Biomedical subjects

Y Xu

Publications and source records attributed to Y Xu.

At least 1,099 records · Page 61Linked to original sources

PubMed1994

Recognizing exons in genomic sequence using GRAIL II.

We have described an improved neural network system for recognizing protein coding regions (exons) in human genomic DNA sequences. This coding region recognition system is part of a new version of GRAIL, GRAIL II, and represents a significant improvement over the coding recognition performance of the previous GRAIL system. GRAIL II divides the process of locating exons into four steps. It first generates an exon candidate pool consisting of all possible (translation start-donor), (acceptor-donor), and (acceptor-translation stop) pairs within all open reading frames of the test sequence. The vast majority of these exon candidates are eliminated from consideration by applying a set of heuristic rules. After reducing the size of the candidate pool, GRAIL II uses three trained neural networks to evaluate the coding potential and accuracy of the edges of starting exon, internal exon and terminal exon candidates. These networks output a set of overlapping candidates for each exon which differ by their scores and position of their edges. Multiple candidates for a given exon are grouped into a cluster based on their locations relative to candidates corresponding to other exons, and the highest scoring candidate for each cluster is used as the "best" prediction of the corresponding exon. Unlike the previous GRAIL version, GRAIL II uses variable-length windows to evaluate exon candidates and its performance is nearly independent of exon length. In addition to several strong indicators of coding potential, the system uses several other types of information including scores for splice junctions, GC composition, and the properties of the regions adjacent to an exon candidate, to aid in the discrimination process. On a large set of sequences from Genbank (3), GRAIL II located 93% of all exons regardless of size with a false positive rate of 12%. Among the true positives, 62% match the actual exons exactly (the exons edges are correct to the base), and 93% match at least one edge correctly. These statistics are further improved, especially the false positive rate and accuracy of the edges, through a process of gene model construction by the Gene Assembly Program (GAP III) (4) module of GRAIL II, which uses the scored exon candidates as input and constructs optimal gene models. The gene modeling system will be described elsewhere.

Amino Acid Sequence↗

PubMed1994

Construction and expression of high efficiency expressing plasmid of transforming growth factor alpha-Pseudomonas aeruginosa exotoxin fusion protein TGF alpha-PE40.

The XbaI/EcoRI cleaved TGF alpha-PE40 gene from plasmid pXY382 was inserted into the same cloning site of the expression vector pCB604 resulting in the plasmid p2X-TP1. E. coli BL21 (lambda DE3) cells were transformed with the p2X-TP1 and then induced with IPTG. The product expressed was accumulated mainly in the form of inclusion bodies. The expression level was closely related to the cell density, induction temperature and medium but not to the inductor dosage and the induction period within certain range. The expressed amount of the fusion protein TGF alpha-PE40 was about 50 mg/L.

Cloning, Molecular↗

PubMed1994

[Etiologic study on the relationship between HBV, HCV and HCC].

A total of 110 HCC patients were sampled randomly in 20 townships of Qidong county (a higher incidence area of HCC in China) from Mar. to Sept. 1989. Each patient was paired with two healthy persons as control. The results showed that the prevalences of HBV and HCV in 110 patients were 85.45% and 17.27% respectively, and were significantly higher that in control (50.45% and 4.09%). Using Conditional Logistic Regression Model. we found that the main risk factors of HCC in Qidong were HBsAg and Pre-S2 for HBV and anti-HCV for HCV. The OR value were 10.22, 2.96 and 2.63, respectively. Drinking tea was the only protective factor (OR = 0.36). Among 110 HCC patients. 13.64% were positive for both HBV and HCV. The OR value was the highest (6.48). 88.18% patients were either HBV or HCV positive. The OR values were similar (3.90 and 3.89). It suggests that the most important risk factor of HCC in Qidong was HBV infection because it had a higher prevalence among the population while the HCV infection having an equal OR value was also a risk factor.

Carcinoma, Hepatocellular↗

PubMed1994

[The effect of wheat germ agglutinin on anion transport in the erythrocyte membranes].

