Biomedical subjects

Guang Gao

Publications and source records attributed to Guang Gao.

At least 19 recordsLinked to original sources

PubMed2006

A universal reference sample derived from clone vector for improved detection of differential gene expression.

BACKGROUND: Using microarrays by co-hybridizing two samples labeled with different dyes enables differential gene expression measurements and comparisons across slides while controlling for within-slide variability. Typically one dye produces weaker signal intensities than the other often causing signals to be undetectable. In addition, undetectable spots represent a large problem for two-color microarray designs and most arrays contain at least 40% undetectable spots even when labeled with reference samples such as Stratagene's Universal Reference RNAs. RESULTS: We introduce a novel universal reference sample that produces strong signal for all spots on the array, increasing the average fraction of detectable spots to 97%. Maximizing detectable spots on the reference image channel also decreases the variability of microarray data allowing for reliable detection of smaller differential gene expression changes. The reference sample is derived from sequence contained in the parental EST clone vector pT7T3D-Pac and is called vector RNA (vRNA). We show that vRNA can also be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This reference sample can be made inexpensively in large quantities as a renewable resource that is consistent across experiments. CONCLUSION: Results of this study show that vRNA provides a useful universal reference that yields high signal for almost all spots on a microarray, reduces variation and allows for comparisons between experiments and laboratories. Further, it can be used for quality control of microarray printing and PCR product quality, detection of hybridization anomalies, and simplification of spot finding and segmentation tasks. This type of reference allows for detection of small changes in differential expression while reference designs in general allow for large-scale multivariate experimental designs. vRNA in combination with reference designs enable systems biology microarray experiments of small physiologically relevant changes.

Calibration↗

PubMed2006

Evaluating genotoxicity associated with microcystin-LR and its risk to source water safety in Meiliang Bay, Taihu Lake.

In recent years cyanobacteria blooms have become a severe problem in Taihu Lake, a large shallow eutrophic lake in China. Microcystins produced by certain genera of cyanobacteria can affect public health in this area because of their acute and chronic toxic effects. In this study, samples of cyanobacteria were collected and extracted by two solvent systems. The extracts were tested with three short-term genotoxicity assays, the ara test, the Ames test, and the SOS/umu test. In addition, temporal variation in the concentrations of microcystin-LR in the water samples was determined and monitored by an ELISA assay. Then the concentration of microcystin-LR in the drinking water was estimated. The risk of microcystin-LR exposure by drinking water was assessed according to tolerable daily intake (TDI). The three genotoxicity assays showed negative results regardless of the solvent system used, and there were clear inconsistencies in the spatiotemporal profiles of genotoxic potential and microcystin concentrations in Taihu Lake. Risk assessment showed that the drinking water from Taihu Lake was not safe from the end of July to the beginning of November because of a high concentration of microcystin-LR. Our study indicated the drinking water from Taihu Lake posed a risk because of the microcystin-LR, although it was neither genotoxic nor associated with genotoxicity of the lake water.

Environmental Monitoring↗

PubMed2006

The ubiquitin-proteasome pathway in viral infections.

The cellular biological function of the ubiquitin-proteasome pathway as a major intracellular protein degradation pathway, and as an important modulator for the regulation of many fundamental cellular processes has been greatly appreciated over the last decade. The critical role of the ubiquitin-proteasome pathway in viral pathogenesis has become increasingly apparent. Many viruses have been reported to evolve different strategies to utilize the ubiquitin-proteasome pathway for their own benefits. Here, we review the general background and function of the ubiquitin-proteasome pathway, summarize our current understanding of how viruses use this pathway to target cellular proteins, and finally, discuss the roles of this pathway in enteroviral infection, and the potential therapeutic application of proteasome inhibition in myocarditis.

Animals↗

PubMed2005

Liposome-mediated transient transfection reduces cholesterol-dependent coxsackievirus infectivity.

