IGEM:Stanford/2009/Ideas and Discussion

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DNA as a Language
Joseph: Interesting idea came up today. DNA is supposed to be the "language of life" but we never really see as a language but more as a biological stepping stone to more important things (cells, organisms, etc). It would be extremely interesting - and feasible - to analyze DNA the same way we would analyze, say, a radio signal picked up by SETI.

DNA, as a language, is unique in that it is one of very few languages (by language I mean a sequence that follows very strict convetions) that are NOT of human society. Even just figuring out whether we actually can analyze and "read" DNA the same way we would read any other language would be an extremely significant breakthrough. In addition, DNA probably follows patterns enough that linguistic studies could yield information about how DNA changes, what direction it changes in, etc. For example, applying Markov models to sections of DNA that code for proteins or genes would be very interesting. I don't want to explain Markov models here but I'll do it at the next meeting. Get pumped!

Photosynthetic Machines
Joseph: I believe somebody mentioned an implementation of photosynthesis last week at the meeting (something about algae)? Energy efficiency is all about using what we have in surplus to either create or re-use what we have very little of. Obviously, photosynthesis would make an amazing source of energy in that it is, as far as we are concerned, limitless. There are other concerns with using photosynthesis (sun is not a steady source of energy on cloudy days, etc.) but these concerns could be addressed later. I also do believe that it would be easier to take a photosynthetic organism and modify it for our purposes than to take an organism initially suitable to our purposes and make it photosynthetic, but I have to go find articles on it first.

Also, just making an organism photosynthetic is not enough. What the organism uses the solar energy for would be the main purpose of the project. For example, some bacteria create bioplastic precursors. Bioplastic is much more environmentally friendly than conventional petroleum-derived plastic; but bioplastic-creating bacteria have their own energy costs. Were we to transfer this characteristic to a photosynthetic organism (even a plant) bioplastic could be created from, essentially, sunlight. I'm sure the actual idea is much more complicated, but it's worth a thought.

Nghi: let's begin listing all organisms that have photosynthetic properties. Classification of photoautotroph The organism we will ultimately choose will be based on the specification of what we want it to do.

--Nghi Nguyen 17:00, 22 January 2009 (EST)After last night's presentation, it seems best to use E.coli or cyanobacteria if we decided to do an energy project.

Bioelectricity
I really like the direction of bioenergy. I also liked the solar biohydrogen research done by James Swartz. To build on top of that, here is a research I found very interesting--Monitoring and Accessing Cellular Photosynthesis for Bioelectricity by Fritz Prinz and Arthur Grossman. They are studying how to capture electricity directly from living cellls through inserting electroders (really really small ones) into the chloroplasts. And using light, a high electron potential is genetrated in stroma and high 02 and H+ potential in lumen. And energy is generated using the gradient. SO thinking along that line, I was thinking that we could manipulate photosynthesis in such way that electricity is generated.

Ming

Microbial Synthesis of Biodiesel
Along the same line of bioenergy, there is a study done by Chaitan Khosla. In this study, E.Coli is used to produced fatty acid alternatives. And these fatty acid alternatives, such as aldehydes, ester and lactones, are then tetsed for their potential as biodisel fuels. Ming

Nghi: Khosla's research

He engineers E. coli to produce fatty acid using three different approaches. 1. inserting genes from other organisms to increase synthesis of fatty acids 2. looking at different types of fatty acid precursors 3. separating two synthesis pathways (fatty acid analogue and triglyceride) to minimize accumulation of glycerol waste

To get a good overview of Khosla's work in polyketide biosynthesis, you should check out this video. -Chris

I have a question: why is glycerol waste bad for the organism?

