Biomedical subjects
Publications and source records attributed to Qing Dai.
Friction, adhesion, and bounce dynamics are found to be asymmetric with respect to sliding direction for a tilted pad sliding at high speed. The differences originate from the nanoscale effects of the mechanical action against the lubricant layer forming an asymmetric meniscus around the pad and from a self-excited vibration induced by friction hysteresis coupled with adhesion hysteresis.
Over 100 different chemical types of modifications have been identified in thousands of sites in tRNAs, rRNAs, mRNAs, small nuclear RNAs, and other RNAs. Some modifications are highly conserved, while others are more specialized. They include methylation of bases and the ribose backbone, rotation, and reduction of uridine, base deamination, elaborate addition of ring structures, carbohydrate moieties, and more. We have developed a systematic approach to detect and quantify the extent of known RNA modifications. The method is based on the enzymatic ligation of oligonucleotides using the modified or unmodified RNA as the template. The efficiency of ligation is very sensitive to the presence and the type of modifications. First, two oligo pairs for each type of modification are identified. One pair greatly prefers ligation using the unmodified RNA template over the modified RNA template or vice versa. The other pair has equal reactivity with unmodified and modified RNA. Second, separate ligations with each of the two oligo pairs and the total RNA mixture are performed to detect the presence or absence of modifications. Multiple modification sites can be examined in the same ligation reaction. The feasibility of this method is demonstrated for three 2'O-methyl modification sites in yeast rRNA.
Amiloride (N-amidino-3,5-diamino-6-chloro-pyrazinecarboxamide hydrochloride) has two sets of hydrogen-bond forming sites suitable for target nucleotides and the phosphodiester DNA backbone by which a thymine base opposite an abasic site in DNA duplexes can be recognized with high selectivity and affinity, and it is applicable to the fluorescence detection of thymidine-related SNPs (single-nucleotide polymorphisms) of PCR amplification products.
Longitudinal shortening of the esophagus during peristaltic contraction has been previously analyzed globally using spaced mucosal clips. This method gives a relatively crude measurement. In this study, local longitudinal shortening (LLS) was evaluated using simultaneous high-resolution endoluminal ultrasound (HREUS) and manometry based on basic principles of muscle mechanics. We sought to determine if there are regional differences in LLS of the esophageal muscle during swallow-induced peristaltic contraction and evaluate shortening of the circular smooth muscle (CSM) and longitudinal smooth muscle (LSM) of the esophagus. Twenty normal subjects underwent simultaneous HREUS/manometry at 4 levels (5, 10, 15, and 20 cm above the upper border of the lower esophageal sphincter [LES] high-pressure zone) in the esophagus with 5-mL swallows of water. Ultrasound images were recorded with synchronized manometric pressure data. The images were digitized and the cross-sectional surface area (CSA) of the LSM, CSM, and total muscle (TM) were measured at baseline (at rest) and at peak intraluminal pressure (implying peak CSM contraction) during swallowing. LLS was calculated for the CSM and LSM using the principle of mass conservation, whereby the change in CSA relative to the resting CSA is quantitatively equal to the relative change in length of a local longitudinal muscle segment.CSM, LSM, and TM all shortened longitudinally, with the circular muscle shortening more than the longitudinal muscle, LLS of the CSM and TM layers at 5 cm above the LES was significantly greater than at 20 cm (CSM: 30% difference, P < .001; TM: 18% difference, P < .05). The greater shortening of LSM at 5 versus 20 cm was found not to be statistically significant (11% difference, P > .05). Peak intraluminal pressure strongly correlated with peak muscle thickness of all layers at all levels (r = 0.96-0.98).LLS increases from the proximal to the distal esophagus during bolus transport. CSM and LSM both shorten longitudinally, with CSM shortening more than LSM. The increase in LLS increases the efficiency of peristaltic contraction and likely contributes to the axial displacement of the LES preceding hiatal opening and esophageal emptying.
