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Biomedical subjects

Yan Fu

Publications and source records attributed to Yan Fu.

At least 37 records · Page 2Linked to original sources
PubMed2005

Roles of forkhead transcription factor Foxc2 (MFH-1) and endothelin receptor A in cardiovascular morphogenesis.

OBJECTIVE: Foxc2/MFH-1 is a member of the forkhead family of transcription factors and Foxc2-deficient mice exhibit aortic arch anomalies (type B interruption of the aortic arch). Endothelin receptor type-A (ETA) is one of the two known endothelin receptors that belong to the G-protein-coupled receptor family. ETA-deficient mice show defects in the great arteries, primarily type B interruption of the aortic arch. Based on similar phenotypes in the cardiovascular system of Foxc2- and ETA-deficient mice, we investigated whether Foxc2 and ETA have a close relationship in aortic arch patterning. METHODS: The Foxc2 and ETA homozygotes were obtained by crossing the Foxc2 and ETA heterozygotes, respectively. The double Foxc2/ETA homozygotes were obtained by crossing the double Foxc2/ETA heterozygotes. RESULTS: We investigated the expression of ETA in Foxc2-null mice and the expression of Foxc2 in ETA-null mice and found that the absence of either Foxc2 or ETA had no effect on the expression of the other. Next, we analyzed mice lacking both Foxc2 and ETA to examine the relationship between Foxc2 and ETA on aortic arch patterning in vivo. We found that the majority of Foxc2/ETA double-mutant embryos died around 11.5 dpc and that all surviving mice had persistent truncus arteriosus. CONCLUSIONS: The results suggest that Foxc2- and ETA-expressing cells additively form the aorticopulmonary septum.

Animals↗
PubMed2005

Comparative analysis of expressed sequence tags from cold-acclimated and non-acclimated leaves of Rhododendron catawbiense Michx.

An expressed sequence tag (EST) analysis approach was undertaken to identify major genes involved in cold acclimation of Rhododendron, a broad-leaf, woody evergreen species. Two cDNA libraries were constructed, one from winter-collected (cold-acclimated, CA; leaf freezing tolerance -53 degrees C) leaves, and the other from summer-collected (non-acclimated, NA; leaf freezing tolerance -7 degrees C) leaves of field-grown Rhododendron catawbiense plants. A total of 862 5'-end high-quality ESTs were generated by sequencing cDNA clones from the two libraries (423 from CA and 439 from NA library). Only about 6.3% of assembled unique transcripts were shared between the libraries, suggesting remarkable differences in gene expression between CA and NA leaves. Analysis of the relative frequency at which specific cDNAs were picked from each library indicated that four genes or gene families were highly abundant in the CA library including early light-induced proteins (ELIP), dehydrins/late embryogenesis abundant proteins (LEA), cytochrome P450, and beta-amylase. Similarly, seven genes or gene families were highly abundant in the NA library and included chlorophyll a/b-binding protein, NADH dehydrogenase subunit I, plastidic aldolase, and serine:glyoxylate aminotransferase, among others. Northern blot analyses for seven selected abundant genes confirmed their preferential expression in either CA or NA leaf tissues. Our results suggest that osmotic regulation, desiccation tolerance, photoinhibition tolerance, and photosynthesis adjustment are some of the key components of cold adaptation in Rhododendron.

Acclimatization↗
PubMed2005

Hypoglycemic activity of jatrorrhizine.

The hypoglycemic activity and its mechanism of Jatrorrhizine (Jat) were studied. The normal mice and alloxan-induced hyperglycemic mice were given with different doses of Jat. Blood glucose and liver glycogen levels were determined by spectrophotometry with glucose-oxidase and iodine reagents respectively. The levels of blood lactic acid (LC) and liver lactate dehydrogenase (LDH) activity were measured to explore the effect of Jat on anaerobic glycolysis. Succinate dehydrogenase (SDH) activity in liver was measured to evaluate the effect of Jat on aerobic glycolysis in liver. It was found that Jat (50 mg/kg, 100 mg/kg) could significantly decrease blood glucose level in a dose- and time-dependent manner in both normal and alloxan-diabetic mice, increase the activity of SDH, but had no significant effects on the LC level and LDH activity. Jat could significantly reduce the content of liver glycogen in normal mice. Moreover, Jat could inhibit the platelet aggregation in rabbits in vitro in a dose-effect relationship. It was concluded that Jat induced the pronounced decrease in blood glucose in normal and hyperglycemic mice. The hypoglycemic activity of Jat may be attributed to the enhancement of aerobic glycolysis.

