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CSD, a database of microbial strains for carbon fixation

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CSD, a database of microbial strains for carbon fixation
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  This article appeared in a journal published by Elsevier. The attachedcopy is furnished to the author for internal non-commercial researchand education use, including for instruction at the authors institutionand sharing with colleagues.Other uses, including reproduction and distribution, or selling orlicensing copies, or posting to personal, institutional or third partywebsites are prohibited.In most cases authors are permitted to post their version of thearticle (e.g. in Word or Tex form) to their personal website orinstitutional repository. Authors requiring further informationregarding Elsevier’s archiving and manuscript policies areencouraged to visit:http://www.elsevier.com/copyright  Author's personal copy Software, Data and Modelling News CSD, a database of microbial strains for carbon fixation Rashmi Saini a , Manash C. Majhi a , Rupam Kapoor b , Anil Kumar a , Rita Kumar a , * a Institute of Genomics and Integrative Biology, Mall Road, New Delhi-110007, India b Department Botany, Delhi University, New Delhi-110007, India a r t i c l e i n f o  Article history: Received 27 December 2008Received in revised form24 February 2009Accepted 28 February 2009Available online 31 March 2009 Keywords: CSDCarbon dioxide utilizing strain databaseGlobal warmingBiological fixationCO2 fixing pathways a b s t r a c t The CSD database contains a list of microorganisms involved in biological fixation of carbon dioxide. Thedatabase allows managing of information related to carbon dioxide fixation utilizing microbes belongingto four different classes i.e. microorganisms, genus listing, mechanisms and literature. The database canhelp in devising biological strategies for reducing carbon dioxide from the environment. It can also serveas comprehensive knowledgebase to search the microbes capable of utilizing carbon dioxide.   2009 Elsevier Ltd. All rights reserved. 1. Database availability  Name of Database: CSD (http://csd.igib.res.in)Developer: Rashmi saini/Manash Chandra Majhi/Rita KumarContact Address:Environmental Biotech Division5th Floor, Lab No: 506, 507Institute of Genomics and Integrative BiologyNew Delhi, India.Tel.: þ 91 011 2766156x154; fax: þ 91 011 27667471.Availability and Cost: Freely available on Internet athttp://csd.igib.res.inYear of first Availability: 2008Hardware Requirement: Any computer with Internet enabled,preferred screen resolution1024  768 or higher.Software Required: Internet Explorer or any other browser.Programming Language: PHP, JavaScript, HTML, XML Software Used: MySQL, ApacheProgram Size: 5.5 MB 2. Overview  Global warming – the most noticeable environmental problemis an unusual rise in earth’s temperature mainly due to the accu-mulation of greenhouse gases. Today global warming hassubstantial but undefined impacts on our ecosystem which areexpected to become more pronounced in the coming years ( Jarviset al., 2009). To overcome the effects of global warming there is anurgent need to think of various innovative ways for fixing CO 2 through physical, chemical and biological processes. Among thethree, the biological fixation using microorganisms has beenaccepted as a potential measure to mitigate global warming. It isbelievedtobeanenvironmentfriendlyandenergyefficientprocessas the biomass formed by fixation of CO 2  can be used for theproduction of bioenergy, microbial biodiesel, biohydrogen. Thesecan serve as an alternative to conventional energy sources such asfossil fuel and hence reduce the pressure to some extent (Bruce,2008). Till now, in many biological fixation processes, the photo-synthetic activity of microalgae have been exploited for mitigatingglobal warming (Wang et al., 2008). But besides microalgae there are some microbes i.e. bacteria and archaea that can too contributein reducing global warming ( Jessup et al., 1998). So far scientists have identified 5 different pathways