1 Pick a problem 2 Design some experiments
1. Pick a problem 2. Design some experiments 3. See where they lead us
GRADING? Combination of papers and presentations • First presentation: 5 points • Research presentation: 10 points • Final presentation: 15 points • Assignments: 5 points each • Poster: 10 points • Intermediate report 10 points • Final report: 30 points Alternatives • Paper(s) instead of 1 or two presentations • Research proposal instead of a presentation • One or two exams?
Topics? 1. Making novel biofuels • blue-green algae that generate electricity • Plants/algae that make methane or hydrogen • Biodiesel • Something else?
Biofuels
Biofuels 1 st gen Ethanol • Yeast makes Et. OH from plant sugar • Corn, sugar cane, sugar beet, sorghum
Biofuels 1 st gen Ethanol • Yeast makes Et. OH from plant sugar • Corn, sugar cane, sugar beet, sorghum • Only use part of plant
Biofuels 1 st gen Ethanol • Yeast makes Et. OH from plant sugar • Corn, sugar cane, sugar beet, sorghum • Only use part of plant • Can yield 1. 3 x more energy than needed to grow, harvest & convert it to ethanol
Biofuels 1 st gen Ethanol • Yeast makes Et. OH from plant sugar • Corn, sugar cane, sugar beet, sorghum • Only use part of plant • Can yield 1. 3 x more energy than needed to grow, harvest & convert it to ethanol • Usually lose C
Biofuels Yeast makes Et. OH from plant sugar • Corn, sugar cane, sugar beet, sorghum • Only use part of plant • Can yield 1. 3 x more energy than needed to grow, harvest & convert it to ethanol • Usually lose C • Use crops for fuel instead of food
Biofuels 1 st gen Ethanol • Yeast makes Et. OH from plant sugar • Inefficient • Only use part of plant • Use crops for fuel instead of food 2 nd gen (cellulosic) Ethanol • Use cell walls as source of sugar for yeast
Biofuels 2 nd gen (cellulosic) Ethanol • Use cell walls as source of sugar for yeast • Can use entire plant
Biofuels 2 nd gen (cellulosic) Ethanol • Use cell walls as source of sugar for yeast • Can use entire plant • Can use non-crops grown on marginal land • Switchgrass (Panicum virgatum)
Biofuels 2 nd gen (cellulosic) Ethanol • Use cell walls as source of sugar for yeast • Can use entire plant • Can use non-crops grown on marginal land • Switchgrass (Panicum virgatum) • C 4 perennial: grows from Mexico to 55˚ N
Biofuels Switchgrass (Panicum virgatum) • C 4 perennial: grows from Mexico to 55˚ N • C 4 = high water efficiency, also deep roots = high nutrient efficiency so grows on poor soil
Biofuels Switchgrass (Panicum virgatum) • C 4 perennial: grows from Mexico to 55˚ N • C 4 = high water efficiency, also deep roots = high nutrient efficiency so grows on poor soil • Can yield 5. 4 x more energy than needed to grow, harvest & convert it to ethanol cf 1. 3 x max for corn
Biofuels Switchgrass (Panicum virgatum) • Can yield 5. 4 x more energy than needed to grow, harvest & convert it to ethanol cf 1. 3 x max for corn • Also used for soil conservation and phytoremediation
Biofuels Switchgrass (Panicum virgatum) • Can yield 5. 4 x more energy than needed to grow, harvest & convert it to ethanol cf 1. 3 x max for corn • Also used for soil conservation and phytoremediation Miscanthus giganteus
Biofuels Miscanthus giganteus • Sterile hybrid of M. sinensis X M. sacchariflorus (both from Asia)
Biofuels Miscanthus giganteus • Sterile hybrid of M. sinensis & M. sacchariflorus (both from Asia) • C 4 perennial that reproduces solely through rhizomes
Biofuels Miscanthus giganteus • Sterile hybrid of M. sinensis & M. sacchariflorus (both from Asia) • C 4 perennial that reproduces solely through rhizomes • Non-invasive cf both parents, even though grows > 4 m tall cf 1 -2 m max for both parents
Biofuels Miscanthus giganteus • Non-invasive cf both parents, even though grows > 4 m tall cf 1 -2 m max for both parents • High N efficiency + C 4 = grows well on barren land
Biofuels Miscanthus giganteus • Non-invasive cf both parents, even though grows > 4 m tall cf 1 -2 m max for both parents • High N efficiency + C 4 = grows well on barren land • Can yield 20 tons biomass/acre cf 7. 6 for corn & 6 for switchgrass
