Biomedical subjects

Ao Li

Publications and source records attributed to Ao Li.

15 recordsLinked to original sources

PubMed2026

Genomic analysis of regulatory mechanisms governing EPS66A biosynthesis in Streptomyces changanensis HL-66.

Streptomyces changanensis HL-66 produces the α-(1,4)/(1,6)-glucan exopolysaccharide EPS66A, a potent plant immune elicitor with promising applications in plant protection. However, its low native fermentation yield limits large-scale application. To investigate the biosynthetic potential and regulatory mechanisms underlying EPS66A production, the whole genome of HL-66 was sequenced and analyzed. The HL-66 genome is 6.82 Mb in size, with a GC content of 74%, and encodes 6081 predicted functional genes. Among these, 1390 genes were annotated to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, 4187 were assigned to Gene Ontology (GO) terms, and 143 were classified into Clusters of Orthologous Groups (COG) categories. antiSMASH analysis identified 22 secondary metabolite biosynthetic gene clusters, including multiple polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) clusters. Functional analyses revealed that the glycosyltransferase gene (GTy) and the global regulatory gene (bldD) are involved in EPS66A biosynthesis. bldD is involved in morphological development and EPS66A production, whereas GTy specifically regulates EPS66A production without affecting growth or development. In both in vivo and potted-plant experiments, EPS66A (200 μg/mL) significantly reduced the severity of tobacco mosaic virus, apple anthracnose leaf spot, walnut bacterial leaf spot, and jujube anthracnose, achieving control efficacies of 90.21%, 87.95%, 77.41%, and 68.55%, respectively, and outperforming a commercial chitosan oligosaccharide control. These findings provide new insights into the genetic architecture and regulatory mechanisms of EPS66A biosynthesis and support its development as a polysaccharide-based green pesticide.

Streptomyces↗

PubMed2026

Comparative analysis of genomic variations among different Cdo1 paralogs for salinity-adaptation in oysters.

Under rapid climate change and anthropogenic activities, oysters, a global aquaculture species, are subjected to exacerbated culturing environments, especially for those living in in-shore estuarine species, such as Suminoe oysters Crassostrea ariakensis. This study aims to investigate the molecular mechanisms of salinity adaptation of C. ariakensis. We performed an expression genome-wide association study (eGWAS) to compare genetic regulation among 5 paralogous copies of a key salinity-related gene, cysteine dioxygenase 1 (Cdo1). A total of 40 significant eSNPs with 82 adjacent eGenes were identified in 2 copies (Cdo1_26639 and Cdo1_1666). We identified only trans-eSNPs for Cdo1_26639 and more cis-eSNPs for Cdo1_1666, and different eGenes for these 2 Cdo1 copies, which indicated that the expressional regulation of these paralogs may undergo distinct pathways. We identified 3 eGenes that exhibited identical expression patterns with Cdo1_26639 and Cdo1_1666, including 6-Pgdh, Trapp and tandem copy of Cdo1_27337. The expression correlation between Cdo1 copies and eGenes was enhanced under salinity stresses, suggesting the crucial role of eGenes in regulating Cdo1's expression in response to salinity changes. Our results provide comprehensive identification and comparison of eSNPs across different paralogous copies of one gene, along with insights into the molecular mechanisms underlying salinity tolerance, and genetic markers for breeding salinity-resistant oysters.

Animals↗

PubMed2006

Prediction of Nepsilon-acetylation on internal lysines implemented in Bayesian Discriminant Method.

