Friday, February 25, 2011
Breaking down lignin
I just saw a short article over at Discover Magazine which mentions work being done by Ratna Sharma-Shivappa at NCSU in developing a process to break down lignin in plants, allowing them to access hidden carbohydrates. Lignin is the woody material found in grasses. By grinding up the grass (miscanthus in her work) and then exposing this to ozone, she is able to break down the lignin while leaving in tack the valuable carbohydrates. These can then be fermented to produce ethanol for fuel.
Wednesday, February 23, 2011
Re-engineering Photosynthesis
New Scientist has an article today titled "A blue-green revolution: Upgrading photosynthesis." In it, the author describes various possible upgrades that could be made to the photosynthetic machinery in modern plants.
The main point is that the chloroplasts in modern plants can trace their ancestry back to a photosynthetic bacteria which was engulfed by another cell some 1.5 billion years ago or so. Since that time, this original chloroplast has been passed down to all photosynthetic algae and plants. Of course it has evolved over time, and there are differences amongst the chloroplasts in various species of plants, but the divergence between these chloroplasts is very small compared to the changes that have occurred in single cell photosynthetic bacteria.
Why wouldn't we expect to see an equal diversification in the chloroplasts in algae and plants vs. photosynthetic bacteria? "Think of the countless cyanobacteria living in the sea. If a mutation enables one cyanobacterium to photosynthesise more efficiently, it will grow and reproduce faster, and its descendants could come to dominate a population within weeks. The rampant gene-swapping among simple cells means other kinds of bacteria could acquire this trait too. Now suppose that same mutation occurs in a chloroplast in a plant. It might not be beneficial in plants, as what is good for chloroplasts can be bad for the host cell. Even if the mutation is beneficial, the odds are the chloroplast is in a leaf that will fall to the ground and die. And even if the mutation occurs in a cell that eventually gives rise to a new plant, the much slower reproduction rate of plants means it will take many decades for the mutation to spread through a population." In other words, the fact that the bacteria are single-celled with short-lifetimes and prolific gene swapping, translates to a faster rate of evolution when compared to multi-cellular, longer lived plants and algae.
So what are the trends we see in today's most fashionable photosynthetic bacteria?
Adjusting to developments in the atmosphere. The modern atmosphere is composed of about 78% Nitrogen, 21% Oxygen, and only 0.039% Carbon Dioxide (although it seems like we're trying to change that balance as fast as we can...). Of course 2 billion years ago when that original photosynthetic bacteria was engulfed and on its way to becoming the ancestor of chloroplasts, the atmosphere had almost no Oxygen, and significantly more Carbon Dioxide, Carbon Monoxide, and other gases.
Proteins like rubisco, which take the carbon from CO2 and use it to help form sugar molecules. The ancient rubisco would take up Oxygen or Carbon Dioxide. Since there was a negligible amount of Oxygen, this didn't matter that much. Now however, with a lot of Oxygen present, rubisco frequently grabs an Oxygen instead of a Carbon Dioxide, which results in a destruction of food instead of creation.
Cyanobacteria on the otherhand have evolved a way to mitigate this. These organisms create carboxysomes, small compartments that allow Carbon Dioxide but keep Oxygen out. Rubisco in carboxysomes is therefore free to spend its time being productive. Moreover, carboxysomes also have an enzyme called carbonic anhydrase, which will convert bicarbonate to CO2, further increasing the amount of CO2 present to form sugar.
A second optimization that is discussed is in Nitrogen fixation. Many plants are unable to take molecular Nitrogen from the air to use as raw Nitrogen in cellular processes. Instead they often rely on symbiotic bacteria near their roots to do this for them, or alternatively, a friendly farmer to throw down some Nitrogen containing fertilizer. The enzyme nitrogenase is capable of fixing molecular Nitrogen for use in plants, but unfortunately, nitrogenase is destroyed by Oxygen. If plants could be designed to produce Nitrogenase at night however, when photosynthesis is not occurring and consequently lower levels of Oxygen are present, this might allow plants to effectively produce their own fertilizer. Or, if nitrogenase could be inserted into a compartment like carboxysome, that also might prove beneficial.
