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Biomedical subjects

Wei Yang

Publications and source records attributed to Wei Yang.

At least 163 records · Page 9Linked to original sources
PubMed2003

Genetic variation of infant reduced folate carrier (A80G) and risk of orofacial and conotruncal heart defects.

How folate reduces the risks of congenital anomalies is unknown. The authors focused on a gene involved in folate transport-reduced folate carrier-1 gene (RFC1). Using data from a California case-control study (1987-1989 births), the authors investigated whether the risks of orofacial clefts or conotruncal heart defects were influenced by a polymorphism of infant RFC1 or by an interaction between the RFC1 gene and maternal periconceptional use of vitamins containing folic acid. A total of 305 liveborn infants with cleft lip with or without cleft palate, 123 with cleft palate, 163 with conotruncal heart defects, and 364 nonmalformed controls were genotyped. Odds ratios of 1.6 (95% confidence interval: 0.9, 2.8) for the G80/G80 genotype and of 2.3 (95% confidence interval: 1.3, 3.9) for the G80/A80 genotype were observed relative to the A80/A80 genotype for conotruncal defects. Among mothers who did not use vitamins, the risk of conotruncal defects was 2.1 (95% confidence interval: 0.7, 5.9) for infants with genotype G80/G80 compared with those with the A80/A80 genotype. Among mothers who did use vitamins, the risk was 1.3 (95% confidence interval: 0.7, 2.7). Substantially elevated risks for either cleft group were not observed irrespective of genotype and use/nonuse of vitamins. Thus, this study found modest evidence for a gene-nutrient interaction between infant RFC1 genotype and periconceptional intake of vitamins on the risk of conotruncal defects.

California↗
PubMed2003

A model for the cooperative free energy transduction and kinetics of ATP hydrolysis by F1-ATPase.

Although the binding change mechanism of rotary catalysis by which F1-ATPase hydrolyzes ATP has been supported by equilibrium, kinetic, and structural observations, many questions concerning the function remain unanswered. Because of the importance of this enzyme, the search for a full understanding of its mechanism is a key problem in structural biology. Making use of the results of free energy simulations and experimental binding constant measurements, a model is developed for the free energy change during the hydrolysis cycle. This model makes possible the development of a kinetic scheme for ATP hydrolysis by F1-ATPase, in which the rate constants are associated with specific configurations of the beta subunits. An essential new element is that the strong binding site for ADP,Pi is shown to be the betaDP site, in contrast to the strong binding site for ATP, which is betaTP. This result provides a rationale for the rotation of the gamma subunit, which induces the cooperativity required for a tri-site binding change mechanism. The model explains a series of experimental data, including the ATP concentration dependence of the rate of hydrolysis and catalytic site occupation for both the Escherichia coli F1-ATPase (EcF1) and Thermophilic Bacillus PS3 F1-ATPase (TF1), which have different behavior.

Adenosine Triphosphate↗
PubMed2003

Replication of a cis-syn thymine dimer at atomic resolution.

Ultraviolet light damages DNA by catalysing covalent bond formation between adjacent pyrimidines, generating cis-syn cyclobutane pyrimidine dimers (CPDs) as the most common lesion. CPDs block DNA replication by high-fidelity DNA polymerases, but they can be efficiently bypassed by the Y-family DNA polymerase pol eta. Mutations in POLH encoding pol eta are implicated in nearly 20% of xeroderma pigmentosum, a human disease characterized by extreme sensitivity to sunlight and predisposition to skin cancer. Here we have determined two crystal structures of Dpo4, an archaeal pol eta homologue, complexed with CPD-containing DNA, where the 3' and 5' thymine of the CPD separately serves as a templating base. The 3' thymine of the CPD forms a Watson-Crick base pair with the incoming dideoxyATP, but the 5' thymine forms a Hoogsteen base pair with the dideoxyATP in syn conformation. Dpo4 retains a similar tertiary structure, but each unusual DNA structure is individually fitted into the active site for catalysis. A model of the pol eta-CPD complex built from the crystal structures of Saccharomyces cerevisiae apo-pol eta and the Dpo4-CPD complex suggests unique features that allow pol eta to efficiently bypass CPDs.

