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Biofiles Volume 5, Number 5 Enzymes and Reagents for Alternative Energy Metabolic strategies in alternative energy Enzyme-based fuel cells Lignocellulosic depolymerization Enzymes for biofuel research Reagents for ethanol and biodiesel analysis Biofilesonline Biofilescontents Your gateway to Biochemicals and Reagents for Life Science Research Introduction 3 BioFiles Online allows you to: Advancements in Enzyme-Based • Easily navigate the content of Fuel Cell Batteries, Sensors and the current BioFiles issue Emissions Reduction Strategies 8 • Access any issue of BioFiles • Subscribe for email notifications Selected Enzymes for Biofuel of future eBioFiles issues Cell Research 10 Register today for upcoming issues and eBioFiles announcements at Enzymes and Reagents for sigma.com/biofiles Ethanol Research 12 Enzymes for Lignocellulosic Greener Products Ethanol Research 12 Sigma-Aldrich is committed to doing our Enzymes for Starch Hydrolysis 20 part to minimize our footprint on the Ethanol Analysis 23 environment. As a life science and high technology company, we recognize your Enzymes for BioDiesel Research 24 need for high quality chemicals comes Lipase 24 first. In cases where it becomes possible to consider alternatives, we have made it Phospholipase C 24 easier for you to find greener options BioDiesel Analysis 25 through our new “Greener Alternatives and Technologies” product lists. Metabolic Standards for Mevalonate and Isoprenoid Pathway Analysis 30 Products Including: • Quality Environmentally-Friendly Enzymes • Ionic Liquids • Greener Alternatives: Solvents • Greener Alternatives: Reagents sigma-aldrich.com/green Life Science Labware Center The Life Science Labware Center allows easy browsing of labware products, including disposables, books, and equipment Features Include: • Corning® cell culture selection guide • Products by top manufacturers • New products by research areas • New lab start-up programs Start using the Life Science Labware center at sigma-aldrich.com/lslabware Technical content: Robert Gates, M. S. M. Order sigma.com/order Technical service sigma.com/techinfo sigma.com/lifescience 3 Introduction Robert Gates Market Segment Manager [email protected] Leveraging nature’s metabolic glucose, and then needlessly polymerize strategies for tomorrow’s this glucose into starch or cellulose. Then energy resources. we often rely on microbial and enzymatic hydrolysis of these biopolymers to give back Although most of the world’s population glucose and then ferment it to yield ethanol. understands that carbon dioxide is the Sugarcane ethanol employs a slightly simpler predominant end product of energy path via sucrose. production from combustible fuels, most of us forget that the “raw material” for most Our challenge for the future may be to find of our combustible fuel sources is also the “straightest metabolic line” between atmospheric carbon dioxide. Photosynthetic carbon dioxide and ethanol, butanol, fatty carbon dioxide fixation is most often the first acids or even hydrogen. The ideal route to step in the synthesis of both our renewable ethanol production might be to devise an fuels and non-renewable fossil fuels. Even enzymatic or cellular system to fix carbon much of our hydrogen production is an dioxide and take the direct route from indirect product of carbon dioxide fixation as ribose-1,5-bis-phosphate to pyruvate to it is often derived from fossil fuels. ethanol and bypass glucose biosynthesis, polymerization and depolymerization. The basic differences between non- We have included the Nicholson/IUBMB renewable fossil fuels and our “new Metabolic Pathway chart on the following generation” renewable fuels is time, energy pages illustrating the specific pathways input and mass. Our non-renewable related to carbon dioxide fixation and fuels, such