BioBuilder as a database development and functional annotation platform for proteins

BACKGROUND: The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. RESULTS: BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database , a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. CONCLUSIONS: As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL

Synthesis of Isoquinolines from Indanones-Total Synthesis of Illudinine

Schmidt reaction of 5-methoxy or 7-methoxyindan-1-ones or their derivatives results exclusively in isocarbostyrils which are converted into 6-methoxy or 8-methoxyisoquinolines in good yields. This strategy has been extended to the total synthesis of illudinine methyl ester (1b) starting from methyl 8-methoxy-2,2-dimethyl-7-oxo-1,2,3,5,6,7-hexahydro-s-indacene-4-carboxylate (4)

ChemInform Abstract: Synthesis Based on Cyclohexadienes. Part 16. Synthesis of Methyl 2,7-Dimethyltricyclo (5.2.2.01,5)undec-5-ene-6-carboxylates

Synthesis of methyl 2, 7-dimethyltricyclo{5.2.2.0(1,5}undec-5-en-6-carboxylates, the tricyclic skeleton present in (+)-allo-cedrol (1) is described using the Diels-Alder strategy. Thus, Birch reduction of the aromatic acid 8 gives 5, the methyl ester of which is isomerised with DBU to a 1:1 mixture of the dienes 6 and 4. Cycloaddition of this mixture with 2-chloroacrylonitrile followed by hydrolysis yields the ketone 60 having the tricyclo{5.2.2.0(1.5)}undec-5-ene framework. Similar reaction with methyl vinyl ketone affords the regioisomeric adducts 61 and 62

Bridgehead substitution of 1-methoxybicyclo[2.2.2]oct 5-en-2-one derivatives: towards the synthesis of (±)-allo-cedrol [khusiol]1

Preparation of the key intermediates, 11 and 21, required for the synthesis of (+/-)-allo-cedrol (khusiol) is reported by a novel methodology involving the substitution at the bridgehead position of 1-methoxybicyclo[2.2.2]oct-5-en-2-one derivative

BioBuilder as a database development and functional annotation platform for proteins

Abstract Background The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. Results BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. Conclusions As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.</p

Gender difference in HIV-1 RNA viral loads.

OBJECTIVES: To test and characterize the dependence of viral load on gender in different countries and racial groups as a function of CD4 T-cell count. METHODS: Plasma viral load data were analysed for > 30,000 HIV-infected patients attending clinics in the USA [HIV Insight (Cerner Corporation, Vienna, VA, USA) and Plum Data Mining LLC (East Meadow, NY, USA) databases] and the Netherlands (Athena database; HIV Monitoring Foundation, Amsterdam, Netherlands). Log-normal regression models were used to test for an effect of gender on viral load while adjusting for covariates and allowing the effect to depend on CD4 T-cell count. Sensitivity analyses were performed to test the robustness of conclusions to assumptions regarding viral loads below the lower limit of quantification (LLOQ). RESULTS: After adjusting for covariates, women had (nonsignificantly) lower viral loads than men (HIV Insight: -0.053 log(10) HIV-1 RNA copies/mL, P = 0.202; Athena: -0.005 log(10) copies/mL, P = 0.667; Plum: -0.072 log(10) copies/mL, P = 0.273). However, further investigation revealed that the gender effect depended on CD4 T-cell count. Women had consistently higher viral loads than men when CD4 T-cell counts were at most 50 cells/microL, and consistently lower viral loads than men when CD4 T-cell counts were greater than 350 cells/microL. These effects were remarkably consistent when estimated independently for the racial groups with sufficient data available in the HIV Insight and Plum databases. CONCLUSIONS: The consistent relationship between gender-related differences in viral load and CD4 T-cell count demonstrated here explains the diverse findings previously published