Tatiana

Hello I'm Tatiana, or Tati for short. I'm from Dover, MA; little more than 30 minutes from Boston. I'm 15, a rising sophomore, and I stumbled upon this camp due to its good reputation while looking for biology-related camps online. I love science because it helps me understand everything around me, and its constantly subject to change and improvement. I'm especially interested in genetics because... it's just really cool, and there's still a lot about it we don't understand. As for sports and hobbies, I love to read and learn independently. This past year I participated in track and field for the first time. Having just completed my freshman year, I've taken two semesters of standard biology in school. I look forward to these next few weeks in camp!



Research Project: Cyanobacterial Energy




 * Problem:** Fossil fuels have been the main source of energy around the world for decades. These fuels, such as oil and coal, pose several problems. They cause pollution which contributes to the greenhouse effect and thus global warming, and they are also non-renewable; we will soon run out of readily available fossil fuels. Alternative energy sources have been developed, such as solar, wind, hydropower, geothermal, nuclear, etc. Bioenergy, however, is the only type of energy that has been able to be used as fuel in current vehicles. Current biofuels are expensive and unable to compete with traditional fuels. Scientists have thus turned to synthetic biology to produce more cost-effective alternatives.


 * Competing technologies and their downfalls:**


 * ** Biofuels from crops: **These are produced from fermentation of the starches and sugars in crops. Crops are costly, in resources and in money. It takes land and water to build them. Deforestation is becoming a problem as forests are cleared to provide this land. Many people also believe that these crops should be used as food sources, not as fuel sources. Using crops to produce biofuels raises economic, ecologic, and ethical controversy. Cyanobacterial energy production eliminates these problems.


 * Solution:** Cyanobacteria are simple prokaryotes that produce a variety of chemicals that can be used as eco-friendly, sustainable fuel. While these are produced naturally, the efficiency of their production is inhibited by naturally limiting factors. Synthetic biology has allowed the modification of these organisms to maximize the production of these fuels.


 * Options:**
 * ** Hydrogen: ** Cyanobacteria may produce hydrogen through two different types of enzymes; hydrogenase or nitrogenase.
 * ** Nitrogenase: ** Heterocysts are bacteria that fix nitrogen. In their nitrogen-fixing processes, they use nitrogenase and produce H 2 as a byproduct. This fixation occurs in an anaerobic environment, which synthetic biologists can produce by inhibiting PSII in these bacteria. The problem with this type of H 2 production is that the H 2 is quickly consumed by an uptake hydrogenase. Biologists are working on engineering a mutant which cannot recycle the hydrogen it produces. Another downfall of this method of production is that it uses a considerable amount of ATP. Hydrogenase presents another, more efficient method of production.
 * ** Hydrogenase: ** Bidirectional hydrogenases naturally found in many bacteria can either oxidize or produce H 2. The problem with this enzyme is that it is intolerant to oxygen, and so oxygen must be constantly removed along with the H 2. To combat this obstacle, certain attempts have been made to introduce enzymes which are less oxygen-sensitive to these bacteria. Another challenge of hydrogenase is its necessity for electron donors which cannot be met through natural metabolic processes of the cell. Synthetic biologists are working on directing electron flow away from other metabolic processes and towards H 2 production
 * Hydrogen is used in fuel cells, producing energy when combined with oxygen. Its only byproduct is pure water.


 * ** Ethanol: ** Ethanol can be produced through fermentation. Previously, it has been harvested from crops. This is a controversial practice, as crops are food sources. Cyanobacteria are not food sources, and they ferment naturally when in the dark, unlike crops. Ethanol production occurs through a series of enzymes. The enzyme PDC converts pyruvates to acetaldehyde, which is in turn converted to ethanol by the enzyme ADH. This production is generally minimal, as it is limited to what the organism needs. Synthetic biology has allowed the engineering of strains that can produce greater amounts of ethanol through the overexpression of relevant enzymes. Ethanol is useful in powering cars; it can be mixed with diesel and used in diesel engines without their modification.




 * ** Butanol: ** Butanol has a higher concentration of energy than ethanol, closer to that of gasoline, and so may be seen as a more favorable alternative. Butanol can be produced through two distinct pathways. The synthetic 2-ketoacid pathway uses intermediates from amino acid production pathways. The intermediate, 2-ketovalerate, is decarboxylated and thus turned to 1-butanol. An alternative pathway, the coA-dependent pathway creates butyryl-CoA from acetyl-CoA and then reduces butyryl-CoA to 1-butanol. This pathway does occur in nature for the production of butanol, along with ethanol and acetone. Introduction of certain enzymes allowed synthetic biologists to concentrate this production, resulting in bacteria which create an average of 20 mL/day of butanol. Butanol is produced directly from CO 2 . Butanol can be used in petroleum engines, or mixed with diesel to be used in diesel engines.