as petroleum and coal required glucose, cellulose, pectin, starch, lignin and thousands of years of collection of solar ethanol production highlighted in yellow. energy to power carbon fixation for the biosynthesis of enormous amounts of Enzymes and their metabolic pathways biomass. That biomass then underwent enter the energy equation from other millions of years of anaerobic decomposition directions. Microbial strains are being to yield today’s fossil fuels. In our attempt to discovered that can ferment cellulosic circumvent or speed up this process, we are biomass to yield hydrogen. Some finding natural “renewable analogs” to some photosynthetic microbes, such as of our fossil fuels, i.e., ethanol and butanol algae, are capable of splitting water to to replace or supplement gasoline and fatty produce hydrogen utilizing solar energy. acid esters to replace diesel. Hydrogenases are being targeted not only for hydrogen production but also for the However, we have not advanced far enough oxidation of H2 in fuel cells. Immobilized in our manufacturing technology to divest enzyme-based fuel cell batteries can ourselves of the need for biological systems utilize multi-enzyme systems that mimic to do the complicated work for us. Current in vivo glycolytic and Krebs Cycle pathways. processes for ethanol production rely on Immobilized enzymes are also being plants to fix carbon dioxide, synthesize studied for the sequestration of carbon a “common currency” molecule such as dioxide emissions. 4 Engineering organisms and enzyme systems below, many of these areas require an (5) D. Klein-Marcuschamer, V. G. Yadav, A. Ghaderi, G. Stephanopoulos, De Novo Metabolic Engineering and to maximize biofuel production could understanding of metabolic pathways and the Promise of Synthetic DNA, Adv. Biochem. Eng. Biotech- require insertion of exogenous enzymatic enzymatic processes. nol. in press (2010). pathways from various organisms into a (6) J. L. Fortman, S. Chhabra, A. Mukhopadhyay, H. Chou, T. S. References Lee, E. Steen, J. D. Keasling, Biofuel alternatives to etha- new host. In addition, alternative metabolic nol: pumping the microbial well, Trends in Biotechnol., 26 (1) S. Atsumi, J. C. Liao, Metabolic Engineering for Ad- 375–381 (2010). pathways such as the mevalonate and vanced Biofuels Production from Escherichia coli, Curr. (7) D. B. Levin, R. Islam, N. Cicek, R. Sparling, Hydrogen Opin. Biotechnol., 19, 414–419 (2008). isoprenoid pathways are being studied as production by Clostridium thermocellum 27405 from (2) H. Alper, G. Stephanopoulos, Engineering for biofuels: cellulosic biomass substrates., Int. J. Hydrogen Energy, sources of biofuel. exploiting innate microbial capacity or importing 31, 1496–1503 (2006) biosynthetic potential?, Nature Reviews, Microbiology, 7, This issue of BioFiles is devoted to how (8) M. L. Ghirardi, S. Kosourov, A. Tsygankov1, A. Rubin, M. 715–723 (2009). Seibert, Cyclic Photobiological Algal H2 Production, Sigma-Aldrich enzymes and reagents are (3) P. P. Peralta-Yahya, J. D. Keasling, Advanced biofuel pro- Proceedings of the 2002 U. S. DOE Hydrogen Program duction in microbes, Biotechnol. J., 5, 147–162 (2010). involved in many of these areas of research. Review (4) J. M. Clomburg, R. Gonzalez, Biofuel production in (9) A. A. Karyakin, S. V. Morozov, E. E. Karyakina, N. A. Zorin As summarized above and illustrated Escherichia coli: the role of metabolic engineering V. V. Perelygin, S. Cosnie, Hydrogenase Electrodes for Fuel and synthetic biology, Appl. Microbiol. Biotechnpl., 86, Cells, International Hydrogenases Conference 2004. 