Biomedical subjects

Yong Deng

Publications and source records attributed to Yong Deng.

6 recordsLinked to original sources

PubMed2006

Evaluating sensor reliability in classification problems based on evidence theory.

This paper presents a new framework for sensor reliability evaluation in classification problems based on evidence theory (or the Dempster-Shafer theory of belief functions). The evaluation is treated as a two-stage training process. First, the authors assess the static reliability from a training set by comparing the sensor classification readings with the actual values of data, which are both represented by belief functions. Information content contained in the actual values of each target is extracted to determine its influence on the evaluation. Next, considering the ability of the sensor to understand a dynamic working environment, the dynamic reliability is evaluated by measuring the degree of consensus among a group of sensors. Finally, the authors discuss why and how to combine these two kinds of reliabilities. A significant improvement using the authors' method is observed in numerical simulations as compared with the recently proposed method.

Algorithms↗

PubMed2004

Scoring hidden Markov models to discriminate beta-barrel membrane proteins.

A new method is presented for identification of beta-barrel membrane proteins. It is based on a hidden Markov model (HMM) with an architecture obeying these proteins' construction principles. Once the HMM is trained, log-odds score relative to a null model is used to discriminate beta-barrel membrane proteins from other proteins. The method achieves only 10% false positive and false negative rates in a six-fold cross-validation procedure. The results compare favorably with existing methods. This method is proposed to be a valuable tool to quickly scan proteomes of entirely sequenced organisms for beta-barrel membrane proteins.

Algorithms↗

PubMed2003

Low concentrations of NaHSO(3) increase cyclic photophosphorylation and photosynthesis in cyanobacterium Synechocystis PCC6803.

Application of NaHSO(3) solution at low concentrations (20-200 muM) to the culture medium enhanced photosynthetic oxygen evolution in cyanobacterium Synechocystis PCC6803 by more than 10%. The slow phase of ms-DLE was strengthened, showing that the transmembrane proton motive force related to photophosphorylation was enhanced. It was also observed that dry weight as well as ATP content under illuminated conditions were both increased after the treatment, indicating that low concentrations of NaHSO(3) could enhance the supply of ATP and thus increase biomass accumulation. In accord with the promotion in the photosynthetic oxygen evolution and ATP content, the transient increase in chlorophyll fluorescence after the termination of actinic light was increased; and meanwhile, the half-time of re-reduction of P700(+) in the presence of DCMU after a pulse light under background far-red light was shortened by approximately 30%, indicating that cyclic electron flow around PS I was accelerated by the treatment. Based on these results it is suggested that the increase in photosynthesis in Synechocystis PCC6803 caused by low concentrations of NaHSO(3) solution might be due to the stimulation of the cyclic electron flow around PS I and thus the increase in photophosphorylation.

Journal Article↗

PubMed2003

Response of NAD(P)H dehydrogenase complex to the alteration of CO2 concentration in the cyanobacterium Synechocystis PCC6803.

An NADPH-specific NDH-1 sub-complex was separated by native-polyacrylamide gel electrophoresis and detected by activity staining from the whole cell extracts of Synechocystis PCC6803. Low CO2 caused an increase in the activity of this sub-complex quickly, accompanied by an evident increase in the expression of NdhK and PSI-driven NADPH oxidation activity that can reflect the activity of NDH-1-mediated cyclic electron transport. During incubation with high CO2, the activities of NDH-1 sub-complex and PSI-driven NADPH oxidation as well as the protein level of NdhK slightly increased at the beginning, but decreased evidently in various degrees along with incubation time. These results suggest that CO2 concentration in vitro as a signal can control the activity of NDH-1 complex, and NDH-1 complex may in turn function in the regulation of CO2 uptake.

Carbon Dioxide↗

PubMed2003

Effects of low CO2 on NAD(P)H dehydrogenase, a mediator of cyclic electron transport around photosystem I in the cyanobacterium synechocystis PCC6803.

The expression and activity of type-1 NAD(P)H dehydrogenase (NDH-1) was compared between cells of Synechocystis PCC6803 grown in high (H-cells) and low (L-cells) CO(2) conditions. Western analysis indicated that L-cells contain higher amounts of the NDH-1 subunits, NdhH, NdhI and NdhK. An NADPH-specific subcomplex of NDH-1 showed higher NADPH-nitroblue tetrazolium oxidoreductase activity in L-cells. The activities of both NADPH-menadione oxidoreductase and light-dependent NADPH oxidation driven by photosystem I were much higher in L-cells than in H-cells. The initial rate of re-reduction of P700(+) following actinic light illumination in the presence of DCMU under background far-red light was enhanced in L-cells. In addition, rotenone, a specific inhibitor of NDH-1, suppressed the relative rate of post-illumination increase in Chl fluorescence of L-cells more than that of H-cells, suggesting that the involvement of NDH-1 in cyclic electron flow around photosystem I was enhanced by low CO(2). Taken together, these results suggest that NDH-1 complex and NDH-1-mediated cyclic electron transport are stimulated by low CO(2) and function in the acclimation of cyanobacteria to low CO(2).

Blotting, Western↗

PubMed2003

[Separation of hydrophobic NAD(P)H dehydrogenase subcomplexes from cyanobacterium Synechocystis PCC6803].

Many efforts have been paid to the separation of an integrated NA(D)PH dehydrogenase (NDH) complex. Several hydrophilic subcomplexes of NDH have been purified from the cyanobacterium Synechocystis PCC6803. However, no hydrophobic NDH subcomplex has ever been separated from cyanobacteria yet. In this paper, two NDH subcomplexes were separated from n-dodecyl beta-D-maltoside(DM)-treated whole cell extracts of Synechocystis PCC6803 by anion exchange chromatography and gel filtration. Both subcomplexes contained the hydrophobic subunit NdhA, suggesting that they were hydrophobic NDH subcomplexes. Of the two subcomplexes, only one subcomplex contained NdhH. These subcomplexes showed NADPH-nitroblue tetrazolium (NBT) oxidoreductase activity and could specifically oxidize NADPH when several quinone analogues were used as electron acceptors, such as ferricyanide, 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), 2,6-dichlorophenol indophenol (DCPIP), duroquinone, ubiquinone-0 (UQ-0), etc.

Cyanobacteria↗