Protein acetylation is an important and reversible post-translational modification (PTM), and it governs a variety of cellular dynamics and plasticity. Experimental identification of acetylation sites is labor-intensive and often limited by the availability of reagents such as acetyl-specific antibodies and optimization of enzymatic reactions. Computational analyses may facilitate the identification of potential acetylation sites and provide insights into further experimentation. In this manuscript, we present a novel protein acetylation prediction program named PAIL, prediction of acetylation on internal lysines, implemented in a BDM (Bayesian Discriminant Method) algorithm. The accuracies of PAIL are 85.13%, 87.97%, and 89.21% at low, medium, and high thresholds, respectively. Both Jack-Knife validation and n-fold cross-validation have been performed to show that PAIL is accurate and robust. Taken together, we propose that PAIL is a novel predictor for identification of protein acetylation sites and may serve as an important tool to study the function of protein acetylation. PAIL has been implemented in PHP and is freely available on a web server at: http://bioinformatics.lcd-ustc.org/pail.

Acetylation↗

PubMed2006

Differentiated cells are more efficient than adult stem cells for cloning by somatic cell nuclear transfer.

Since the creation of Dolly via somatic cell nuclear transfer (SCNT), more than a dozen species of mammals have been cloned using this technology. One hypothesis for the limited success of cloning via SCNT (1%-5%) is that the clones are likely to be derived from adult stem cells. Support for this hypothesis comes from the findings that the reproductive cloning efficiency for embryonic stem cells is five to ten times higher than that for somatic cells as donors and that cloned pups cannot be produced directly from cloned embryos derived from differentiated B and T cells or neuronal cells. The question remains as to whether SCNT-derived animal clones can be derived from truly differentiated somatic cells. We tested this hypothesis with mouse hematopoietic cells at different differentiation stages: hematopoietic stem cells, progenitor cells and granulocytes. We found that cloning efficiency increases over the differentiation hierarchy, and terminally differentiated postmitotic granulocytes yield cloned pups with the greatest cloning efficiency.

Adult Stem Cells↗

PubMed2006

PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory.

BACKGROUND: As a reversible and dynamic post-translational modification (PTM) of proteins, phosphorylation plays essential regulatory roles in a broad spectrum of the biological processes. Although many studies have been contributed on the molecular mechanism of phosphorylation dynamics, the intrinsic feature of substrates specificity is still elusive and remains to be delineated. RESULTS: In this work, we present a novel, versatile and comprehensive program, PPSP (Prediction of PK-specific Phosphorylation site), deployed with approach of Bayesian decision theory (BDT). PPSP could predict the potential phosphorylation sites accurately for approximately 70 PK (Protein Kinase) groups. Compared with four existing tools Scansite, NetPhosK, KinasePhos and GPS, PPSP is more accurate and powerful than these tools. Moreover, PPSP also provides the prediction for many novel PKs, say, TRK, mTOR, SyK and MET/RON, etc. The accuracy of these novel PKs are also satisfying. CONCLUSION: Taken together, we propose that PPSP could be a potentially powerful tool for the experimentalists who are focusing on phosphorylation substrates with their PK-specific sites identification. Moreover, the BDT strategy could also be a ubiquitous approach for PTMs, such as sumoylation and ubiquitination, etc.

Amino Acid Sequence↗

PubMed2006

Missing value estimation for DNA microarray gene expression data by Support Vector Regression imputation and orthogonal coding scheme.

BACKGROUND: Gene expression profiling has become a useful biological resource in recent years, and it plays an important role in a broad range of areas in biology. The raw gene expression data, usually in the form of large matrix, may contain missing values. The downstream analysis methods that postulate complete matrix input are thus not applicable. Several methods have been developed to solve this problem, such as K nearest neighbor impute method, Bayesian principal components analysis impute method, etc. In this paper, we introduce a novel imputing approach based on the Support Vector Regression (SVR) method. The proposed approach utilizes an orthogonal coding input scheme, which makes use of multi-missing values in one row of a certain gene expression profile and imputes the missing value into a much higher dimensional space, to obtain better performance. RESULTS: A comparative study of our method with the previously developed methods has been presented for the estimation of the missing values on six gene expression data sets. Among the three different input-vector coding schemes we tried, the orthogonal input coding scheme obtains the best estimation results with the minimum Normalized Root Mean Squared Error (NRMSE). The results also demonstrate that the SVR method has powerful estimation ability on different kinds of data sets with relatively small NRMSE. CONCLUSION: The SVR impute method shows better performance than, or at least comparable with, the previously developed methods in present research. The outstanding estimation ability of this impute method is partly due to the use of the most missing value information by incorporating orthogonal input coding scheme. In addition, the solid theoretical foundation of SVR method also helps in estimation of performance together with orthogonal input coding scheme. The promising estimation ability demonstrated in the results section suggests that the proposed approach provides a proper solution to the missing value estimation problem. The source code of the SVR method is available from http://202.38.78.189/downloads/svrimpute.html for non-commercial use.

