Biomedical subjects

Qiong Gao

Publications and source records attributed to Qiong Gao.

7 recordsLinked to original sources

PubMed2006

Resources for integrative systems biology: from data through databases to networks and dynamic system models.

In systems biology, biologically relevant quantitative modelling of physiological processes requires the integration of experimental data from diverse sources. Recent developments in high-throughput methodologies enable the analysis of the transcriptome, proteome, interactome, metabolome and phenome on a previously unprecedented scale, thus contributing to the deluge of experimental data held in numerous public databases. In this review, we describe some of the databases and simulation tools that are relevant to systems biology and discuss a number of key issues affecting data integration and the challenges these pose to systems-level research.

Animals↗

PubMed2006

Dynamic modeling of chemical fate and transport in multimedia environments at watershed scale-I: theoretical considerations and model implementation.

A geo-referenced environmental fate model was developed for analyzing unsteady-state dispersion and distribution of chemicals in multimedia environmental systems. Chemical transport processes were formulated in seven environmental compartments of air, canopy, surface soil, root-zone soil, vadose-zone soil, surface water, and sediment. The model assumed that the compartments were completely mixed and chemical equilibrium was established instantaneously between the sub-compartments within each compartment. A fugacity approach was utilized to formulate the mechanisms of diffusion, advection, physical interfacial transport, and transformation reactions. The governing equations of chemical mass balances in the environmental compartments were solved simultaneously to reflect the interactions between the compartments. A geographic information system (GIS) database and geospatial analysis were integrated into the chemical transport simulation to provide spatially explicit estimations of model parameters at watershed scale. Temporal variations of the environmental properties and source emissions were also considered in the parameter estimations. The outputs of the model included time-dependent chemical concentrations in each compartment and its sub-compartments, and inter-media mass fluxes between adjacent compartments at daily time steps.

Computer Simulation↗

PubMed2006

Dynamic modeling of chemical fate and transport in multimedia environments at watershed scale-II: trichloroethylene test case.

A multimedia environmental fate model was developed to study the temporal dynamics and spatial distribution of a chemical pollutant at watershed scale. The theoretical considerations and implementation of the model were described in the accompanying paper (Part I). This paper presents the result of a test simulation on the transport of trichloroethylene (TCE) in the Connecticut River Basin. The simulation results were reported as time series of concentrations and inter-media transport fluxes in the compartments of atmosphere, plant, soil, surface water, and sediment. Predicted concentrations from the test simulation were compared with published field data or predictions by validated models. The temporal trends in TCE predictions were evaluated by comparing the simulation results with monthly TCE concentrations in various environmental compartments and monthly fluxes of inter-media transport processes. Results indicated that the simulation results were in reasonable agreement with reported data in the literature. The results also revealed that the mass transport of TCE from the atmosphere compartment to soil and surface water was a major route of TCE dispersion in the environment.

Ecosystem↗

PubMed2006

FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets.

FLIGHT (www.flight.licr.org) is a new database designed to help researchers browse and cross-correlate data from large-scale RNAi studies. To date, the majority of these functional genomic screens have been carried out using Drosophila cell lines. These RNAi screens follow 100 years of classical Drosophila genetics, but have already revealed their potential by ascribing an impressive number of functions to known and novel genes. This has in turn given rise to a pressing need for tools to simplify the analysis of the large amount of phenotypic information generated. FLIGHT aims to do this by providing users with a gene-centric view of screen results and by making it possible to cluster phenotypic data to identify genes with related functions. Additionally, FLIGHT provides microarray expression data for many of the Drosophila cell lines commonly used in RNAi screens. This, together with information about cell lines, protocols and dsRNA primer sequences, is intended to help researchers design their own cell-based screens. Finally, although the current focus of FLIGHT is Drosophila, the database has been designed to facilitate the comparison of functional data across species and to help researchers working with other systems navigate their way through the fly genome.

Animals↗

PubMed2006

pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.

pSTIING (http://pstiing.licr.org) is a new publicly accessible web-based application and knowledgebase featuring 65 228 distinct molecular associations (comprising protein-protein, protein-lipid, protein-small molecule interactions and transcriptional regulatory associations), ligand-receptor-cell type information and signal transduction modules. It has a particular major focus on regulatory networks relevant to chronic inflammation, cell migration and cancer. The web application and interface provide graphical representations of networks allowing users to combine and extend transcriptional regulatory and signalling modules, infer molecular interactions across species and explore networks via protein domains/motifs, gene ontology annotations and human diseases. pSTIING also supports the direct cross-correlation of experimental results with interaction information in the knowledgebase via the CLADIST tool associated with pSTIING, which currently analyses and clusters gene expression, proteomic and phenotypic datasets. This allows the contextual projection of co-expression patterns onto prior network information, facilitating the identification of functional modules in physiologically relevant systems.

Amino Acid Motifs↗

PubMed2003

Explanation of vegetation succession in subtropical southern China based on ecophysiological characteristics of plant species.

A stomatal conductance model and a photosynthesis model were applied to field measurements of transpiration and photosynthesis of seven tree species growing in subtropical southern China. Parameter values of drought resistance and tolerance and biochemical assimilation capacity were obtained by means of nonlinear statistical regression, and were used to quantify species succession. The analysis indicated that the models adequately described the ecophysiological behavior of the trees under various environmental conditions. We found a general pattern of decreased drought resistance and tolerance, but increased biochemical assimilation capacity from pines to heliophilus broadleaf trees to mesophilus broadleaf trees. Succession was explained on the basis of these physiological characteristics together with positive feedbacks caused by changes in soil physical properties. The ecophysiological explanation of succession implies that: (1) fitness of a species for a particular succession stage at a particular location can be measured by stomatal behavior and biochemical assimilation capacity under local climate and soil conditions; (2) selection of species for a particular location at a particular succession stage can be guided by the parameter values provided in this study; and (3) succession may be accelerated by selecting trees with large root systems and large soil-root conductances that facilitate soil hydraulic redistribution of water.

China↗

PubMed2002

Variations of plant life form diversity along the Northeast China Transect and its direct gradient analysis.

Plant life form diversity and its direct gradient analysis on a larger scale climate change gradient were tested, based on the data from Northeast China Transect platform. The results showed that the species numbers, life form richness and life form diversity were relative higher at the eastern forests and the ecotone between typical vegetation, while those on the meadow grasslands and typical steppes were lower. Although plant life forms can reflect the climate variations, life form diversity is not consistent with the major global gradient along the NECT.

China↗