Biomedical subjects

Da-Wei Li

Publications and source records attributed to Da-Wei Li.

10 recordsLinked to original sources

PubMed2006

Development of an ID-ELISA for the detection of Rice black-streaked dwarf virus in plants.

The Rice black-streaked dwarf virus (RBSDV) virion is composed of two layers of capsid proteins and 10 segments of double-stranded genomic RNA (S1-S10). Due to the fragility of the RBSDV outer capsid, it is very difficult to obtain intact virus particles for preparation of antiserum needed in virus detection. In this work, the major outer capsid protein (P10) encoded by S10 of RBSDV was expressed in Escherichia coli cells as a glutathione-S-transferase (GST) fusion protein. After purification of GST-P10 through affinity chromatography, P10 was released from the fusion protein by thrombin digestion and the purified P10 protein was used to immunize rabbits. The resulting polyclonal antiserum specifically recognized RBSDV from infected plant tissue and a planthopper vector in Western blotting assays. To facilitate screening of large numbers of samples, an indirect enzyme-linked immunosorbent assay (ID-ELISA) protocol capable of detecting RBSDV in very dilute wheat leaf extracts was developed. Based on the results, we conclude that efficient and economic detection of RBSDV can be performed routinely using polyclonal antiserum against P10 expressed in prokaryotic cells.

Animals↗

PubMed2005

Examination of membrane fusion by dissipative particle dynamics simulation and comparison with continuum elastic models.

A dissipative particle dynamics model is applied to probe the lipidic membrane fusion. This model is verified by reproducing the lipid phase behavior. The classical stalk model has been visited and modified. The tilt deformation of the lipids and the noncircular shape of the stalk are supported. The stalk is shown to undergo asymmetric expansion to form the trans-monolayers contact (TMC). Unlike previous models, an energy barrier between the stalk and the TMC has been identified, implying that the TMC should be a metastable formation. This shows good agreement with the fusion experiments. Two typical elastic continuum models are compared with our result and possible modifications to the two elastic models are suggested. The effect of spontaneous curvature of lipid on selection of fusion pathway is also examined. It is observed that a bent stalk with pore or an inverted micellar intermediate will have more chance to occur than traditional stalk when the spontaneous curvature of the lipid becomes more negative.

Journal Article↗

PubMed2005

Consecutive rotation of crystallographic orientation in lateral growth.

A consecutive rotation of crystallographic orientation has been observed in lateral crystallization of NH4Cl on a glass substrate, which induces a periodic distribution of faceted and roughened regions on the surface of a crystallite aggregate. Experimental observation indicates that this phenomenon derives from the asymmetric surface energies at the growth front, which deform the nascent nucleus and tilt the crystallographic orientation in the nucleation-mediated layered growth. We suggest that this effect is significant for a class of lateral growth where nucleation plays a dominate role.

Journal Article↗

PubMed2005

Analysis of nucleotide sequences and multimeric forms of a novel satellite RNA associated with beet black scorch virus.

The full-length sequence of a satellite RNA (sat-RNA) of Beet black scorch virus isolate X (BBSV-X) was determined. This agent is 615 nucleotides long and lacks extensive sequence homology with its helper virus or with other reported viruses. Purified virus particles contained abundant single-stranded plus-sense monomers and smaller amounts of dimers. Single-stranded RNAs from total plant RNA extracts also included primarily monomers and smaller amounts of dimers that could be revealed by hybridization, and preparations of purified double-stranded RNAs also contained monomers and dimers. Coinoculation of in vitro transcripts of sat-RNA to Chenopodium amaranticolor with BBSV RNAs was used to assess the replication and accumulation of various forms of sat-RNA, including monomers, dimers, and tetramers. Dimeric sat-RNAs with 5- or 10-base deletions or 15-base insertions within the junction regions accumulated preferentially. In contrast, the replication of monomeric sat-RNA was severely inhibited by five-nucleotide deletions in either the 5' or the 3' termini. Therefore, sequences at both the 5' and the 3' ends of the monomers or the presence of intact juxtaposed multimers is essential for the replication of sat-RNA and for the predomination of monomeric progeny. Comparisons of the time courses of replication initiated by in vitro-synthesized monomeric or multimeric sat-RNAs raised the possibility that the dimeric form has an intermediate role in replication. We propose that replication primarily involves multimers, possibly as dimeric forms. These forms may revert to monomers by a termination of replication at 5' end sequences and/or by internal initiation at the 3' ends of multimeric junctions.