Algorithms↗

PubMed2006

[Analysis and discrimination of Collocalia esculenta L. via FTIR spectroscopy].

Collocalia esculenta L. is called Yanwo in China. Thirty kinds of dry yanwo were identified by Fourier transform infrared spectroscopy (FTIR) . The results indicated that there were some obvious differences in FTIR between the dry yanwo and the natural yanwo, mainly represented in some absorption peaks of protein, amino acid (1 634, 1 535 cm(-1)) and amylase (1 034 cm9-1)). Meanwhile, the shape, position and intensity of the peaks from methylene (2 935 cm(-1)), protein and amino acid (1 647, 1 533, 1 447 cm(-1)) in dry yanwo were similar to those of the glutin. Therefore, different amounts of glutin were added in dry yanwo samples. The content of candy in some dry candy yanwo products was as high as 99%, but the content of yanwo was only 1%. The characteristic peaks of yanwo in these products even could not be found. So the quality of yanwo in the market could not be guaranteed from these results. FTIR is fast and direct to analyse and evaluate the quality of yanwo product.

Animals↗

PubMed2006

[Prediction of protein solvent accessibility with Markov chain model].

Residues in protein sequences can be classified into two (exposed / buried) or three (exposed/intermediate/buried) states according to their relative solvent accessibility. Markov chain model (MCM) had been adopted for statistical modeling and prediction. Different orders of MCM and classification thresholds were explored to find the best parameters. Prediction results for two different data sets and different cut-off thresholds were evaluated and compared with some existing methods, such as neural network, information theory and support vector machine. The best prediction accuracies achieved by the MCM method were 78.9% for the two-state prediction problem and 67.7% for the three-state prediction problem, respectively. A comprehensive comparison for all these results shows that the prediction accuracy and the correlative coefficient of the MCM method are better than or comparable to those obtained by the other prediction methods. At the same time, the advantage of this method is the lower computation complexity and better time-consuming performance.

Algorithms↗

PubMed2005

LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST.

Subcellular location of a protein is one of the key functional characters as proteins must be localized correctly at the subcellular level to have normal biological function. In this paper, a novel method named LOCSVMPSI has been introduced, which is based on the support vector machine (SVM) and the position-specific scoring matrix generated from profiles of PSI-BLAST. With a jackknife test on the RH2427 data set, LOCSVMPSI achieved a high overall prediction accuracy of 90.2%, which is higher than the prediction results by SubLoc and ESLpred on this data set. In addition, prediction performance of LOCSVMPSI was evaluated with 5-fold cross validation test on the PK7579 data set and the prediction results were consistently better than the previous method based on several SVMs using composition of both amino acids and amino acid pairs. Further test on the SWISSPROT new-unique data set showed that LOCSVMPSI also performed better than some widely used prediction methods, such as PSORTII, TargetP and LOCnet. All these results indicate that LOCSVMPSI is a powerful tool for the prediction of eukaryotic protein subcellular localization. An online web server (current version is 1.3) based on this method has been developed and is freely available to both academic and commercial users, which can be accessed by at http://Bioinformatics.ustc.edu.cn/LOCSVMPSI/LOCSVMPSI.php.