The use of high-frequency ultrasound transducers in the gastrointestinal tract (GI) has already yielded remarkable findings concerning the anatomy, physiology and pathophysiology of the GI tract and of various motility disorders. These transducers have made completely invisible portions of the GI tract (the longitudinal smooth muscle, muscles of the upper esophageal sphincter, components of the gastroesophageal junction high-pressure zone, and the muscle of the anal sphincter complex) accessible to investigation. Use of simultaneous ultrasound and manometry has allowed the exploration of the normal physiology of peristaltic contraction. The components of the high-pressure zone of the distal and proximal esophagus have been isolated and the movement of these components has been studied individually and as a group. Various esophageal motility disorders have been investigated including achalasia, scleroderma, Barrett's esophagus and diffuse esophageal spasm. The possible etiology of the symptoms of esophageal chest pain and heartburn (sustained esophageal contractions of the longitudinal smooth muscle), have been studied. The possible underlying pathophysiology of GERD (the missing gastric clasp and sling fiber pressure profile) has been explored. Three-dimensional high-frequency ultrasound imaging has allowed the peristaltic contraction sequence to be viewed in a completely new and unique manner. The biomechanics of both esophageal contraction and the gastroesophageal junction high-pressure zone have been investigated and the mechanical advantage of esophageal shorting has been studied. The mechanism of action of standard surgical and newer endoscopic therapies for GERD has been defined. Future applications of this technology are limited only by our imagination.
The recognition ability of pteridine derivatives for nucleobases opposite an abasic (AP) site in an oligodeoxynucleotide (ODN) duplex is enhanced by using a propylene residue (Spacer-C3) as an AP site. The recognition ability is further enhanced both by attaching methyl groups to a fluorescent ligand and by measuring the fluorescence response at 5 degrees C; 6.2 x 10(6) M(-1) of the binding constant is attained between 2-amino-6,7-dimethyl-4-hydroxypteridine and guanine opposite the AP site in water.
OBJECTIVE: The purpose of this study was to evaluate the accuracy of velocity parameters for the diagnosis of renal artery stenosis (RAS) with color Doppler sonography and to determine the optimal threshold values for these parameters. METHODS: The study group was composed of 187 renal arteries, which were examined by color Doppler sonography and angiography. Four Doppler parameters, including the peak systolic velocities (PSVs) in the renal and interlobar arteries, the renal-aortic ratio, and the renal-interlobar ratio (RIR), were measured. Receiver operating characteristic curve analysis was performed to determine the optimal parameter. The sensitivity, specificity, and negative and positive predictive values at various threshold values were calculated. RESULTS: Doppler sonographic examination was technically successful in 96% of renal arteries (180/187). The RIR was determined to be the best parameter. With threshold values of RIR greater than 5, PSV greater than 150 cm/s in the renal artery, renal-aortic ratio greater than 2, and PSV less than 25 cm/s in the interlobar artery, the sensitivity values were 88%, 81%, 70%, and 74%, respectively. An RIR greater than 5 and PSV less than 15 cm/s in the interlobar artery provided the optimal combination of parameters, with sensitivity and specificity of 91% and 87%, respectively. CONCLUSIONS: The RIR is the best velocity parameter in the detection of RAS (> or =50%), and its best cutoff is 5. Valuing influencing factors of PSV in the renal artery will help reduce misdiagnosis. The combination of RIR greater than 5 and PSV less than 15 cm/s in the interlobar artery provides the best diagnostic efficiency of RAS.
2'-Amino-2'-deoxynucleosides and oligonucleotides containing them have proven highly effective for an array of biochemical applications. The guanosine analogue and its phosphoramidite derivatives have been accessed previously from 2'-amino-2'-deoxyuridine by transglycosylation, but with limited overall efficiency and convenience. Using simple modifications of known reaction types, we have developed useful protocols to obtain 2'-amino-2'-deoxyguanosine and two of its phosphoramidite derivatives with greater convenience, fewer steps, and higher yields than reported previously. These phosphoramidites provide effective synthons for the incorporation of 2'-amino-2'-deoxyguanosine into oligonucleotides.
