Biomedical subjects

Tong-Ruei Li

Publications and source records attributed to Tong-Ruei Li.

4 recordsLinked to original sources

PubMed2005

Immune signaling pathways regulating bacterial and malaria parasite infection of the mosquito Anopheles gambiae.

We show that, in the malaria vector Anopheles gambiae, expression of Cecropin 1 is regulated by REL2, an NF-kappaB-like transcription factor orthologous to Drosophila Relish. Through alternative splicing, REL2 produces a full-length (REL2-F) and a shorter (REL2-S) protein isoform lacking the inhibitory ankyrin repeats and death domain. RNA interference experiments show that, in contrast to Drosophila Relish, which responds solely to Gram-negative bacteria, the Anopheles REL2-F and REL2-S isoforms are involved in defense against the Gram-positive Staphylococcus aureus and the Gram-negative Escherichia coli bacteria, respectively. REL2-F also regulates the intensity of mosquito infection with the malaria parasite, Plasmodium berghei. The adaptor IMD shares the same activities as REL2-F. Microarray analysis identified 10 additional genes regulated by REL2, including CEC3, GAM1, and LRIM1.

Alternative Splicing↗

PubMed2004

Exploring the portability of informatics capabilities from a clinical application to a bioscience application.

This report describes XDesc (eXperiment Description), a pilot project that serves as a case study exploring the degree to which an informatics capability developed in a clinical application can be ported for use in the biosciences. In particular, XDesc uses the Entity-Attribute-Value database implementation (including a great deal of metadata-based functionality) developed in TrialDB, a clinical research database, for use in describing the samples used in microarray experiments stored in the Yale Microarray Database (YMD). XDesc was linked successfully to both TrialDB and YMD, and was used to describe the data in three different microarray research projects involving Drosophila. In the process, a number of new desirable capabilities were identified in the bioscience domain. These were implemented on a pilot basis in XDesc, and subsequently "folded back" into TrialDB itself, enhancing its capabilities for dealing with clinical data. This case study provides a concrete example of how informatics research and development in clinical and bioscience domains has the potential for synergy and for cross-fertilization.

Clinical Medicine↗

PubMed2003

Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila.

We demonstrate the use of a chromosomal walk (or "tiling path") printed as DNA microarrays for mapping protein-DNA interactions across large regions of contiguous genomic DNA in Drosophila melanogaster. Microarrays were constructed with genomic DNA fragments 430-920 bp in length, covering 2.9 million base pairs of the Adh-cactus region of chromosome 2 and 85,000 base pairs of the 82F region of chromosome 3. We performed DNA localization mapping for the heterochromatin protein HP1 and for the sequence-specific GAGA transcription factor, producing a comprehensive, high-resolution map of in vivo protein-DNA interactions throughout these regions of the Drosophila genome.

Amino Acid Motifs↗

PubMed2003

Tissue-specific gene expression and ecdysone-regulated genomic networks in Drosophila.

During insect metamorphosis, each tissue displays a unique physiological and morphological response to the steroid hormone 20-hydroxyecdysone (ecdysone). We assayed gene expression in five tissues during metamorphosis onset. Larval-specific tissues display major changes in genome-wide expression profiles, whereas tissues that survive into adulthood display few changes. In one larval tissue, the salivary gland, we used a computational approach to identify a regulatory motif and a cognate transcription factor involved in regulating a set of coexpressed genes. During the metamorphosis of another tissue, the midgut, genes encoding factors from the hedgehog, Notch, EGF, dpp, and wingless pathways are activated by the ecdysone regulatory network. Mutation of the ecdysone receptor abolishes their induction. Cell cycle genes are also activated during the initiation of midgut metamorphosis, and they are also dependent on ecdysone signaling. These results establish multiple new connections between the ecdysone regulatory network and other well-studied regulatory networks.

Amino Acid Sequence↗