Animals↗
PubMed2005

Evaluation of five ab initio gene prediction programs for the discovery of maize genes.

Five ab initio programs (FGENESH, GeneMark.hmm, GENSCAN, GlimmerR and Grail) were evaluated for their accuracy in predicting maize genes. Two of these programs, GeneMark.hmm and GENSCAN had been trained for maize; FGENESH had been trained for monocots (including maize), and the others had been trained for rice or Arabidopsis. Initial evaluations were conducted using eight maize genes (gl8a, pdc2, pdc3, rf2c, rf2d, rf2e1, rth1, and rth3) of which the sequences were not released to the public prior to conducting this evaluation. The significant advantage of this data set for this evaluation is that these genes could not have been included in the training sets of the prediction programs. FGENESH yielded the most accurate and GeneMark.hmm the second most accurate predictions. The five programs were used in conjunction with RT-PCR to identify and establish the structures of two new genes in the a1-sh2 interval of the maize genome. FGENESH, GeneMark.hmm and GENSCAN were tested on a larger data set consisting of maize assembled genomic islands (MAGIs) that had been aligned to ESTs. FGENESH, GeneMark.hmm and GENSCAN correctly predicted gene models in 773, 625, and 371 MAGIs, respectively, out of the 1353 MAGIs that comprise data set 2.

Alternative Splicing↗
PubMed2005

Preprocessing of tandem mass spectrometric data based on decision tree classification.

In this study, we present a preprocessing method for quadrupole time-of-flight (Q-TOF) tandem mass spectra to increase the accuracy of database searching for peptide (protein) identification. Based on the natural isotopic information inherent in tandem mass spectra, we construct a decision tree after feature selection to classify the noise and ion peaks in tandem spectra. Furthermore, we recognize overlapping peaks to find the monoisotopic masses of ions for the following identification process. The experimental results show that this preprocessing method increases the search speed and the reliability of peptide identification.

Amino Acid Sequence↗
PubMed2005

[Study of chemical constituents of the essential oil from Inula britannica L. by GC-MS].

OBJECTIVE: The chemical components of the essential oil from Inula britannica L., which were collected from Yuncheng area of Shanxi province, were analyzed by GC-MS. METHODS: The essential oil was extracted from Inula britannica L. by steam distillation, the components were separated with the capillary chromatographic columns, the amount of the components from the essential oil was determined by normalization method. The components separated were identified by data search system. The chromatographic conditions were as follows: DB-5 (30m x 0.25mm, 0.25 microm) capillary column; High purity helium was used as carrier gas, and the flow rate was 1.0 ml/min; Column temperature: 70 degrees C keeping 2min, from 70 degrees C to 230 degrees C at rising rate 10 degrees C/min and keeping 10 min; Split ratio 15:1; Injector temperature 250 degrees C. RESULTS: 62 peaks were identified representing 68.4% of the total contents. Main component was 1-Benzoxepin-3-ol,2,3,4,5-tetrahydro-(4. 276% ). CONCLUSION: The method is so reliable, stable, and good reproducible that can be applied to the analysis of the essential oil from Inula britannica L.

Asteraceae↗
PubMed2005

[Newly progress in applications of Saccharomyces cerevisiae cell-surface engineering].

Saccharomyces cerevisiae cell-surface engineering is a newly genetic expressing system for fusion heterologous gene. With its ability of post-translational modification, and the convenience to identify and screen the expressed products, it is undergoing a marvelous progress in its newly applications, which include using as whole-cell biocatalyst, antigen/antibody library, bioadsorbent, biosensor, combinatory protein library, immunoassays and affinity purification. It performs a more and more important role in exploring the function and application of protein molecules.

Biosensing Techniques↗
PubMed2005

[Preparation and determination of 1-O-acetylbritannilactone in Inula Britannica L].

