cryptic plasmid pSKU146 from the wall-less plant pathogen Spiroplasma kunkelii encodes an adhesin and components of a type IV translocation-related conjugation system.

A cryptic plasmid of the wall-less plant pathogenic mollicute, Spiroplasma kunkelii CR2-3X, was cloned and its sequence analyzed. The 14,615 bp plasmid, designated pSKU146, has a nucleotide content of 28 mol% G + C, and contains 18 potential protein-coding regions (open reading frames, ORFs), of which six encode proteins that exhibit similarity to virulence-associated proteins involved in cell-to-cell adhesion or conjugal DNA transfer. One ORF encodes a 96 kDa protein, SkARP1, that is highly similar to SARP1 adhesin involved in attachment of Spiroplasma citri to insect vector gut membrane. Five ORFs encode proteins similar to TraE and Mob in walled bacteria, and to ORFs found in the integrative, conjugative element (ICEF) of Mycoplasma fermentans, respectively. Presence of domains similar to proteins of the Type IV secretion system in pathogenic bacteria suggests that spiroplasma possesses a related translocation system. Plasmid pSKU146 also contains two identical oriT regions each containing a nick sequence characteristic of the IncP conjugative plasmid family, as well as a 58 bp palindromic sequence, palSK1. Features in pSKU146 suggest that the plasmid functions as a mobile genetic element in conjugative transmission of spiroplasma pathogenicity-related genes.

Adhesins, Bacterial↗

PubMed2005

Lineage-specific decay of folate biosynthesis genes suggests ongoing host adaptation in phytoplasmas.

Phytoplasmas are nonculturable cell wall-less, obligate intracellular pathogens of plants and insect vectors. In their descent from walled bacterial ancestors, phytoplasmas underwent massive genome reduction, resulting in some of the smallest cellular genomes known in nonsymbiotic bacteria. While requirements for in vitro culture of phytoplasmas remain unknown, two opposing reports have appeared concerning genes encoding the ability of phytoplasmas to synthesize folates de novo. One study found pseudogene homologs of folP and folK, obviating folate synthesis in "Candidatus Phytoplasma asteris"-related strain CPh, whereas, a separate study found intact genes encoding a complete folate biosynthesis pathway in "Ca. Phytoplasma asteris"-related strain OY. To resolve the apparent conflict, we hypothesized that evolutionary adaptation to the availability of folate and/or other metabolites in host cells is an ongoing process in the phytoplasma clade that is reflected in part by differences among phytoplasmas in the status of genes of the folate biosynthesis pathway. By studying folP and folK loci in 11 closely related phytoplasmas, we determined that these essential folate biosynthesis genes are intact in some phytoplasmas but are deteriorating in closely related strains. We suggest that the status of the folate biosynthesis pathway and the course of gene decay are lineage-specific, predicting the eventual, lineage-related loss of recognizable folP and folK homologs in phytoplasma genomes.

Adaptation, Physiological↗

PubMed2005

Phylogenetic positions of 'Candidatus Phytoplasma asteris' and Spiroplasma kunkelii as inferred from multiple sets of concatenated core housekeeping proteins.

Phytopathogenic mollicutes, which include spiroplasmas and phytoplasmas, are cell wall-less bacteria that parasitize plant hosts and insect vectors. Knowledge of the evolution of these agents is important in understanding their biology. The availability of the first complete phytoplasma and several partial spiroplasma and phytoplasma genome sequences made possible an investigation of evolutionary relationships between phytopathogenic mollicutes and other micro-organisms, especially Gram-positive bacteria, using a comparative genomics approach. Genome data from a total of 41 bacterial species were used in the analysis. Sixty-one conserved proteins were selected from each species for the construction of a hypothetical phylogenetic tree. The genes encoding these selected proteins are among a core of genetic elements that constitute a hypothetical minimal genome. The proteins were concatenated into five superproteins according to their functional categories, and phylogenetic trees were reconstructed using distance, parsimony and likelihood methods. Phylogenetic trees based on the five sets of concatenated proteins were congruent in both clade topology and relative branching length. Spiroplasma kunkelii and phytoplasmas clustered together with other mollicutes, forming a monophyletic group. Phytoplasmas diverged from spiroplasmas and mycoplasmas at early stages in the evolution of mollicutes. Branch lengths on the phylogenetic trees were noticeably longer in the Mollicutes clade, suggesting that the genes encoding the five sets of proteins evolved at a greater rate in this clade than in other clades. This observation reinforces the concept that mollicutes have rapidly evolving genomes.

Bacterial Proteins↗

PubMed2005

Histone H3 Ser10 phosphorylation-independent function of Snf1 and Reg1 proteins rescues a gcn5- mutant in HIS3 expression.

Gcn5 protein is a prototypical histone acetyltransferase that controls transcription of multiple yeast genes. To identify molecular functions that act downstream of or in parallel with Gcn5 protein, we screened for suppressors that rescue the transcriptional defects of HIS3 caused by a catalytically inactive mutant Gcn5, the E173H mutant. One bypass of Gcn5 requirement gene (BGR) suppressor was mapped to the REG1 locus that encodes a semidominant mutant truncated after amino acid 740. Reg1(1-740) protein does not rescue the complete knockout of GCN5, nor does it suppress other gcn5- defects, including the inability to utilize nonglucose carbon sources. Reg1(1-740) enhances HIS3 transcription while HIS3 promoter remains hypoacetylated, indicating that a noncatalytic function of Gcn5 is targeted by this suppressor protein. Reg1 protein is a major regulator of Snf1 kinase that phosphorylates Ser10 of histone H3. However, whereas Snf1 protein is important for HIS3 expression, replacing Ser10 of H3 with alanine or glutamate neither attenuates nor augments the BGR phenotypes. Overproduction of Snf1 protein also preferentially rescues the E173H allele. Biochemically, both Snf1 and Reg1(1-740) proteins copurify with Gcn5 protein. Snf1 can phosphorylate recombinant Gcn5 in vitro. Together, these data suggest that Reg1 and Snf1 proteins function in an H3 phosphorylation-independent pathway that also involves a noncatalytic role played by Gcn5 protein.