Liposome-mediated gene delivery provides a powerful strategy for the study of gene function and for gene therapy. Coxsackievirus B3 is an important human pathogen associated with various diseases. Here we reported that liposome-mediated transient transfection of plasmid cDNA inhibited coxsackieviral replication at the levels of RNA, protein and viral progeny release. These inhibitory effects were observed in various cell types and by using different liposome reagents. We further showed that the inhibition was likely due to the lack of virus attachment. Moreover, we showed that addition of cholesterol restored, at least in part, the viral infectivity. Interestingly, we found that membrane cholesterol levels were unchanged during transfection, indicating that disruption rather than depletion of membrane cholesterol contributes to the inhibitory effects of transfection. Our data suggest that liposome-mediated cDNA transient transfection inhibits coxsackievirus infectivity via inhibition of viral attachment, which is likely occurring through the changes of membrane cholesterol integrity.

Blotting, Western↗

PubMed2005

Quasi-consensus-based comparison of profile hidden Markov models for protein sequences.

A simple approach for the sensitive detection of distant relationships among protein families and for sequence-structure alignment via comparison of hidden Markov models based on their quasi-consensus sequences is presented. Using a previously published benchmark dataset, the approach is demonstrated to give better homology detection and yield alignments with improved accuracy in comparison to an existing state-of-the-art dynamic programming profile-profile comparison method. This method also runs significantly faster and is therefore suitable for a server covering the rapidly increasing structure database. A server based on this method is available at http://liao.cis.udel.edu/website/servers/modmod

Algorithms↗

PubMed2005

Comparison of microbial community between two shallow freshwater lakes in middle Yangtze basin, East China.

In order to investigate the role of the microbial community in aquatic ecology and nutrient transformations in the development of eutrophication in large shallow freshwater lakes along Yangtze River, the microbial community in the depth-related sediment in Lake Chaohu and Lake Longganhu were compared. Lake Chaohu is one of the three most polluted lakes in China. However, the neighboring Lake Longganhu, a mesotrophic lake, is relatively pristine. The total phosphorous (TP) and total nitrogen (TN) concentration in water was detected at 0.193 mgl(-1) and 3.035 mgl(-1) for Lake Chaohu, 0.051 mgl(-1) and 0.774 mgl(-1) for Lake Longganhu, respectively. The population of the microorganisms with various ecological nutrient transforming functions (e.g. phosphate solubilizing, denitrifying and cellulose decomposing) and a batch of environmental parameters concerning the nutrient accumulating and transforming (e.g. total organic carbon, total nitrogen, and total phosphorous concentrations) were assayed in the depth-related sediment samples from several defined points in both lakes. The sediment samples from Lake Chaohu showed higher density of actinomycetes (P<0.05) and phosphate-solubilizing bacteria (P<0.001) and less profusion of denitrifying bacteria (P<0.05) and cellulolytic microbes (P<0.001), compared with those of Lake Longganhu. The data suggested that the current microbial community in the sediment of Lake Chaohu is in favor of sustaining or further accelerating the process of the lake eutrophication. A possible positive feedback loop which consists of sustained growth of microorganisms and gradual decline of lake eutrophic status is worth further discussing.

Actinobacteria↗

PubMed2005

An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes.

MOTIVATION: Knowledge of the transmembrane helical topology can help identify binding sites and infer functions for membrane proteins. However, because membrane proteins are hard to solubilize and purify, only a very small amount of membrane proteins have structure and topology experimentally determined. This has motivated various computational methods for predicting the topology of membrane proteins. RESULTS: We present an improved hidden Markov model, TMMOD, for the identification and topology prediction of transmembrane proteins. Our model uses TMHMM as a prototype, but differs from TMHMM by the architecture of the submodels for loops on both sides of the membrane and also by the model training procedure. In cross-validation experiments using a set of 83 transmembrane proteins with known topology, TMMOD outperformed TMHMM and other existing methods, with an accuracy of 89% for both topology and locations. In another experiment using a separate set of 160 transmembrane proteins, TMMOD had 84% for topology and 89% for locations. When utilized for identifying transmembrane proteins from non-transmembrane proteins, particularly signal peptides, TMMOD has consistently fewer false positives than TMHMM does. Application of TMMOD to a collection of complete genomes shows that the number of predicted membrane proteins accounts for approximately 20-30% of all genes in those genomes, and that the topology where both the N- and C-termini are in the cytoplasm is dominant in these organisms except for Caenorhabditis elegans. AVAILABILITY: http://liao.cis.udel.edu/website/servers/TMMOD/

Algorithms↗

PubMed2005

Stress-activated protein kinases are involved in coxsackievirus B3 viral progeny release.