419–434 (2010). Biomass O CH3 O HO OCH CH3O O 3 OH O HO HO OH OH CH3O O H O HO OCH3 HO OH CH3O HO O O OH HO O O OCH3 CH O OCH OH OCH 3 O OCH O 3 O CH 3 O 3 3 O Fuels OH CH3 O HO CH3O Non-Renewable O O CH3 OH O O O OH O Fossil Fuels OH HO CH3 O H O OH H C H OH H HO OH Lignin Solar Energy O O Methane (Natural Gas) CH2OH O OH OCH3 OH CH OH OH H H H O 2 HO O O H C C C H OH OH H H H CH2OH HO O O OH Propane OH CH2OH O O OH OH H H H H H H H CH2OH O H C C C C C C C H OH O H H H H H H H OH CH2OH n O O Gasoline CO2 CH2O OH OH Cellulose O OH OH OH H H H H H H H H H H H H H H Fixation OH C Anaerobic H C C C C C C C C C C C C C C H OH H H H H H H H H H H H H H H Decomposition ombustion OH CH2OH CH2O CH2OH CH2OH O O O O Diesel Glucose OH OH OH OH O O O O O OH OH OH OH CO2 OH n OH OH Carbon Dioxide Starch OS O OH NH2 COOH S O CH3 S O O CO2 O OH H H3C CH2 CH2 CH2 CH2 CH2 CH2 C CH3 S O N CH2 CH2 CH2 CH2 CH2 CH2 CH2 O HO O OOH Carbon Dioxide H3C CH2 CH2 CH2 CH2 CH2 CH2 C CH 2 CH C CH CH CH CH CH O 2 H2 2 2 2 2 2 CH2O OH O O OH H3C CH2 CH2 CH2 CH2 CH2 CH2 C CH3 CH C CH CH CH CH CH O 2 H2 2 2 2 2 2 OH HO H Coal OH Lipids OH Glucose H2 Anabolic InVivo Enzymatic Conversions Hydrogen H3C–CH2 OH Ethanol Microbial, Enzymatic and Chemical Conversions O H3C CH2 CH2 CH2 CH2 CH2 CH2 C CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 O BioDiesel Renewable Fuels Todays fuel sources originate primarily from the biosythesis of hydrocarbons originating from photosynthetic carbon dioxide fixation. The combustion of these fuels results in production of carbon dioxide. Ideally, this might someday be a “closed-CO2-loop” system with solar power as the only energy input. Many of the structures shown are basic examples of simple unbranched molecules intended to represent heterogeneous mixtures. Order sigma.com/order Technical service sigma.com/techinfo sigma.com/lifescience 5 The New Enzyme Explorer Redesigned Format and Expanded Resources. The Enzyme Explorer Indices provide The Enzyme Explorer Learning Center Allow the New Protease Finder to help paths to find more than 3,000: includes: you locate both the endo and exoproteases needed for precision protein cleavage.
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  • Course Title: Systemic Bacteriology & Mycology

    Course Title: Systemic Bacteriology & Mycology

    COURSE TITLE: BACTERIOLOGY COURSE CODE: MIPA-219 RECOMMENDED BOOKS 1. Essentials of Veterinary Microbiology (Fifth Edition) By G. R. Carter, M. M. Chengappa and C. A. W. Roberts 2. Veterinary Bacteriology and Virology By I. A .Merchant and R. A. Packer 3. Text Book of Veterinary Microbiology By S. N. Sharma and S. C. Adlakha 4. Pathogenesis of Bacterial Infections in Animals By C. L. Gyles and C. O. Thoen 5. Veterinary Microbiology and Microbial disease By P. J. Quinn, B. K. Markey, M. E. Carter, W. J. C. Donnelly, F. C. Leonard 6. Topley and Wilson‟s Microbiology and Microbial Infections (Volume-3; 9th Edition) By L. Collier, A. Balows and M.Sussman For Practical Class Purposes 1. Diagnostic Procedures in Veterinary Bacteriology and Mycology By G. R. Carter and J. R. Cole, Jr. 2. Color Atlas and Textbook of Diagnostic Microbiology (Fifth Edition) By Elmer W. Koneman et.al 1 BACTERIAL CLASSIFICATION AND NOMENCLATURE Systematic Bacteriology Systematic Bacteriology is a branch of Microbiology which embraces the classification and nomenclature of bacteria. Taxonomy Taxonomy is defined as the science of classification (orderly arrangement of organisms). Nomenclature Nomenclature is naming an organism by international rules according to its characteristics. Identification Identification refers - i. To isolate and distinguish desirable organisms from undesirable ones. ii. To verify the authenticity or special properties of a culture. Isolate An isolate is a pure culture derived from a heterogenous, wild population of microorganisms. Classification Classification can be defined as the arrangement of organisms into taxonomic groups (taxa) on the basis of similarities or relationships. Biochemical, physiologic, genetic and morphologic properties are often necessary for an adequate description of a taxon.