Biomedical subjects

Dequan Li

Publications and source records attributed to Dequan Li.

6 recordsLinked to original sources

PubMed2025

Glutamate molecular structure and protein affect the inhibition of breast cancer cell metastasis: Cell-derived exosomes inhibitory effects through the MAPK signaling pathway.

The aim of this study was to investigate the inhibitory effect of glutamate molecular structure and protein on breast cancer cell metastasis and the potential inhibitory mechanism of cell-derived exosomes via MAPK signaling pathway. Breast cancer cell lines with high metastatic potential were selected by in vitro cell culture technique. The effects of specific inhibitors of glutamic acid on the proliferation and metastasis of breast cancer cells were studied. Changes in protein expression profiles were analyzed by proteomics techniques to identify key proteins associated with breast cancer metastasis. Breast cancer cells were treated with inhibitors of the MAPK signaling pathway to evaluate their effect on cell metastasis and compare with exosome treatment. The results showed that the specific inhibitors of glutamate molecular structure could significantly inhibit the proliferation and metastasis of breast cancer cells. Proteomic analysis revealed several down-regulated proteins that are closely related to breast cancer metastasis.

Humans↗

PubMed2006

IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics.

UNLABELLED: A software package, IndexToolkit, aimed at overcoming the disadvantage of FASTA-format databases for frequent searching, is developed to utilize an indexing strategy to substantially accelerate sequence queries. IndexToolkit includes user-friendly tools and an Application Programming Interface (API) to facilitate indexing, storage and retrieval of protein sequence databases. As open source, it provides a sequence-retrieval developing framework, which is easily extensible for high-speed-request proteomic applications, such as database searching or modification discovering. We applied IndexToolkit to database searching engine pFind to demonstrate its effect. Experimental studies show that IndexToolkit is able to support significantly faster searches of protein database. AVAILABILITY: The IndexToolkit is free to use under the open source GNU GPL license. The source code and the compiled binary can be freely accessed through the website http://pfind.jdl.ac.cn/IndexToolkit. In this website, the more detailed information including screenshots and documentations for users and developers is also available.

Database Management Systems↗

PubMed2006

Molecular cloning and expression of a gene encoding alcohol acyltransferase (MdAAT2) from apple (cv. Golden Delicious).

Volatile esters are major aroma components of apple, and an alcohol acyltransferase (AAT) catalyzes the final step in ester biosynthesis. The gene MdAAT2, which encodes a predicted 51.2 kDa protein containing features of other acyl transferases, was isolated from Malus domestica Borkh. (cv. Golden Delicious). In contrast to other apple varieties, the MdAAT2 gene of Golden Delicious is exclusively expressed in the fruit. The MdAAT2 protein is about 47.9 kDa and mainly localized in the fruit peel, as indicated by immunoblot and immunolocalization analysis. Northern blot and immunoblot analysis showed that the transcription and translation of MdAAT2 have a positive correlation with apple AAT enzyme activity and ester production, except in the later ripening stage, suggesting that MdAAT2 is involved in the regulation of ester biosysthesis and that a post-translation modification may be involved in regulation of AAT enzyme activity. Tissue disk assays of fruit peel revealed that using extraneous alcohols can recover the corresponding ester formation. Transcription and translation of MdAAT2 were both depressed by 1-methylcyclopropene (1-MCP) treatment and subsequent ester production was also prevented. These results suggest that: (1) ester production is mainly regulated by MdAAT2; (2) ethylene is also involved in this regulatory progress and (3) ester compounds rely principally on the availability of substrates.

Acyltransferases↗

PubMed2005

pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry.

SUMMARY: Research in proteomics requires powerful database-searching software to automatically identify protein sequences in a complex protein mixture via tandem mass spectrometry. In this paper, we describe a novel database-searching software system called pFind (peptide/protein Finder), which employs an effective peptide-scoring algorithm that we reported earlier. The pFind server is implemented with the C++ STL, .Net and XML technologies. As a result, high speed and good usability of the software are achieved.

Algorithms↗

PubMed2005

Effects of elevated intraocular pressure on mouse retinal ganglion cells.

We developed and characterized a mouse model of elevated intraocular pressure (IOP) to investigate the underlying cellular and genetic mechanisms of retinal ganglion cell (RGC) death. IOP was unilaterally increased in C57BL/6J mice by photocoagulation of the episcleral and limbal veins. IOP was measured using an indentation tonometer. RGC survival was measured by retrograde labeling using DiI applied to the superior colliculous. The mechanism of RGC death was investigated using TUNEL staining, immunostaining for cleaved caspase-3, and Western blot for Bcl-2 and Bax expression. RT-PCR was used to measure changes in Bcl-2, Bax, Bad, Bak, P53, ICE and Fas. Mean IOP was increased in the treated eyes from 13+/-1.8 to 20.0+/-2.8 mmHg at four weeks and 17+/-2.2 mmHg at eight weeks. RGC loss was 15.6+/-3.4% at two weeks and 27.3+/-4.5% at four weeks after laser photocoagulation. TUNEL staining and caspase-3 positive cells were increased in the ganglion cell layer (GCL) in the treated eyes and seldom found in the control eyes. Bcl-2 expression in control group was higher than in the experimental group, while Bax expression in the control group was less than in experimental group. This mouse model resulted in a consistent, sustained increase in IOP with a reduction in the number of RGCs in the treated eye. The RGCs in eyes with elevated IOP were TUNEL-positive, with increased caspase-3 and decreased Bcl-2, consistent with apoptosis as the mechanism of neuronal cell death.

Animals↗

PubMed2004

Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry.

MOTIVATION: The correlation among fragment ions in a tandem mass spectrum is crucial in reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information in a tunable and comprehensive manner has been lacking. RESULTS: This paper provides a promising approach to utilizing the correlative information for improving the peptide identification accuracy. The kernel trick, rooted in the statistical learning theory, is exploited to address this issue with low computational effort. The common scoring method, the tandem mass spectral dot product (SDP), is extended to the kernel SDP (KSDP). Experiments on a dataset reported previously demonstrate the effectiveness of the KSDP. The implementation on consecutive fragments shows a decrease of 10% in the error rate compared with the SDP. Our software tool, pFind, using a simple scoring function based on the KSDP, outperforms two SDP-based software tools, SEQUEST and Sonar MS/MS, in terms of identification accuracy. SUPPLEMENTARY INFORMATION: http://www.jdl.ac.cn/user/yfu/pfind/index.html

Algorithms↗