Amino Acid Sequence↗
PubMed2003

Novel concepts mediate word retrieval from human episodic associative memory: evidence from event-related potentials.

Effects of conceptual fusion on episodic associative retrieval were examined. Subjects attempted to fuse sequentially displayed (800 ms offset) word pairs; pairs subjects were unable to fuse were instead considered associated by juxtaposition. Next, dense-array event-related potentials (ERPs) were recorded while the pairs were redisplayed, half reversed in order. Subjects pressed a button to indicate whether each pair was presented in the previous order. Behavioral results showed that retrieval of fused pairs was faster and more accurate than for juxtaposed pairs. ERP topography to the first word of fused pairs was different from juxtaposed pairs, indicating that fusion can mediate associative retrieval of constituent items. Estimates of current source density at the cortical surface showed that fusion-mediated retrieval elicited left inferior-prefrontal/anterior-temporal activity not typically observed in episodic memory retrieval studies.

Adolescent↗
PubMed2003

Monovalent cation dependence and preference of GHKL ATPases and kinases.

The GHKL phosphotransferase superfamily, characterized by four sequence motifs that form the ATP-binding site, consists of the ATPase domains of type II DNA topoisomerases, Hsp90, and MutL, and bacterial and mitochondrial protein kinases. In addition to a magnesium ion, which is essential for catalysis, a potassium ion bound adjacent to the triphosphate moiety of ATP in a rat mitochondrial protein kinase, BCK (branched-chain alpha-ketoacid dehydrogenase kinase), has been shown to be indispensable for nucleotide binding and hydrolysis. Using X-ray crystallographic, biochemical, and genetic analyses, we find that the monovalent cation-binding site is conserved in MutL, but both Na(+) and K(+) support the MutL ATPase activity. When Ala100 of MutL is substituted by proline, mimicking the K(+)-binding environment in BCK, the mutant MutL protein becomes exclusively dependent on Na(+) for the ATPase activity. The coordination of this Na(+) ion is identical to that of the K(+) ion in BCK and involves four carbonyl oxygen atoms emanating from the hinges of the ATP lid and a non-bridging oxygen of the bound nucleotide. A similar monovalent cation-binding site is found in DNA gyrase with additional coordination by a serine side chain. The conserved and protein-specific monovalent cation-binding site is unique to the GHKL superfamily and probably essential for both ATPase and kinase activity. Dependence on different monovalent cations for catalysis may be exploited for future drug design specifically targeting each individual member of the GHKL superfamily.

Adenosine Triphosphatases↗
PubMed2003

Rational design of a calcium-binding protein.

Calcium ions play key roles as structural components in biomineralization and as a second messenger in signaling pathways. We have introduced a de novo designed calcium-binding site into the framework of a non-calcium-binding protein, domain 1 of CD2. The resulting protein selectively binds calcium over magnesium with calcium-binding affinity comparable to that of natural extracellular calcium-binding proteins (K(d) of 50 microM). This experiment is the first successful metalloprotein design that has a high coordination number (seven) metal-binding site constructed into a beta-sheet protein. Our results demonstrate the feasibility of designing a single calcium-binding site into a host protein, taking into account only local properties of a calcium-binding site obtained by a survey of natural calcium-binding proteins and chelators. The resulting site exhibits strong metal selectivity, suggesting that it should now be feasible to understand and manipulate signaling processes by designing novel calcium-modulated proteins with specifically desired functions and to affect their stability.

Binding Sites↗
PubMed2003

In vitro and in vivo studies of MutS, MutL and MutH mutants: correlation of mismatch repair and DNA recombination.

We have used the recently determined crystal structures of Escherichia coli (E. coli) MutS, MutL and MutH to guide construction of 47 amino-acid substitutions in these proteins and analyzed their behavior in mismatch repair and recombination in vitro and in vivo. We find that the active site of the MutH endonuclease is composed of regions from two separate structural domains and that the C-terminal 5 residues of MutH influence both DNA binding and cleavage. We also find that the non-specific DNA-binding activity of MutL is required for mismatch repair and probably functions after strand cleavage by MutH. Alteration of residues in either the mismatch recognition domain, the ATPase active site, or the domain interfaces linking the two activities can diminish the differential binding of MutS to homoduplex versus heteroduplex and results in the loss of mismatch-specific MutH activation. Finally, every mutation that abolishes mismatch repair is deficient in blocking homeologous recombination, suggesting that mismatch repair and prevention of homeologous recombination use the same MutS-MutL complexes for signaling in E. coli.