The wheat germ agglutinin (WGA) has been recognized as the lectin that can agglutinate human erythrocytes. It is reported recently that the binding of WGA to the glycophorin blocks the morphological conversions of discocyte<-->echinocyte. Glycophorin is thought to be associated with Band 3, the anion transport protein, via the cytoskeleton proteins Band 4.1, spectrin and ankyrin. The effect of WGA on the anion transport across the erythrocyte membranes was measured by NO2- transport and NH4 Cl isotonic swelling, two different methods developed by our laboratory in recent years. The results showed that the rate of anion transport was decreased, depending on WGA concentration. This effect became saturated when WGA concentration reached 2-3 micrograms/ml. We have also observed that in certain conditions when the morphological conversion of discocyte-->elliptocyte was induced by high concentration of WGA, the rate of anion transport could be reversely increased. Furthermore, the effect of WGA on erythrocyte osmotic fragility was studied. The results indicated that the osmotic fragility was reduced after adding WGA to the erythrocyte suspension, which means the erythrocyte cytoskeleton is more stable under this condition. All effects that WGA exerted above were instantly abolished by adding N-acetylglucosamine which has specific binding sites on WGA. In conclusion, the binding of WGA to the sialic acid groups of glycophorin can lead to the conformational changes in saccharides and such changes will be transferred via glycophorin, cytoskeleton to Band 3, which causes the final change of anion transport. The effect is indirect, so the change is small (approximately 10%).(ABSTRACT TRUNCATED AT 250 WORDS)

Acetylglucosamine↗

PubMed1994

The roots of dentistry in ancient China.

The history of dentistry in China is closely aligned with the remarkable developments in Chinese medicine over at least six millennia. Rudimentary dental extractions were performed as early as 6000 BC, when the first signs of adornment with human teeth were described. There were actually four distinct periods of medical development in China: the Mystical Period; the Golden Period; the Controversial Period; and the Transitional Period. The Golden Period was marked by the appearance of the first textbooks to describe preventive and restorative dental techniques, as well as the first colleges. Dentistry then moved through the dark times of the Controversial Period, when war mongering stymied progress. Lasting until 1800 AD, it came to an end with the domination of Western medicine and dentistry. This paper chronicles the development of dentistry in China, revealing that it has been a part of Chinese life for a long time.

China↗

PubMed1994

Characterization of chondrocyte alkaline phosphatase as a potential mediator in the dissolution of calcium pyrophosphate dihydrate crystals.

OBJECTIVE: To characterize chondrocyte alkaline phosphatase (ALP) distribution and expression in cartilage and monolayer cultures. METHODS: Sections of bovine articular cartilage or chondrocyte monolayer cultures were stained for ALP activity. Surface ALP was released with bacterial phosphatidylinositol specific phospholipase C (PI-PLC). The levels of ALP mRNA were determined by Northern blot analysis using a cDNA probe to bovine ALP. RESULTS: Chondrocyte ALP activity dissolves calcium pyrophosphate dihydrate (CPPD) crystals. About 5% of the total chondrocytes contained ALP activity. The ALP positive cells were present only in the deep layers of articular cartilage adjacent to the subchondral bone. Thirty to forty percent of the total ALP activity was present on the chondrocyte surface and was released by PI-PLC. Both chondrocyte ALP activity and mRNA levels decreased with time in culture. However, continuous dexamethasone treatment stimulated the expression of ALP in ALP positive chondrocytes, sufficiently to replace all of the chondrocyte surface ALP released following PI-PLC treatment. CONCLUSION: Since ALP hydrolyzes pyrophosphate and dissolves CPPD crystals, our data suggest that regulation of chondrocyte ALP activity and expression in cartilage may prove useful for the development of a specific therapy CPPD arthropathy.

Alkaline Phosphatase↗

PubMed1994

[New species of Haloarcula].

