Deepti

-Tenth Doctor
 * Hello! Oka-*nauseated expression* New teeth. That's weird. So where was I? Oh, that's right- Barcelona! **

So, I'm Deepti Kamma, almost 16, and as you can see, absolutely obsessed with Doctor Who (and British shows in general). I was a sophomore last year, because still don't want to accept the fact that I will be a junior next year (And no, this is not denial….And I am not in denial that I am in denial…Hush now). I was born in India and came to America when I was three. I have lived in Massachusetts for around 12 years now. I go to Norwood High. I am here at BLI because I wanted to expand my knowledge of science. (*Broaden your minds* as Professor Trelawney would say…I'm a Potterhead as well) In school, it's all the conventional side of science. But here, in BLI, I have the opportunity to see an entirely different, wonderfully new side of the subject. The beautiful thing about science is its variation and the subject itself is so multi-faceted. Any topic you take is so detailed and leads you on other paths. My interest in science first started when I was around 4 or 5. My mom used to work in the labs at Dana Farber Cancer Institute and we would often go and visit her. I fell in love with the white countertops, the bottles containing various fluids, the centrifuges twirling away small vials. It was there I got my first look at science in real life and I swore that I would work in a lab when I grew up, that I too would wear the clean white lab coat. And as I advanced in my academics, science was always my favorite subject. I could have a headache through Algebra and English, but the minute I walked into the labs, I felt okay. I took Honors Biology in freshman year, and Honors Chemistry last year. Next year, I will takes Honors Physics and AP Biology. I also plan to take AP Chemistry and Anatomy in my senior year. In my future, I would like to work in the research field. No matter what I do, I know that I will always have my passion for science, and hopefully, that will take me to many places.

Speaking of places, I love traveling. On par with science courses, I absolutely love history as well. I have tons of history books (that weigh a ton), and often read of them when I can. (Yeah…I'm that person). I wold like to travel the world. And not just to France and China and Australia, but Kenya, Serbia, and New Zealand, Mongolia, It is my life goal to see every country in the world (but not just on a map). I mean to visit every nation. Yeah, sounds very ambitious, but that is what makes a goal a goal. So other than dreaming and planning future trips, I like to read (I love reading, I can't get enough….Siriusly, if there are letters on a page, I will read them…). I also like to write and draw. I have many obsessions in my life. My mind is roughly divided into many parts, each side constantly thinks about its designated topic. I am absolutely positive that the portion of my brain originally designed to be Math has been taken over by the portion of my brain that memorizes random stuff. (I can recite the entirety of the Lord of the Rings movies right now). I completely obsess over Harry Potter, BBC series Sherlock, Lord of the Rings, Doctor Who, tennis (Professional tennis is the best, though I am absolutely terrible at tennis in real life), Coldplay, British stuff, I should mention Doctor Who again because...Wibbly Wobbly, Timey Wimey stuff happened, and so many more…*Oscar music swells up in the background* I would like to thank the Academy, the library, my crazy friends at the lunch table, and the Internet for these obsessions...

It might surprise you that I have never done anything surprising in my life...Wait that was pathetic, Umm...I really really like memes and puns. Especially puns. Siriusly, it's not even like 'Oh, that was clever! And mildly funny!" I laugh at puns. Like falling out of my chair during Chemistry. They're the best. Here's one:

I would tell you a chemistry joke, but all the good ones Argon.