Biofuels Miscanthus giganteus • Can yield 20 tons biomass/acre cf 7. 6 for corn & 6 for switchgrass • could supply 12% of the EU's energy by 2050 Trees • Poplar • Grows very fast (for a tree) • Can be genetically transformed • Can add or edit genes
Biofuels Trees • Poplar • Eucalyptus
Biofuels Trees • Poplar • Eucalyptus Can be harvested in 4 -5 years
Biofuels Trees • Poplar • Eucalyptus Can be harvested in 4 -5 years Low maintenance
Biofuels Trees • Poplar • Eucalyptus Can be harvested in 4 -5 years Low maintenance Yield <4 tons biomass/acre cf 20 for M. giganteus
Biofuels Trees • Poplar • Eucalyptus Can be harvested in 4 -5 years Low maintenance Yield <4 tons biomass/acre cf 20 for M. giganteus Sawdust, other waste cell walls
Biofuels 2 nd gen (cellulosic) Ethanol • Use cell walls as source of sugar for yeast • Can use entire plant • Can use non-crops grown on marginal land • Problem: lignin & other wall chems
Biofuels 2 nd gen (cellulosic) Ethanol • Problem: lignin & other wall chems
Biofuels 2 nd gen (cellulosic) Ethanol • Problem: lignin & other wall chems • Chemical hydrolysis
Biofuels Problem: lignin & other wall chems • Chemical hydrolysis • Digest cell walls with enzymes
Biofuels Problem: lignin & other wall chems • Chemical hydrolysis • Digest cell walls with enzymes • Need a cocktail
Biofuels Problem: lignin & other wall chems • Chemical hydrolysis • Digest cell walls with enzymes • Need a a cocktail Fermenting other sugars
Biofuels Fermenting other sugars • Use other microbes • Mutate yeast
Biofuels Fermenting other sugars • Use other microbes • Mutate yeast Mutate plants to make simpler cell walls
Biofuels Fermenting other sugars • Use other microbes • Mutate yeast Mutate plants to make simpler cell walls • 10% of Arabidopsis genes are estimated to be involved in plant cell wall metabolism
Biofuels Mutate plants to make simpler cell walls • 10% of Arabidopsis genes are estimated to be involved in plant cell wall metabolism • Many mutants reduce lignin synthesis
Biofuels Mutate plants to make simpler cell walls • 10% of Arabidopsis genes are estimated to be involved in plant cell wall metabolism • Many mutants reduce lignin synthesis • Easier to digest cell walls
Biofuels Mutate plants to make simpler cell walls • 10% of Arabidopsis genes are estimated to be involved in plant cell wall metabolism • Many mutants reduce lignin synthesis • Easier to digest cell walls • Easier for pathogens to attack
Biofuels Mutate plants to make simpler cell walls • 10% of Arabidopsis genes are estimated to be involved in plant cell wall metabolism • Many mutants reduce lignin synthesis • Easier to digest cell walls • Easier for pathogens to attack • More prone to xylem collapse
Biofuels Biodiesel = fatty acid methyl esters • Trans-esterify oils to make them volatile
Biofuels Biodiesel = fatty acid methyl esters • Trans-esterify oils to make them volatile • Renewable Fuels Standard (RFS 2): US must use > 1 billion gallons/year in 2012 through 2022 (cf ~40 billion/year total)
Biofuels Biodiesel = fatty acid methyl esters • Trans-esterify oils to make them volatile • Renewable Fuels Standard (RFS 2): US must use > 1 billion gallons/year in 2012 through 2022 (cf ~40 billion/year total) • > 50% reduction in CO 2 cf petrodiesel
Biofuels Biodiesel = fatty acid methyl esters • Trans-esterify oils to make them volatile • Renewable Fuels Standard (RFS 2): US must use > 1 billion gallons/year in 2012 through 2022 (cf ~40 billion/year total) • > 50% reduction in CO 2 cf petrodiesel • 2. 1 billion gallons of biodiesel were used in 2015 • Diamond Green Diesel in LA can make 275 million gallons/yr
Biofuels Biodiesel = fatty acid methyl esters • Trans-esterify oils to make them volatile • Renewable Fuels Standard (RFS 2): US must use > 1 billion gallons/year in 2012 through 2022 • > 50% reduction in CO 2 cf petrodiesel • Oils can be from seeds, algae, used cooking oil, animals
Biofuels Oils can be from seeds, algae, used cooking oil, animals Also use coconut & other oils directly in diesel engines • Just need to be sufficiently fluid to reach cylinder • Add double bonds to fatty acids or make them shorter
Biofuels • Oils from plants and algae
Biofuels • Algal oil production
