Biomedical subjects

Vicki Vance

Publications and source records attributed to Vicki Vance.

3 recordsLinked to original sources

PubMed2006

CSRDB: a small RNA integrated database and browser resource for cereals.

Plant small RNAs (smRNAs), which include microRNAs (miRNAs), short interfering RNAs (siRNAs) and trans-acting siRNAs (ta-siRNAs), are emerging as significant components of epigenetic processes and of gene networks involved in development and in homeostasis. Here we present a bioinformatics resource for cereal crops, the Cereal Small RNA Database (CSRDB), consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing. The smRNA sequences have been mapped to the rice genome and to the available maize genome sequence and these results are presented in two genome browser datasets using the Generic Genome Browser. Potential RNA targets for the smRNAs have been predicted and access to the resulting smRNA/RNA target pair dataset has been made available through a MySQL based relational database. Various ways to access the data are provided including links from the genome browser to the target database. Data linking and integration are the main focus for this interface, and internal as well as external links are present. The resource is available at http://sundarlab.ucdavis.edu/smrnas/ and will be updated as more sequences become available.

Databases, Nucleic Acid↗

PubMed2005

Computational prediction of miRNAs in Arabidopsis thaliana.

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in animals and plants. Comparative genomic computational methods have been developed to predict new miRNAs in worms, flies, and humans. Here, we present a novel single genome approach for the detection of miRNAs in Arabidopsis thaliana. This was initiated by producing a candidate miRNA-target data set using an algorithm called findMiRNA, which predicts potential miRNAs within candidate precursor sequences that have corresponding target sites within transcripts. From this data set, we used a characteristic divergence pattern of miRNA precursor families to select 13 potential new miRNAs for experimental verification, and found that corresponding small RNAs could be detected for at least eight of the candidate miRNAs. Expression of some of these miRNAs appears to be under developmental control. Our results are consistent with the idea that targets of miRNAs encompass a wide range of transcripts, including those for F-box factors, ubiquitin conjugases, Leucine-rich repeat proteins, and metabolic enzymes, and that regulation by miRNAs might be widespread in the genome. The entire set of annotated transcripts in the Arabidopsis genome has been run through find MiRNA to yield a data set that will enable identification of potential miRNAs directed against any target gene.

Algorithms↗

PubMed2004

The potyviral suppressor of RNA silencing confers enhanced resistance to multiple pathogens.

Helper component-protease (HC-Pro) is a plant viral suppressor of RNA silencing, and transgenic tobacco expressing HC-Pro has increased susceptibility to a broad range of viral pathogens. Here we report that these plants also exhibit enhanced resistance to unrelated heterologous pathogens. Tobacco mosaic virus (TMV) infection of HC-Pro-expressing plants carrying the N resistance gene results in fewer and smaller lesions compared to controls without HC-Pro. The resistance to TMV is compromised but not eliminated by expression of nahG, which prevents accumulation of salicylic acid (SA), an important defense signaling molecule. HC-Pro-expressing plants are also more resistant to tomato black ring nepovirus (TBRV) and to the oomycete Peronospora tabacina. Enhanced TBRV resistance is SA-independent, whereas the response to P. tabacina is associated with early induction of markers characteristic of SA-dependent defense. Thus, a plant viral suppressor of RNA silencing enhances resistance to multiple pathogens via both SA-dependent and SA-independent mechanisms.

Cysteine Endopeptidases↗