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== About ==
 
== About ==
As amateurs/novices,we hope to bring our training in the arts and
+
We consider ourselves amateurs/novices within the context of the IGEM competition. Our endeavor as “outsiders” is to bring our training in the arts and design to synthetic biology. Over this summer, we learnt the tools and techniques of synthetic biology and developed a piece of life which reflects our concerns, namely, the cultural, ethical and aesthetic implications of Synthetic Biology. Using a DIY approach and getting our hands “wet” was a critical element in the learning process. This approach allowed us to engage in constructive discussions with scientists working in the field. Our construct synthesizes Geosmin, an enzyme normally produced by cyanobacteria and actinobacteria. The biosynthesis of geosmin from farnesyl diphosphate is catalyzed by a single enzyme germacradienol/germacrene D synthase. E. coli, does not bear a gene that codes for germacradienol/germacrene D synthase. We have expressed this gene in different strains of  E. coli, under control of the pTrc  promoter present in the pTrc99a vector. Geosmin is responsible for producing the earthy smell that occurs in the air when rain falls after a dry spell of weather.
design as 'outsiders' and (hopefully) critical thinkers to synthetic
 
biology, which, no doubt is a powerful tool and paradigm in looking at
 
the life sciences.
 
During the course of the workshop we hope to not only learn the tools
 
and techniques of synthetic biology and come up with a piece of life
 
which reflects our concerns but also use the process to engage with
 
the political, ethical and cultural implications of Synthetic Biology.
 
  
 
== People ==
 
== People ==
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[[File:Whiteboard.jpg|820px|none|Click for a closer look]]  
 
[[File:Whiteboard.jpg|820px|none|Click for a closer look]]  
  
-bacteria that prevents corrosion
+
Major Outcomes -
  
-Time keeper or clock
+
* [[Ideas for Bacteria.]]
 
 
-Combustible bacteria
 
 
 
-Related to weather - smell of rain
 
 
 
-Bacteria that is resistant to Scientific Probing/Instruments
 
 
 
-Mirror of bacteria
 
 
 
-Buoyant bacteria
 
 
 
-Interactive bacteria(painting)
 
 
 
-Another creature made from bacteria
 
 
 
-Bacteria and sound
 
  - Bacteria visualizations. (Both colour changes and 'choreographed' movement)
 
 
 
-Neuro transmitters- bacteria as sensors for emotions
 
 
 
-Glue
 
 
 
-Bacteria that detects cravings
 
 
 
-Magnetic bacteria
 
 
 
-Self mutating Bacteria
 
 
 
-Lie detector
 
 
 
-Bacteria creates an identity
 
 
 
-Bacteria becoming material on death
 
 
 
-Constructing a 'Bacterial Ecology'
 
 
 
-Bacteria that acts like oil
 
  - A lubricant
 
  - A liquid that can withstand high temperatures
 
  
 
* Facilitate a group of children to design their 'perfect creature' through visual/tactile media and then draw from these experiences and ideas to build another structure.
 
* Facilitate a group of children to design their 'perfect creature' through visual/tactile media and then draw from these experiences and ideas to build another structure.
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== Workshop ==
 
== Workshop ==
  
=== '''May 15th''' ===
 
 
-We discussed two Claire Pentacost Readings-[http://www.clairepentecost.org/beyond_face.htm Beyond Face ] and [http://www.clairepentecost.org/lab%20of%20symbolic_text.htm Critical Inventory of BioArt ].
 
-The gist of the Pentacost readings were that artists work with the symbolic and that the Artist's consent to work and learn in public is important.
 
-We also discussed the political and cultural implications of Scientific Authority.
 
-We also looked at Tuur Van Balen's [http://www.tuurvanbalen.com/projects/urbanbiogeography Urban Geography project]
 
-Most of the Ideas[see above] today, dealt with the use of bacteria as
 
    -a) A sensor or Reactor - (to Inputs,emotions,light..etc)
 
    -b) A Producer (of energy, proteins..etc)
 
      -c) A Material
 
 
-Is there Any way in which we can look at Bacteria from a purely non-symbiotic / non-anthropomorphic viewpoint?
 
-Can we use our technological "progress" to give a non-selfish gift back to our ecological siblings?
 