through which microbes canfix CO 2  into biomass (Rudolf, 2007; Tributsch, 2003). This infor- mation can contribute to devise the technologies that emphasizeon the role of microbes in curbing the emission of greenhouse gasi.e. CO 2  from the industrial process. *  Correspondence to: Rita Kumar, Environmental Biotech Division, 5th Floor,Room No: 506, 507, Institute of Genomics and Integrative Biology, New Delhi, India.Tel.:  þ 91 011 2766156x154; fax:  þ 91 011 27667471. E-mail addresses:  rshm.saini12@gmail.com (R. Saini), manashbio@gmail.com(M.C. Majhi), kapoor_rupam@yahoo.com (R. Kapoor), anilcbt@yahoo.com (A. Kumar), rita@igib.res.in (R. Kumar). Contents lists available at ScienceDirect Environmental Modelling & Software journal homepage: www.elsevier.com/locate/envsoft 1364-8152/$ – see front matter    2009 Elsevier Ltd. All rights reserved.doi:10.1016/j.envsoft.2009.02.016 Environmental Modelling & Software 24 (2009) 1133–1134  Author's personal copy Thus the CSD database organizes information about CO 2 absorbing microbes in a systematic manner that providesresearchers with easy access to relevant information about theconcerned microbes. 3. Visualization The main aim of CSD, version 1.0, is to integrate all the dataavailable to date for the fixation of CO 2  using microbial strains. TheCSD web interface enables us to categorize all the informationwithin various classes on a single page (Fig. 1). Firstly, ‘‘Microor-ganisms’’, which assembles all the microbial species involved inculling CO 2  from their surrounding environment. Second, ‘‘Genuslist’’ contains data describing the genus of all species reportedunder Ist class. Each genus is linked to NCBI (National center forbiotechnology information) page that not only enables users tofurtherexplorethe knowledgeon relatedspecies, but also providesthe taxonomic characteristics of the genus. The third class ‘‘Mech-anism’’ informs about the mode of incorporation of CO 2  in themetabolic pathways of these organisms. More detailed informationabout these pathways has beenprovided as a hyperlink to MetaCycdatabase.Lastly the ‘‘Literature’’ class presents the list of research papersfrom which the data has been extracted. The database is expectedto expand further in order to keep up with the pace of scientificresearch in this area. Besides these classes there are other twoimportant features in the database that will help users in manyways. Foremost the search tool option that will facilitate rapidsearchtothedatafora particularmicrobial species.Secondly, otherrelevant databases as mentioned in the CSD will help theresearchers to collect more information. 4. Conclusions In the present work (CSD), we describe a comprehensive data-base for managing scattered information regarding microbialCO 2  utilization. This platform of comprehensive knowledge willdefinitely motivate researchers to device new biological approachto curb global warming. Information is managed in a simple anduser friendly way and it can be retrieved by simple search tool. Weare thankful to open databases like NCBI, MetaCyc to which linkshave been made for the detailed information. References Bruce, E.R., 2008. Opportunities for renewable bioenergy using microorganisms.Biotechnology and Bioengineering 100 (2), 203–212. Jarvis, A., Leedal, D., Taylor, C.J., Young, P., 2009. Stabilizing global mean surfacetemperature: a feedback control perspective. Environmental Modelling &Software 24 (5), 665–674. Jessup, M.S., Geertje, V.K., Wim, G.M.,1998. SOMETHING FROM ALMOST NOTHING:carbon dioxide fixation in chemoautotrophs. Annual Review of Microbiology52, 191–230.Rudolf, K.T., 2007. A fifth pathway of carbon fixation. Science 318, 1732–1733.Tributsch, H., 2003. Coupling bio-geochemical processes to regenerative energy foran industrial carbon cycle. Hydrometallurgy 71, 293–300.Wang, B., Li, Y., Wu, N., Lan, C.Q., 2008. CO2 bio-mitigation using microalgae.Applied Microbiology and Biotechnology 79, 707–718. Fig. 1.  Screen shot showing CSD web page. R. Saini et al. / Environmental Modelling & Software 24 (2009) 1133–1134 1134
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