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Yu Shao

Publications and source records attributed to Yu Shao.

10 recordsLinked to original sources
PubMed2006

The functional effects of physical interactions among Toll-like receptors 7, 8, and 9.

Toll-like receptors (TLRs) TLR1, TLR2, TLR4, and TLR6 are evolutionarily conserved, highly homologous, and localized to plasma membranes of host cells and recognize pathogen-associated molecular patterns (PAMPs) derived from bacterial membranes. These receptors cooperate in a pairwise combination to elicit or inhibit the inflammatory signals in response to certain PAMPs. The other TLRs that are evolutionarily closely related and highly homologous are TLR7, TLR8, and TLR9. They are all confined to the membranes of endosomes and recognize similar molecular structures, the oligonucleotide-based PAMPs. However, the cooperative interactions among these receptors that may modulate the inflammatory signaling in response to their cognate agonists are not reported. We report here for the first time the functional effects of one TLR on the other among TLR7, TLR8, and TLR9. The results indicate that TLR8 inhibits TLR7 and TLR9, and TLR9 inhibits TLR7 but not vice versa in HEK293 cells transfected with TLRs in a pairwise combination. This is concluded by selectively activating one TLR over the other by using small molecule TLR agonists. We also show that these inhibitory interactions are the result of direct or indirect physical interactions between the TLRs. The murine TLR8 that does not respond to any known human TLR8 agonists also inhibits both murine and human TLR7. The implications of the inhibitory interactions among these TLRs in host-pathogen recognition and subsequent inflammatory responses are not obvious. However, given the complexity in expression pattern in a particular cell type and the variation in distribution and response to different pathogens and stress signals in different cell types, the inhibitory physical interactions among these TLRs may play a role in balancing the inflammatory outcome from a given cell type to a specific challenge.

Animals↗
PubMed2006

Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation.

Antisense oligodeoxynucleotides (oligos) are widely used for functional studies of both prokaryotic and eukaryotic genes. However, the identification of effective target sites is a major issue in antisense applications. Here, we study a number of thermodynamic and structural parameters that may affect the potency of antisense inhibition. We develop a cell-free assay for rapid oligo screening. This assay is used for measuring the expression of Escherichia coli lacZ, the antisense target for experimental testing and validation. Based on a training set of 18 oligos, we found that structural accessibility predicted by local folding of the target mRNA is the most important predictor for antisense activity. This finding was further confirmed by a direct validation study. In this study, a set of 10 oligos was designed to target accessible sites, and another set of 10 oligos was selected to target inaccessible sites. Seven of the 10 oligos for accessible sites were found to be effective (>50% inhibition), but none of the oligos for inaccessible sites was effective. The difference in the antisense activity between the two sets of oligos was statistically significant. We also found that the predictability of antisense activity by target accessibility was greatly improved for oligos targeted to the regions upstream of the end of the active domain for beta-galactosidase, the protein encoded by lacZ. The combination of the structure-based antisense design and extension of the lacZ assay to include gene fusions will be applicable to high-throughput gene functional screening, and to the identification of new drug targets in pathogenic microbes. Design tools are available through the Sfold Web server at http://sfold.wadsworth.org.

Algorithms↗
PubMed2004

A stability-indicating HPLC method for the determination of glucosamine in pharmaceutical formulations.

A stability-indicating high performance liquid chromatographic (HPLC) method was developed for the assay of glucosamine in bulk forms and solid dosage formulations. The HPLC separation was achieved on a Phenomenex Luna amino column (150 mm x 4.6 mm, i.d., 5 microm particle size) using a mobile phase of acetonitrile-phosphate buffer (75:25, v/v, pH 7.50) at a flow rate of 1.5 ml min(-1) and UV detection at 195 nm. The method was validated for specificity, linearity, solution stability, accuracy, precision, limit of detection, and limit of quantitation. The detector response for glucosamine hydrochloride was linear over the selected concentration range from 1.88 to 5.62 mg ml(-1) with a correlation coefficient 0.9998. The accuracy was between 98.9 and 100.5%. The precision (R.S.D.) amongst six sample preparations was 1.1%. The limit of detection and the limit of quantitation are 0.037 and 0.149 mg ml(-1), respectively. The sample and standard solutions were stable for 1 week. The method was successfully used for analysis of active-excipient compatibility samples used for development of a solid dosage formulation in our laboratory and subsequent stability studies. The method was also used for the analysis of glucosamine in several commercially available solid dosage forms.

Chemistry, Pharmaceutical↗
PubMed2004

Five hierarchical levels of sequence-structure correlation in proteins.

This article reviews recent work towards modelling protein folding pathways using a bioinformatics approach. Statistical models have been developed for sequence-structure correlations in proteins at five levels of structural complexity: (i) short motifs; (ii) extended motifs; (iii) nonlocal pairs of motifs; (iv) 3-dimensional arrangements of multiple motifs; and (v) global structural homology. We review statistical models, including sequence profiles, hidden Markov models (HMMs) and interaction potentials, for the first four levels of structural detail. The I-sites (folding Initiation sites) Library models short local structure motifs. Each succeeding level has a statistical model, as follows: HMMSTR (HMM for STRucture) is an HMM for extended motifs; HMMSTR-CM (Contact Maps) is a model for pairwise interactions between motifs; and SCALI-HMM (HMMs for Structural Core ALIgnments) is a set of HMMs for the spatial arrangements of motifs. The parallels between the statistical models and theoretical models for folding pathways are discussed in this article; however, global sequence models are not discussed because they have been extensively reviewed elsewhere. The data used and algorithms presented in this article are available at http://www.bioinfo.rpi.edu/~bystrc/ (click on "servers" or "downloads") or by request to bystrc@rpi.edu .