 
-Replace financial transactions with Bacteria
 
 
=== '''May 16th''' ===
 
 
Here's some creatures we created using techno-scientific jargon and aesthetics:
 
<gallery>
 
File:Non-standard_registry_of_names.jpg|IUpasana's Non Standard Regisitry of Names
 
File:Upasana.jpg|Upasana's Ideas
 
File:Bacteria_own.jpg|Neha's ''Materialistica Destructica''
 
File:DOC160509-16052009101732_Page_07.jpg|Neha's Graph
 
File:Page_1.jpg| Avni's ''actinodopaine''
 
File:Description_of_the_Amebitoni_Bacteria.png|Amebitoni_Bacteria
 
File:2.jpg|Immuno Bacteria
 
File:Sanya1.jpg|Plastico Collecticus
 
File:bactiprint.jpg|Id bacteria-Akash
 
File:bacteria.jpg|
 
</gallery>
 
 
 
Today's reading was called [http://www.patriciapiccinini.net/essay.php?id=30 Speculative Fabulations for Technoculture's Generation] by Donna Haraway.
 
 
-The article is primarily a review of the Australian artist Patricia Piccinini's work and a recapitulation of Haraway's philosophies .
 
 
-One of the things enduring about the reading was her appeal to "love" our creations, not in a tech.no- phillic sense but in a more nurturing and caring way.
 
 
=== '''May 17th''' ===
 
 
'''Hybrid Creatures From Mythology:'''
 
[[Gallery]]
 
*[[The May 17th Notebook]]
 
 
=== '''May 19th''' ===
 
 
We spent the day in NCBS picking up some standard biological techniques-Gel electrophoresis
 
And looking at some of the microscopy equipment at NCBS.
 
 
*[[Mukund's Brief Overview on Synthetic Biology Basics]]
 
 
*[[Gel Electrophorosis]]
 
 
*([[Talk:ArtScience_IGEM_team|Click here to discuss]])
 
 
*[[Streaking and Spreading to obtain bacterial colonies]]
 
 
*[[Imaging]]
 
 
*[[Discussion over Lunch]]
 
 
 
[[Some Images Of Our Day ]]
 
 
Non-categorised images [[here]]
 
 
=== '''May 21st''' ===
 
 
We put down all the information that we had about learnt about geosmin. We then put down the various paths we could take in order to produce the results we wanted. This exercise cleared certain doubts we had, but also raised a lot of questions.
 
 
<gallery>
 
File:geosmin_synthesis.jpg|The Scientific Representation
 
File:Rain_scenario_1.jpg
 
File:RAin_scenario_2.jpg
 
File:rain_scenario_3.jpg
 
File:Bactothing2.png|The Artistic Representation
 
</gallery>
 
 
[[First Prototype of the Bacteria]]
 
 
=== ''May 22nd'' ===
 
 
'''Today's Reading:'''
 
 
[[File:Jenshauser.png|400px|thumb|left|Some basics of Gene Expression and production of Proteins and Enzymes by Genes]]
 
 
===May 25th===
 
 
Presentation ideas- Bollywood sculpture?
 
 
<gallery>
 
File:Nehasculpture.jpg
 
File:krupakar_sc.jpg
 
File:sandeep-machine.png|Its this big box. There is a projection of a window looking out into rain. All the paraphanalia can fit in the space below. fog machine?. The curtain goes all round.
 
File:Installation_idea.jpg
 
</gallery>
 
 
 
'''How to read a scientific Paper''' by Mukund
 
 
1) Scan through the entire article quickly and find out what they are saying or trying to say.
 
 
2) Do not get lost in the references beyond 2 layers
 
 
 
How to create a gel electrophoresis chamber:
 
 
[[http://learn.genetics.utah.edu/content/labs/gel/gelchamber]]
 
 
 
'''Today's Reading:'''
 
 
[http://www.elowitz.caltech.edu/publications/Repressilator.pdf A synthetic Oscillatory network of transcriptional regulators]
 
 
<br/>
 
 
===May 27th===
 
http://openwetware.org/wiki/DIYbio:Notebook/Open_Gel_Box_2.0/RFC1
 
 
http://umassigem.blogspot.com/
 
 
http://diybio.org/2009/03/20/extract-dna-from-strawberries/
 
 
 
===May 28th===
 
 
'''Bio-Sculptures:'''
 
 
Avni's 'Chicken in a Kaleidoscope'
 
 
Neha's '''From a Spider'''
 
 
<gallery>
 
File:Spider.jpg| '''Spider-artist?'''  A spider made to crawl through watercolor on white paper in a one-holed plastic box overnight.
 