Adenosine Triphosphatases↗
PubMed2003

Crystal structure and biochemical analysis of the MutS.ADP.beryllium fluoride complex suggests a conserved mechanism for ATP interactions in mismatch repair.

During mismatch repair ATP binding and hydrolysis activities by the MutS family proteins are important for both mismatch recognition and for transducing mismatch recognition signals to downstream repair factors. Despite intensive efforts, a MutS.ATP.DNA complex has eluded crystallographic analysis. Searching for ATP analogs that strongly bound to Thermus aquaticus (Taq) MutS, we found that ADP.beryllium fluoride (ABF), acted as a strong inhibitor of several MutS family ATPases. Furthermore, ABF promoted the formation of a ternary complex containing the Saccharomyces cerevisiae MSH2.MSH6 and MLH1.PMS1 proteins bound to mismatch DNA but did not promote dissociation of MSH2.MSH6 from mismatch DNA. Crystallographic analysis of the Taq MutS.DNA.ABF complex indicated that although this complex was very similar to that of MutS.DNA.ADP, both ADP.Mg(2+) moieties in the MutS. DNA.ADP structure were replaced by ABF. Furthermore, a disordered region near the ATP-binding pocket in the MutS B subunit became traceable, whereas the equivalent region in the A subunit that interacts with the mismatched nucleotide remained disordered. Finally, the DNA binding domains of MutS together with the mismatched DNA were shifted upon binding of ABF. We hypothesize that the presence of ABF is communicated between the two MutS subunits through the contact between the ordered loop and Domain III in addition to the intra-subunit helical lever arm that links the ATPase and DNA binding domains.

Adaptor Proteins, Signal Transducing↗
PubMed2003

Maternal periconceptional alcohol consumption and risk for conotruncal heart defects.

BACKGROUND: In this study we investigated whether the risk of delivering infants with conotruncal heart defects was increased among mothers who consumed alcohol during the periconceptional period (i.e., 1 month before conception to 3 months after conception). METHODS: Data were obtained from a population-based case-control study of California births from 1987-1988. Information concerning alcohol consumption was obtained via telephone interviews with mothers of 207 (87% of eligibles) case infants and 481 (76%) nonmalformed control infants. RESULTS: Bivariate results indicated that relative to nonconsumers, women who consumed alcohol less than once a week had a 1.3-fold increased risk of delivering infants with a conotruncal heart defect (95% confidence interval (CI) 1.0, 1.9), and women who consumed alcohol once a week or more had a 1.9-fold increased risk (95% CI 1.0, 3.4). The risks associated with consuming five or more drinks per drinking occasion were 1.6 (95% CI 0.8, 3.2) for less than once a week, and 2.4 for once a week or more (95% CI 0.6, 9.7). The results for the phenotypic subgroups were similar to those for all cases. Adjustment for potential covariates resulted in somewhat weaker, but still elevated, risks. CONCLUSIONS: This study found that the risk of conotruncal heart defects in offspring was moderately elevated among women who consumed alcoholic beverages during the periconceptional period, and that risk was higher with increased frequency of drinking or increased number of drinks consumed per occasion. Most of the risk estimates were imprecise, and chance could not be ruled out as an explanation for the observed findings.

Adult↗
PubMed2003

Damage repair DNA polymerases Y.

The newly found Y-family DNA polymerases are characterized by low fidelity replication using an undamaged template and the ability to carry out translesion DNA synthesis. The crystal structures of three Y-family polymerases, alone or complexed with DNA and nucleotide substrate, reveal a conventional right-hand-like catalytic core consisting of finger, thumb and palm domains. The finger and thumb domains are unusually small resulting in an open and spacious active site, which can accommodate mismatched base pairs as well as various DNA lesions. Although devoid of a 3'-->5' exonuclease activity, the Y-family polymerases possess a unique "little finger" domain that facilitates DNA association, catalytic efficiency and interactions with auxiliary factors. Expression of Y-family polymerases is often induced by DNA damage, and their recruitment to the replication fork is mediated by beta-clamp, clamp loader, single-strand-DNA-binding protein and RecA in Escherichia coli, and by ubiquitin-modified proliferating cell nuclear antigen in yeast.