Biofuels Problem: are shifting from growing food to growing fuel! • Raises price of soybeans, corn, etc • Cut down forests to grow oil crops in tropics • Is this environmentally sound? • Depends on real costs of growing, processing and delivering products
Biofuels Is this environmentally sound? • Depends on real costs of growing, processing and delivering products • NO! for corn-based ethanol! (But yes for sugar canebased ethanol in Brazil)
Biofuels Is this environmentally sound? • Depends on real costs of growing, processing and delivering products • NO! for corn-based ethanol! (But yes for sugar canebased ethanol in Brazil) • Probably yes for cellulosic ethanol
Biofuels Is this environmentally sound? • Depends on real costs of growing, processing and delivering products • NO! for corn-based ethanol! • Probably yes for cellulosic ethanol • Maybe for soy-based biodiesel
Biofuels Is this environmentally sound? • Depends on real costs of growing, processing and delivering products • NO! for corn-based ethanol! • Probably yes for cellulosic ethanol • Maybe for soy-based biodiesel • Maybe for other biodiesel
Biofuels Is this environmentally sound? • What are the real costs? • What else could be grown?
Biofuels Maybe for other biodiesel • What are the real costs? • What else could be grown? • Best to grow in places unsuitable for other crops • Pickleweed in salt marshes
Biofuels What else could be grown? • Best to grow in places unsuitable for other crops • Pickleweed in salt marshes, switchgrass, miscanthus or trees on lousy soil
Biofuels What else could be grown? • Algae (up to 60% oil) can generate 10 x more oil/acre • Grow in sewage, etc?
Biofuels What else could be grown? • Algae (up to 60% oil) can generate 10 x more oil/acre • Grow in sewage, etc? • Engineer or mutate to divert more photosynthate to lipids, ethanol, biogasoline, H 2 or electricity?
Biofuels Engineer or mutate to divert more photosynthate to lipids, ethanol, biogasoline, H 2 or electricity?
conversion of CO 2 to ethylene (C 2 H 4) in Synechocystis 6803 transformed with efe gene. Use ethylene to make plastics, diesel, gasoline, jet fuel or ethanol
Changing Cyanobacteria to make a 5 carbon alcohol
Engineering the light reactions? 1. Absorb full spectrum
Engineering the light reactions? 1. Absorb full spectrum 2. Improve efficiency of transport w/in PSI & PSII (or recover the energy)
Engineering the light reactions? 1. Absorb full spectrum 2. Improve efficiency of transport w/in PSI & PSII (or recover the energy) 3. Transport electrons to another acceptor • From OEE • From PQH 2 • From Fd
Engineering the light reactions? 1. Absorb full spectrum 2. Improve efficiency of transport w/in PSI & PSII (or recover the energy) 3. Transport electrons to another acceptor • From OEE • From PQH 2 • From Fd: use hydrogenase to make H 2
Engineering the light reactions? 1. Transport electrons to another acceptor • From OEE • From PQH 2 • From Fd: use hydrogenase to make H 2 or couple Pt catalysts to PSI to generate it directly from ascorbic acid via Cyt. C 6
Engineering the light reactions? 1. Transport electrons to another acceptor • From OEE • From PQH 2 • From Fd: use hydrogenase to make H 2 or couple Pt catalysts to PSI to generate it directly from ascorbic acid via Cyt. C 6 • Or use N 2 ase to make H 2
Biofuels Plants that make electricity? transfer e- from H 2 O to anode via direct contact, nanowires or a mediator
Biofuels What else could be grown? • Plants that release H 2? • Plants that make electricity? What else could be done? • Burn plants to make electricity? • 2 x better energy recovery than ethanol or diesel
Biofuels What else could be done? • Burn plants to make electricity? • 2 x better energy recovery than ethanol or diesel Process plant material directly to glucose?
Biofuels Conclusion: Renewable fuels are feasible • Bioethanol/biodiesel are stopgaps • Bioelectricity is best long-term plan • Direct current (eg solar panels? )
Biofuels Conclusion: Renewable fuels are feasible • Bioethanol/biodiesel are stopgaps • Bioelectricity is best long-term plan • Direct current (eg solar panels? ) • Hydrogen via water-splitting?