In response to the glycerol question, I don't know why it's bad for the organism, but the following article is a simple but useful explanation I found about why glycerol is waste when it comes to fuels: http://www.guardian.co.uk/technology/2008/dec/04/biofuels-glycerol-green-technology. According to this article, it's hard to burn but production of biodiesel produces it in large quantities, and no one really knows what to do with it. Some groups are trying to unlock the hydrogen in glycerol to produce H2 for alternative energy, because it's more hydrogen-rich in methane and they think it might form a more efficient H2 production pathway. Alternatively, some groups are looking into shunting glycerol through a metabolic process that converts it into the building blocks for bioplastic polymers.[www.rsc.org/ej/GC/2008/b714292g.pdf] -Ariana

A Jackpot of Ideas for Energy Projects @ Stanford
Click link here: Of interest, molecular solar cells and artificial photosynthesis

I also enjoyed the paper: "Engineering for the Direct Biological Conversion of Sunlight into Hydrogen"  here: --research by James Swartz in the Chem E department. He is designing an oxygen-tolerant hydrogenase protein. When this protein is incorporated into a living cell, it may enable the efficient production of H from sunlight and water, using biological agents as catalysts. Swartz is also conducting research on creating an improved water filter using biosensors that are sensitive to chemicals and ions in water.

Other faculty at Stanford we may ask to be advisors/follow research:

KC Huang--regulate cell membranes/shape...we could combine this with the research of Dr. Somerville, who is altering plant cell wall structure and dynamics for enhanced biomass production.

For CS people: Altman and Covert are in BioE and are building computer models of complex biological processes.

Bryant: molecular motors/transport.

The article about the synthetic plastics is awesome! I searched about limonene oxide, and found this article (http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TGM-4K48MFP-4&_user=145269&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000012078&_version=1&_urlVersion=0&_userid=145269&md5=e0378a94f59bd05af584ef0a8da0945c) that describes a set of ideal (or rather, acceptably efficient,) conditions for the reaction to take place: hydrogen peroxide as an oxidant agent, alumina as a catalyst, and ethyl acetate as solvent. As a reactive oxygen species, hydrogen peroxide is toxic to cells, but perhaps there would be a way to create a unique vesicle for the reaction that is similar to/linked with a peroxisome? I guess then we'd also have to figure out a way to export the product from the vesicle or just lyse it and the cell. Here's a website for basic information about bioplastics and biopolymers: http://www.biobasics.gc.ca/english/View.asp?x=790#biotech. I also saw some articles in Journal of the American Chemical Society (JACS) that mentioned Zn (II)-based catalysts as an efficient means of creating copolymers/biopolymers of epoxides (including limonene oxide) and carbon dioxide. (http://pubs.acs.org/doi/abs/10.1021/ja982601k) -Ariana

Color Changing Moss

 * Physcomitrella patens

Hydrocarbon Production
Is it possible to increase the metabolic capabilities of biological system in order to produce hydrocarbons?

Literature: Expanding metabolism for biosynthesis of nonnatural alcohols, http://www.pnas.org/content/105/52/20653.full

Another paper: Microdiesel: E.coli engineered for fuel production PMID: 16946248

Fourth Generation Biofuel
So, 4th G technology combines genetically optimized feedstocks (high biomass, low lignin content), which are designed to capture large amounts of carbon, and genomically synthesized microbes, which are made to efficiently make fuels. The capture and sequestration of CO2 characterizes 4th G biofuels a carbon negative source of fuel. Can we make an organism or a plant that will inhale CO2 better and excrete more sugars? A similar idea was proposed last year of fixing CO2. It was mentioned one company was working on this: Click. It was also proposed if it was possible to precipitate CO2 - maybe into limestone? Can we flush this out even more? How about this? I'm not saying we should use these exact ideas but we can brainstorm on what's possible with the friendly molecule.

I just wanted to contribute to this idea and say that Amyris and EcoRock are two start up companies working. The latter works specifically with flushing CO2 into cement and they're a really powerful startup. I know that when Vinod Khosla came to speak here at Stanford last year, he had a few companies like EcoRock in his venture group's portfolio. (Anusuya). It's a really important technique for sequestering CO2 and it would be awesome if we could make it have a biological basis and be sustainable. (Anusuya)

Synthetic gene oscillator
Two recent papers in Nature: tunable oscillator and gene oscillator

Maybe we can use this is as a component of a project that is dependent upon light.