The main point is that the chloroplasts in modern plants can trace their ancestry back to a photosynthetic bacteria which was engulfed by another cell some 1.5 billion years ago or so. Since that time, this original chloroplast has been passed down to all photosynthetic algae and plants. Of course it has evolved over time, and there are differences amongst the chloroplasts in various species of plants, but the divergence between these chloroplasts is very small compared to the changes that have occurred in single cell photosynthetic bacteria.
Why wouldn't we expect to see an equal diversification in the chloroplasts in algae and plants vs. photosynthetic bacteria? "Think of the countless cyanobacteria living in the sea. If a mutation enables one cyanobacterium to photosynthesise more efficiently, it will grow and reproduce faster, and its descendants could come to dominate a population within weeks. The rampant gene-swapping among simple cells means other kinds of bacteria could acquire this trait too. Now suppose that same mutation occurs in a chloroplast in a plant. It might not be beneficial in plants, as what is good for chloroplasts can be bad for the host cell. Even if the mutation is beneficial, the odds are the chloroplast is in a leaf that will fall to the ground and die. And even if the mutation occurs in a cell that eventually gives rise to a new plant, the much slower reproduction rate of plants means it will take many decades for the mutation to spread through a population." In other words, the fact that the bacteria are single-celled with short-lifetimes and prolific gene swapping, translates to a faster rate of evolution when compared to multi-cellular, longer lived plants and algae.
So what are the trends we see in today's most fashionable photosynthetic bacteria?
Adjusting to developments in the atmosphere. The modern atmosphere is composed of about 78% Nitrogen, 21% Oxygen, and only 0.039% Carbon Dioxide (although it seems like we're trying to change that balance as fast as we can...). Of course 2 billion years ago when that original photosynthetic bacteria was engulfed and on its way to becoming the ancestor of chloroplasts, the atmosphere had almost no Oxygen, and significantly more Carbon Dioxide, Carbon Monoxide, and other gases.
Proteins like rubisco, which take the carbon from CO2 and use it to help form sugar molecules. The ancient rubisco would take up Oxygen or Carbon Dioxide. Since there was a negligible amount of Oxygen, this didn't matter that much. Now however, with a lot of Oxygen present, rubisco frequently grabs an Oxygen instead of a Carbon Dioxide, which results in a destruction of food instead of creation.
Cyanobacteria on the otherhand have evolved a way to mitigate this. These organisms create carboxysomes, small compartments that allow Carbon Dioxide but keep Oxygen out. Rubisco in carboxysomes is therefore free to spend its time being productive. Moreover, carboxysomes also have an enzyme called carbonic anhydrase, which will convert bicarbonate to CO2, further increasing the amount of CO2 present to form sugar.
A second optimization that is discussed is in Nitrogen fixation. Many plants are unable to take molecular Nitrogen from the air to use as raw Nitrogen in cellular processes. Instead they often rely on symbiotic bacteria near their roots to do this for them, or alternatively, a friendly farmer to throw down some Nitrogen containing fertilizer. The enzyme nitrogenase is capable of fixing molecular Nitrogen for use in plants, but unfortunately, nitrogenase is destroyed by Oxygen. If plants could be designed to produce Nitrogenase at night however, when photosynthesis is not occurring and consequently lower levels of Oxygen are present, this might allow plants to effectively produce their own fertilizer. Or, if nitrogenase could be inserted into a compartment like carboxysome, that also might prove beneficial.