Yeah, that was pretty bad. Sorry... =<><><><><><><><><><><><><><><><><><><><><><><><><><><><>= =__ **Research: Artemisinin** __= There are an estimated 400 million reported cases of malaria, which result in around 1-3 million deaths. Malaria kills more than 2,000 people a day. Many of the victims were children in Africa, often under the age of five. This mosquito-borne infectious disease greatly affects the subtropical and tropical climates of the world, with the multitude of cases in sub-Saharan Africa and south Asia. The warm climate and humidity provide an excellent habitat for the mosquito larvae. Unfortunately, these areas are also the developing countries of the globe.
 * The Issue **

The people in these regions are often hard pressed for adequate medical protection and they cannot afford the effective vaccines, and thus, many meet their ends. However, there is hope. There have been various treatments and vaccines, most notably quinine and chloroquine. Unfortunately, evolution kicked in. Various strains of mosquitos have developed resistance to the oft used antimalarial drugs. Enter to the global medical stage: artemisinin. In nature, artemisinin is found in the sweet wormwood plant, // Artemisia annua // (pictured below). The compound is then isolated and then manufactured as a drug. Recent studies have displayed that the antimalarial drug artemisinin has had a nearly 100% success rate in its patients. All point to artemisinin as the miracle drug of malaria. But just how does it fight the mosquito parasite? It goes into a telephone booth and changes- No. The process is quite simple. The drug basically releases oxygen based free radicals that target the mosquito parasite in the red blood cells. After the WHO (World Health Organization) declared artemisinin as the most effective weapon against malaria, ACTs (artemsinin-combination therapies) have become the standard treatment for the //P. falciparum// strain of the parasite. But there is a catch. A slight wrinkle in the silk. It has been mentioned earlier that artemsinin needs to be extracted from its natural source, the sweet wormwood. This means that the entire, global supply of the most effective drug against malaria is dependent on a crop that is temperamental, picky, and only able to grow in certain regions. Certain years may yield a plentiful harvest, and people are able to get their hands on treatment. But what about a decline? The prices would rise, and the people would have to suffer. The steady call for artemsinin for treatment has been pressurizing the delicate plant. The rapid increase of demand has left the supply exhausted. Herein lies the problem. We can no longer be reliant on a specific crop that produces that little amount of artemisinin. And it is here that we turn to the area of miracles: Synthetic Biology.
 * Miracle Plant **
 * Problems With Natural Synthesis **

The Institute at OneWorld Health and PATH’s Drug Development branch launched the program to synthesize a new source of artemsinin. The UC Berkeley team headed by Jay Keasling were also partnered with Amyris Inc and the pharmaceutical Sonafi. Extensive funding from the Bill & Melinda Gates Foundation were crucial to the research. These groups invested copious amounts of capital and effort into the ambitious project. Due to the relative new technologies of synthetic biology, there was not a great chance that the project would succeed as hoped. The doubts were replaced by relief soon after though. Jay Keasling and his team announced initial success in their endeavors in 2003. They figured that implanting genes into //E. coli// bacteria would enable them to produce a precursor to artemisinin, called amorphadiene, or artemisinic acid. These genes were obtained from three distinct organisms, among them yeast and the //Artemisia annua//. The team was able to make the //E. coli// bypass its natural metabolic pathway, in favor of the transplanted pathway. The product, the artemisinic acid, is then chemically transformed into artemisinin. The process can be seen below. The gray box represents the various metabolic pathways of the bacteria, eventually producing the artemisinic acid.
 * Here Come the Heroes **
 * The Process **

It is much cheaper, and far more efficient, to have the bacteria produce the precursor and turn the acid into artemisinin than it is to naturally extract the artemisinin from the plant. Thus, it is far more affordable for the impecunious families of the devastated victims. No longer is the global supply of artemisinin from the untrustworthy plants. Pharmaceutical company Sonafi has become the first producer of the semi-synthetic method of producing artemisinin. Furthermore, the process has been approved by the Pre-qualification of Medicines Programme (PQP), a subgroup of WHO. Sonafi plans to produce 35 tons of artemisinin this year alone, and roughly 55 tons this following year. This translates to an estimated figure between 80 and 150 ACT treatments. The company also announced that roughly one-third of the world's artemisinin would be synthetically produced this year. It was officially released April 11, 2013. Jay Keasling and his team at UC Berkeley subsequently launched Zagaya (“Spear”) to ensure that artemisinin is given at affordable costs to all people in the regions. Artemisinin is a part of the isoprenoid family. Isoprenoids are organic compounds composed of two or more hydrocarbons.
 * Success and Recent Advancements **
 * Ramifications **