Biofuels Conclusion: Renewable fuels are feasible • Bioethanol/biodiesel are stopgaps • Bioelectricity is best long-term plan • Direct current (eg solar panels? ) • Hydrogen via water-splitting? • Something else?
Biofuels Conclusion: Renewable fuels are feasible • Bioethanol/biodiesel are stopgaps • Bioelectricity is best long-term plan • Direct current (eg solar panels? ) • Hydrogen via water-splitting? • Something else? • Photosynthetic vehicles & houses?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis? • DNA synthesis?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis? • DNA synthesis? • Lipid synthesis?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis? • DNA synthesis? • Lipid synthesis? • Hydrogen synthesis?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis? • DNA synthesis? • Lipid synthesis? • Hydrogen synthesis? How to test?
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis? • DNA synthesis? • Lipid synthesis? • Hydrogen synthesis? How to test? • Alter external conditions
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis? • DNA synthesis? • Lipid synthesis? • Hydrogen synthesis? How to test? • Alter external conditions • Alter internal conditions by bioengineering
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Will change allocation of photosynthate • Will invest their income in energy stores cf growth Predictions? • Growth? • Photosynthesis? • Respiration? • Protein synthesis? • DNA synthesis? • Lipid synthesis? • Hydrogen synthesis? How to test? • Alter external conditions • Alter internal conditions by bioengineering • Then measure growth, physiology and biofuels
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin)
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG
Finding Genes to Clone Working hypothesis: find way to alter metabolism to increase investment in biofuels 1. Increase production of photosynthate so will store some • Increase Calvin cycle • Increase light reactions
Finding Genes to Clone Working hypothesis: find way to alter metabolism to increase investment in biofuels 1. Increase production of photosynthate so will store some • Increase Calvin cycle • Increase light reactions 2. Alter allocation of photosynthate
Finding Genes to Clone Working hypothesis: find way to alter metabolism to increase investment in biofuels 1. Increase production of photosynthate so will store some • Increase Calvin cycle • Increase light reactions 2. Alter allocation of photosynthate • Alter N or S uptake
Finding Genes to Clone Working hypothesis: find way to alter metabolism to increase investment in biofuels 1. Increase production of photosynthate so will store some • Increase Calvin cycle • Increase light reactions 2. Alter allocation of photosynthate • Alter N or S uptake • Alter N or S assimilation
Finding Genes to Clone Working hypothesis: find way to alter metabolism to increase investment in biofuels 1. Increase production of photosynthate so will store some • Increase Calvin cycle • Increase light reactions 2. Alter allocation of photosynthate • Alter N or S uptake • Alter N or S assimilation 3. Alter biochemical pathways • Push more into lipid synthesis
Finding Genes to Clone Working hypothesis: find way to alter metabolism to increase investment in biofuels 1. Increase production of photosynthate so will store some • Increase Calvin cycle • Increase light reactions 2. Alter allocation of photosynthate • Alter N or S uptake • Alter N or S assimilation 3. Alter biochemical pathways • Push more into lipid synthesis • Alter free fatty acid recycling
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature • Light: intensity & duration
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature • Light: intensity & duration
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature • Light: intensity & duration • Turn down light reactions with atrazine
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature • Light: intensity & duration • Turn down light reactions with atrazine • Bioengineer internal changes • Nutrients (including HCO 3 -) by altering transporters
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature • Light: intensity & duration • Turn down light reactions with atrazine • Bioengineer internal changes • Nutrients (including HCO 3 -) by altering transporters • Light reactions
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature • Light: intensity & duration • Turn down light reactions with atrazine • Bioengineer internal changes • Nutrients (including HCO 3 -) by altering transporters • Light reactions • H 2 production via N 2 ases, H+ pumps, etc • Redirect photosynthate • K/O FFA recycling
Hypothesis: manipulating the internal environment of cyanobacteria will affect biofuel production • Alter external conditions • Nutrients • N, S, P, cofactors (including biotin) • Salinity/ water potential • Na. Cl vs KCl vs mannitol/sorbitol/PEG • p. CO 2: p. CO 2 in air and [HCO 3 -] in medium • Temperature • Light: intensity & duration • Turn down light reactions with atrazine • Bioengineer internal changes • Nutrients (including HCO 3 -) by altering transporters • Light reactions • H 2 production via N 2 ases, H+ pumps, etc • Redirect photosynthate • K/O FFA recycling
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