CisML: an XML-based format for sequence motif detection software

SUMMARY: CisML is an XML-based format for sequence motif detection software. This proposed standard is applicable to many types of sequence motif detection programs. It is intended to facilitate the integration of data and the comparison of results from different software packages, and to simplify the development of downstream tools. XSL stylesheets are provided for easy generation of text, html and graphical reports from CisML-formatted data. AVAILABILITY: http://zlab.bu.edu/CisML/ SUPPLEMENTARY INFORMATION: Example CisML-formatted data and XSL stylesheets for report generation are available along with the sample output.     

Anti-inflammatory flavonoids and pterocarpanoid from Crotalaria pallida and C. assamica

One new isoflavone, 5,7,4'-trihydroxy-2'-methoxyisoflavone (3) and seven, and four known compounds were isolated from the barks of Crotalaria pallida and the seeds of C. assamica, respectively. The known compounds, apigenin (1) and 2'-hydroxygenistein (2), isolated from C. pallida, showed significant concentration-dependent inhibitory effects on the release of beta-glucuronidase and lysozyme from rat neutrophils in response to formyl-Met-Leu-Phe/cytochalasin B (fMLP/CB) with IC(50) values of 2.8+/-0.1 and 17.7+/-1.9, and 5.9+/-1.4 and 9.7+/-3.5 microM, respectively. The known compounds, daidzein (4) and 2'-hydroxydaidzein (6), isolated from C. pallida, inhibited of the release of lysozyme and beta-glucuronidase from rat neutrophils in response to fMLP/CB with IC(50) values of 26.3+/-5.5 and 13.7+/-2.6 microM, respectively. Compounds 1 and 4 also showed significant concentration-dependent inhibitory effects on superoxide anion generation in rat neutrophils stimulated with fMLP/CB with IC(50) values of 3.4+/-0.3 and 25.1+/-5.0 microM, respectively. Compounds 1 and 5, previously isolated from C. pallida, showed the inhibition of NO production in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages and LPS/interferon-gamma (IFN-gamma)-stimulated N9 microglial cells with IC(50) values of 10.7+/-0.1 and 13.9+/-1.1 microM, respectively. Flavonoids, suppressed chemical mediators in inflammatory cells, may have value in treatment and prevention of central and peripheral inflammatory diseases associated with excess production of chemical mediators.     

The Stanford Microarray Database

The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.). SMD makes use of many public resources to connect expression information to the relevant biology, including SGD [Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H. et al. (2000) Nucleic Acids Res., 28, 77-80], YPD and WormPD [Costanzo,M.C., Hogan,J.D., Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E., Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et al. (2000) Nucleic Acids Res., 28, 73-76], Unigene [Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Nucleic Acids Res., 28, 10-14], dbEST [Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332-333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45-48] and can be accessed at http://genome-www.stanford.edu/microarray.     

Distinguishing two types of gray mullet, Mugil cephalus L. (Mugiliformes: Mugilidae), by using glucose-6-phosphate isomerase (GPI) allozymes with special reference to enzyme activities

The resident and migratory types of gray mullet, Mugil cephalus, on the coast of Taiwan can not be separated morphologically. Allozyme analysis was applied to estimate genetic variation between the two types of gray mullet and to test whether they belong to different populations. After starch gel electrophoresis, different allelic frequency spectra of glucose-6-phosphate isomerase-A (GPI-A) between stocks was observed. The resident stock contained Gpi-A(135) and Gpi-A(100), whereas the migratory type contained Gpi-A(100) only. In addition, GPI activities of locus A showed two distinct profiles between the two alleles. The results broadly revealed that Gpi-A allelic frequency was not regulated by temperature changes even after 6 months of thermal acclimation. This suggests that natural selection may play a role in shaping the allelic frequency change during the migratory journey. These findings suggest that the Gpi-A allelic difference can be used for population discrimination.     

Distinguishing malignant from normal oral tissues using FTIR fiber-optic techniques

Oral tissue samples were studied using mid-IR fiber-optic attenuated total reflectance spectroscopy and other spectral techniques. The 1745 cm(-1) band, which is assigned to the ester group (C==O) vibration of triglycerides, is a reliable marker that is present in normal tissues but absent or a weak band in malignant oral tissues. Other bands such as C--H stretching bands and the amide bands are also helpful in distinguishing malignant tissues from normal tissues. Subtraction spectra confirmed the above conclusion. In addition, Raman spectroscopic measurements were in agreement with the results observed from FTIR spectra.     

Synthesis of glucose oxidase and catalase by Aspergillus niger in resting cell culture system

The synthesis of glucose oxidase and catalase by Aspergillus niger was investigated using a resting cell culture system without growth being established. Calcium carbonate induced the synthesis of both enzymes and calcium chloride inhibited it. The optimal pH for the biosynthesis of glucose oxidase and catalase was 6.0 and 5.7, respectively. The effects of other bivalent cations, reductive compounds and metabolic products on enzyme synthesis were also tested. The biosynthesis of glucose oxidase and catalase was promoted by MnCO3, thioglycolic acid, pyroracemic acid and gluconic acid.     

Insights into the function of Rim protein in photoreceptors and etiology of Stargardt's disease from the phenotype in abcr knockout mice.

Rim protein (RmP) is an ABC transporter of unknown function in rod outer segment discs. The human gene for RmP (ABCR) is affected in several recessive retinal degenerations. Here, we characterize the ocular phenotype in abcr knockout mice. Mice lacking RmP show delayed dark adaptation, increased all-trans-retinaldehyde (all-trans-RAL) following light exposure, elevated phosphatidylethanolamine (PE) in outer segments, accumulation of the protonated Schiff base complex of all-trans-RAL and PE (N-retinylidene-PE), and striking deposition of a major lipofuscin fluorophore (A2-E) in retinal pigment epithelium (RPE). These data suggest that RmP functions as an outwardly directed flippase for N-retinylidene-PE. Delayed dark adaptation is likely due to accumulation in discs of the noncovalent complex between opsin and all-trans-RAL. Finally, ABCR-mediated retinal degeneration may result from "poisoning" of the RPE due to A2-E accumulation, with secondary photoreceptor degeneration due to loss of the RPE support role.     

Sugar complexes with neodymium nitrate. Spectroscopic and structural studies of two Nd(NO3)3-galactitol complexes

Two different Nd(NO3)3-galactitol complexes, 2Nd(NO3)3.C6H14O6.8 H2O and Nd(NO3)3.C6H14O6 have been obtained and were characterized by FT-IR and X-ray diffraction techniques. The spectral differences of the two complexes were consistent with the crystal-structure data.     

FT-Raman spectroscopic investigation of lens proteins of tilapia treated with dietary vitamin E

FT-Raman spectroscopy was employed to explore the structural changes of lens proteins in Tilapia lenses affected by dietary vitamin E supplementation. The microenvironment of major lens constituents including thiol compounds, tyrosine, and tryptophan exhibited significant change upon vitamin E treatment, while the protein secondary structure was unaltered and remained as an antiparallel beta-pleated sheet. These structures in the cortex were more susceptible to vitamin E treatment than in the nucleus. Protein sulfhydryls in the cortex were predominantly in the reduced form, while in the nucleus both the oxidized and reduced forms coexisted as evidenced by the vibrational mode of SH (2580 cm(-1)) and SS (507 cm(-1)), respectively. Both tyrosine and tryptophan were more accessible to water or more exposed in the cortex than in the nucleus. The symmetrically inverse response of vitamin E, between Raman intensity of 1090 cm(-1) and the glutathione level, was consistent with a close relationship of GSH and vitamin E in defending the lens from external insults.