Binding Sites↗
PubMed2003

Small molecule integrin antagonists that bind to the beta2 subunit I-like domain and activate signals in one direction and block them in the other.

Leukocyte integrins contain an inserted (I) domain in their alpha subunits and an I-like domain in their beta(2) subunit, which directly bind ligand and regulate ligand binding, respectively. We describe a novel mechanistic class of integrin inhibitors that bind to the metal ion-dependent adhesion site of the beta(2) I-like domain and prevent its interaction with and activation of the alpha(L) I domain. The inhibitors do not bind to the alpha(L) I domain but stabilize alpha/beta subunit association and can show selectivity for alpha(L)beta(2) compared to alpha(M)beta(2). The inhibitors reveal a crucial intersection for relaying conformational signals within integrin extracellular domains. While blocking signals in one direction to the I domain, the antagonists induce the active conformation of the I-like domain and stalk domains, and thus transmit conformational signals in the other direction toward the transmembrane domains.

Allosteric Regulation↗
PubMed2003

Product-assisted catalysis in base-excision DNA repair.

Most spontaneous damage to bases in DNA is corrected through the action of the base-excision DNA repair pathway. Base excision repair is initiated by DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in DNA and catalyze their excision. How such proteins accomplish the feat of catalyzing no fewer than five sequential reaction steps using a single active site has been unknown. To help answer this, we report the structure of a trapped catalytic intermediate in DNA repair by human 8-oxoguanine DNA glycosylase. This structure and supporting biochemical results reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an enzyme-catalyzed reaction.

Amino Acid Substitution↗
PubMed2003

Neural tube defects associated with maternal periconceptional dietary intake of simple sugars and glycemic index.

BACKGROUND: Maternal diabetes, prepregnancy obesity, hyperinsulinemia, and intakes of sweets have been associated with increased risks of neural tube defects (NTDs). The interdependence of these factors suggests a common pathogenesis via altered glycemic control and insulin demand. OBJECTIVE: We investigated whether maternal periconceptional dietary intakes of sucrose, glucose, fructose, and foods with higher glycemic index values influence the risk of having NTD-affected pregnancies. DESIGN: In a population-based case-control study, all hospitals in 55 of the 58 counties in California participated. In-person interviews were conducted with the mothers of 454 NTD cases (including fetuses and infants who were electively terminated, stillborn, or born alive) and with the mothers of 462 nonmalformed controls within an average of 5 mo from the term delivery date. The risk of having an NTD-affected pregnancy was the main outcome measure. RESULTS: Risks of having an NTD-affected pregnancy were not substantially elevated in relation to periconceptional intakes of glucose or fructose. Elevated risks of approximately 2-fold were observed for higher intakes of sucrose and foods with higher glycemic index values. Elevated risks were observed for high sucrose intake irrespective of whether adjustment was made for other covariates such as maternal folic acid intake. For higher glycemic index values, adjusted elevated risks of > or = 4-fold were observed in women whose body mass index (in kg/m(2)) was > 29. CONCLUSION: Our observed associations support observations that potential problems in glucose control are associated with NTD risk even among nondiabetic women.

Adult↗
PubMed2003

Effect of NF-kappaB and p38 MAPK in activated monocytes/macrophages on pro-inflammatory cytokines of rats with acute pancreatitis.