Three strains of pleomorphic halobacteria (A5, B2 and B-B2) were isolated from salt lakes of Xinjiang, China. Based on the Bergey's Manual of Systematic Bacteriology, Volume 3 (1989) and the analytical results of polar lipids, the three strains could be included in the genus Haloarcula. But since they differ from normally accepted two species of this genus in cell shape and physiological and biochemical features, it is suggested that the three strains belong to a new species, called Haloarcu la aidinensis sp. nov.

China↗

PubMed1994

Identification and characterization of pleural neurons that inhibit tail sensory neurons and motor neurons in Aplysia: correlation with FMRFamide immunoreactivity.

Neurons on the rostral edge of the ventral surface of the right pleural ganglion were identified as elements of the circuit mediating the defensive tail withdrawal reflex of Aplysia. These neurons produced IPSPs in tail sensory neurons and were classified into two groups, RPI4 and RPI5, according to their affinity for an antibody directed against FMRFamide. RPI4 was not FMRFamide immunoreactive, and RPI5 was. RPI4 and RPI5 were found to have different electrophysiological profiles. The summated IPSPs in sensory neurons produced by RPI4 developed more rapidly and had a shorter duration than those produced by RPI5. In addition, RPI4 produced IPSPs in the tail motor neurons, whereas RPI5 did not. Both RPI4 and RPI5 received excitatory synaptic inputs from stimulation of the pleural-abdominal connective as well as peripheral nerves P8 and P9, which innervate the tail and posterior part of the animal's body. These inputs were sufficient to elicit spikes. In RPI4, the excitatory synaptic inputs were followed by short and transient hyperpolarization, whereas in RPI5, the excitatory synaptic inputs were followed by slow and long-lasting hyperpolarization. Excitatory inputs elicited in RPI4 by stimulation of peripheral nerves appeared to be mediated, at least in part, by activation of tail sensory neurons. Intracellular stimulation of sensory neurons produced EPSPs in RPI4 that appeared to be monosynaptic. These results suggest that inhibitory interneurons underlying the circuit of the tail withdrawal reflex may play roles in mediating or modulating neuronal responses to tail stimulation. By inhibiting tail sensory and motor neurons, these interneurons may reduce the effectiveness of an animal's response to stimulation of the tail.

Animals↗

PubMed1994

[Amplification of 16S rDNAs from halobacteria by means of PCR technique].

The 16S rDNAs have been amplified from four halobacteria Haloarcula vallismortis (EM201), Haloferax denitrificans (EM303). A5 and B2 through a set of specific primers using the PCR technique. The molecule of the PCR products is about 1.47 kb. The hybridization results also show that these PCR products have DNA homology with halobacteria.

Base Sequence↗

PubMed1993

Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4.

The three-dimensional structure of a yeast ubiquitin-conjugating enzyme, encoded by the Saccharomyces cerevisiae UBC4 gene, has been determined at 2.7 A. The structure was solved using molecular replacement techniques and refined by simulated annealing to an R-factor of 0.198. Bond lengths and angles in the molecule have root mean square deviations from ideal values of 0.018 A and 4.0 degrees, respectively. Ubc4 is an alpha/beta protein with four alpha-helices and a four-stranded antiparallel beta-sheet. The ubiquitin-accepting cysteine is located in a cleft between two loops. Comparison with the recently determined structure of a different plant enzyme suggests that class I ubiquitin-conjugating enzymes are highly conserved in their three-dimensional folding. Except for two extra residues at the N- and the C-terminus of the plant enzyme, the C alpha atoms of the two enzymes can be superimposed with a root mean square deviation of only 1.52 A. Greater variations are found between the surfaces of the two molecules, as most of the identical residues between the two enzymes are either buried or clustered on the surface that lies adjacent to the ubiquitin-accepting cysteine. We suggest that this conserved surface functions in protein-protein binding during ubiquitin thiol ester formation.

Amino Acid Sequence↗

PubMed1993

Action of toosendanin on the membrane current of mouse motor nerve terminals.

