Prakrithy Pradeep

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Introduction




Prakrithy.jpg


I am Prakrithy, a student at Srishti School of Art, Design and Technology. Now, you might ask what an art and design student finds so interesting in iGEM. The answer lays in the fact that I studied Science (Physics, Chemistry, Maths and Biology) in class 11 and 12, at National Public School, Koramangala, Bangalore. Courtesy my biology teacher, who taught us the basics of Genetics, I became very interested in the subject. And it is this interest that pushed me to this course, and competition. I don't remember all the details of those classes back then, but I do seem to have retained bits and pieces of it. But it's never too late to try to rectify those faults in memory, no?



24th May 2011 - A New Beginning


First day of IGEM...what do I say? I was disoriented at first...very disoriented. I mean a science classroom in an art college. I agree I might be stereotyping. I didn’t really know what to expect. Here I was, an art and design student doing a synthetic biology project.

Having studied biology earlier, especially genetics, (not in depth, but whatever CBSE had deemed necessary for their students to know) I remembered bits and pieces of our classes, in that dark classroom of my school. It surprised me that I’d begun this venture with a seemingly clean slate, surprised that I had not retained much of what I had studied earlier.

That’s where we began. A discussion on what we thought synthetic biology was. Awkward silences and many pauses. The ice had yet to be broken. New faces weren’t the issue, the foreign nature of the subject of our discussion was. So we plodded on. About genes, DNA, traits. Life. What form of life could be without form? A formless form of life? God? Plasma? Viruses? That opened us up. We discussed ideas, and concepts. And got our very first assignment! To think of the most insane form of life we could think up. Then was time for research. I researched synthetic biology, gene expression, DNA, genes, nucleic acids, formation of DNA, and a whole host of other random terms that hit me at that time that I don’t seem to have retained anywhere my head (Note to self: Must remember to go check up all those again!!). A tutorial on scientific jargon later, we were dismissed for the day.

Totally blank, and honestly, a bit lost, to thinking and innovating. All in a day's work, I guess. But I do know this for sure, I am definitely looking forward to where we will be going from here.




An Idea


Spicy Bacteria.jpg


Spices like chillies & pepper feel "hot" beacuse they contain certain chemicals like capsaicin and piperine. Our body (mainly our mouth) feels a sensation of burning pain, as a result of these chemicals. Our sensory neurons contain a functional cDNA encoding for a capsaicin receptor. The receptor is a non-selective cation channel that is also activated by increases in temperature. Similarly, other spices will all have acting chemicals, mostly organic. Each spice will also have corresponding receptors, or mechanisms, to induce responses.

Most of the spices and condiments used are plant parts. This implies that they do contain cells (living or dead. Cells contain DNA, which would be responsible for the production of the chemicals responsible for the flavours of the spices. We would be able to identify the exact DNA sequences that code for the necessary chemicals by DNA sequencing. Once the sequences are identified, they can be introduced into the DNA of a suitable, safe bacteria.

This bacteria would produce the different chemicals (for the spices) in certain fixed quantities when introduced into the food. This would reduce the chances of dishes getting "spoilt" due to the usage of incorrect mixtures and quantities of spices.

This idea is what I call the "spicy bacteria".




Day 2 – 25th May 2011


After discussing each of our ideas for new life forms, we researched DNA extraction and BioBricks. After breaking for lunch, we extracted our very own DNA, and buried it in a way that we chose!!!

In a few very simple steps, I’ll show you how to extract your DNA.

STEP 1: Gargle your mouth with salt water.

STEP 2: Empty the contents of your mouth into a test-tube.

STEP 3: Along the sides of the test-tube, pour liquid detergent.

STEP 4: After allowing the detergent to settle at the bottom, pour some chemist’s alcohol along the sides of the test-tube.

STEP 5: VOILA! You will observe a white cloud rising through the alcohol. That is your DNA.

Here's a photo of my DNA...


DNA.jpg


I chose to bury my DNA in the ground itself, at the base of a tree. I had two reasons for this. One, we are a part of nature, and that is where we end as well. So, why should my DNA be any different from any other part of me? Also, my name means nature, in most of the Indian languages (including Sanskrit). So i felt back to nature would be the most fitting way for my DNA to go.