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[reaction: see text] A general method for efficient N(6)-arylation of 2'-deoxyadenosine via copper-catalyzed direct coupling with aryl iodides and bromides is described. The method is useful for aryl halides with either electron-donating or electron-withdrawing groups.
It has been demonstrated that the immunodominant region of the HCV core protein and the hepatitis B surface antigen (HBsAg) have high degree of reactivity. In order to construct a chimeric protein that carries HCV and HBV epitopes and possesses immunogenicity to both HCV and HBV, four epitopes derived from residues aa2-21 (epitope C1), aa22-40 (epitope C2) of the core protein, residues aa315-328 (epitope E) of E1 protein of HCV, and residues aa124-147 (epitope S) of HBsAg were chosen to be displayed in a conformation-specific manner on the outer surface of the Flock House virus capsid protein and expressed in E. coli cells. The reactivity of these epitopes with antisera from hepatitis C and hepatitis B patients and induction of immune response in guinea pigs were determined. The results showed that when displayed in this system, the chimeric protein carrying only epitope S could react with anti-HBsAg positive human sera, elicit an anti-HBsAg response in guinea pigs. The chimeric protein carrying epitopes C1, C2 and E could react with antibodies to different HCV genotypes, elicit an anti-HCV response in guinea pigs. The chimeric protein carrying epitopes C1, C2, E, and S could react with antibodies against HCV and HBV, elicit anti-HCV and anti-HBsAg responses in guinea pigs. The results suggested that these epitopes displayed in this form could be considered for development of epitope-based vaccines against HCV/HBV infections.
[structure: see text] The first syntheses of the adducts formed in the reactions of o-quinone metabolites of carcinogenic polycyclic aromatic hydrocarbons (BPQ and BAQ) at 2'-deoxyadenosine and 2'-deoxyguanosine sites in DNA are reported. These syntheses entail Pd-catalyzed coupling of protected amine derivatives of catechols with suitably protected halopurine analogues of 2'-deoxyribonucleosides.
The farnesoid X receptor (FXR) is activated by bile acids, natural agonists for this nuclear receptor. FXR-target genes play important roles in cholesterol and lipid metabolism. We have found that a series of 5beta-cholanic acid derivatives, even though without a hydroxyl group or any other substituent on the steroidal rings, can activate FXR more potently than hydroxylated bile acids in a reporter gene assay. The most potent compound among these derivatives, N-methyl-5beta-glycocholanic acid (NMGCA), induces the formation of receptor/coactivator complex in a gel-shift assay and also increases the expression of FXR target genes in human hepatoma HepG2 cells. Furthermore, in rats, NMGCA causes hypolipidemic effects as well as induction of the FXR target genes in liver. Our results suggest that NMGCA and its derivatives are important FXR activators in the study of the physiological functions of FXR and are potentially useful as pharmaceutical agents for treatment of cholesterol and lipid-related diseases.
By using UV thermal denaturation and isothermal titration calorimetry (ITC), we examine the binding behaviors of a hydrogen bond-forming ligand, 2-acetylamino-7-methyl-1,8-naphthyridine (AcMND), with a guanine base opposite an abasic site (AP site) in a DNA duplex (5'-TCC AGX GCA AC-3'/3'-AGG TCG CGT TG-5', X = AP site, G = target). In the presence of AcMND, the melting temperature (Tm) of the AP site-containing DNA duplex increases by 8.6 degrees C while hardly any change in Tm is observed for a corresponding normal duplex that has no AP sites. The examination by ITC reveals that, in solutions buffered to pH 7.0 (at 10 degrees C, I = 0.11 M), AcMND is able to recognize guanine base with a 1:1 binding constant of 3.4x10(5) M(-1). The ligand-nucleotide interaction is clearly enthalpy driven, with deltaH(o) of -12.5 kcal/mol. We discuss these binding functions of AcMND at the AP site with a view towards development of ligand-based assay for SNPs (single-nucleotide polymorphisms) typing.