By perineurial recording, the actions of toosendanin on three potassium currents and two calcium currents in the nerve terminal were observed in the intercostal nerve triangularis stein muscle of the mouse. Toosendanin partially blocked the voltage-dependent fast K+ current and irreversibly increased the voltage-dependent slow Ca2+ current. The increase in the Ca2+ current of the nerve terminal accounts for the facilitation of transmitter release and the antibotulismic effect of toosendanin.

Animals↗

PubMed1993

Functional polymorphism in the parental imprinting of the human IGF2R gene.

The murine genes coding for insulin-like growth factor II (Igf2) and its specific receptor (Igf2r) are parentally imprinted, with exclusive expression from the paternal (Igf2) or maternal (Igf2r) gene copy. We have demonstrated that the human IGF2 gene is imprinted, like its murine homologue. To examine whether the human IGF2R is also imprinted, we used CA repeat polymorphisms of the cDNA sequence to distinguish expression from each copy. Unlike the mouse, most subjects equally expressed both gene copies. However, two out of 14 informative fetuses showed exclusive expression from the maternal gene copy. We conclude that the human IGF2R gene is parentally imprinted, like its murine homologue, but only in a minority of individuals. This is the first direct demonstration of imprinting as a polymorphic trait, a property that had been observed in transgene methylation and predicted from the behavior of certain human tumors.

Animals↗

PubMed1993

Autocrine release of angiotensin II mediates stretch-induced hypertrophy of cardiac myocytes in vitro.

Hypertrophy is a fundamental adaptive process employed by postmitotic cardiac and skeletal muscle in response to mechanical load. How muscle cells convert mechanical stimuli into growth signals has been a long-standing question. Using an in vitro model of load (stretch)-induced cardiac hypertrophy, we demonstrate that mechanical stretch causes release of angiotensin II (Ang II) from cardiac myocytes and that Ang II acts as an initial mediator of the stretch-induced hypertrophic response. The results not only provide direct evidence for the autocrine mechanism in load-induced growth of cardiac muscle cells, but also define the pathophysiological role of the local (cardiac) renin-angiotensin system.

Actins↗

PubMed1993

Method for isolation of non-esterified fatty acids and several other classes of plasma lipids by column chromatography on silica gel.

A method is described for isolation from human plasma of non-esterified fatty acids, cholesteryl esters, triglycerides, cholesterol and diglycerides, monoglycerides, and some phospholipids by extraction and silica gel column chromatography. All of these lipid classes except diglycerides and cholesterol were separated cleanly in seven elution steps. Diglycerides and cholesterol were isolated together. Recovery of model compounds which represent the most significant classes of plasma lipids during the column chromatographic step was nearly complete. The overall recovery of added heptadecanoic acid from plasma specimens was 81% after both sample isolation steps. The overall recovery of added synthetic pentadecanoic acid and heptadecanoic acid ester lipid homologues from plasma was 80-91% after both sample preparation steps. About 6 h are required for extraction and isolation in duplicate of these lipid classes from twenty plasma specimens. Alternatively, non-esterified fatty acids can be isolated from twenty plasma specimens in duplicate within 4 h by a variation of the full procedure.

Cholesterol Esters↗

PubMed1993

Heat-shock protein hsp90 governs the activity of pp60v-src kinase.