Artificial Intelligence↗

PubMed2005

[The role of different subtypes of G protein in the secretory function of macrophages stimulated by activated complement following severe burn injury].

OBJECTIVE: To investigate the influence of activated complement on the secretory function of peritoneal macrophage (PMphi) in the production of nitric oxide (NO) and tumor necrosis factor-alpha (TNF-alpha), especially in the role of different G-protein subtypes in this process after burns. METHODS: The mice inflicted by 18% TBSA full-thickness scald was established and employed as the model. And the mice were divided into A (the complements were preserved and activated) and B (with intraperitoneal injection of CVF to deplete complement before scald) groups. The plasma of the mice in the two groups was collected at 6 postburn hour (PBH) and cultured with PMphi from normal mice. The PMphi were pretreated with pertussis toxin (PT) and with cholera toxin (CT). The NO and TNF-alpha levels in the supernatant of normal PMphi culture with different pretreatment were measured by Greiss assay. RESULTS: The NO and TNF-alpha contents in group A [(80 +/- 12) micromol/L, (46 +/- 6)%] were obviously higher than those in group B [(34 +/- 5) micromol/L, (26 +/- 5)%, P < 0.01]. The NO content produced by PMphi (45 +/- 10 micromol/L) in A group decreased (P < 0.01), while the TNF-alpha activity (58 +/- 10)% increased by PT pretreatment (P < 0.05). On the contrary, the NO content produced by PMphi (105 +/- 18 micromol/L) in group A increased (P < 0.01), while the TNF-alpha activity (27 +/- 6)% decreased by CT pretreatment (P < 0.01). CONCLUSION: These results indicates that the secretory function of normal PMphi can be enhanced by complement activation after thermal injury, which might partly be due to the effect of activated complement components through complement receptor coupled G-protein. In the secretory function of complement stimulated Mphi, Gi protein has a major role in the production of NO, Gs protein is mainly involved in the secretion of TNF-alpha.

Animals↗

PubMed2002

[The role of the change in glucocorticoid receptor in stress-induced gastric ulcer in severely burned rats].

OBJECTIVE: To investigate the role of the change in glucocorticoid receptor in stress-induced gastric ulcer in severely burned rats. METHODS: Wistar rats inflicted with 30% TBSA full-thickness burn were employed as the model. The dynamic postburn change in the glucocorticoid receptor in gastric mucosal tissue and gastric mucosal injury (injury index) were observed. RESULTS: The gastric mucosal cortisol content increased as of 3 postburn hours (PBHs) and peaked at 12 PBHs. But the cytoplasmic glucocorticoid receptor content in the gastric mucosal cells decreased evidently. In addition, the gastric mucosal injury index increased obviously at 12 and 24 PBHs. CONCLUSION: The decrease of gastric mucosal cytoplasmic glucocorticoid receptor content might be closely related to the stress-induced gastric mucosal injury.

Animals↗

PubMed2000

Cardiac contraction and calcium transport function after severe burn injury in rats.

OBJECTIVE: To examine the function change of myocardial calcium transports and determined what role the change plays in cardiac dysfunction after severe burn injury in rats. METHODS: The contraction and relaxation properties of the left ventricle (LV) were studied in the isolated hearts preparations of Wistar rats at 3, 8, and 24 h after a 30% TBSA (total body surface area) full-thickness burn. The calcium transport function of the sarcoplasmic reticulum (SR) was measured by the millipore filtration technique. RESULTS: The maximal rate of LV pressure (plus minusdp/dtmax) of the burn group was significantly lower than that of the control group (P<0.01). In addition, the calcium-dependent ATPase activity and the coupling ratio of SR were also markedly depressed. CONCLUSIONS: It indicates that the decrease in the SR calcium transport function is one of the important mechanisms for the cardiac contractile dysfunction after severe burn injury.

Journal Article↗

PubMed2000

Protective effect of early enteral feeding on postburn impairment of liver function and its mechanism in rats.

