Biomedical subjects

Xiangjun Liu

Publications and source records attributed to Xiangjun Liu.

9 recordsLinked to original sources

PubMed2026

Network pharmacology-based prediction and experimental validation of the anti-hyperuricemic effects of oolong tea polyphenols.

OBJECTIVE: This study aimed to identify candidate therapeutic targets of oolong tea polyphenols (TP) against hyperuricemia (HUA) using network pharmacology and bioinformatics, and to validate the predicted molecular mechanism through in vivo experimentation. METHODS: Drug and disease targets were retrieved from public databases, and overlapping targets were identified by Venn diagram analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the shared targets, and a protein-protein interaction (PPI) network was constructed to identify hub genes. For in vivo validation, an HUA mouse model was established by 15 days of oral potassium oxonate (PO) administration. Model mice then received TP by gavage at low (0.5 g⋅kg-1⋅d-1), medium (1 g⋅kg-1⋅d-1), or high (2 g⋅kg-1⋅d-1) doses for an additional 15 days. Serum biochemical markers, histopathological changes, and pathway-related protein expression were assessed by enzyme-linked immunosorbent assay (ELISA), hematoxylin and eosin (HE) staining, and western blot analysis, respectively. RESULTS: Network pharmacology analysis identified 59 overlapping targets between TP and HUA; GO and KEGG enrichment analyses revealed that these targets were primarily associated with hormone metabolism and the PI3K-AKT signaling pathway. In the animal experiment, TP dose-dependently reduced serum uric acid (SUA) levels in hyperuricemic mice. At the molecular level, low and medium doses of TP suppressed phosphorylation of phosphatidylinositol 3-kinase (PI3K), protein kinase B (AKT), and mammalian target of rapamycin (mTOR), whereas the high dose paradoxically activated this pathway and concomitantly elevated interleukin-1β levels. These findings indicate that TP modulates uric acid metabolism through a non-monotonic, dose-dependent mechanism. CONCLUSION: By combining network pharmacology with animal experiments, this study identified the PI3K/AKT/mTOR signaling pathway as a likely mediator of the anti-hyperuricemic action of oolong tea polyphenols (TP). A medium dose of TP achieved the most balanced outcome, attenuating inflammation and preserving hepatic and renal architecture; the high dose, by contrast, paradoxically elevated interleukin-1β (IL-1β) and overactivated PI3K/AKT/mTOR signaling, underscoring the importance of dose calibration. These data suggest that a medium dose of TP may represent a feasible dietary strategy against hyperuricemia. Further work-including monomer identification, direct target validation, and clinical evaluation-is warranted to confirm and extend these preclinical findings.

PI3K/Akt/mTOR signaling pathway↗

PubMed2006

Integrated genome-wide gene expression map and high-resolution analysis of aberrant chromosomal regions in squamous cell lung cancer.

The recognition of recurrent aberrant regions in cancer is important to the discovery of candidate cancer related genes. Here we first constructed a genome-wide gene expression map of squamous lung carcinoma from the Stanford Microarray Database. High-resolution detection of aberrant chromosomal regions was performed by using moving-median method. 84% (27 of 32) of our results were consistent with the previous studies of comparative genomic hybridization or loss of heterozygosity. One overrepresented region in Xq28 was newly discovered to be related to squamous cell lung carcinoma. These observations could be of great interest for further studies.

Carcinoma, Squamous Cell↗

PubMed2006

GNBSL: a new integrative system to predict the subcellular location for Gram-negative bacteria proteins.

This paper proposes a new integrative system (GNBSL--Gram-negative bacteria subcellular localization) for subcellular localization specifized on the Gram-negative bacteria proteins. First, the system generates a position-specific frequency matrix (PSFM) and a position-specific scoring matrix (PSSM) for each protein sequence by searching the Swiss-Prot database. Then different features are extracted by four modules from the PSFM and the PSSM. The features include whole-sequence amino acid composition, N- and C-terminus amino acid composition, dipeptide composition, and segment composition. Four probabilistic neural network (PNN) classifiers are used to classify these modules. To further improve the performance, two modules trained by support vector machine (SVM) are added in this system. One module extracts the residue-couple distribution from the amino acid sequence and the other module applies a pairwise profile alignment kernel to measure the local similarity between every two sequences. Finally, an additional SVM is used to fuse the outputs from the six modules. Test on a benchmark dataset shows that the overall success rate of GNBSL is higher than those of PSORT-B, CELLO, and PSLpred. A web server GNBSL can be visited from http://166.111.24.5/webtools/GNBSL/index.htm.