Stress-activated protein kinases (SAPKs), consisting of c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase (p38 MAPK), are activated upon various environmental stimuli, including viral infections. Cellular survival and death signaling events following coxsackievirus B3 (CVB3) infection have been studied in relationship to viral replication, but the role of SAPKs has not been scrutinized. In this study, we found that the phosphorylation of JNK1/2 and p38 MAPK was increased during active replication of CVB3 and that their phosphorylation was independent of CVB3-induced caspase activation or production of reactive oxygen species. The roles of these kinases in CVB3 infection were further evaluated using specific inhibitors: SP600125 for JNK1/2 and SB203580 for p38 MAPK. JNK1/2 inhibitors reduced CVB3-induced phosphorylation of activating transcription factor 2, and the p38 MAPK inhibitor reduced CVB3-induced phosphorylation of heat shock protein 27. Although inhibition of these kinases by specific inhibitors did not affect CVB3 viral protein synthesis, inhibition of p38 MAPK but not of JNK1/2 resulted in significant reduction of viral progeny release, suppression of CVB3-induced cell death, and blockage of CVB3-induced caspase-3 activation in infected cells. We conclude that SAPK pathways play critical roles in the life cycle of CVB3, particularly in viral progeny release.

Cell Survival↗

PubMed2005

Segmenting deformable surface models using haptic feedback.

Clinically relevant segmentation often incorporates physician insight in the segmentation process (eg. overestimation of tumors). This is a primary reason in the continued use of per-slice based segmentation approaches. Segmenting structures directly by interacting with a volume space provides the advantages of being time efficient and accurate in contrast to per-slice based methods. In this approach volume navigation and parameter specification become critical towards the accuracy of the results obtained. In this paper we present some preliminary results in our research towards segmentation using a haptic device for navigation and parameter specification in an immersive environment. To incorporate the physician's requirements we model the results as a deformable surface model and the user interacts with the surface to obtain the final segmentation.

Diagnostic Imaging↗

PubMed2005

[Parameter determination of algae growth based on ecological tank experiment].

A dynamic simulation experiment of algae in an ecological tank was performed at the Taihu Laboratory for Lake Ecosystem Research. During the experiment, water from Taihu Lake was infused into the ecological tank and samples were taken continually to observe algae growth under varying conditions, such as temperature, sunlight and nutrients. Based on the experiment, an algae growth model, considering nitrogen and phosphorus cycle, was developed by using the advanced PHREEQC model. After that, a detailed calibration and validation of parameters in the model were done on the basis of experimental results. The least square method was used to determine the optimal set of parameters. The calculated values of algae and nutrient concentrations show fairly satisfying fittness with measured data.

China↗

PubMed2005

[Attenuation of photosynthetically available radiation (PAR) in Meiliang Bay under different winds and waves].

Based on the successive underwater irradiance measurement in situ from Jul. 12 to 17 in 2003, the attenuation of photosynthetically available radiation (PAR) and euphotic depth in Meiliang Bay were analyzed under different winds and waves. The results showed that the downward PAR attenuation coefficients ranged from 2.63 to 4.7 m(-1), with an average of 3.63 +/- 0.47 x m(-1), and the corresponding euphotic depth ranged from 0.98 to 1.75 m, with an average of 1.29 +/- 0.18 m, which demonstrated that phytoplankton and macrophyte could not grow below 1.5 m due to the lack of adequate solar radiation. The total suspended solids resulted from wind and wave increased the attenuation of light, with the downward attenuation coefficients of PAR being 2.63, 3.72 and 4.37 x m(-1) under small, medium and large wind and wave, respectively. Significant linear correlations were found between transparence, PAR attenuation coefficient, euphotic depth and total suspended solid, especially inorganic suspended solid, while chlorophyll a was the most nonsignificant light attenuator. Multiple stepwise linear regressions showed that inorganic suspended solid was the most important light attenuator dominating the light attenuation in wind-exposed Meiliang Bay.