The other members of the family are used in combating other diseases, such as the anti cancer drug taxol. Such, the potential mass production of Artemisinin through the pathways of // E.coil // offer the same solution for these applications. The methods used by Keasling’s team should also apply to the other members of the isoprenoid family. One such example is the potential anti cancer drug, Eleutherobin, which is now found from a rare source. (in a rare form of marine coral). With the pathways used for the bacterial production of Artemisinin, the same can be used for that drug. Keasling has succeeded in opening the floodgates, by refining the techniques of synthetic biology and applying them to advocate for the amelioration of the world. After all, that is what science is for, is it not?

In his own words: Jay Keasling and his team talk about the project and what it means to help the world through science. [|Watch] If you can and are willing, please help Jay Keasling and his endeavors for a better future through the foundation Zagaya [|here] =<><><><><><><><><><><><><><><><><><><><><><><><><><><><>= =__ **Synthetic Biology Application Design** __= = = Lyme disease (Lyme // borreliosis // ) is the most prevalent vector-borne disease in the Northern Hemisphere. The infection is transmitted from ticks of the genus // Ixodes //, and most oft by the black legged tick ( // Ixodes scapularis // ). There are approximately 2, 500 cases of Lyme disease reported in the United States annually. The demographics with the highest percentage of diagnoses- Children (aged 5-14) and Adults (aged 45-54). == Lyme disease is not at all like wine or awesome grandparents. It does not get better as time goes on. In fact, it worsens...tenfold. People infected with Lyme disease must get diagnosed and treated immediately. In some cases, late treatments are not effective. Lyme disease is particularly terrible, with an assortment of symptoms ranging from chronic pains to fever, flu-like illnesses, and even paralyzation in some cases. The infection is sort of like a pickpocket, displaying various, distinct ailments that often have no relation to each other. If the infection is left alone, these manifestations augment and increase in severity. The worst case scenarios occur. Therefore, with Lyme disease, it is crucial for early detection and treatment. While treatment is easy, detection is a little harder to accomplish. My bacteria will sense the foreign substance, i.e. the pathogen //Borrelia burgdorferi// (seen above) that initiates the Lyme disease infection. Subsequently, the bacteria will glow, as it expresses the GFP in its modified genes. This allows the easy and simple detection of the //B. burgdorferi// which is the hallmark of the manifestation of Lyme disease, and thus, the person infected is able to ensure early treatment. This will save the victim a multitude of both money investments and pain from symptoms that are involved in the late stages of Lyme disease. Studies are being conducted to understand the vector and host transmission of the disease, in order to formulate a better vaccine of some sort. Research is also being conducted to study exactly how the Borrelia burgdorferi combats the human immune system, such as the use of the immunosuppresive tick salivary protein Salp15. The presence of a bulls eye rash (erythema migrans) is a common detection method of Lyme disease. However, not many people display the rash. Blood tests are another possibility for diagnosis. The blood tests test for the detection of antibodies to Borrelia burgdorferi. However, these tests are not accurate in the early stages. It is difficult to diagnose Lyme disease through the standard tests. The negative result on such tests does not entirely rule out the possibility of acquiring lyme disease. And the person positively diagnosed may not show visible symptoms. Such, there are no clear and accurate, and most importantly, __early__, diagnostic tests for Lyme disease. The pathogen is the spirochete //Borrelia Burgdorferi//, the spirochetes have a unique cell surface, giving the bacteria a specific, unique trait to target. The //Borrelia Burgdorferi// have specific outer surface proteins under the category of Osp. The expression of OspC is particularly important in the transmission of the Lyme disease from the tick to the human. OspA and OspB are by far the most common, but there is an increase in the production of the OspC protein after the infection. The bacteria I would genetically modify is //Staphylococcus epidermidis//, which is a Gram positive bacterium that is naturally found on skin. Ergo, it not usually pathogenic, but patients with weak immune systems should take precautions. Also, people with surgical implants and prosthetics should take warning as well, as S. epidermidis has a tendency to form biofilms on any plastic device.However, //S. epidermidis ATCC 12228// is a strain that does NOT produce the biofilm complications. And it is this specific strain of the bacteria that will be used in the project. The bacteria always had the capability to sense the foreign compounds and degrade them. [|See] here under the Xenobiotics Degradation and Metabolism. This shows that the bacteria is naturally capable of recognizing a foreign pathogen and, possibly, even degrading it. Thus, we can modify so that the bacteria would sense the presence of the pathogen //B. burgdorferi// and express the GFP. The green fluorescent protein would then light up under an ultraviolet (UV) light. This is the signal, which means that the person has been infected with Lyme disease.
 * The Issue **
 * Why? **
 * Your Mission...You Should You Choose to Accept It... **
 * Not-Cool-Enough Existing Technologies **
 * The Weapon **
 * The General Process **