Amino Acid Sequence↗

PubMed2005

Construction of a eukaryotic expression plasmid encoding partial S gene fragments of the SARS-CoV and its potential utility as a DNA vaccine.

The spike (S) protein, a main surface antigen of the SARS coronavirus (SARS-CoV), is considered to be one of the most important protective antigen candidates for targets for vaccine design against the virus. In this study, a secreted recombinant expression plasmid, pVAX-S1, encoding the partial S protein with a signal peptide, was constructed and used to immunize BALB/c mice through electroporation. It was demonstrated that the eukaryotic expression vector pVAX-S1 was successfully constructed by restriction enzyme and sequence analysis. The expressed protein could be detected specifically by Western blot analysis. The serum IgG level of the vaccine group mice was significantly higher than that of the corresponding control group at day 14 after vaccination (P < 0.05). The vaccine group demonstrated significantly higher S1 protein lymphocyte proliferation index (LPI) than the control groups (P < 0.05). Furthermore, in the experimental group, a decrease in the ratio of CD4(+) to CD8(+) T-lymphocytes and an increase level of IFN-gamma in serum were observed. However, interleukin-4 (IL-4) was not detectable in two groups. These results strongly demonstrated that the pVAX-S1 plasmid could induce humoral and cellular immune responses in mice, and may be a potential candidate for a DNA vaccine against the SARS coronavirus.

Animals↗

PubMed2005

[Spatial distribution pattern of Larix chinensis population in Taibai Mt].

Larix chinensis is an endangered species only distributed in Qinling Mountains of China. It has a concentrated distribution in Taibai Mt., and plays an important role in environmental protection in the high altitude. After an investigation on fifteen 400 m2 plots, a comparative study on the spatial distribution pattern of L. chinensis population and its dynamics was made by the tests of discrete distribution pattern and aggregation intensity. The results showed that at different sampling areas, L. chinensis populations all performed the pattern of clustering distribution. As the sampling area increased, the congregating intensity of L. chinensis population appeared the pattern of high-->low-->high, but the highest congregation occurred in the areas of 100 m2 and 25 m2. The clustering intensity went down from low to high altitude, and the area with the highest clustering intensity occurred on that of 25 m2 in low altitude, 150 m2 in middle altitude, and 100 m2 in higher altitude. The clustering intensity in shade slope was higher than that in sunny slope, and the area with the highest clustering intensity was 100 m2 on shade slope, and 150 m2 on sunny slope. With the population age increased, the distribution pattern had a trend from clustering to random, the clustering intensity decreased somewhat, and the area with the highest clustering intensity was 150 m2 in young or old stages, and 100 m2 in middle stage. The distribution pattern of L. chinensis population was related to its ecological characteristics, community composition, and environmental factors. In situ conservation should be strengthened in the future. In lower altitude or on shade slope, the measurements of thinning no-aim in tree and shrub species should be taken; while in higher altitude area or sunny slope, thinning shrub species in patch form would be better for L. chinensis populations block renovating. The fostering area for L. chinensis populations should be suit to the area with the highest clustering intensity of populations.

China↗

PubMed2004

BOD: a customizable bioinformatics on demand system accommodating multiple steps and parallel tasks.

The integration of bioinformatics resources worldwide is one of the major concerns of the biological community. We herein established the BOD (Bioinformatics on demand) system to use Grid computing technology to set up a virtual workbench via a web-based platform, to assist researchers performing customized comprehensive bioinformatics work. Users will be able to submit entire search queries and computation requests, e.g. from DNA assembly to gene prediction and finally protein folding, from their own office using the BOD end-user web interface. The BOD web portal parses the user's job requests into steps, each of which may contain multiple tasks in parallel. The BOD task scheduler takes an entire task, or splits it into multiple subtasks, and dispatches the task or subtasks proportionally to computation node(s) associated with the BOD portal server. A node may further split and distribute an assigned task to its sub-nodes using a similar strategy. In the end, the BOD portal server receives and collates all results and returns them to the user. BOD uses a pipeline model to describe the user's submitted data and stores the job requests/status/results in a relational database. In addition, an XML criterion is established to capture task computation program details.