Base Sequence↗

PubMed2005

Predicting protein subcellular location using digital signal processing.

The biological functions of a protein are closely related to its attributes in a cell. With the rapid accumulation of newly found protein sequence data in databanks, it is highly desirable to develop an automated method for predicting the subcellular location of proteins. The establishment of such a predictor will expedite the functional determination of newly found proteins and the process of prioritizing genes and proteins identified by genomic efforts as potential molecular targets for drug design. The traditional algorithms for predicting these attributes were based solely on amino acid composition in which no sequence order effect was taken into account. To improve the prediction quality, it is necessary to incorporate such an effect. However, the number of possible patterns in protein sequences is extremely large, posing a formidable difficulty for realizing this goal. To deal with such difficulty, a well-developed tool in digital signal processing named digital Fourier transform (DFT) [1] was introduced. After being translated to a digital signal according to the hydrophobicity of each amino acid, a protein was analyzed by DFT within the frequency domain. A set of frequency spectrum parameters, thus obtained, were regarded as the factors to represent the sequence order effect. A significant improvement in prediction quality was observed by incorporating the frequency spectrum parameters with the conventional amino acid composition. One of the crucial merits of this approach is that many existing tools in mathematics and engineering can be easily applied in the predicting process. It is anticipated that digital signal processing may serve as a useful vehicle for many other protein science areas.

Algorithms↗

PubMed2004

Long duration of anticoagulant activity and protective effects of acharan sulfate in vivo.

INTRODUCTION: We previously reported that a new glycosaminoglycan, acharan sulfate (AS) from the African giant snail Achatina fulica showed anticoagulant activity in vitro, but was much less active when compared to heparin. In the present study, the anticoagulant activity of AS was investigated in vivo. METHODS: AS and heparin were administered to mice and rats in various doses and the anticoagulant activities were measured by aPTT assay. Both were also compared in a thrombin-induced lethality animal model. As one of the possible mechanisms, AS-thrombin interaction was studied by using surface plasmon resonance spectroscopy. RESULTS: Intravenous administration of AS to mice prolonged the clotting time (aPTT) in a time and dose-dependent manner. Although the anticoagulant activity was low in rats, it steadily increased over 5 h after administration of AS (30 mg/kg). In contrast, the increase in aPTT induced by 5 mg/kg of heparin was restored to a normal level after 3 h. In a thrombin-induced lethality model in mice, AS (20 mg/kg) protected against lethality by 80%, while heparin (20 mg/kg) did not show any protective activity beyond 3.5 h post-administration. AS could be also detected in plasma even 5 h after i.v. administration to rats. The binding constant (K(D)) of AS to thrombin was 7.27 x 10(-6) M, corresponding to moderate binding affinity. CONCLUSIONS: These results show that the longer duration of AS in blood could prolong the clotting time determined by aPTT and offering protection against thrombin-induced lethality. One possible mechanism may result from AS-thrombin interaction.

Animals↗

PubMed2004

Understanding SARS with Wolfram approach.

Stepping acquired immunodeficiency syndrome (AIDS), severe acute respiratory syndrome (SARS) as another type of disease has been threatening mankind since late last year. Many scientists worldwide are making great efforts to study the etiology of this disease with different approaches. 13 species of SARS virus have been sequenced. However, most people still largely rely on the traditional methods with some disadvantages. In this work, we used Wolfram approach to study the relationship among SARS viruses and between SARS viruses and other types of viruses, the effect of variations on the whole genome and the advantages in the analysis of SARS based on this novel approach. As a result, the similarities between SARS viruses and other coronaviruses are not really higher than those between SARS viruses and non-coronaviruses.

Algorithms↗

PubMed2004

Refolding and characterization of recombinant human GST-PD-1 fusion protein expressed in Escherichia coli.

Programmed death-1 (PD-1) is a costimulatory molecule of CD28 family expressed on activated T, B and myeloid cells. The engagement of PD-1 with its two ligands, PD-L1 and PD-L2, inhibits proliferation of T cell and production of a series of its cytokines. The blockade of PD-1 pathway is involved in antiviral and antitumoral immunity. In this study, human PD-1 cDNA encoding extracellular domain was amplified and cloned into expression plasmid pGEX-5x-3. The fusion protein GST-PD-1 was effectively expressed in E. coli BL21 (DE3) as inclusion bodies and a denaturation and refolding procedure was performed to obtain bioactive soluble GST-PD-1. Fusion protein of above 95% purity was acquired by a convenient two-step purification using GST affinity and size exclusion columns. Furthermore, a PD-L1-dependent in vitro bioassay method was set up to characterize GST-PD-1 bioactivity. The results suggested that GST-PD-1 could competently block the interaction between PD-L1 and PD-1 and increase the production of IL-2 and IFN-gamma of phytohemagglutinin-activated T cells.