Alleles↗

PubMed2005

The effects of stellate ganglion block on visual evoked potential and blood flow of the ophthalmic and internal carotid arteries in patients with ischemic optic neuropathy.

Ischemic optic neuropathy (ION) is a common disease that can cause a loss of visual acuity in the elderly. We treated ION patients with stellate ganglion block (SGB) and investigated its effects on picture visual evoked potential (P-VEP) and blood flow in the ophthalmic artery (OA) and internal carotid artery (ICA). Twelve ischemic eyes in 12 patients diagnosed by the same ophthalmologist were investigated in this study. All patients were treated with daily SGB on the affected side with 2-3 mL of 2% lidocaine for a treatment period of 10-15 days. In ION eyes before SGB, compared with healthy eyes, the latency of P-VEP P(100) was delayed (123 +/- 14 ms versus 98 +/- 3 ms; P < 0.05), and the amplitude was reduced (4.24 +/- 1.76 microV versus 10.26 +/- 4.09 microV; P < 0.05). After SGB, the latency and amplitude returned to normal (103 +/- 6 ms versus 98 +/- 3 ms; 10.43 +/- 4.88 microV versus 10.26 +/- 4.09 microV; P > 0.05). Before treatment, the blood flow velocities of the OA and the ICA on the ischemic side were slow and the resistance indexes were high, but SGB reduced these changes. SGB did not affect the OA and the ICA on the healthy side. We conclude that SGB improves P-VEP and OA and ICA blood flow in ION eyes. Further studies are needed to confirm that this is an effective method for the treatment of ION.

Adult↗

PubMed2005

Analysis of the monosaccharide components in Angelica polysaccharides by high performance liquid chromatography.

An analytical method of on-line high performance liquid chromatography (HLPC) was developed to simultaneously separate and identify the monosaccharide composition of three Angelica polysaccharide fractions (APF), named APF1, APF2 and APF3. In this method, APF were hydrolyzed into component monosaccharides and subsequently labeled with 1-phenyl-3-methyl-5-pyrazolone (PMP), and then the labeled monosaccharide derivatives were separated by a reverse-phase C18 column and monitored by UV absorbance at 250 nm. The results showed that nine monosaccharide derivatives have been well separated by HPLC under optimized conditions and the composition analysis of monosaccharides from APF samples could be achieved using acid hydrolysis and a set of monosaccharide standards. With this method, the within-day and day to day precisions of the composition determinations were 3.41-4.87% and 3.12-4.93% (RSD), respectively. The method was successfully applied to the determination of the component monosaccharides of Angelica polysaccharides.

Angelica sinensis↗

PubMed2005

[The sequence polymorphism of Y-chromosome DNA and mtDNA of Dong Ethnic of Congjiang, Guizhou].

To study the patrilineal and matrilineal genetic structure and the origin of Dong Ethnic of Congjiang Guizhou. Study the distribution of Y-chromosome haplotypes which consisted of 10 SNPs of Y-DNA and mtDNA haplogroups consisted of 11 SNPs by using PCR-RFLP method. The result is three haplotypes H6,H11,H14 were detected, the frequency of H11 is 92.5%. Six haplogroups were identified by mtDNA analysis, 75% of the people can be identified. The patrilineal genetic structure of Dong of Guizhou is simple, Principle component indicated that the structure is closer to Zhuang-Dong branch of Sino-Tibetan language family. The matrilineal genetic structure of Dong of Guizhou is complicated.

Asian People↗

PubMed2005

[5, 10-methylenetetrahydrofolate reductase polymorphism in three nationalities of Guizhou in China].

OBJECTIVE: To study the genetic polymorphisms of methylenetetrahydrofolate reductase (MTHFR) among the Han, Buyi and Miao populations in Guizhou and to provide genetic data for establishment of the genetic polymorphism bank of Guizhou Minorities. METHODS: The technique of polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) was used to detect the genotype and allele frequencies at two mononucleotide sites (677 and 1298) of MTHFR among the Han population in Libo county, the Buyi population in Libo county and the Miao population in Leishan county. RESULTS: At the site of 677, the T allele frequencies were found to be 22.8%, 16.1%, 10.6%, for the Han, Buyi, Miao populations respectively. At the site of 1298, the C allele frequencies were 28.9%, 39.1%, 48.7% for the Han, Buyi, Miao populations respectively. The frequencies for the combined heterozygote of 677CT/1298AC were 16.66%, 22.7%, 11.1% for the three populations respectively. Moreover, one case with combined homozygote of 677TT/1298CC was seen in the Miao population. CONCLUSION: The polymorphisms of the two mononucleotide sites (677 and 1298) of MTHFR are diverse in different populations. The C allele frequencies at the site of MTHFR 1298 of the Miao population in Leishan county and the Buyi population in Libo county are high, and the C allele frequency in the Miao population is higher than those hitherto reported in literature.

Base Sequence↗