AIM: Proinflammatory cytokines TNF-alpha and IL-6 play a main role in acute pancreatitis (AP). Cytokine biosynthesis runs through two major signaling pathways at the level of proteins: nuclear transcription factor-kappaB (NF-kappaB) and p38 mitogen-activated protein kinase (p38 MAPK). The aim of the study was to investigate the effect of NF-kappaB and p38 MAPK in activated monocytes/macrophages on cytokines of rats with acute pancreastitis. METHODS: Taurocholate (3% and 5%) at doses of 1 mL/kg was administered into the biliopancreatic duct of male Sprague-Dawley (SD) rats to reduce acute edematous pancreariris (AEP) and acute necrotizing pancreatitis (ANP). Pancreatic tissues were prepared immediately after death. At this point, blood was obtained for determination of serum amylase and pro-inflammatory TNF-alpha and IL-6. Activated monocytes/macrophages were captured from blood and so were ascites. NF-kappaB and p38 MAPK in activated monocytes/macrophages were measured by immunohistochemistry method. Pancreatic tissue samples were prepared for routine light microscopy, using hematoxylin and eosin (HE) staining. RESULTS: The serum levels of amylase were 3,056.00+/-1,232.35 IU/L and 4,865.12+/-890.34 IU/L at 3 and 6 hours in ANP group, which were significantly higher than those (3,056.00+/-1,232.35 IU/L and 3,187.17+/-821.16 IU/L) (P<0.05, respectively) in AEP group. In ascites the levels were 3.32+/-1.01 g and 3.76+/-1.12 g at 3 and 6 hours in ANP group, which were significantly higher than those (1.43+/-1.02 g and 2.56+/-1.21 g) (P<0.05, respectively) in AEP group. The serum levels of TNF-alpha were 54.27+/-23.48 pg/ml and 67.83+/-22.02 pg/ml in AEP group and 64.28+/-20.79 pg/ml and 106.59+/-43.71 pg/ml in ANP group, and the serum levels of IL-6 were 428.12+/-140.30 pg/ml and 420.13+/-139.40 pg/ml in AEP group and 1,600.32+/-309.78 pg/ml and 2,203.76+/-640.85 pg/ml in ANP group, which were far significantly higher than those in sham group (P<0.001, respectively). The serum level of TNF-alpha 6 hours after establishment of the studied model and that of IL-6 at 3 and 6 hours in ANP group were significantly higher than those in AEP (P<0.05, P<0.001, P<0.05). In ANP group, the levels of serum TNF-alpha and IL-6 6 hours after establishment of the studied model were significantly higher than those 3 hours after establishment of studied model (P<0.05, P<0.05, respectively). Three and 6 hours after establishment of the model, typical pathological changes of AEP and ANP were found, such as large numbers of inflammatory cells, edema, hemorrhage, necrosis, large amount of ascites. In AEP, NF-kappaB and p38 MAPK in activated monocytes/macrophages were moderately found at 3 and 6 hours after introduction of the model. However, in ANP, the expression of NF-kappaB and p38 MAPK in activated monocytes/macrophages was upregulated evidently at 3 and 6 hours after introduction of the model, reaching their highest levels at 6 hours after introduction of the model, which were consistent with the levels of TNF-alpha and IL-6. CONCLUSION: Cytokine TNF-alpha and IL-6 play a main role in acute pancreatitis, expression of NF-kappaB and p38 MAPK in activated monocytes/macrophages might play a major role in cytokine transcription and biosynthesis.

Acute Disease↗
PubMed2003

Antitumor and immunomodulatory activity of resveratrol on experimentally implanted tumor of H22 in Balb/c mice.

AIM: To study the antitumor and immunomodulatory activity of resveratrol on experimentally implanted tumor of H22 in Balb/c mice. METHODS: The cytotoxicity of peritoneal macrophages (Mphi) against H22 cells was measured by the radioactivity of ((3)H)TdR assay, mice with H22 tumor were injected with different concentrations of resveratrol, and the inhibitory rates were calculated and IgG contents were determined by single immunodiffusion method. the plaque forming cell (PFC) was measured by improved Cunningham method, the levels of serum tumor necrosis factor-alpha (TNF-alpha) were measured by cytotoxic assay against L929 cells. RESULTS: Resveratrol 2.5 mg x L(-1), 5.0 mg x L(-1), 10.0 mg x L(-1), 20.0 mg x L(-1) (E:T=10:1, 20:1) promoted the cytotoxicity of Mphi against H22 cells. Resveratrol ip 500 mg x kg(-1), 1 000 mg x kg(-1) and 1,500 mg x kg(-1) could curb the growth of the implanted tumor of H22 in mice. The inhibitory rates were 31.5 %, 45.6 % and 48.7 %, respectively (P<0.05), which could raise the level of serum IgG and PFC response to sheep red blood cell. Resveratrol 1,000 mg x kg(-1) and 1,500 mg x kg(-1) and BCG 200 mg x kg(-1) ip could increase the production of serum TNF-alpha in mice H22 tumor. However, the effect of resveratrol was insignificant (P>0.05). CONCLUSION: Resveratrol could inhibit the growth of H22 tumor in Balb/c mice. The antitumor effect of resveratrol might be related to directly inhibiting the growth of H22 cells and indirectly inhibiting its potential effect on nonspecific host immunomodulatory activity.