Tuesday, February 15, 2011
Converting the world's energy supplies to solar, wind, and hydro
The latest Stanford Report has an article about a study by Mark Z. Jacobson and Mark Delucci which argues that the world's energy supplies can be provided solely through solar, wind, and hydropower. Moreover, they claim that energy from such sources are near price parity with our current energy portfolio, owing to a decrease in deaths and other health consequences of air pollution associated with fossil fuels and to the fact that electrical energy is approximately 30% more efficient than energy from fossil fuels.
Such a plan would require a complete replacement of existing infrastructure though. Cars would need to be replaced by electric cars, airplanes replaced by planes fueled by hydrogen (formed using electricity), power plants shuttered etc. This seems both inefficient and an unlikely scenario to me, which is why I think biofuels are a more realistic solution, at least in the mid-term, provided we can improve on their efficiencies.
Nevertheless, it's an interesting approach, and I especially liked data points like
"...to power100 percent of the world for all purposes from wind, water and solar resources, the footprint needed is about 0.4 percent of the world's land (mostly solar footprint) and the spacing between installations is another 0.6 percent of the world's land (mostly wind-turbine spacing)"
and
"The actual footprint required by wind turbines to power half the world's energy is less than the area of Manhattan." If half the wind farms were located offshore, a single Manhattan would suffice."
That wouldn't be a bad investment.
Such a plan would require a complete replacement of existing infrastructure though. Cars would need to be replaced by electric cars, airplanes replaced by planes fueled by hydrogen (formed using electricity), power plants shuttered etc. This seems both inefficient and an unlikely scenario to me, which is why I think biofuels are a more realistic solution, at least in the mid-term, provided we can improve on their efficiencies.
Nevertheless, it's an interesting approach, and I especially liked data points like
"...to power100 percent of the world for all purposes from wind, water and solar resources, the footprint needed is about 0.4 percent of the world's land (mostly solar footprint) and the spacing between installations is another 0.6 percent of the world's land (mostly wind-turbine spacing)"
and
"The actual footprint required by wind turbines to power half the world's energy is less than the area of Manhattan." If half the wind farms were located offshore, a single Manhattan would suffice."
That wouldn't be a bad investment.
Wednesday, February 9, 2011
Looking for Novel Cellulose Degrading Enzymes in Cow Guts
Scientific American has an interesting article out about a research team at the Joint Genome Institute which is looking for novel enzymes that may help to degrade cellulose. Almost all ethanol currently produced comes from the fermentation of simple sugars. In the U.S., the simple sugars often come from corn. The problem is that this is not terribly efficient. First, corn for fuel comes from the same land as corn for crops, meaning that the more fuel produced from corn, the less available for food, and we see rising food prices. Second, the simple sugars we extract from corn come almost entirely from the kernels. So we grow these great big corn stalks, take the kernels and through away the stalk and cob, which account for the vast majority of the mass in the plant. The reason we do this is because the stalk and cob are primarily composed of cellulose, a complex sugar which is not easily fermentable. What would be nice is if we could break the cellulose down into simple sugars, and then we could use existing technology to ferment these into ethanol for fuel. If we were able to break down cellulose, we could even skip corn, and concentrate on plants that don't compete with our food supply. The most commonly referred to possibility is switch grass, a very hardy plant which can grown in all sorts of soil and environments that are typically hostile to traditional agriculture.
So back to the SciAm article. The JGI researchers figured that cows eat all sort of grass that is chalk full of cellulose. So, they took a cow which essentially has a door inserted on its side, allowing for easy access to the rumen, the cow's first stomach. They placed a bag of switch grass inside and waited 3 days. They then removed the bag and sequenced the DNA of all microbes found feeding on the switchgrass. Of course there were thousands if not millions of different species of microbes there, but in their sequencing process they were able to divy out the contributions from the various microbes. (This is a technique called metagenomic analysis.) They then searched the sequenced genes looking for DNA sequences which are similar to known DNA sequences of genes that work on carbohydrates. They identified over 27,000 genes. They actually took 90 of these genes, expressed the genes, took the resulting enzymes and looked to see if they do in fact help breakdown cellulose. Over half of them did.