As for the gene that would be used in the detection, I would use the pGLO plasmid. (below) This particular piece has often been used in various experiments and has shown efficient and adequate results. The GFP is a part of the pGLO plasmid. Thus, the pGLO plasmid would be transplanted into the //S. epidermidis//, to ensure that the code for the GFP is inside the bacteria. The promoter for the plasmid translation would be launched by the detection of the foreign substance //B. burgdorferi//. And thus, the GFP would be expressed. While that looks simple enough, there was a little problem that arose. The GFP reporter gene can only be expressed in the presence of arabinose, a sugar. However, we are able to overcome that setback by using synthetic biology once again. We can put in two systems that interact with one another, one to produce the arabinose, and the other to consequently express the GFP. Therefore, the device would look something like this:
 * **Presence of Borrelia burgdorferi** || **Gene Expression of GFP** ||
 * 0 || 0 ||
 * 1 || 1 ||
 * A Closer Look **
 * A Slight Complication **

Sensor, detecting the B. burgdorferi => Launches the promoter that expresses the gene that produces the arabinose => The presence of arabinose will allow the GFP is to be expressed => The second promoter begins the expression of the pGLO plasmid, and the GFP is expressed.

It would be especially fine for the system to function as a bacterial Toggle switch. This would mean that the gene, once expressed, would stay ON continuously until turned off by an outside force. This would allow the person using the product to have enough time to observe the glowing bacteria. My bacteria would be far more advanced than the existing technologies. One main advantage is that it offers an early diagnosis test. Rather than wait a month or two, the person can now do a Lyme disease test immediately and effectively. Also, the plan is to put the bacteria into a spray bottle or lotion of some kind. This is helpful because people would not have to come into the doctors' offices to have the tests done. They can do it anywhere and everywhere (With a fox, In a box, etc.) Just make sure there is a UV light source! As stated before, time is of the virtue for Lyme disease treatment. And the early bird gets to enjoy life. **Possible Complications** // S. epidermidis // is a strain of bacteria that is found naturally on human skin. Ergo, it should have no ill effects. While some strains have been known to cause complications by producing biofilms on implanted plastic devices, the particular strain // S. epidermidis ATCC 1222 // 8has not been shown to cause biofilms. There should be no complications for people who have protheses of some sort. Take note, the Lyme disease pathogen is clever and evil. It has outwitted the human immune system many times. There is no guarantee that the bacteria would be able to detect the // B. burgdorferi // at all. However, this is why we need to instill more effort into studying this situation. The only way to effectively test the diagnostic test would be to enlist peopel who have confirmed positive for Lyme disease. There should be no complications from the GM bacteria, as they are naturally found on human skin. There are no discernible safety concerns resulting from the // S. epidermidis. // Further research is definitely needed, and urged.
 * Advantages **