Adjuvants, Immunologic↗
PubMed2003

[Surface expression and co-localization of NMDA receptor and AMPA receptor on dendritic tree of hippocampal neurons in culture].

OBJECTIVE: To investigate the developmental profiles on surface expression and co-localization of NMDA receptor clusters and AMPA receptor clusters on dendrite in cultured hippocampal neurons of rats. METHODS: Green fluorescent protein tagged GluR2 subunit (GFP-GluR2) and FLAG tagged NR2B subunit (FLAG-NR2B) were transfected into cultured hippocampal neurons at 5 days in vitro (DIV5). FLAG-NR2B containing NMDA receptor clusters and GFP-GluR2 containing AMPA receptor clusters expressed on membrane surface were then labeled in living neurons using anti FLAG mAb/Cy3-conjugated anti-mouse antibody and anti-GFP pAb/Alex488-conjugated anti-rabbit antibody. RESULT: The numbers of receptor cluster per 100 microm dendrite in the neurons at DIV7 and DIV19 were 39.7+/-5.0 and 64.7+/-6.1 (P<0.01) for NR2B-NMDAR, 59.1+/-3.3 and 99.7+/-6.4 (P<0.01) for GluR2-AMPAR, and 29.9+/-4.5 and 37.5+/-2.5(P<0.05) for the co-localized, respectively. At DIV7 and DIV19, 75.4% and 57.9% NR2B-NMDAR clusters were co-localized with GluR2-AMPAR; and 50.6% and 37.6% GluR2-AMPAR clusters were co-localized with NR2B-NMDAR, respectively. CONCLUSION: The density of NR2B-NMDAR containing and GluR2-AMPAR containing receptor clusters increases during development of hippocampal neurons in culture. Although the co-localized clusters are increased as well in an unit length of dendrite, the extent to which the two receptor clusters are co-localized decreases. These data imply a possible change in the partnership of AMPA receptor subtype and NMDA receptor subtype at newly formed synapses during development.

Animals↗
PubMed2003

[Surface expression of NMDA receptors composed of NR1 subunit and NR2A subunit mutants with partially deleted C-terminus in HEK293 cells].

OBJECTIVE: To examine the potential function of NMDA receptor NR2A subunit C-terminus in assembling and surface expression of the receptor in HEK293 cells. METHODS: Five vectors GFP- NR2ADeltaC1- DeltaC5 were constructed for expressing N-terminally GFP-tagged NR2A with C-terminal deletion at different regions by using conventional techniques of molecular cloning. The deleted region for NR2ADeltaC1-Delta C5 was 897L-1017S, 1024D-1142P, 1149D-1347G, 1354S-1464V, and 897L-1464V. These plasmids were transfected alone or co-transfected with NR1-1a into HEK293 cells. The surface NMDA receptors were immuno-stained using rabbit antibody against GFP and Cy3 conjugated secondary antibody in living cells. RESULT: The vectors GFP-NR2ADeltaC1-DeltaC5 were generated and all of them expressed GFP fluorescence in the transfected cells. Surface NMDA receptors were detected by immuno-labeling with anti-GFP in the cells co-transfected by NR1-1a and any one of GFP-NR2ADeltaC1-DeltaC5. However, no surface expression of NR2A proteins was found in the transfected cells with any one of these plasmids alone. CONCLUSION: Within the region downstream from the 897L of NR2A subunit, neither a particular domain directly interacted with ER retention domain in NR1-1a C1 cassette, nor that determining ER retention of NR2A subunit itself has been found, indicating that more complicated mechanisms might exist in which the subunit assembling and targeting to plasma membrane of NMDA receptors undergo.

Cell Line↗