To prepare reference substance for quality control of Inula Britannica L., 1-O-acetylbritannilactone was extracted and separated from chloroform extraction of Inula Britannica L. Chemical structure of the 1-O-acetylbritannilactone product was elucidated by ultraviolet spectrometry (UV), infrared spectroscopy (IR), nuclear magnetic resonance (NMR) and mass spectrometry (MS), and the results were in agreement with the reference. The purity of the 1-O-acetylbritannilactone product was 99.5%, which satisfies the need of reference substances of traditional Chinese medicines. A method of high performance liquid chromatography-evaporative light scattering detection (HPLC-ELSD) is described for the determination of 1-O-acetylbritannilactone in Inula Britannica L. The chromatographic conditions include Hypersil ODS-2 column, a mixture of methanol-water (52: 48, v/v) with the flow rate of 1.0 mL/min used as mobile phase. The temperature of drift tube of the ELSD was 90 degrees C. Flow rate of carrier gas was 2.5 L/min. Linear range of 1-O-acetylbritannilactone was 1.37 - 8.21 microLg (r = 0.999 8). The average recovery of 1-O-acetylbritannilactone was 100.2% with the relative standard deviation (RSD) of 1.3% (n = 6). The method is simple, accurate, time saving and reproducible.

Chromatography, High Pressure Liquid↗
PubMed2004

Low stability of nucleocapsid protein in SARS virus.

The nucleocapsid protein (N protein) is one of the major virion structural proteins of a newly identified coronavirus, which has been confirmed as the causative agent of severe acute respiratory syndrome (SARS). The major function of N protein is to assemble the RNA of coronavirus. In the present study, the gene encoding the N protein was cloned and the protein was expressed, purified, and refolded as shown by (1)H NMR measurement. The maximal Trp emission wavelength occurs near 331 nm, suggesting substantial burial of Trp residues. Circular dichroism measurements indicate that N protein contains little alpha-helical structure. Acid titration shows that N protein begins to unfold near pH 5 and is fully denatured near pH 2.7, and the acid unfolding process is reversible. The physical and chemical properties of N protein indicate that its stability is low. N protein is denatured reversibly at pH 7.4 either by urea (with C(m) of 2.77 M and m value of 2.74 kcal mol(-1) M(-1)) or GdmCl (with C(m) of 1.46 M and m value of 4.50 kcal mol(-1) M(-1)). In the heat-induced denaturation in phosphate-buffered saline buffer, N-protein starts to unfold at 35 degrees C and is completely denatured at 55 degrees C, where SARS virus was also reported to be inactivated. We propose that the low stability of N protein may be critical for the stability and function of SARS virus.

Cations, Monovalent↗
PubMed2004

Types and frequencies of sequencing errors in methyl-filtered and high c0t maize genome survey sequences.

The Maize Genome Sequencing Consortium has deposited into GenBank more than 850,000 maize (Zea mays) genome survey sequences (GSSs) generated via two gene enrichment strategies, methylation filtration and high-C(0)t (HC) fractionation. These GSSs are a valuable resource for generating genome assemblies and the discovery of single nucleotide polymorphisms and nearly identical paralogs. Based on the rate of mismatches between 183 GSSs (105 methylation filtration + 78 HC) and 10 control genes, the rate of sequencing errors in these GSSs is 2.3 x 10(-3). As expected many of these errors were derived from insufficient vector trimming and base-calling errors. Surprisingly, however, some errors were due to cloning artifacts. These G.C to A.T transitions are restricted to HC clones; over 40% of HC clones contain at least one such artifact. Because it is not possible to distinguish the cloning artifacts from biologically relevant polymorphisms, HC sequences should be used with caution for the discovery of single nucleotide polymorphisms or paramorphisms. The average rate of sequencing errors was reduced 6-fold (to 3.6 x 10(-4)) by applying more stringent trimming parameters. This trimming resulted in the loss of only 11% of the bases (15,469/144,968). Due to redundancy among GSSs this more stringent trimming reduced coverage of promoters, exons, and introns by only 0%, 1%, and 4%, respectively. Hence, at the cost of a very modest loss of gene coverage, the quality of these maize GSSs can approach Bermuda standards, even prior to assembly.

DNA, Plant↗
PubMed2004

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.

