Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2

<p>Abstract</p> <p>Background</p> <p>The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished using multiple complementary methods that include ESTs, homology searches and <it>ab initio </it>gene predictions. Previously, the Genie gene-finding algorithm was trained on a small set of <it>Chlamydomonas </it>genes and shown to improve the accuracy of gene prediction in this species compared to other available programs. To improve <it>ab initio </it>gene finding in <it>Chlamydomonas</it>, we assemble a new training set consisting of over 2,300 cDNAs by assembling over 167,000 <it>Chlamydomonas </it>EST entries in GenBank using the EST assembly tool PASA.</p> <p>Results</p> <p>The prediction accuracy of our cDNA-trained gene-finder, GreenGenie2, attains 83% sensitivity and 83% specificity for exons on short-sequence predictions. We predict about 12,000 genes in the version <it>v3 Chlamydomonas </it>genome assembly, most of which (78%) are either identical to or significantly overlap the published catalog of <it>Chlamydomonas </it>genes <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. 22% of the published catalog is absent from the GreenGenie2 predictions; there is also a fraction (23%) of GreenGenie2 predictions that are absent from the published gene catalog. Randomly chosen gene models were tested by RT-PCR and most support the GreenGenie2 predictions.</p> <p>Conclusion</p> <p>These data suggest that training with EST assemblies is highly effective and that GreenGenie2 is a valuable, complementary tool for predicting genes in <it>Chlamydomonas reinhardtii</it>.</p

Plasma Dynamics

Contains reports on ten research projects split into two sections.National Science Foundation (Grant ENG77-00340)U.S. Department of Energy (Contract EY-76-S-02-2766)U.S. Air Force - Office of Scientific Research (Grant AFOSR-77-3143)U.S. Department of Energy (Contract ET-78-C-01-3019)U.S. Department of Energy (Contract ET-78-S-02-4681)U.S. Department of Energy (Contract ET-78-S-02-4682)U.S. Department of Energy (Grant EG-77-G-01-4107)U.S. Department of Energy (Contract ET-78-S-02-4714)U.S. Department of Energy (Contract ET-78-S-02-4886)U.S. Department of Energy (Contract ET-78-S-02-4690

Plasma Dynamics

Contains reports on ten research projects divided into two sections.National Science Foundation (Grant ENG79-07047)U.S. Air Force - Office of Scientific Research (Grant AFOSR-77-3143)U.S. Department of Energy (Contract DE-ACO2-78ET51013)U.S. Department of Energy (Contract DE-ASO2-78ET53073.AO02)U.S. Department of Energy (Contract ET-78-S-02-4682)U.S. Department of Energy (Contract DE-AS02-78ET53074)U.S. Department of Energy (Contract DE-ASO2-78ET53050)U.S. Department of Energy (Contract DE-AS02-78ET51002)U.S. Department of Energy (Contract DE-ASO2-78ET53076

Plasma Dynamics

Contains research objectives and summary of research on eighteen research projects split into seven sections and reports on four research projects.U.S. Atomic Energy Commission (Contract AT(l1-1)-3070)National Science Foundation (Grant GK-37979X1

The Novel Deacetylase Inhibitor AR-42 Demonstrates Pre-Clinical Activity in B-Cell Malignancies In Vitro and In Vivo

While deacetylase (DAC) inhibitors show promise for the treatment of B-cell malignancies, those introduced to date are weak inhibitors of class I and II DACs or potent inhibitors of class I DAC only, and have shown suboptimal activity or unacceptable toxicities. We therefore investigated the novel DAC inhibitor AR-42 to determine its efficacy in B-cell malignancies.In mantle cell lymphoma (JeKo-1), Burkitt's lymphoma (Raji), and acute lymphoblastic leukemia (697) cell lines, the 48-hr IC(50) (50% growth inhibitory concentration) of AR-42 is 0.61 microM or less. In chronic lymphocytic leukemia (CLL) patient cells, the 48-hr LC(50) (concentration lethal to 50%) of AR-42 is 0.76 microM. AR-42 produces dose- and time-dependent acetylation both of histones and tubulin, and induces caspase-dependent apoptosis that is not reduced in the presence of stromal cells. AR-42 also sensitizes CLL cells to TNF-Related Apoptosis Inducing Ligand (TRAIL), potentially through reduction of c-FLIP. AR-42 significantly reduced leukocyte counts and/or prolonged survival in three separate mouse models of B-cell malignancy without evidence of toxicity.Together, these data demonstrate that AR-42 has in vitro and in vivo efficacy at tolerable doses. These results strongly support upcoming phase I testing of AR-42 in B-cell malignancies

Functional Relationship between Protein Disulfide Isomerase Family Members during the Oxidative Folding of Human Secretory Proteins

We systematically depleted PDI family members and show that whereas ERp72 and P5 contributed minimally to oxidative protein folding, PDI and ERp57 were the predominant catalysts. Depletion of PDI or ERp57 alone modestly delayed folding, but depletion of both led to generalized protein misfolding and degradation