Light
I'm not sure how to start a new topic, but this idea is kind of dependent on light I suppose. In reading about things going on in biotech these days, I stumbled upon the work of Karl Deisseroth and his optogenetics. Anyway, I was wondering if it would be possible to modify his concept a little so that we could stimulate the actual neurons that are responsible for vision. Basically what I was thinking was infecting human neurons with DNA that codes for proteins which are responsible for detecting different wavelengths of light. Essentially, we could extract the DNA from one of the many hundreds of bacteria out there with light-activated ion channels and put that DNA into some kind of virus which tends to attack neurons responsible for vision. The virus would then unload it's DNA into the neurons and so the neurons would have some way of reacting to light, thereby bypassing the need to process photons with the eye. Also, I don't know if this has been done already, but I would think it would definitely be possible to create a camera using a similar concept as described above. -Leon

To dive into this idea a bit more, the light absorbing cells are in fact Photoreceptor cells. What would be a more achievable and synthetic biology approach to answer this question? (particularly avoiding viruses which make it tricky for engineering) I'm thinking that a proof of concept of making a light-insensitive organism to a light sensitive organism would be a good proof of concept. Also take a look at Voigt's paper

Dual Action Solar Cell??
So I don't know if this is possible and we would need someone who is good with electrical information i think, but this idea came to me and I thought it could be interesting. What if we reengineered a pv solar cell so that it absorbed the necessary wavelength of light to operate, but then allowed some wavelengths to pass through... as if it was transparent. Then we could engineer a plant cell to absorb the wavelength of light that passes through the solar cell. For example, some bacteria are photosynthetic I believe and may use different wavelengths than plants. We could introduce those genes into the plants so then they would operate beneath the solar cell. Thus, on a large scale operation, farmers could place huge tracts of solar cells over their land generating electricity while at the same time their crops would be able to grow. Ir even placing the solar cells on rooftops in cities but still having lawns or gardens beneath them....just an idea (Suzie)

Decomposing Oil
Another concern about the energy issue is what to do with all of the waste- especially the plastics that take years to decompose. Instead of finding ways to engineer new plastics, we could engineer bacteria that would actually break down the specific plastics and then that decomposition could be used as a biomass fuel for energy sources. I am pretty sure research is trying to develop this (I remember reading about it somewhere.. for example http://science.slashdot.org/article.pl?sid=08/05/24/0335242&from=rss.. or just google it) however, we could do something similar or try to make it more efficient.. (Suzie)

I was considering something similar to what Suzie proposed-- I also thought that it might be interesting to consider engineering a pathway for the degradation of plastic to design a strain of microbe that is intended for use in a compost for plastics. While looking at some articles and information about bioplastics, I found the following article (http://www.guardian.co.uk/environment/2008/apr/26/waste.pollution) about the dangers of polylactic acid (Pla), a supposedly ecologically-friendly bioplastic that may cause more environmental stress than more traditional non-bioplastics. Pla products are often recycled with other plastics, but this results in the contamination of recycled plastics, or they are tossed into landfills, where a substantial amount of methane is released as they degrade without oxygen. Would it be possible to design an anaerobic bacteria that efficiently degrades Pla without leftover residues (and perhaps link it to another project that reduces methane output/ uses methane as a substrate for another metabolic process? This article, which discusses methane recycling in wetlands through symbiotic relationships, seemed relevant: http://www.nature.com/nature/journal/v436/n7054/full/nature03802.html.) -Ariana

Joseph: I like this idea as well, but I think we could also bypass the problem of material waste completely if we could find organic alternatives to normally non-biodegradable materials. We've all seen the silverware made out of starch. We have bioplastics which are much more environmentally friendly and easier to decompose. What is to stop us from finding ways to make the materials inherently more environmentally conscious?

Along the lines of Suzie's and Ariana's proposals, I know that a big problem in industries is how to get rid of side products from chemical reactions used to crack oil or create other biochemicals. For example, how to reduce sulfur emissions in processing plants without using scrubbers - if we could think about creating a biological scrubber system that works with sulfur and is efficient I think that would be profound. This shouldn't be too hard since bacteria often already process hydrogen sulfide (Anusuya)

Plaque-Digesting RBC or Lymphocyte
Designing a synthetic red blood cell or some sort of lymphocyte to digest arterial wall plaque by inserting collagenase genes that are activated in the presence of plaque or to release a limited amount of anticoagulant or antiplatelet substances in the presence of an embolism? Just a thought... -Ariana UC Berkeley did a similar project Bactoblood of creating an RBC out of E. coli to carry out specific functions, however plaque-digesting wasn't part of their project. Correct me if I'm wrong but I assume the plaque-digestion would help individuals with high cholesterol? Maybe we can expand the project and target diabetes, etc.?

