Biomedical subjects

Wenying Xu

Publications and source records attributed to Wenying Xu.

6 recordsLinked to original sources

PubMed2006

A novel nuclear-localized CCCH-type zinc finger protein, OsDOS, is involved in delaying leaf senescence in rice.

Leaf senescence is a developmentally programmed degeneration process, which is fine tuned by a complex regulatory network for plant fitness. However, molecular regulation of leaf senescence is poorly understood, especially in rice (Oryza sativa), an important staple crop for more than half of the world population. Here, we report a novel nuclear-localized CCCH-type zinc finger protein, Oryza sativa delay of the onset of senescence (OsDOS), involved in delaying leaf senescence in rice. The expression of OsDOS was down-regulated during natural leaf senescence, panicle development, and pollination, although its transcripts were accumulated in various organs. RNAi knockdown of OsDOS caused an accelerated age-dependent leaf senescence, whereas its overexpression produced a marked delay of leaf senescence, suggesting that it acts as a negative regulator for leaf senescence. A genome-wide expression analysis further confirmed its negative regulation for leaf senescence and revealed that, in particular, the jasmonate (JA) pathway was found to be hyperactive in the OsDOS RNAi transgenic lines but impaired in the OsDOS overexpressing transgenic lines, indicating that this pathway is likely involved in the OsDOS-mediated delaying of leaf senescence. Furthermore, methyl JA treatments of both seeds and detached leaves from the RNAi and the overexpressing transgenic lines showed hyper- and hyporesponses, respectively, consistent with the negative regulation of the JA pathway by OsDOS. Together, these results indicate that OsDOS is a novel nuclear protein that delays leaf senescence likely, at least in part, by integrating developmental cues to the JA pathway.

Amino Acid Sequence↗

PubMed2006

A multivariate prediction model for microarray cross-hybridization.

BACKGROUND: Expression microarray analysis is one of the most popular molecular diagnostic techniques in the post-genomic era. However, this technique faces the fundamental problem of potential cross-hybridization. This is a pervasive problem for both oligonucleotide and cDNA microarrays; it is considered particularly problematic for the latter. No comprehensive multivariate predictive modeling has been performed to understand how multiple variables contribute to (cross-) hybridization. RESULTS: We propose a systematic search strategy using multiple multivariate models [multiple linear regressions, regression trees, and artificial neural network analyses (ANNs)] to select an effective set of predictors for hybridization. We validate this approach on a set of DNA microarrays with cytochrome p450 family genes. The performance of our multiple multivariate models is compared with that of a recently proposed third-order polynomial regression method that uses percent identity as the sole predictor. All multivariate models agree that the 'most contiguous base pairs between probe and target sequences,' rather than percent identity, is the best univariate predictor. The predictive power is improved by inclusion of additional nonlinear effects, in particular target GC content, when regression trees or ANNs are used. CONCLUSION: A systematic multivariate approach is provided to assess the importance of multiple sequence features for hybridization and of relationships among these features. This approach can easily be applied to larger datasets. This will allow future developments of generalized hybridization models that will be able to correct for false-positive cross-hybridization signals in expression experiments.

Algorithms↗

PubMed2005

Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.).

Previously, we identified 253 cDNAs that are regulated by pollination/fertilization in rice by using a 10K cDNA microarray. In addition, many of them also appeared to be involved in drought and wounding responses. To investigate this relationship, we obtained their expression profiles after dehydration and wounding treatments in this study. Venn diagram analysis indicated that 53.8% (136/253) and 21% (57/253) of the pollination/fertilization-related genes are indeed regulated by dehydration and wounding, respectively, and nearly half of the genes expressed preferentially in unpollinated pistils (UP) are responsive to dehydration. These results indicated that an extensive gene set is shared among these responses, suggesting that the genetic programs regulating them are likely related. Among them, the genetic network of water stress control may be a key player in pollination and fertilization. Additionally, 39.5% (100/253) cDNAs that are related to pollination/fertilization appear not to be regulated by the stress treatments (dehydration and wounding), suggesting that the existence of additional genetic networks are involved in pollination/fertilization. Furthermore, comparative analysis of the expression profiles of the 253 cDNAs under 18 different conditions (various tissues, treatments and developmental status) revealed that the genetic networks regulating photosynthesis, starch metabolisms, GA- and defense-responses are involved in pollination and fertilization. Taken together, these results provided some clues to elucidate the molecular mechanisms of pollination and fertilization in rice.

Cluster Analysis↗

PubMed2004

Determining oxygen diffusion coefficients in polymer films by lifetimes of luminescent complexes measured in the frequency domain.

Polymer films doped with luminescent ruthenium complexes are proving to be important oxygen sensors. We describe a technique using lifetime measurements in the frequency domain for determining the diffusion coefficient of oxygen through various polymer supports. These fundamental measurements will allow for more rational design of improved sensors. Three types of polymers were doped with [Ru(4,7-diphenyl-1,10-phenanthroline)3]Cl2. We monitored the luminescence versus time after applying a step increase in the oxygen pressure at the surface of the film. We modeled the decrease in apparent lifetime as a function of time using the diffusion coefficient of oxygen in the polymer as the only adjustable parameter. The model accurately predicted the lifetime versus time curves, and diffusion coefficients agreed well with those obtained from intensity measurements. The advantages and disadvantages of the lifetime technique to those used earlier are discussed.

Diffusion↗

PubMed2002

Multicomponent lifetime-based pH sensors utilizing constant-lifetime probes.

A multicomponent luminescent sensor system is described that uses probe species with constant lifetimes to generate an analyte-dependent change in the apparent sensor lifetime. This new sensing scheme not only allows for lifetime-based measurement techniques to be applied to sensors that employ static quenching interactions but also provides the ability to vary the sensitivity of the sensor system with simple changes in instrumental parameters. A model for the multicomponent sensor is presented, followed by data measured using a prototype pH sensor based on the model.

Biosensing Techniques↗

PubMed2002

Method for measuring oxygen diffusion coefficients of polymer films by luminescence quenching.

To ascertain the relationship between the physical properties of polymer supports and the observed response of luminescence-based oxygen sensors, a quenching-based method was developed to measure oxygen diffusion in polymers. The method offers advantages over existing quenching-based techniques since it allows a simple correction for films of high optical density, and the computations do not assume uniform oxygen concentration throughout the film. Diffusion coefficients (D) were measured for a series of sensors with [Ru(Ph2phen)3]Cl2 (Ph2phen = 4,7-diphenyl-1,10-phenanthroline) asthe luminophore and polystyrene, poly(trimethylsilylmethyl methacrylate), poly(butyl methacrylate), poly(trimethylsilylmethyl methacrylate-co-butyl methacrylate), or poly(trimethylsilylmethyl methacrylate-co-1H, 1H-heptafluorobutyl methacrylate) as the support. The solvent from which the films were cast was varied, and filler materials such as hydrophobic, amorphous silica or tributyl phosphate plasticizer were added. Results are interpreted by a domain model in which the local environment of the sensor, rather than the bulk properties of the polymer, is the most critical parameter in sensor design.

Journal Article↗