MOTIVATION: The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information in a tunable and comprehensive manner has been lacking. RESULTS: This paper provides a promising approach to utilizing the correlative information for improving the peptide identification accuracy. The kernel trick, rooted in the statistical learning theory, is exploited to address this issue with low computational effort. The common scoring method, the tandem mass spectral dot product (SDP), is extended to the kernel SDP (KSDP). Experiments on a dataset reported previously demonstrate the effectiveness of the KSDP. The implementation on consecutive fragments shows a decrease of 10% in the error rate compared with the SDP. Our software tool, pFind, using a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy. SUPPLEMENTARY INFORMATION: http://www.jdl.ac.cn/user/yfu/pfind/index.html

Algorithms↗
PubMed2004

A strategy for assembling the maize (Zea mays L.) genome.

UNLABELLED: Because the bulk of the maize (Zea mays L.) genome consists of repetitive sequences, sequencing efforts are being targeted to its 'gene-rich' fraction. Traditional assembly programs are inadequate for this approach because they are optimized for a uniform sampling of the genome and inherently lack the ability to differentiate highly similar paralogs. RESULTS: We report the development of bioinformatics tools for the accurate assembly of the maize genome. This software, which is based on innovative parallel algorithms to ensure scalability, assembled 730,974 genomic survey sequences fragments in 4 h using 64 Pentium III 1.26 GHz processors of a commodity cluster. Algorithmic innovations are used to reduce the number of pairwise alignments significantly without sacrificing quality. Clone pair information was used to estimate the error rate for improved differentiation of polymorphisms versus sequencing errors. The assembly was also used to evaluate the effectiveness of various filtering strategies and thereby provide information that can be used to focus subsequent sequencing efforts.

Algorithms↗
PubMed2004

Determination of human complement3 by solid substrate room temperature phosphorescence immunoassay with a labelled avidin-biotin bridge.

A solid substrate room temperature phosphorescence immunoassay (SS-RTP-IA) for the determination of human complement3 (C3) based on a sandwich type assay and a labelled avidin-biotin (LAB) type assay was described. The anti-human complement3 and avidin were labeled with eosin5-isothiocyanate. On a polyamide membrane (PM), SS-RTP signals (lambda(ex)/lambda(em) = 535/678 nm) of immune complexes obtained by both assays were linear with the concentration of complement3 in the range of 6.25-100 ng/ml. The detection limits are 1.37 ng/ml for sandwich assay and 2.74 ng/ml for labeled avidin-biotin assay. (For a sample volume of 0.4 microl per spot, the mass detection limits are 0.546 and 1.09 pg/spot, respectively. If the molecular weight of human complement3 is 185,000, the detection limits are 2.95 and 5.91 amol per spot.) The results of determination of complement3 in 20 human sera obtained by labeled avidin-biotin SS-RTP-IA are correlated well with those obtained by ELISA. This study shows that SS-RTP-IA by whichever direct, sandwich or labeled avidin-biotin type assay can combine very well the characteristics of both the high sensitivity of SS-RTP and specificity of the immunoreaction.

Antibodies↗
PubMed2004

Potential role of p53 mutation in chemical hepatocarcinogenesis of rats.

AIM: Inactivation of p53 gene is one of the most frequent genetic alterations in carcinogenesis. The mutation status of p53 gene was analyzed, in order to understand the effect of p53 mutation on chemical hepatocarcinogenesis of rats. METHODS: During hepatocarcinogenesis of rats induced by 3'-methyl-4- dimethylaminoazobenzene (3'-Me-DAB), prehepatocarcinoma and hepatocarcinoma foci were collected by laser capture microdissection (LCM), and quantitatively analyzed for levels of p53 mRNA by LightCycler(TM) real-time RT-PCR and for mutations in p53 gene exons 5-8 by direct sequencing. RESULTS: Samples consisting of 44 precancerous foci and 24 cancerous foci were collected by LCM. A quantitative analysis of p53 mRNA showed that p53 mRNA peaked at an early stage (week 6) in the prehepatocarcinoma lesion, more than ten times that of adjacent normal tissue, and gradually decreased from week 6 to week 24. The expression of p53 mRNA in adjacent normal tissue was significantly lower than that in prehepatocarcinoma. Similar to prehepatocarcinoma, p53 mRNA in cancer was markedly higher than that in adjacent normal tissue at week 12, and was closer to normal at week 24. Direct p53 gene sequencing showed that 35.3% (24/68) (9 precancer, 15 cancer) LCM samples exhibited point mutations, 20.5% of prehepatocarcinoma LCM samples presented missense mutations at exon 6/7 or/and 8, and was markedly lower than 62.5% of hepatocarcinoma ones (P<0.01). Mutation of p53 gene formed the mutant hot spots at 5 codons. Positive immunostaining for p53 protein could be seen in prehepatocarcinoma and hepatocarcinoma foci at 24 weeks. CONCLUSION: p53 gene mutation is present in initial chemical hepatocarcinogenesis, and the mutation of p53 gene induced by 3'-Me-DAB is an important factor of hepatocarcinogenesis.