I dug a small hole in the ground and poured the solution containing my DNA into it. I covered up the hole with soil, and marked the spot with a broken coconut shell, some twigs and leaves I found around. The markings were chosen in order to ensure that my DNA's "grave" would stand out. And i realized it wouldn't stand out especially not in the grassy, plant filled yard of our college.

Here's a photo of the burial site.


Burial.jpg




Day 3 – 26th May 2011


Today, we began with research into the equipment necessary for laboratories – a basic science one, and a microbiology one too. We considered the equipment we’d need for our very own microbiology lab. And we’re going to be building most of these. This task has been given out to certain groups of people. The group I am a part of is going to be making a desiccator and a laminar airflow cabinet. Our group discussed the equipment we’d chosen, studied its structure and normal construction. We also had to look at low-cost, high efficiency substitutes and alternate methods of construction for the very same equipment. We discussed all of that without coming to any concrete conclusions.

After lunch, our senior, Aaron, taught us how to make a microscope out of a webcam. All we need to do was open the webcam up, and reverse the lens. Fantastic, isn't it? We thought so too. But the only issue with this microscope was it's stability. The stability of our microscope would depend on the hand of the holder. From this issues, rose our next challenge. To design a stable, safe structure with adequate lighting, for "finishing" our microscope.


Webcam.jpg




Day 4 – 27th May 2011


Our day began with a few questions. I’ve put them down here, with my answers to each of them


1. What is life, according to you?

Life. Dictionaries define it as “the state of being which begins with generation, birth, or germination, and ends with death; also, the time during which this state continues”. To me, life is something you can’t define. Life is not something you can summarize in a few words, or sentences. Life is existence. But it’s also so much more.

2. Do you think you have the right to modify a living thing?

Every living organism has the right to choose how it lives. That in a way, denies us the right to choose how it lives by modifying it. But in a way, nature itself modifies it’s organisms, and if nature has the right, we should also be given the rights.

3. What is design according to you?

Design is innovation, or modification, to attain functionality, ergonomics and aesthetics.


These questions were followed by some research into cell structure, the difference between a prokaryotic cell and a eukaryotic one, the cell organelles and their functions, etc.

We also had to build the stable structure to hold our microscope. Our structure was ready in the morning itself. But we had issues coming up with a lighting solution. We discussed this and came up with a plausible, usable solution. After that we went about in our efforts to document the building of our microscope.

Lego.jpg




Growing My Own Bacteria


Bacteria, for growth, need nutrition, warmth and humidity.

I tried using an unconventional medium for bacterial growth - starch, water and curd.

I prepared the curd at home itself, using warm milk and a drop of curd.


Curd.jpg


I let the starch settle into a near-jelly form, and then added a drop of curd onto it's surface.

I am not sure if I will be successful or not, but it was worth a try.



Day 5 - 30th May 2011



Today, we watched the movie Gattaca (1997), in the morning. The setting of the movie, and certain aspects of the society depicted there, was familiar.

After the movie, we looked through Synthetic Biology for Artists & Designers. We also went through the parts offered by BioBrick, and were asked to come up with a new life form using the available parts.

The starch based medium seems to be good enough for the bacteria to grow, thought it does seem to be growing mould and fungi as well.




New Life Form?

I wanted to create a life form that was going to make cooking easier, and maybe healthier also.

When I looked through the registry of parts, I found this particular gene sequence that coded for a protein that when metabolised would make everything taste better. BBa_J14012 is a BioBrick that codes for the genX protein.

I also found a BioBrick that was a nutrition promoter, BBa_J49006. This is a bad food dependent promoter. Hence, it promotes the nutritional value in bad foods.

So if this two sequences were introduced into Cyanocobalamin, which help in the production of vitamin B12 during the process of digestion, the overall effect would be very highly beneficial.

The modified bacteria could be introduced into foods of all kinds, hence, increasing their nutritional value, while also improving their taste.