During or immediately after synthesis in vertebrate cells, the oncogenic protein-tyrosine kinase pp60v-src associates with the approximately 90-kDa heat-shock protein (hsp90). In this complex, pp60v-src is not functional as a kinase. When pp60v-src is subsequently found inserted into the plasma membrane, it is active as a kinase and is no longer associated with hsp90. We have taken advantage of genetic manipulations possible in Saccharomyces cerevisiae to investigate the function and specificity of the association between hsp90 and pp60v-src. Expression of pp60v-src is known to be toxic to S. cerevisiae cells. We find that this toxicity is due to a very specific effect on growth, arrest at a particular point in the cell cycle. In cells expressing v-src, a mutation that lowers the level of hsp90 expression (i) relieves cell cycle arrest and rescues growth, (ii) reduces the level of tyrosine phosphorylation mediated by pp60v-src, (iii) changes the pattern of tyrosine phosphorylation, and (iv) reduces the concentration of pp60v-src. We conclude that hsp90 does not simply suppress pp60v-src kinase activity during transit to the plasma membrane, as previously suggested, but also stabilizes the protein and affects both its activity and specificity. This function of hsp90 is highly selective for pp60v-src: the same hsp90 mutation has no effect on the activity or specificity of the exogenous pp160v-abl tyrosine kinase; similarly, it does not affect the specificity and has only a very small effect on the activity of the exogenous pp60c-src kinase.

Cell Cycle↗

PubMed1993

Defective stimulation of cyclic AMP by prostaglandin E2 in colonic epithelial cells in colitis.

The present study investigated the effect of vasoactive intestinal peptide and prostaglandin E2 on cyclic adenosine monophosphate levels in isolated colonocytes during experimental colitis. Intra-rectal trinitrobenzenesulfonic acid induced a colitis-like inflammation in the rabbit distal colon. Basal levels of cyclic adenosine monophosphate were similar in control and colitic colonocytes. Levels were increased by prostaglandin E2 and vasoactive intestinal peptide in control cells. Colonocytes from colitic tissue responded to vasoactive intestinal peptide normally, but exhibited an attenuated response to prostaglandin E2. We conclude during colitis the epithelium exhibits a specific alteration in prostaglandin E2 receptor number, affinity or adenylate cyclase coupling.

Animals↗

PubMed1993

Molecular cloning and expression of a cDNA encoding a novel isoenzyme of protein kinase C (nPKC). A new member of the nPKC family expressed in skeletal muscle, megakaryoblastic cells, and platelets.

At least seven bacteriophage lambda clones encoding structurally related but unique polypeptides with PKC activity have been isolated from mammalian brain, epidermis, and lung cDNA libraries. The possibility that additional isoenzymes are expressed in human blood platelets or megakaryoblastoid human erythroleukemia cells was examined by polymerase chain reaction amplification of reverse transcribed RNA employing oligonucleotide primers corresponding to conserved peptide sequences. cDNAs encoding a novel PKC-related sequence, designated PKC-theta, and four (alpha, beta, delta, and eta) previously identified isoenzymes were isolated from reverse transcribed total RNA of human erythroleukemia cells and platelets. PKC-theta lacks a conserved region (C2) that is present in the calcium-dependent isoenzymes and therefore belongs to the group of novel, or nPKC, isoenzymes. Significantly increased [3H] phorbol 12,13-dibutyrate binding and cytoskeleton-associated calcium-independent PKC activity were found in COS cells expressing the transfected cDNA. Northern transfer analysis of mRNA from various human tissues revealed high level expression of PKC-theta in skeletal muscle, lung, and brain, and minimal expression in cardiac muscle, placenta, and liver. These findings extend the PKC family and suggest a novel approach to the study of diversity within this pathway of intracellular signal transduction.

Amino Acid Sequence↗

PubMed1993

Molecular cloning and sequencing of a human somatostatin receptor, hSSTR4.

We recently reported the cloning of a somatostatin receptor (SSTR) subtype from a rat genomic library designated rSSTR4. In the present study, we report the cloning of the human SSTR4 gene. A human genomic library was screened with a 1.2 kb fragment of rSSTR4 containing the full open reading frame and a genomic clone, hSSTR4, was isolated. The deduced amino acid sequence of this clone encoded a protein of 388 amino acids and is a member of the G-protein coupled receptor superfamily. Comparison of rat and human SSTR4 sequences demonstrated 89% identity. In addition, the sequence of hSSTR4 shows 61%, 46%, and 47% sequence identity with previously identified isoforms hSSTR1, hSSTR2, and hSSTR3, respectively.

Amino Acid Sequence↗