Animals↗
PubMed2004

[The application of DNA sequencing in studying haplotypes of PAI-1 gene in patients with coronary artery disease].

OBJECTIVE: Using simple and efficient DNA sequencing method to determine the haplotypes derived from 4G/5G and G/A polymorphisms in promoter of plasminogen activator inhibitor-1 (PAI-1) gene and trying to associate those haplotypes with coronary artery disease(CAD). METHODS: The frequencies and genotype distribution of the two PAI-1 gene variants in 93 CAD patients and 145 control subjects were determined via denaturing high-performance liquid chromatography (DHPLC) method. The heterozygotes for both polymorphism sites were directly sequenced to define the haplotypes based on the principle that heterozygotes of 4G/5G genotype were one guanine deletion and therefore one base shift from this site in sequencing graph results in particular wave pattern on -844G/A site. RESULTS: Only A-4G and G-5G haplotypes were detected in carriers heterozygous for both -6754G/5G and -844G/A polymorphisms sites though there are G-4G and A-5G haplotypes in carriers homozygous for both sites. No significant differences in haplotypes distribution were seen between CAD patients and control subjects. CONCLUSION: The DNA sequencing is objective and correct in determining haplotypes derived from two polymorphisms with distance less than about 400 bp apart and with one insertion/deletion polymorphism. And the haplotypes derived from -675 4G/5G and -844G/A polymorphisms are not associated with pathogenosis of CAD.

Aged↗
PubMed2004

[Analysis of gene expression profiles in heart tissues from two breeds of pigs].

To study the expression profiles in the heart tissues of domestic pigs,five un-normalized cDNA libraries from Danish adult female Landrace heart, biceps femoris, aorta, left ventricle tissues and Chinese adult female Erhualian heart tissue were constructed. Totally 35 180 expressed sequence tags (ESTs) were randomly sequenced. Using functional clustering and statistic methods, three gene clusters and 47 genes highly expressed in Landrace heart tissue were found. These genes are corresponding to the chaperone activity, motor activity and physiology process, implying the functional importance of the protection and movement process in heart. Between the two pig breeds, most of the differentially expressed genes are related with energy metabolism and catalytic activity, of which the majority are highly expressed in Landrace. The results indicate that the physiological activities of Landrace heart are more active and effective than Erhualian heart.

Animals↗
PubMed2003

pRB2/p130 target genes in non-small lung cancer cells identified by microarray analysis.

The retinoblastoma gene family consisting of RB/p105, p107, and RB2/p130 cooperate to regulate cell-cycle progression through the G1 phase of the cell cycle. Previous data demonstrated an independent role for the reduction or loss of pRb2/p130 expression in the formation and/or progression of lung carcinoma. Rb2/p130 is mutated in a human cell line of lung small cell carcinoma as well as in primary lung tumors. To identify potential pRb2/p130 target genes in an unbiased manner, we have utilized an adenovirus-mediated expression system of pRb2/p130 in a non-small lung cancer cell line to identify specific genes that are regulated by pRb2/p130. Using oligonucleotide arrays, a number of Rb2/p130 downregulated genes were identified and their regulation was confirmed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) and Western blot analysis. As a result, 40 genes showed greater than 2.0-fold modification in their expression level after the RB2/p130 viral transduction. In conclusion, coupling adenoviral overexpression with microarray and semiquantitative RT-PCR analyses proved to be a versatile strategy for identifying pRb2/p130 target genes and for better understanding the expression profiles of these genes. Our results may also contribute to identifying novel therapeutic biomarkers in lung carcinoma.

Adenoviridae↗