Genome-Wide Microarrray Analysis Reveals Roles for the REF-1 Family Member HLH-29 in Ferritin Synthesis and Peroxide Stress Response

In Caenorhabditis elegans, the six proteins that make up the REF-1 family have been identified as functional homologs of the Hairy/Enhancer of Split (HES) proteins. These transcription factors act in both Notch dependent and Notch-independent pathways to regulate embryonic events during development; however, their post-embryonic functions are not well defined. As a first step toward understanding how the REF-1 family works together to coordinate post-embryonic events, we used gene expression microarray analysis to identify transcriptional targets of HLH-29 in L4/young adult stage animals. Here we show that HLH-29 targets are genes needed for the regulation of growth and lifespan, including genes required for oxidative stress response and fatty acid metabolism, and the ferritin genes, ftn-1 and ftn-2. We show that HLH-29 regulates ftn-1 expression via promoter sequences upstream of the iron-dependent element that is recognized by the hypoxia inducible factor, HIF-1. Additionally, hlh-29 mutants are more resistant to peroxide stress than wild-type animals and ftn- 1(RNAi) animals, even in the presence of excess iron. Finally we show that HLH-29 acts parallel to DAF-16 but upstream of the microphthalmia transcription factor ortholog, HLH-30, to regulate ftn-1 expression under normal growth conditions

HES-Mediated Repression of Pten in Caenorhabditis elegans

The Hairy/Enhancer-of-Split (HES) group of transcription factors controls embryonic development, often by acting downstream of the Notch signaling pathway; however, little is known about postembryonic roles of these proteins. In Caenorhabditis elegans, the six proteins that make up the REF-1 family are considered to be HES orthologs that act in both Notch dependent and Notch-independent pathways to regulate embryonic events. To further our understanding of how the REF-1 family works to coordinate post-embryonic cellular events, we performed a functional characterization of the REF-1 family member, HLH-25. We show that, after embryogenesis, hlh-25 expression persists throughout every developmental stage, including dauer, into adulthood. Like animals that carry loss-of-function alleles in genes required for normal cell cycle progression, the phenotypes of hlh-25 animals include reduced brood size, unfertilized oocytes, and abnormal gonad morphology. Using gene expression microarray, we show that the HLH-25 transcriptional network correlates with the phenotypes of hlh-25 animals, and that the C. elegans Pten ortholog, daf-18, is one major hub in the network. Finally, we show that HLH-25 regulates C. elegans lifespan and dauer recovery, which correlates with a role in the transcriptional repression of daf-18 activity. Collectively, these data provide the first genetic evidence that HLH-25 may be a functional ortholog of mammalian HES1, which represses PTEN activity in mice and human cells

AN APPLICATION OF ASSOCIATION RULE MINING TO HLA-A*0201 EPITOPE PREDICTION

This paper presents a novel approach to epitope prediction based on the clustering of known T-cell epitopes for a given MHC class I allele (HLA-A*0201). A combination of association rules (ARs) and sequence-structure patterns (SSPs) was used to do the clustering of training set epitopes from the Antijen database. A regression model was then built from each cluster and a peptide from the test set was declared to be an epitope only if one or more of the models gave a positive prediction. The sensitivity (TP/TP+FN) of the AR/SSP regression models approach was higher than that of a single regression model built on the entire training set, and was also higher than the sensitivity measures for SYFPEITHI, Rankpep, and ProPred1 on the same test set

Pooling evidence to identify cell cycle-regulated genes

Most of the biological studies have embraced statistical approaches to make inferences. It is common to have several, independent experiments to test the same null hypothesis. The goal of research on pooling evidence is to combine the results of these tests to ask if there is evidence from the collection of studies to reject the null hypothesis. In this study, we evaluated four different pooling techniques (Fisher, Logit, Stouffer and Liptak) to combine the evidence from independent microarray experiments in order to identify cell cycle-regulated genes. We were able to identify a better set of cell cycle-regulated genes using the pooling techniques based on our benchmark study on budding yeast (Saccharomyces cerevisiae). Our gene ontology study on time series data of both the budding yeast and the fission yeast (Schizosaccharomyces pombe) showed that the GO terms that are related to cell cycle are significantly enriched in the cell cycle-regulated genes identified using pooling techniques. © Springer-Verlag Berlin Heidelberg 2006