Day 6 – 31st May 2011



Our group had already completed making our microscope, except for a stable lighting source. We finally decided on fairy lights, combined with a 9 volt square battery and a battery holder.

The rest of the day, we spent time working on the documentation of the making of the microscope.




Day 7 – 1st June 2011



Due to the poor health conditions of majority of the students, class was cancelled for the day.



Day 8 - 2nd June 2011



The morning was spent perfecting the microscopes, and we finally finished the lighting set-up for our microscope. We viewed a couple of specimens under the microscope. The following images have been captured using our microscope.


PaperFibre.jpg

The above image shows the fibres on a piece of newspaper.


FungalSpores.jpg

The above images shows fungal spores.


ButterflyWing.jpg

The above image shows the scales on the wing of a common garden butterfly.

I am also setting up a new bacterial sample, from water from a swimming pool. This one uses the sample (water from the pool), sugar, salt and chicken broth. Considering the fact that it contains chlorine, and shouldn't be allowing bacteria to grow, it'd prove the "safety" of the pool water.

Shivers (a movie directed by David Cronenberg) is about a doctor’s attempts to bring out the inner sexual animal in man, using a parasite. He fooled his co-workers, and sponsors, into thinking that he was working on creating an alternative to organ transplant, by using parasites. The doctor was unable to accurately predict what the modified parasite would do. This lead to the parasite spreading from his teenaged mistress to quite a few other residents of a “sterile” high-end apartment block, and spreading uncontrollable sexual desire.

This movie, to me, highlighted the unpredictable nature of the effects, the consequences of any modifications that we make in any organisms. It also highlights the unpredictability of the behaviour of the organisms. The behaviour of the modified organism in the laboratory is not adequate enough to predict its behaviour in the outside (real) world. The parasites modified an entire society and, in a manner, the entire purpose of a community.

How will this sudden change in the very purpose of their lives affect the community? Will it have adverse effects on their functioning? What about their environment? How will the delicate balance of nature be affected? Would it be affected? Who are we to change the very nature of the place we call home so drastically?

These are just a few of the questions that come to mind.



Day 9 - 3rd June 2011


Today we started the day by watching an interview of David Cronenberg. He spoke about issues he'd faced as a result of filming Shivers.

We also watched an interview of the famous physicist, Richard Feynman. He spoke of the necessity for us to understand that by knowing the name of something, we do not actually know it. His view on how the world works was quite interesting, but I do not find it as something I necessarily need to agree or disagree with. Everyone is entitled to their views, and that doesn't give anyone else the rights to credit or discredit them.

We also watched a few videos on the basis of life, and genetics. The videos also spoke about the history of genetics, and the principles of inheritance, as stated by Mendel.

Another important thought that came to mind today was the right of humans to modify organisms. I had earlier said, "Every living organism has the right to choose how it lives. That in a way, denies us the right to choose how it lives by modifying it. But in a way, nature itself modifies it’s organisms, and if nature has the right, we should also be given the rights."

Nature's modifications occur over millions of years. It's consequences have been experienced in smaller magnitudes over time. But would it be the same when we drastically cause changes, that have been happening over millions of years, in a matter of days or months? Again, the predictability of the consequences of these changes comes into question. Will their magnitudes be bearable? As of today, only God knows!



Day 10 – 4th June 2011


Cells are the very basis of life, and the basis of a cell, is its DNA. It was this we studied today. DNA. We studied mainly by watching videos.

We first saw a video on genes and how they are linked to chromosomes, how characters transferred from parent to progeny through their genes. The next video was about the discovery of DNA, its structure, and how it was accepted as the genetic material. The third and last video was about circumstantial and experiential evidence for DNA being accepted, among the scientific community, as the genetic material.



Day 11 – 6th June 2011


Today we studied proteins, how they are coded for by DNA, their structures, and their role in the phenotypic expression of genes. We also studied some chromosomal anomalies and how they were initially diagnosed and all the other history you could’ve asked for (pertaining to chromosomal anomalies and their diagnosis only).

We also contemplated multiple designs for the desiccator. A desiccator is meant to keep chemicals free from moisture. Since we needed an airtight container with two chambers (one for the chemical containers, and the other for the desiccant) allowing the passage of air between the two chambers, I thought that the design of a traditional Indian coffee filter was perfect.


