In The Institute for Genomic Research Rice Genome Annotation project (), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42 653 non-transposable element-related genes encoding 49 472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13 237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31 739 gene models), representing ∼50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

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Fimbrial production by Porphyromonas gingivalis was inactivated by insertion-duplication mutagenesis, using the cloned gene for the P. gingivalis major fimbrial subunit protein, fimA. by several criteria, this insertion mutation rendered P. gingivalis unable to produce fimbrilin or an intact fimbrial structure. A nonfimbriated mutant, DPG3, hemagglutinated sheep erythrocytes normally and was unimpaired in the ability to coaggregate with Streptococcus gordonii G9B. The cell surface hydrophobicity of DPG3 was also unaffected by the loss of fimbriae. However, DPG3 was significantly less able to bind to saliva-coated hydroxyapatite than wild-type P. gingivalis 381. This suggested that P. gingivalis fimbriae are important for adherence of the organism to saliva-coated oral surfaces. Further, DPG3 was significantly less able to cause periodontal bone loss in a gnotobiotic rat model of periodontal disease. These observations are consistent with other data suggesting that P. gingivalis fimbriae play an important role in the pathogenesis of human periodontal disease.

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also known as EDG-8, binds sphingosine-1-phosphate (S1P) with high affinity and specificity. In this paper we examined the signal transduction pathways regulated by the binding of S1P to EDG-8. In Chinese hamster ovary cells heterologously expressing EDG-8, S1P inhibited forskolin-induced cAMP accumulation and activated c-Jun NH 2 -terminal kinase. Surprisingly, S1P inhibited serum-induced activation of extracellular regulated protein kinase 1 and 2 (ERK1/2). Treatment with pertussis toxin, which ADP-ribosylates and inactivates G i , blocked S1P-mediated inhibition of cAMP accumulation, but had no effect on c-Jun NH 2 -terminal kinase activation or inhibition of ERK1/2. The inhibitory effect of S1P on ERK1/2 activity was abolished by treatment with orthovanadate, suggesting the involvement of a tyrosine phosphatase. A subunit selective [35 S] guanosine 5-3-O-(thio)triphosphate binding assay demonstrates that EDG-8 activated G i/o and G 12 but not G s and G q/11 in response to S1P. In agreement, EDG-8 did not stimulate phosphoinositide turnover or cAMP accumulation. The ability of S1P to induce mitogenesis in cells expressing the EDG-1 subfamily of G protein-coupled receptors is well characterized. In contrast, S1P inhibited proliferation in Chinese hamster ovary cells expressing EDG-8 but not empty vector. The antiproliferative effect, like S1P-mediated ERK1/2 inhibition, was orthovanadate-sensitive and pertussis toxin-insensitive. Our results indicate that EDG-8, a member of the EDG-1 subfamily, couples to unique signaling pathways.The lysophospholipids sphingosine-1-phosphate (S1P) 1 and lysophosphatidic acid (LPA) are endogenous ligands of the EDG family of G protein-coupled receptors (GPCRs) (1-3). Presently, eight EDG receptors have been cloned and are divided into two or three homology clusters or subfamilies (4 -13). EDG-1, -3, -5, and -8 exhibit high sequence homology to one another and have high affinity for S1P (14 -17). EDG-2, -4, and -7 form a second cluster and are high affinity receptors for LPA (1,5,8,18). EDG-6 displays intermediate homology between the two clusters and binds S1P with moderate to high affinity (7, 19). S1P-activated EDG receptors are coupled to multiple effector pathways, including activation/inhibition of adenylyl cyclase, stimulation of phosphoinositide (PI) hydrolysis, mobilization of Ca 2ϩ (20 -26), induction of DNA synthesis (27-29), and stimulation of the MAP kinase family members ERK1/2, SAPK/JNK, and p38 (17, 20 -24). For example, activation of EDG-1, -3, or -5 by S1P leads to a pertussis toxin (PTX)-sensitive stimulation of ERK1/2 (17, 20 -22, 24), suggesting the involvement of G i/o proteins. In contrast, EDG-5 stimulates both stress-activated protein kinases, SAPK/JNK and p38, in a PTX-insensitive manner (23), indicating that EDG receptor coupling to MAP kinase family members involves PTX-sensitive and -insensitive