Fresh Water↗

PubMed2004

Structural determinants of RhoA binding and nucleotide exchange in leukemia-associated Rho guanine-nucleotide exchange factor.

Rho guanine-nucleotide exchange factors (RhoGEFs) activate Rho GTPases, and thereby regulate cytoskeletal structure, gene transcription, and cell migration. Leukemia-associated RhoGEF (LARG) belongs to a small subfamily of RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. Herein we describe the atomic structures of the catalytic Dbl homology (DH) and pleckstrin homology (PH) domains of LARG alone and in complex with RhoA. These structures demonstrate that the DH/PH domains of LARG can undergo a dramatic conformational change upon binding RhoA, wherein both the DH and PH domains directly engage RhoA. Through mutational analysis we show that full nucleotide exchange activity requires a novel N-terminal extension on the DH domain that is predicted to exist in a broader family of RhoGEFs that includes p115-RhoGEF, Lbc, Lfc, Net1, and Xpln, and identify regions within the LARG PH domain that contribute to its ability to facilitate nucleotide exchange in vitro. In crystals of the DH/PH-RhoA complex, the active site of RhoA adopts two distinct GDP-excluding conformations among the four unique complexes in the asymmetric unit. Similar changes were previously observed in structures of nucleotide-free Ras and Ef-Tu. A potential protein-docking site on the LARG PH domain is also evident and appears to be conserved throughout the Lbc subfamily of RhoGEFs.

Amino Acid Sequence↗

PubMed2004

DNA damage induces downregulation of histone gene expression through the G1 checkpoint pathway.

Activation of the G(1) checkpoint following DNA damage leads to inhibition of cyclin E-Cdk2 and subsequent G(1) arrest in higher eucaryotes. Little, however, is known about the molecular events downstream of cyclin E-Cdk2 inhibition. Here we show that, in addition to the inhibition of DNA synthesis, ionizing radiation induces downregulation of histone mRNA levels in mammalian cells. This downregulation occurs at the level of transcription and requires functional p53 and p21(CIP1/WAF1) proteins. We demonstrate that DNA damage induced by ionizing radiation results in the suppression of phosphorylation of NPAT, an in vivo substrate of cyclin E-Cdk2 kinase and an essential regulator of histone gene transcription, and its dissociation from histone gene clusters in a p53/p21-dependent manner. Inhibition of Cdk2 activity by specific inhibitors in the absence of DNA damage similarly disperses NPAT from histone gene clusters and represses histone gene expression. Our results thus suggest that inhibition of Cdk2 activity following DNA damage results in the downregulation of histone gene transcription through dissociation of NPAT from histone gene clusters.

CDC2-CDC28 Kinases↗

PubMed2004

A season-dependent variation of genotoxicity of surface water samples from Taihu Lake, Yangzte delta.

The present study is to assess a year round change of genotoxicity of surface water in Taihu Lake, Yangtze delta. The water samples were collected in spring, summer, autumn and winter of 2001, respectively. The bacterial L-arabinose resistance forward mutation test (ara test), along with the Ames test, was performed for the evaluation of time profile of mutagenicity of the surface water samples. The strong genotoxic potentials were detected in the near-shore area, especially in the vicinity to the major city. All the samples collected from the lake center and areas distant from dense human activity showed genotoxicity-free in year round time. Intensified human activity along the lake may play an important role for the genotoxic pollution. By comparison of the samples from year round, the winter samples showed the strongest mutagenic potential of all seasons, which indicates that meteorological and hydrological factors also affect the water quality. The impact of dense human activity, improper management and season change should be put into consideration for designing an effective remediation project in the lake basin area.

Arabinose↗

PubMed2004

Growth and phosphate uptake kinetics of Microcystis aeruginosa under various environmental conditions.