IndianCoffeeFilter.jpg

Using the coffee filter as our main theme, and working on increasing the size of the entire unit, we came up with a design for it.


Dessicator-Initial.jpg



Day 12 - 7th June 2011


As most of our class had gone to SJP Road to buy the materials necessary for the construction of our lab equipment, class was scheduled to begin later post-lunch.

When I had gone to the market to buy the materials necessary to build the dessicator (two airtight containers, that would fit one above the other), I realised that my initial design would have certain flaws.

The dessicant would need to be recycled, by removing the chamber, and drying it. The dessicant chamber, being located below the chemicals' chmanber, would mean that it would prove difficult to remove the dessicant chamber without disturbing the chemicals.

Hence, I had to come up with a new design.


Image will be up soon!


Day 13 - 8th June 2011


Today was the day we started brainstorming. The class was divided into three groups of four, and got to work with a large sheet of paper, and some pens.


At Work PP.jpg

Below are a few ideas that our group shortlisted, and worked on.


HappyFeet PP.jpg


Blend In PP.jpg

The third shortlisted idea - "Morph" - would function like an audio visualizer, albeit a live, 3-dimensional one. It would respond to different frequencies, wavelengths of sound in a different manner, hopefully using light, and motion as its visible responses.



Day 14 - 10th June 2011


The day was spent preparing a presentation for the ideas selected from our brainstorming. For this, we also had to do deeper research on each of our ideas, and how doable they are.



Day 15 - 11th June 2011


We presented our ideas (Morph and Blend-In) to a few of our seniors and team-mates. We were asked to research futher into our ideas, and see how achievable our ideas were.



Day 16 - 13th June 2011


We watched videos on what genetics is all about, how plasmids are introduced into bacteria.

The following link was quite interesting:

www.youtube.com/watch?v=GNMJBMtKKWU

The next video we watched showed the origin of DNA recombinant technology, its progress during the following years, ita practical applications, and its usage in large scale.

We also discussed some of the adverse effects and legal issues that had arisen due to the large scale implementation of the same.



Day 17 - 14th June 2011


We looked through a few biology textbooks written and illustrated by artists.

We saw a few brilliant illustrations by Ron Estrine, Paul Slick, Masami Teraoka, Philip Kirkland, Diane MacDermott and many other artists.


Biology Today.jpg


You can find more of the illustrations at: 50watts.com/1163951/An-Artist-s-Interpretation-of-a-Flashback-Biology-Today-1

Inspired by the psychedelic illustrations we'd seen, we were asked to come up with illustrations of one of our ideas.

The below image is the digital version of my illustration and flowchart.


Ideas illustrated.jpg


Flowchart CamBac.jpg



Day 18 - 15th June 2011


As we started woking on the laminar airflow, we realised there were certain issues with it. And had to come up with solutions to the same.

IMAGE WILL BE UP SOON!



Day 19 - 16th June 2011


Today, we visited Vishweswariah Museum. This was fun and interesting.

IMAGES WILL BE UP SOON!



Day 20 - 17th June 2011


We have finally started working on the new design of the laminar airflow.

We spent the afternoon at a bio-symposium at National Centre for Biological Sciences(NCBS), in the Gandhi Krishi Vignana Kendra(GKVK) campus.

The focus of the Bio-symposium was on bio-mimicry, and robotics based on the same.

For example, a robot that would walk on water, like a water strider.

Water Strider.jpg


And, a robot mimicking a gecko.

Sticky Bot.jpg

We also got to hear an ornithopter specialist, and to see a demo of one of his own ornithopters.

Ornithopter.jpg



The next week


We finished working on most of the equipments.



12th July 2011


We started ideating on possible projects. A few of the shortlisted ones were Anti-venom bacteria and Zombie bacteria. Our class was spilt into two groups, and were to reserach further into this.

There are many different animals that are venomous, including arthropods, spiders, scorpions and snakes. We decided to mainly target snake venoms. In countries like India and Africa, the mortality due to snake bites were far greater than that in countries like the US. This is mainly due to the lack of medical facilities with the antivenom readily available.