 * ** Photanol: ** Photanal is the combination of chemiotrophic organisms and phototrophic organisms to create “photofermentative” metabolic pathways in the resulting microorganisms. Photanol may significantly increase the production of biofuels through the use of microorganisms e.g. cyanobacteria. The only products consumed in this system are H 2 O and CO 2.
 * ** Phototrophs: ** Phototrophs are organisms which use energy from the sun’s light (photons) to power metabolic processes. One of these processes is the production of different types of C 3 sugars during the Calvin Cycle of photosynthesis. These C 3 sugars are used by these organisms in subsequent anabolic processes.
 * ** Chemiotrophs: ** Chemiotrophs are organisms which obtain energy through oxidation of organic and inorganic compounds in their environment. In chemiotrophs, the same C 3 sugars produced by phototrophs play a role in catabolic processes. Chemiotrophs often break more complex sugars down into these C 3 sugars, and then further degrade the latter into CO 2 under aerobic conditions, and other products under anaerobic conditions.
 * ** Combining the two: ** synthetic biologists are working on engineering a combinations of phototrophs and chemiotrophs. An organism such as this one would, using phototrophic systems, be able to produce C 3 sugars using only sunlight, water, and CO 2, and subsequently use chemiotrophic systems to these sugars into products that can be used for as biofuels. The only byproduct of these processes would be O 2.



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Design Project: Polypropylene Biodegrading Bacteria


 * Problem:** Plastics are unable to biodegrade because they do not occur in nature. This means that no microorganisms have had the opportunity to evolve to break them down. This is a problem because plastic products remain in our environment, posing threats to wildlife.


 * Solution:** As there are no natural organisms which can break plastics down, my bacteria will be genetically modified to break down the polypropylene into its constituent propylene.


 * Competing technologies:**


 * ** Biodegradable plastics ** have been created and are currently in circulation. However, they are made of organic materials, which must be taken from crops. Additionally, disposal of biodegradable plastics is tricky. They cannot be recycled along with other plastics, as they could contaminate them. These plastics are meant to be composted, but would take around 2 years to decompose in the average household compost.


 * ** Recycling ** is another option, but poses many challenges. In fact, plastic is one of the most difficult materials to recycle. Different types of plastics cannot be recycled together, as they create structurally weak plastics. Additionally, plastic often takes enormous amounts of energy to recycle, as it must be melted down completely. This energy is produced through the burning of fossil fuels, harming the environment.


 * Some biologists have ** selected for bacteria, ** separating the strains which are better able to break down plastic in succession until they had forced the evolution of strains which biodegrade plastic in various conditions. There are various problems with this proposed solution. It is not efficient and often the bacteria cannot act unaided by other processes. Certain bacteria require that the polypropylene must be blended with other substances, such as starches, or requires various types of bacteria along with carefully maintained conditions to biodegrade. Additionally, the traditional biodegradation proposes the breakdown of polypropylene into products that include CO2 and, under certain conditions, CH4 (methane) and H2S (hydrogen sulfide). CO2 and CH4 are both greenhouse gasses, and H2S is corrosive and poisonous. None of these compounds are particularly useful.

**Advantages of propylene as a product:**


 * Polypropylene is generally a product created from fossil fuels. The processes used to gain these fossil fuels is not ecofriendly, and the fuels themselves are not sustainable. If we are able to reduce polypropylene back to its constituent propylene, we can use the product to recreate propylene without using more resources.


 * Propylene is not only used in the creation of polypropylene; a few of the products of which it is involved in the production of:
 * 1) **Acetone:** is a solvent and common household cleaning agent
 * 2) **Phenol:** is used to create precursors to various plastics. It is also an antiseptic and is commonly used in the production of cosmetics**.**
 * 3) **Isopropanol:** is used as a solvent, in disinfecting pads, and has various in labs.


 * My bacteria:**

My bacteria would have to be able to detect the presence of polypropylene compounds, and secrete, in response, something that would cleave the carbon-carbon covalent bonds that link its monomers.

Very few methods exist for severing these bonds; they are very stable. This makes sense when we consider that plastic is meant to be durable. One possibility that I considered was a modified endonuclease.

Endonucleases generally cleave covalent bonds in the backbone of DNA. NEases are endonucleases that cleave only one side of the strand of DNA. A nuclease like this one would be ideal for breaking the single-stranded polypropylene molecule. Certain endonucleases cleave these covalent bonds by inserting a covalent intermediate- a compound which goes between the phosphate and sugar compounds to break the bond. In DNA, this compound would be a nucleophile. These enzymes cleave at the right spots by identifying the designated base pair combinations at their recognition sites. Two major modifications would have to be made to this endonuclease. Firstly, the recognition site would have to be built to recognize the CH3/H patterns running along the polypropylene and attempt to cleave at the C-C bonds between them. Secondly, the covalent intermediate would not be a nucleophile, but a transformation metal. The insertion of a transformation metal turns the highly stable C-C bond into a far weaker C-M-C bond, making the carbon bonds liable to break under reasonable heat pressure.

Another possibility is the integration of hydroxyethylphophonate dioxygenase (HEPD), a rather unique enzyme that breaks a carbon-carbon bonds using oxygen and ferric superoxide. However, it is uncertain whether this compound would work similarly in polypropylene.

[] [|http://en.wikipedia.org/wiki/Plastic#Polystyrene] [] [] [] [] [] [] [] [|http://en.wikipedia.org/wiki/Restriction_enzyme#Recognition_site] [] [] [] [] []