To expand the question, what other problems exist in the blood that can be easily solved by a modified blood cell? On issue with RBC is that they lack DNA and some other typical functions. Also, if you go the plaque route, what is the human's natural mechanism of removal? Could this be implemented into a modified RBC? - Chris

That sounds really really neat- and would have a really helpful effect in general. I know health-wise we could find quite a bit of support. If we could engineer them to target plaque, we could also look into other things as well, such as toxins in the blood. Or like you said, if we targeted glucose or insulin perhaps we would have a new treatment for diabetes. What about tumor cells? I'm not sure about the details, but let's say a certain enzyme is released in areas of rapidly dividing cells, we could target the blood cell to dissolve the cells releasing the enzyme... I would have to do more research.

Recombinant B cells with a Wider Vision
A few months ago I read a few articles about engineering cells to incorporate unnatural amino acids (by this I mean synthetically-created amino acids that are not one of the traditional twenty) into their proteomes. For this process, an entirely orthogonal tRNA-codon-aminoacyl-tRNA synthetase system is introduced into host cells. The following article is a really good review about the subject: http://www.nature.com/nrm/journal/v7/n10/abs/nrm2005.html. Of course, there are a variety of applications that follow from this idea, but one in particular that intrigued me (I may have read about it as a potential application somewhere, but I don't know if any group has tried it yet) would be to design B cells to enable them to incorporate certain unnatural amino acids into the genes that are translated into antibodies. Already B cells have the capability to make antibodies that target a vast repertoire of microbial/pathogenic ligands through VDJ gene splicing, but introducing alternative amino acids would expand this repertoire even more, perhaps making it possible for the resulting antibodies to recognize a wider range of pathogens. -Ariana

CVL: Looking at the idea, the incorporation of non-natural AAs could result in an immune rejection. However, for antibody production in, say, hybridomas, this would be a great asset! That or maybe a cell-free system.

This may not be what you were talking about exactly, but Annelise Barron here at Stanford engineers peptoids, which are things that look like amino-acids but have their functional groups coming off of a different place. -Isis

The thought of immune rejection had crossed my mind, but if the antibodies were isolated and processed into a vaccine, would that render the vaccine unusable by causing an acute hyper-rejection rather than the normal immunostimulating response? When I first thought of the idea, what initially came to mind was as you said--hybridomas--for the production of monoclonals for use in Westerns, ELISAs, etc. This might be especially useful if we were to try to produce antibodies that have been problematic in industry due to low stability and added, say, codons that code for PEGylated or D amino acids into the antibody genes to increase the antibodies' half-life. -Ariana

Staving off Global Warming
As it becomes clearer that global warming is a product of human activities, scientists are growing concerned that levels of warming may reach a threshold of catastrophic positive feedback before we can curb our greenhouse gas production. As such researches are looking for ways to temporarily relieve the situation and buy time for later innovations that will solve the problem of greenhouse emissions. Popularized ideas include installing giant solar screen in space that will cast the Earth in partial shadow and spraying sulfate particulates into the upper atmosphere to reflect sunlight. An idea that I have is to engineer cyanobacteria, such as algae, to express artificial chlorophylls that absorb all across the EM spectrum, instead just in the green portion of the visible light band. Not only would these cyanobacteria absorb sunlight and help ameliorate warming, but they would also be able to better convert CO2 already in the atmosphere into glucose and other organic carbon compounds. A first step for iGEM would be to try to come up with artificial chlorophylls that have differing sizes of resonant regions (i.e. conjugate pi bond systems) so that they absorb in different regions of the EM spectrum.