Algorithms↗
PubMed2004

[Eosinophilic granuloma of the jaw: an analysis of 21 cases].

PURPOSE: To study the clinical features and treatment of eosinophilic granuloma of the jaw (EGJ) in 21 cases. METHODS: 21 patients with EGJ treated from 1983 to 2002 were reviewed, including the sexes, ages, extent of lesions, clinical features and treatment methods. RESULTS: The male to female rate was 13:8. 76% of the cases were among 2-10 years. The median age was 8 years, 18 lesions were in the mandible, 1 was in the maxilla and 2 involved the mandible and maxilla. CONCLUSIONS: EGJ was rarely seen clinically, lack of specificity. Pathology can confirm the diagnosis. Surgery is still the major treatment modality. Combination of radiotherapy or chemotherapy maybe valuable. The prognosis of the patients was generally good.

Age Factors↗
PubMed2004

[Photocatalytic functional ceramic and its speciality of photodecomposition].

Photocatalytic ceramic was prepared by coating photocatalytic membrane on ceramic matrix. The photocatalytic behavior of the TiO2 coated ceramic for degradation of oleic acid, ethylene, SO2, NOx and sterilization was studied by using XRD, chromatogram, in-situ IR and spectrophotometer. The results showed that the photocatalytic ceramic prepared by special conditions have the function of environmental conservation such as the photodegradating organic contaminants, removing inorganic baleful gas and killing bacteria. Degradation ratio of ethylene, oleic acid, SO2 and NOx reached 95%-100% respectively for the photocatalytic functional ceramic.

Air Pollution, Indoor↗
PubMed2003

Structural identification of nonvolatile dimerization products of glucosamine by gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, and nuclear magnetic resonance analysis.

The degradation profile of glucosamine bulk form stressed at 100 degrees C for 2 h in an aqueous solution was studied. Column chromatography of acetylated product mixture led to isolation of two pure compounds (1b and 2b) and a mixture of at least three isomers (3b). 1a and 2a were identified as 5-(hydroxymethyl)-2-furaldehyde (5-HMF) and 2-(tetrahydroxybutyl)-5-(3',4'-dihydroxy-1'-trans-butenyl)pyrazine, respectively, by utilizing a variety of analytical techniques, such as GC-MS, LC-MS, on-line UV spectrum, (1)H and (13)C NMR, and DEPT, as well as (1)H-(1)H COSY. 3a was identified as 2-(tetrahydroxybutyl)-5-(2',3',4'-trihydroxybutyl)pyrazine, commonly known as deoxyfructosazine. In addition, glucosamine solid dosage form was exposed to 40 degrees C/75% relative humility for 10 weeks. Methanol extract of glucosamine solid dosage form was analyzed after acetylation by LC-MS, resulting in degradants 3b and 4b. 3a and 4a were, therefore, determined as deoxyfructosazine and 2,5-bis(tetrahydroxybutyl)pyrazine (fructosazine), respectively. Furthermore, the mechanisms of formation of identified degradation products are proposed and briefly discussed.

Chromatography, High Pressure Liquid↗
PubMed2003

Predicting interresidue contacts using templates and pathways.

We present a novel method, HMMSTR-CM, for protein contact map predictions. Contact potentials were calculated by using HMMSTR, a hidden Markov model for local sequence structure correlations. Targets were aligned against protein templates using a Bayesian method, and contact maps were generated by using these alignments. Contact potentials then were used to evaluate these templates. An ab initio method based on the target contact potentials using a rule-based strategy to model the protein-folding pathway was developed. Fold recognition and ab initio methods were combined to produce accurate, protein-like contact maps. Pathways sometimes led to an unambiguous prediction of topology, even without using templates. The results on CASP5 targets are discussed. Also included is a brief update on the quality of fully automated ab initio predictions using the I-sites server.

Algorithms↗
PubMed2002

Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA.

MOTIVATION: The Monte Carlo fragment insertion method for protein tertiary structure prediction (ROSETTA) of Baker and others, has been merged with the I-SITES library of sequence structure motifs and the HMMSTR model for local structure in proteins, to form a new public server for the ab initio prediction of protein structure. The server performs several tasks in addition to tertiary structure prediction, including a database search, amino acid profile generation, fragment structure prediction, and backbone angle and secondary structure prediction. Meeting reasonable service goals required improvements in the efficiency, in particular for the ROSETTA algorithm. RESULTS: The new server was used for blind predictions of 40 protein sequences as part of the CASP4 blind structure prediction experiment. The results for 31 of those predictions are presented here. 61% of the residues overall were found in topologically correct predictions, which are defined as fragments of 30 residues or more with a root-mean-square deviation in superimposed alpha carbons of less than 6A. HMMSTR 3-state secondary structure predictions were 73% correct overall. Tertiary structure predictions did not improve the accuracy of secondary structure prediction.

Algorithms↗