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

Cardioprotective effect of Elepahnopus scaber Linn. on the Isolated rat heart in Ischemia-Reperfusion induced myocardial damage

ABSTRACT The current study was carried out to determine the protective role of hydro-alcoholic extract of Elephantopus scaber Linn. (HAEES) on ischemia-reperfusion induced myocardial injury in rats. HAEES was screened for in-vitro antioxidant activity using standard methods, to investigate the free radicals scavenging activity which are produced by ischemia-reperfusion induced oxidative stress. Ischemia-reperfusion induced injury in isolated rat hearts by global no-flow ischemia (15 min) can be assessed by measuring the changes in Hemodynamic parameters of heart, level of cardiac marker enzymes in heart perfusate and HTH, antioxidant system and histological changes when compared to post-ischemic condition of ischemia-reperfusion control group. HAEES have shown good antioxidant activity in DPPH, nitric oxide, hydroxyl and superoxide radical methods. Pretreatment with HAEES and ischemia-reperfusion induced injury have shown good cardioprotective effect in terms of significant recovery in DT, changes in biochemical parameters in perfusate and HTH, antioxidants level and histological changes in isolated rat hearts

Nephroprotective Activity of Psidium Guajava Linn. Leaves Extract against Cisplatin Induced Nephrotoxicity In Rats

ABSTRACT Cisplatin is an effective chemotherapeutic agent successfully used in the treatment of a wide range of tumors; however, nephrotoxicity has restricted its clinical use. Several studies have shown that reactive oxygen species are involved in cisplatin-induced nephrotoxicity. The aim of this study was to investigate nephroprotective activity of hydroalcoholic extract of Psidium guajava Linn. (HAPG) leaves in cisplatin induced nephrotoxicity in rats. Rats received a single injection of cisplatin (7.5 mg/kg, i.p.) on 5 th day. HAPG was given to two groups (200 mg/kg and 400 mg/kg body weight p.o.) for 9 days. The HAPG treatment was able to ameliorate the reduced body weight, urinary creatinine, blood total protein and increased kidney weight, urine volume, urinary sodium, urinary potassium, urinary glucose, blood urea, blood creatinine levels due to cisplatin induced nephrotoxicity. HAPG significantly increased the tissue GSH levels and reduced lipid peroxide levels. Further it was confirmed by the histopathological observation that the degenerative changes caused by cisplatin were also restored by treatment with HAPG. These results suggested that HAPG possess nephroprotective activity against cisplatin induced kidney damage

Nephroprotective Activity of Benincasa hispida (Thunb.) Cogn. Fruit Extract against Cisplatin Induced Nephrotoxicity in Rats

ABSTRACT Cisplatin is one of the most effective chemotherapeutics against a wide range of cancers including head, neck, ovarian and lung cancers. But its usefulness is limited by its toxicity to normal tissues, including cells of the kidney and proximal tubule. The purpose of the present study is to investigate whether the hydro alcoholic whole fruit extract of Benincasa hispida (Thunb.) Cong.(HABH) could decrease the intensity of toxicity in cisplatin induced albino wistar rats. A single dose of cisplatin (7.5 mg/kg i.p.) induced nephrotoxicity, manifested biochemically by a significant increase of urine volume, kidney weight, urinary sodium, urinary potassium, urinary glucose, blood urea, blood creatinine and decreased in body weight, urinary creatinine and blood total protein level with multiple histological damages. Nephrotoxicity was further confirmed by a significant decrease in glutathione (GSH) and increase in lipid peroxides in kidney homogenates. Administration of HABH (200, 400 mg/kg per day p.o.) 5 days before and 5 days after cisplatin injection produced a significant protection against nephrotoxicity induced by cisplatin. The amelioration of nephrotoxicity was evidenced by significant reductions in blood urea, blood creatinine, urinary glucose, urinary sodium, urinary potassium , urine volume with a significant weight gain. In addition HABH tended to normalize decreased level of blood total protein and urinary creatinine. Moreover, HABH prevented the rise of lipid peroxidation and the reduction of GSH activities in the kidney. These results suggest that HABH has a protective effect on nephrotoxicity induced by cisplatin

Antimicrobial effects of Indian medicinal plants against acne-inducing bacteria

Propionibacterium acnes and Staphylococcus epidermidis have been recognized as pus-forming bacteria triggering an inflammation in acne. The present study was conducted to evaluate antimicrobial activities of Indian medicinal plants against these etiologic agents of acne vulgaris. Ethanolic extracts of Hemidesmus indicus (roots), Eclipta alba(fruits), Coscinium fenestratum (stems), Curcubito pepo (seeds), Tephrosia purpurea (roots), Mentha piperita (leaves), Pongamia pinnata (seeds), Tinospora cordyfolia (barks), Euphorbia hirta (roots), Tinospora cordyfolia (roots), Thespesia populnea(roots), and Jasminum officinale (flowers) were tested for antimicrobial activities by disc diffusion and broth dilution methods. The results from the disc diffusion method showed that 07 medicinal plants could inhibit the growth of Propionibacterium acnes. Among those Hemidesmus indicus, Coscinium fenestratum , Tephrosia purpurea , Euphorbia hirta, Tinospora cordyfolia , Curcubito pepo and Eclipta albahad strong inhibitory effects. Based on a broth dilution method, the Coscinium fenestratum extract had the greatest antimicrobial effect. The MIC values were the same (0.049 mg/ml) for both bacterial species and the MBC values were 0.049 and 0.165 mg/ml against Propionibacterium acnes and Staphylococcus epidermidis, respectively. In bioautography assay, the Coscinium fenestratum extract produced strong inhibition zones against Propionibacterium acnes. Phytochemical screening of Coscinium fenestratum revealed the presence of alkaloid which could be responsible for activity. Taken together, our data indicated that Coscinium fenestratum had a strong inhibitory effect on Propionibacterium acnes and Staphylococcus epidermidis

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

BioBuilder as a database development and functional annotation platform for proteins-2

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>te interactions. Here protein 1 indicates the protein that is being annotated and protein 2 is the interacting protein. The 'Check' function assists if protein 2 already exists in the database. This feature avoids the redundancy that would arise from entering the same interactions from different proteins. An option to annotate non-protein types of interacting molecules such as drugs, DNA or carbohydrates is also available

BioBuilder as a database development and functional annotation platform for proteins-0

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>est and sends it to ZPublisher. The ZPublisher acts as an object request broker, finding the requested object, and delivering the objects back to the ZServer in their requested form. BioBuilder was built on top of the Zope core application code. Part of the application code is stored in the file system and other parts are in object database (ZODB)

BioBuilder as a database development and functional annotation platform for proteins-3

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>of shapes and colors as shown in the screenshot

BioBuilder as a database development and functional annotation platform for proteins-1

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>n is complete, it is submitted for review. An external reviewer can then assess the quality by using the 'Edit Gene' option