AIM:To study the protective effect of early enteral feeding (EEF) on the postburn impairment of liver function and its mechanism.METHODS:Wistar rats with 30% of total body surface area (TBSA) full-thickness burn were employed. The effects of EEF on the postburn changes of gastric intramucosal pH, endotoxin levels in portal vein, water contents of hepatic tissue, blood concentrations of tumor necrosis factor (TNF-alpha), plasma activities of alanine aminotransferase (ALT) and asparate aminotransferase (AST), as well as the blood contents of total (TB) and direct bilirubin (DB), total protein (TP) and albumin (ALB) were serially determined within 48h postburn.RESULTS:EEF could significantly improve gastric mucosal acidosis, reduce portal vein endotoxin level and water content of hepatic tissue, as well as plasma concentrations of TNF-alpha at all timepoints after severe burns (P < 0.01); postburn elevation of the plasma activities of ALT, AST and the contents of TB, DB were effectively prevented, whereas the plasma concentrations of TP and ALB were markedly increased 24h and 48h posturn in EEF group compared with that of the burn without EEF group (P < 0.01 ).CONCLUSION:EEF has significant beneficial effects on the improvement of hepatic function in rats after severe burn, and is probably related with an increase in splanchnic blood flow, reduction of the absorption of gut-origin endotoxin and the consequent release of inflammatory mediators.

Journal Article↗

PubMed2000

Reduced gastric acid production in burn shock period and its significance in the prevention and treatment of acute gastric mucosal lesions.

AIM:To investigate the changes of gastric acid production and its mechanism in shock period of severe burn in rats.METHODS:A rat model with 30% TBSA full thickness burn injury was employed and the gastric acid production,together with gastric mucosal blood flow (GMBF) and energy charge (EC) were measured serially within 48h postburn.RESULTS:The gastric acid production in the acute shock period was markedly inhibited after severe burn injury.At the 3rd h postburn,the gastric juice volume, total acidity and acid output were already significantly decreased (P < 0.01 =, and reached the lowest point, 0.63mL/L ± 0.20mL/L, 10.81mmol/L ± 2.58mmol/L and 2.23mmol/h ± 0.73mmol/h respectively, at the 12th h postburn. Although restored to some degree 24h after thermal injury, the variables above were still statistically lower, compared with those of control animals at the 48th h postburn. The GMBF and EC were also significantly reduced after severe burns, consistent with the trend of gastric acid production changes.CONCLUSION:Gastric acid production, as well as GMBF and EC was predominantly decreased in the early postburn stage, suggesting that gastric mucosal ischemia and hypoxia with resultant disturbance in energy metabolism, but not gastric acid proper, might be the decisive factor in the pathogenesis of AGML after thermal injury, and that the preventive use of anti-acid drugs during burn shock period was unreasonable in some respects. Therefore, taking effective measures to improve gastric mucosal blood perfusion as early as possible postburn might be more preferable for the AGML prevention and treatment.

Journal Article↗

PubMed1999

Significance of runaway calcium homeostasis in cultured cardiomyocytes in development of hypoxia, burnt serum-induced injury.

OBJECTIVE: This study aimed at understanding of the role of calcium homeostasis in cardiomyocytes from hypoxia, burnt serum-induced injury. METHODS: Alterations in cytosolic free calcium concentration (Ca(i)), calcium influx and viability of the cardiomyocytes in vitro after hypoxia, burnt serum stimulus were observed. RESULTS: Ca(i) increased markedly, in the meantime, the cellular transmembrane calcium influx increased and the viability of the cells decreased significantly following hypoxia, burnt serum-induced injury. CONCLUSIONS: In our study cytosolic calcium ion was transported abnormally in the cardiomyocytes after burn, to result in Ca(i) increase and runaway calcium homeostasis, thus the normal cellular function was disturbed. This may be one of the important factors in the development of burn-induced cardiac injury.

Journal Article↗