Computational Biology↗

PubMed2004

[Root growth dynamics of Adenophora potaninii populations and its relation with environmental factors in northwest Sichuan Province].

In this paper, the dynamics of the root biomass and form development of Adenophora potaninii populations in different natural habitats in Northwest Sichuan were studied, and the factors influencing the root growth and form development were analyzed. The root biomass accumulation process of the mean individuals of the whole A. potaninii population in its life could be expressed by Logistic equation. From 1-3 years, the root length grew fast, but the root biomass accumulated slowly. From 4 years old, the root system developed in high speed, and the fast growth period of the root system could maintain until 15 year old. The basic patterns of root biomass accumulation process of different A. potaninii populations at different altitudes were similar to that of the whole population. However, the root system accumulation and root development was related closely with habitant conditions, and the root forms of different populations at different altitudes were significantly different (P < 0.05). At middle altitude (2800-3300 m), the biomass and form of root system could achieve a higher level, and the good harvest of root biomass could be obtained because of the favorable soil and climate conditions, and the less external disturbance of human beings. Therefore, this area could be an important base for A. potaninii population to grow. Whereas at the lower altitude (2600-2800 m), the biomass accumulation and the form development of root system were confined and maintained at a lower level because of the drought climate and the external disturbance of human beings. At the higher altitude (3300-3500 m) area with the harsh habitats, especially with lower temperature and lower pH, the root biomass of the mean individuals was significantly lower, and the individual form of root system was smaller, compared with that at middle altitude area. In order to use natural A. potaninii resource sustainablely, all the area should be planned, and the reasonable rotational prohibition of grazing and digging should be carried out.

Altitude↗

PubMed2004

[Analysis on age structure and dynamics of Kindonia uniflora populations].

Kindonia uniflora is a perennial clone herbaceous plant, and also, a native endangered plant in China. This paper studied its age structure, life table and survivorship curve in different habitats in Taibai mountain area. The results indicated that the age structure and dynamics of K. uniflora populations in the Betula utilis forest at altitude 2500-2700 m, in the Abies fargesii forest at altitude 2700-2900 m, and in the Larix chinensis forest at altitude 2900-3100 m had the similar pattern and developing tendency. The number of younger ramets at 1-2 years old or older than 5 years was less, and the number of ramets at 3-5 years old was the highest in the age structures. The negative values of dx (dead number), qx (mortality rate) and Kx (Killing rate) in the life table showed the increasing rate of the population sizes during the age stage. The survivorship curve of K. uniflora populations in different habitats belonged to Deevey C after 3-5 years old. The mortality rate of populations during 5-10 years stage was higher, and was stable after 10 years old. As for the characters of asexual propagation and clone growth, the rhizomes of the populations were in humus of soil, and developed and expanded as guerilla line style. During growth season, only one leaf grew above ground at every inter-node, and the population growth and development were rarely influenced by external factors. The forest communities, such as Betula utilis, Abies fargesii and Larix chinensis forest, in which K. uniflora populations lived, were at middle or higher mountain, where there were rarely disturbance from human being. Therefore, the habitats for K. uniflora populations to live were relatively stable. As the altitude increased, the disturbances from human being became less, the density of K. uniflora populations increased, the life cycle expanded, the peak of population death delayed, and the population living strategy changed to adapt to the habitats. K. uniflora populations preferred to live in cool climate, thick humus of soil and under shaded forest, therefore, the habitat of communities of Abies fargesii, Larix chinensis forest at altitude 2700-3100 m were better than that in Betula utilis forest. The growth and development of K. uniflora populations depended on the habitats; therefore, the communities in which K. uniflora population lived should be conserved firstly. The in-situ conservation of the populations should be encouraged.

Altitude↗

PubMed2002

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.

Animals↗