SBLAST: Structural Basic Local Alignment Searching Tools using Geometric Hashing

While much research has been done on finding similarities between protein sequences, there has not been the same progress on finding similarities between protein structures. Here we report a new algorithm (SBLAST) which discovers the largest common substructures between two proteins using a trianglebased variant of the geometric hashing of protein structures algorithm. The algorithm selects triples (triangles) of selected Cα atoms from all proteins in a protein structure database and creates a hash table using a key based on the three inter-atomic distances. Hash table hits from the triangles of a query protein are extended recursively to determine the largest common substructures less than a threshold deviation level (rmsd). Comparisons between a query protein and a preprocessed protein database can be performed in parallel. Because SBLAST does not rely on protein sequence alignment, common substructures can be detected in the absence of sequence conservation. SBLAST has been tested using the ASTRAL subset of the PDB. 1

Identification of Abnormal Cervical Regions from Colposcopy Image Sequences

Cervical cancer is the third most common cancer in women worldwide and the leading cause of cancer death in women of the developing countries. Cancer death rate can be greatly reduced by regular screening. One of the steps during a screening program is the detection of the abnormal cells that could evolve into cancer. In this paper, we propose an algorithm that automatically identifies the abnormal cervical regions from colposcopy image sequence. Firstly, based on the segmentation of three different image regions, a set of low-level features is extracted to model the temporal changes in the cervix before and after applying acetic acid. Second, a support vector machine (SVM) classifier is trained and used to make predictions on new input feature vectors. As the low-level features are very insensitive to accurate image registration, only a rough normalization step is needed to sample image patches. Our preliminary results show that our algorithm is accurate and effective. Furthermore, our algorithm only needs to sample patches from six image frames within a five-minute time period. Hence, the proposed algorithm also could be applied to improve the accuracy of the mobile telemedicine for cervical cancer screening in low-resource settings

<i>ftn-1</i> Expression Profile in Wild Type Nematodes.

<p>Stable transgenic lines bearing the EcoRV <i>ftn-1</i> promoter covering 1060 bp upstream and 19 bp downstream of the translation start were examined for expression using fluorescence microscopy as described in Methods. Effects of <i>hlh-29</i> or <i>hlh-30</i> on <i>ftn-1</i> promoter activities were achieved by feeding bacterial strains producing dsRNA for either <i>hlh-29</i> or <i>hlh-30</i> since embryonic stages. Magnified regions emphasize the vulval region in the bright field (BF) images and the posterior intestinal <i>ftn</i>-1 expression in the GFP and merged images.</p

Lifespan Measurements With or Without 24 mM FAC.

<p>Lifespan Measurements With or Without 24 mM FAC.</p

<i>ftn-1</i> mRNA Levels in Adult Stage Animals.

<p>A) RT-qPCR measurements of <i>ftn-1</i> mRNA under normal iron conditions in indicated genetic backgrounds, relative to levels in wild-type animals. B) RT-qPCR measurements of <i>ftn-1</i> mRNA levels in wild-type animals and <i>hlh-29</i> mutants subjected to <i>hif-1</i> RNAi. C) RT-qPCR measurements of <i>ftn-1</i> mRNA in wild-type animals and <i>hlh-29</i> mutants after treatment with BP or FAC. D) RT-qPCR measurements of <i>hlh-29</i> mRNA levels in wild-type animals after treatment with BP or FAC. E) Expression of an integrated transgenic reporter of <i>ftn-1</i> activity in young adult wild-type animals and <i>hlh-29</i> mutants. In panels A - D, error bars represent standard error of the mean (SEM), wild-type = black bars; <i>hlh-29</i> = grey bars; <i>daf-16</i> = striped bars; <i>hlh-29</i>;<i>daf-16</i> = spotted bars. *P-value <0.05, **P-value <0.005, *** -value <0.0005).</p