Animals↗

PubMed2004

[Observation of maxillary mucosa restoration after the endoscopic sinus surgery operation of chronic sinusitis and nasal polyps].

OBJECTIVE: To understand the restoration process of the mucosa through the continual endoscopic, microscopic, transmission electron microscopic and scanning electron microscopic observation of the nasal mucosa after endoscopic sinus surgery (ESS). This restoration process of mucosa can be used to appraise the effectiveness of the operation. METHODS: Thirty-one cases (53 sides) with chronic nasal sinusitis and nasal polyps were selected randomly, which had been undergone ESS operation during January to December, 2001. Biopsy of posterior frontanelle of the maxillary sinus were performed to observe the mucosa changes before the ESS and at 2-3 weeks, 8-11 weeks and 13-16 weeks after the ESS, respectively. RESULTS: Epithelia shedding, proliferation, squamous metaplasia, glandular and fibrous tissue proliferation and lymphocytes infiltration were observed in all cases before the ESS. The microtubule abnormal and mitochondria diminishing and expanding existed in all cases. The morphological changes were not significant within 2-3 weeks after the ESS compared to the changes before the ESS. Eight-eleven weeks after the ESS, the nasal cavity turned clean and smooth. The number of pillar cells increased and the cilia swelling, short cilia, and many pillar cells with microvillus were seen. The number of goblet cells increased. Pathological glandular and fibrous proliferation were seen in all cases (53 sides). The operated cavity was clean and covered completely by epithelia (50 sides) 13-16 weeks after ESS. The length of cilia increased and arrangement of the cilia line was in the same direction. The structure of microtubules was clear. The mitochondria was elongated and became dense (49 sides). The pathological repairing was at work (3 sides). CONCLUSIONS: After the ESS, the recovery of the mucus needs 3 months. Some pathological changes are irreversible and the cilia pathological change is related with its restoration. The more cilia reserved and timely local cleaned after ESS, the more helpful to the restoration of the cilia morphology and function. The effective of ESS can be evaluated through the histological-morphological changes. timely local cleaned after ESS, the more helpful to the restoration of the cilia morphology and function. The effective of ESS can be evaluated through the histological-morphological changes.

Adolescent↗

PubMed2003

Sequence analysis of the complete genome of rice black-streaked dwarf virus isolated from maize with rough dwarf disease.

The complete nucleotide sequences of 10 genomic segments (S1-S10) from an isolate of rice black-streaked dwarf virus causing rough dwarf disease on maize (RBSDV-Hbm) in China were determined, a total of 29,142 base pairs (bp). Each segment possessed the genus-specific termini with conserved nucleotide sequences of (+) 5'-AAGUUUUU......CAGCUNNNGUC-3' and a perfect or imperfect inverted repeat of seven to eleven nucleotides immediately adjacent to the terminal conserved sequence. While the coding strand of most RBSDV-Hbm segments contained one open reading frame (ORF), there were two non-overlapping ORFs in S7 and S9, and one small overlapping ORF downstream of the major ORF in S5. Homology comparisons suggest that S1 encodes a RNA-dependent RNA polymerase (RdRp), with 63.5% and 32.6% identity to the putative RdRp encoded by Fiji disease virus (FDV) and Nilaparvata lugens reovirus (NLRV), respectively. The proteins encoded by S2, S3, and S4 showed various degrees of similarity to those encoded by the corresponding segments of FDV or NLRV. In S5 and S6, low identities were found to those of FDV only, but not to NLRV. Sequence analyses showed that RBSDV-Hbm had the most similarities in the genome organizations and the coding assignments with a RBSDV isolated from rice in China, in which each pair of the corresponding segments shared sequence identities of 93.8-98.9% and 93.5-100% at nucleotide or amino acid levels, respectively. In addition, phylogenetic analyses suggested that RBSDV-Hbm had the closest evolutionary relationship to RBSDV in Fijivirus.

Conserved Sequence↗