Growth and uptake of exogenous phosphate by Microcystis aeruginosa in batch culture under different temperature, photoperiod, and turbulence were studied by the method of phosphate isotope tracer. Relatively high temperature, long photoperiod and strong turbulence increased the cell density of M. aeruginosa in these batch cultures. The initial rapid uptake of phosphate by M. aeruginosa was independent of the temperature, photoperiod, and turbulence. Similarly, maximum exogenous phosphate uptake was not related to these environmental factors. However, elevated temperature and turbulence shortened the time, required to obtain maximum P accumulation. The growth of M. aeruginosa could alleviate the phosphorous leakage. Total amounts of exogenous phosphate uptake to M. aeruginosa and the phosphorus leakage of M. aeruginosa were significantly influenced by the growth state of M. aeruginosa closely correlated with the environmental factors. The maximum volume of exogenous phosphate uptake to M. aeruginosa was 46% of added exogenous phosphate in water with 16 hours of photoperiod. Thus, total amounts of exogenous phosphate uptake to M. aeruginosa were more strongly affected by the photoperiod length than temperature and turbulence.

Centrifugation↗

PubMed2004

Truncated hepatitis C virus core protein encoded in hepatocellular carcinomas.

Studies have suggested that a truncated form of the hepatitis C virus (HCV) core protein can enter hepatocyte nuclei and might play a role in HCV-associated hepato-carcinogenesis. In the present study, the HCV core gene from hepatocellular carcinomas (HCC) and/or adjacent non-tumorous liver tissues from eight patients was amplified by nested RT-PCR and sequenced. Mutations in the HCV core gene that would encode a truncated core protein were found in 4 of the 8 patients. Since truncated core proteins have been shown to be capable of entry into the hepatocyte nucleus (unlike HCV itself, which is an exclusively cytoplasmic virus), the detection of mutated sequences encoding them in these four HCC patients suggests that these mutations may have played a role in the development of these HCCs.

Adult↗

PubMed2004

[Chlorophyll a content and primary productivity of phytoplankton in Meiliang Bay of Taihu Lake].

Based on the investigations on primary productivity of phytoplankton and related factors at four stations in Meiliang Bay of Taihu Lake from May 1998 to August 1999, this paper studied the distribution of phytoplankton chlorophyll a, its primary productivity, and their relationships with environmental factors. The results showed that there were obvious temporal and spatial differences in chlorophyll a and primary productivity. The high values of chlorophyll a content and primary productivity were recorded in spring and summer. Generally, chlorophyll a content and primary productivity decreased from inner to outer in the bay. The vertical profile of primary productivity showed that the maximum of primary productivity was recorded at 20-50 cm water depth in spring, summer and autumn, while there was no remarkable difference in winter. The primary productivity exponentially increased with water temperature from 10 to 30 degrees C. There was a significant positive correlation between chlorophyll a content and primary productivity. The correlation coefficients between nutrients and primary productivity varied greatly, which presented that nutrient was not the limiting factor for phytoplankton growth. The analysis of P-I curves based on different photosynthesis-irradiance models showed that obvious light inhibition was occurred at surface water in spring and summer.

Biomass↗

PubMed2003

Intracellular phosphorus metabolism of Microcystis aeruginosa under various redox potential in darkness.

Phosphorus metabolism of Microcystis aeruginosa was studied under gradient redox potential from 252 mV to -70 mV in darkness. The release of phosphorus occurred in all the treatments, and this process was accelerated in darkness when the redox potential was lowered. Low redox potential in darkness stimulated the accumulation of polyphosphate (PolyP) and the degradation of polyglucose. The synthesis of PolyP delayed the decrease of intracellular orthophosphate. The death of M. aeruginosa was slowered when the redox potential was low in darkness. The accumulation of PolyP under low redox potential in the dark was very important to M. aeruginosa for endurance through the unfavorable growth conditions for maintaining phosphorus concentration, energy storage, and other physiological functions. The ability to accumulate PolyP in the dark and negative redox potential may be of considerable advantage in the low-light, organically rich, and low-redox habitats.

Anaerobiosis↗