It would be interesting to screen a larger set of these enzymes in a high-throughput fashion, identify a set of the most effective enzymes, and then perform multiple rounds of directed evolution, selecting for the most efficient enzyme during each round. This might give an indication of how much low-hanging fruit there is in improving the efficiency of such enzymes...
So back to the SciAm article. The JGI researchers figured that cows eat all sort of grass that is chalk full of cellulose. So, they took a cow which essentially has a door inserted on its side, allowing for easy access to the rumen, the cow's first stomach. They placed a bag of switch grass inside and waited 3 days. They then removed the bag and sequenced the DNA of all microbes found feeding on the switchgrass. Of course there were thousands if not millions of different species of microbes there, but in their sequencing process they were able to divy out the contributions from the various microbes. (This is a technique called metagenomic analysis.) They then searched the sequenced genes looking for DNA sequences which are similar to known DNA sequences of genes that work on carbohydrates. They identified over 27,000 genes. They actually took 90 of these genes, expressed the genes, took the resulting enzymes and looked to see if they do in fact help breakdown cellulose. Over half of them did.
It would be interesting to screen a larger set of these enzymes in a high-throughput fashion, identify a set of the most effective enzymes, and then perform multiple rounds of directed evolution, selecting for the most efficient enzyme during each round. This might give an indication of how much low-hanging fruit there is in improving the efficiency of such enzymes...
Tuesday, February 8, 2011
Making Hydrogen from Spinach
Another fun teaser article on New Scientist today. A group of scientists at Oak Ridge National Labs has produced an in vitro system to produce hydrogen gas. They took the LHC-II (light harvesting complex II) from spinach, and added in some copoloymers and sodium hexachloroplatinate. The copolymers and LHC-II self-assembled into small sheets. When light is shined on them, LHC-II absorbs the photons releasing electrons, which are then transfered to the platinum, which can then catalyze the reduction of protons to form hydrogen gas. They observed the reaction for over 100 hours. It was unclear to me whether the platinum was consumed during this process, or if it can be continuously reused. If it is consumed or must be recharged in some way in order to catalyze further reactions, it seems cost may be an issue. Nevertheless, hydrogen is an incredibly clean fuel, so it's always exciting to see work done there! The full scientific article is here. Hopefully I'll get a chance to read it later in the week.
Tuesday, February 1, 2011
Storing Hydrogen with Nanobeads
The New Scientist has an interesting article today about using plastic nanobeads to store hydrogen efficiently. Hydrogen is a great fuel, but it has energy density issues (i.e. you need a large volume of hydrogen to store enough energy to be useful.) You can store it as a liquid, but this requires it to be kept extremely cold. One proposed solution has been to store Hydrogen in hydrides. However, these materials can burst into flames when exposed to Oxygen in the air, not exactly a desired trait when designing a car for instance.
The work discussed in this article uses nanobeads of ammonia-borate which essentially surround the hydrogen and protect it from exposure to oxygen. When heated however, they'll release the hydrogen, allowing its use as a fuel. The beads in this form actually function as a liquid, so it should be easy to adapt existing infrastructure to their use. Apparently there still remain challenges in recharging the beads with Hydrogen though.
The company making the nanobeads is Cella Energy.
The work discussed in this article uses nanobeads of ammonia-borate which essentially surround the hydrogen and protect it from exposure to oxygen. When heated however, they'll release the hydrogen, allowing its use as a fuel. The beads in this form actually function as a liquid, so it should be easy to adapt existing infrastructure to their use. Apparently there still remain challenges in recharging the beads with Hydrogen though.
The company making the nanobeads is Cella Energy.
New DOE Bioenergy Portal
The DOE just released a new portal for Bioenergy concerns here. It appears less focused on the biology behind bioenergy, and more focused on industry infrastructure, but it's also a work in progress so that may change.
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