Snake venoms are mainly of two types - Cytotoxins and Neurotoxins. These are further divided on the basis of their action. We found a few possible methods that we could use for this purpose.

Mongoose, and European hedgehogs are immune to certain snake venoms. If we were able to trace the gene sequences in each responsible for their immunity, and are able to introduce into bacteria, and make them somehow transmit it to the humans.

Also, the European common snake has toxins in its bloodstream that is analogous to viper venom. As a result of this toxin, the european common snake is immune to viper venom.

Or if we could somehow induce the production of antivenom (in bacteria, which would be present in our body) on contact with the venom.

We need to do more research, and find more information on this.



13th July 2011


We were told that we would be meeting Dr.Mukund Thattai, and presenting our ideas to him. We had to prepare a presentation for the same.


AntiVenomBacteria.JPG


ACh.JPG



14th July 2011


We were to finalise our presentation for our meeting with Mukund, which is going to be tomorrow.

We are working on it, making illustrations and so on.

A few of the illustrations are below.


Illustrations PP.jpg



15th July 2011


We met Mukund today. He was interested in learning our reasons for choosing design, and for our interest in iGEM. After the introductions, we were asked to put forward the ideas we had been working on.

Below are the main slides of our presentation.


Venom Prak.jpg


At the end of our presentation, he gave us some very valuable advice - to be ourselves, and to not try to emulate what any scientist can do. What we take to iGEM is our perspectives as artists, and that is exactly what sets us apart from the crowd, and that's something we should hold onto.


30th July 2011


I designed a few layouts for the iGEM wiki.


Prak Layout.jpg


This one was done by Achala and me.


Prakrithy Layout1.jpg



31st August 2011

Brainstorm of Soil Mapping

  • Urban Bacterial Theater
  • Desire Line Drawing
    • Capture the paths of people on a park using Stop Motion
    • Sample along those paths
  • Hospital Waste Samples
    • Human Parts thrown out back?
    • Nurse Costume
  • Family History
  • Super Hero
    • Saving the Day
    • Radiation / Mutation i.e. Spiderman, Incredible Hulk
  • Disaster Mapping
    • Fukishima, Chernobyl, Bhopal etc...
    • E-Waste Sites
  • "Space Dusters" / Space Crashers = Mediorite Landing
  • Retracing a walk
    • Recursion / Remembering
    • Gandhi Sea March
    • Silk Road
    • Ghengis Kahn
  • Topography / BioTrekking
  • Farmer / Drought / IR Mapping
  • Costume = Bullet Belt
  • Blood Soil
    • Conflict Areas / Borders
    • Israel / Palestine
    • Kashmir
    • Tropic of Cancer - Bhuj
  • Tea Plantation
    • Basket Costume for Collecting samples
    • Terroir
  • Ant Hills / Termite Mounds
    • Costume = A Bacteria Zoologist / Arcehologist
  • Paranormal Activity
    • Soil Ghost Hunters
  • Soul in the Soil
    • Graveyard / Tower of Silence
  • Sending Soil on a Journey
    • Put a potted plant on a train and take samples at each end
  • Soil Sadu
    • Ask for soil samples instead of alms
    • Wiseman / karma
  • Culture Soil
    • Compare different cultures / paint clothes
  • National PCR
    • Compare national data (GDP, GINI) with PCR data
  • Sunrise Sampling
    • Grab samples as the sun comes up across the world
  • Airplane dust
    • Collect samples on the plane
  • Sea beds
    • Since it is no ones land. International waters
  • Oil Refinery / Shipping Ports
    • Look for oil contamination / Map the flow of energy
  • Shadows & Soils
    • Microclimates on ONE site based on where sun hits or doesn't
  • Tracing the path of Ganga
  • Zoology of the Future
    • Junkyard is seperated out by object - sample each site
  • Old vs. New Airport in BLR
  • Oldest Building in BLR and site that is being built on now
  • Schools vs. Old Age Homes
  • Difference between "holy" soil & normal soil