Another thought came up as I wrote this: maybe it'd be even easier just to engineer cyanobacteria to produce more chloroplasts? In a feedback loop, more chloroplasts means more glucose production, which can be used to feed the bacteria who need more glucose to produce more chloroplasts. This project may be more feasible for the iGEM team than the above idea. -Mark

What if we separated the project to accomplish both? One could target a way to increase chloroplast production, maybe by incorporating the genes from a cell that divides quickly like an RBC, and another work on integrating the genes for a greater wavelength absorption. These we may need to engineer ourselves, but could we use what is already in nature? I wonder whether different plants and bacteria absorb different wavelengths already. For example, do red algae absorb a different spectrum that blue/green algae?...Just a thought (Suzie) Oh! and if we could do both of these, maybe we could eventually incorporate the final product to be those other organic compounds..maybe to create bioplastics or something.

As to engineering chlorophyll to accept a wider range of wavelengths, here's an article I read a while ago about genetically modifying GFP to get different absorption spectra: http://pubs.acs.org/doi/abs/10.1021/jo026570u. The group relied on a fascinating technique involving the addition of orthogonal amino-acid/tRNA systems so that the resulting GFP would have synthetic amino acids with different absorption properties. Could we use this principle to modify these photosystems? -Ariana

Isis Trenchard 01:39, 22 January 2009 (EST): I think this is a really interesting idea and I have a few comments/ideas.
 * 1) First, to make chlorophyll absorb different wavelengths, we would have to modify the chemical structure which conveniently has already been done by nature. There are a bunch of photosynthetic pigments that cover most of the spectrum.
 * 2) I think what would be interesting would be to try to express these pigments in not-native hosts. Like have a green algae express a red algae pigment thereby expanding its photosynthetic range (?) (note: expression of the pigment doesn't really mean it will increase photosynthesis because it would have to link in with the endogenous photosynthetic machinery... its hard to tell if that would happen on its own or not.)
 * 3) Major problem: the pathways to synthesize these molecules are complicated and require multiple enzymatic steps. Take chlorophyll biosynthesis for example. This makes it really hard to just transfer the pathway into a new host
 * 4) (presentation idea?!) It might be interesting to see if there is much overlap between the biosynthetic pathways of the different pigments... that way we may only need to introduce a few enzymes to get pigment expression. It is also important to check if the enzymes are even clonable.

Chris VanLang Good search Ariana. Can anyone find an example with editing the chloroplast absorbing units? Unlike GFP, chloroplasts are made with different types of chlorophylls. How would you then expand the range of absorption. Also you should consider how the energy cascades to generate sugars.

Check out this article: http://www.cell.com/current-biology/abstract/S0960-9822(08)01680-1. It's about reducing global warming by bioengineering more reflective plants; I saw it as a link from an article from today's NY Times--seemed kind of relevant to this post. -Ariana

Altering lengths of the reproductive cycle of various lab organisms
Yesterday, during Feng's presentation, he mentioned that popular lab organisms such as E. coli, S. cerevisiae, cyanobacteria, and green microalgae all reproduced at different rates. One of our considerations is whether we would have enough attempts to complete our project given the frequency of reproduction for a species, which is a reason we probably won't be using microalgae. What if we were able to make S. cerevisiae, cyanobateria, or green microalgae reproduce at faster rates? This will help solve problems in the sense that it will reduce the waiting periods for scientists all around, reducing (possibly precious) time. Scientists have split the cell cycle of a eukaryotic cell into the resting phase, interphase, and metaphase. What if we could identify the biomechanical pathways that a cell uses to trigger interphase and tamper with the regulation of various key proteins? The G1 checkpoint is a control mechanism that tells a cell whether or not to enter the S phase, where its genome would be duplicated. It is often the "rate-limiting step," if you will, of the cell cycle. Is it possible to tamper with the inhibitors that restrict a cell from entering the S phase? (Bobby)

Along the lines of iGEM projects, if we were to do this would we couple it with another project, such as taking the faster growing algae and simultaneously trying to get biofuel production or would it stand on its own as a project???

Would it not be more challenging (and thus more rewarding) to tackle an organism that typically has a slow rate of growth? One such example with biofuel and biopharmaceutical value would be Streptomyces -CVL

Stanford Research
http://news-service.stanford.edu/news/2009/january14/med-aging-011409.html Above is a link to a brief srticle on some research with aging.. just some cool connections of biological pathways

http://news-service.stanford.edu/news/2009/january7/cancer-010709.html Another cool link