We report on a highly selective fluorescence ligand for thymine (T) base opposite an abasic site (AP site) in DNA duplexes. From the examination of the binding behaviors in solutions buffered to pH 7.0, we find that 6-chloro-3,5-diamino-2-pyrazinecarbonitrile (CDPC) can selectively recognize T with high affinity (Ka = 2.9 x 10(5) M(-1)), and the fluorescence intensity at 424 nm is significantly quenched only when binding to T. It is highly likely that the selective interaction of CDPC with T is explained by a pseudo-base pairing, for which three point hydrogen bonds are formed along the Watson-Crick edge of the target T. These binding functions of CDPC at the AP site are presented to develop ligand-based fluorescence assay for SNPs (single-nucleotide polymorphisms) typing.
OBJECTIVE: The purpose of this study was to evaluate the mechanical index (MI) displayed on clinical ultrasound scanners as a predictor of exposure conditions related to the destruction of sonographic microbubble contrast agents. METHODS: Sonazoid (GE Healthcare, Oslo, Norway) and Optison (GE Healthcare, Princeton, NJ) microbubbles were injected into a tissue-mimicking flow phantom. Gray scale imaging was performed with 4 different scanners and 3 different transducers (3.5 MHz curved linear, 2.5 MHz convex, and 7.5 MHz linear array), and the MI displayed by the scanner was varied from 0.2 to 1.5 by changing the system output power. All other scanning parameters were kept constant. Downstream changes in echogenicity were monitored with a PowerVision 7000 scanner (Toshiba America Medical Systems, Tustin, CA) as an indirect measure of bubble destruction. Video intensity changes within the flow tube were determined as a function of MI for the different scanner/transducer combinations, and the best linear fit was determined. RESULTS: At a displayed MI of 0.7, different scanner/transducer combinations exhibited a range in video intensity from +16% to -3% of baseline for Sonazoid and from +8% to -71% for Optison. At an MI of 0.3, reductions in video intensity of up to 32% were produced. These results indicate a wide range in bubble destruction at identical MI values. Likewise, regression analysis found no linear fits for all scanner/transducer combinations (r2 < 0.046). CONCLUSIONS: The MI displayed on clinical ultrasound scanners does not predict the degree of microbubble destruction and should not be used by itself to define exposure conditions for destruction of microbubble contrast agents.
OBJECTIVE: To evaluate in vivo immunological protective efficacy and safety of expressed recombinant rotavirus epitopes in mice. METHODS: Using the Flock House virus capsid protein as a vector, three epitopes derived from rotavirus Vp4 amino acid 223-242 [rotavirus epitope A, (REA)], 243-262 [rotavirus epitope B, (REB)], and 234-251 [rotavirus epitope C, (REC)] were genetically engineered on the surface of the vector protein and expressed in pET-3 (E. coli BL21 [DE3]) system into multiple epitopes, REABC, which comprises REA, REB, and REC. Kunming strain mice were inoculated with the recombinant epitopes REABC, and then challenged perorally by cell culture-adapted rotavirus Wa (type G1P1A) and SA11 (type G3P2). Infection syndrome was observed, and virus antigen in stools of mice and serum neutralizing antibody activities were determined and analyzed. RESULTS: The recombinant epitopes REABC significantly induced rotavirus specific neutralyzing antibodies against WA and SA11, reduced virus reproduction, elicitted immune memory in inoculated mice, and protected inoculated mice from challenge by WA or SA11 (P<0.001). CONCLUSION: The recombinant epitopes have high immunological protective efficacy and mild side effects in mice. It may be used as an epitope-based vaccine candidate in human.
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