File:Spider2.jpg| An attempt to trace its movement in colors. Perhaps record a pattern?Would this be art?
 
</gallery>
 
 
 
Sandeep's Mustard seeds
 
 
=== May 29th ===
 
 
<gallery>
 
 
File:TheArtScientistA.jpg|Neha's 'TheArtScientist'-Page 1
 
 
File:The Art ScientistB.jpg|TheArtScientist-Page 2
 
  
</gallery>
 
  
  
=== May 30th ===
 
  
All DNA pictures have been uploaded. Take your pick [[Special:ListFiles|here]]
+
{| border=&quot;0&quot; cellspacing=&quot;0&quot; cellpadding=&quot;4&quot; align=&quot;center&quot;
+
![[Week One]]
1) '''Extracting DNA from Banana:''' <<[[Read here]]
+
![[Week Two]]
 +
![[Week Three]]
 +
![[Week Four]]
 +
|-
 +
![[Week Five]]
 +
![[Week Six]]
 +
![[Week Seven]]
 +
![[Week Eight]]
 +
|}
  
2) '''Exracting DNA from Saliva:'''
+
&lt;br/&gt;
  
'''Images of our DNA we extracted from saliva:'''
+
=== Other ===
 
 
<gallery>
 
File:NehasDNA.JPG|Neha's DNA
 
File:KrupakarsDNA.JPG|Krupakar's DNA
 
File:DhruvsDNA.JPG|Dhruv's DNA
 
File:SandeepsDNA.JPG|Sandeep's DNA
 
</gallery>
 
 
 
===May 31st===
 
 
 
Some interesting articles:
 
 
 
http://www.thenewatlantis.com/publications/the-promise-and-perils-of-synthetic-biology
 
 
 
http://www.nature.com/msb/journal/v2/n1/full/msb4100104.html
 
 
 
An interesting work:
 
 
 
http://www.edgarlissel.de/data/mnemosyne_II_01e.html
 
(The photosensitive stripes are made of bacteria)
 
 
 
===June 3rd===
 
'''''Registry of Parts Exercise'''''
 
 
 
Sanya: Bacteria that indicates rise in and regulates body temperature.[[Media:Light.jpg]]
 
 
 
[[Upasana]]
 
 
 
[[Neha's Bacterial Jewellery]]
 
 
 
===June 5th===
 
 
 
'''Beginning laboratory procedures:'''
 
 
 
1) [[Bacterial Transformation : The Process]] | [[The Bacterial Transformation Gallery]]
 
 
 
2) Preparing the Plasmid (minprep)
 
 
 
3) Digesting the DNA
 
 
 
4) Running the gel (Gel Electrophoresis)
 
 
 
5) Elution
 
 
 
===June 8th===
 
 
 
Preparing the Plasmids
 
 
 
''' A Brief of what we did: ''' <br/>
 
 
 
The plasmids that contained the pBAD and Lysis genes that were prepared were extracted from the bacteria cultures. The unwanted protein around the DNA was then removed. After that the DNA was cleansed of any remaining salt. The plasmids were then cut at certain points such that only the required gene could be extracted. These cut parts were prepared for gel electrophoresis.
 
 
 
[[Preparing the pBAD and Lysis plasmids for gel electrophoresis|The process]] | [[The Plasmid Preparation Miniprep Gallery]]
 
 
 
===June 9th===
 
[[The June 9th Image Gallery]]
 
 
 
Images of the various results attained:
 
 
 
<gallery>
 
File:Gelimage090609.png
 
File:Not working.jpg
 
File:PBAD-insert f.png
 
</gallery>
 
 
 
'''For June 10th:'''
 
 
 
*(Lysis= K112808)
 
 
 
pBAD- promoter
 
Lysis-big construct- gene for cell lysis
 
Gel image of released pBAD(I0500), after digestion with EcoRI+PstI:
 
 
 
Each pBAd and Lysis has 4 restriction enzymes E, X,S, P.
 
 
 
pBAD is digested with EcoRI +SPeI
 
Lysis is digested with EcoRI + XbaI
 
 
 
A small interlink sequence between E and X will break open and spread as one band
 
 
 
'''For June 11th:'''
 
 
 
These bands will be kept overnight in 37 degrees Celsius.
 
 
 
Then these will be run through a preparative gel which takes about 3 hours.
 
 
 
The next step is to elute  the released products which wold take 1.5 hours.
 
 
CIP treatment will be done
 
[Calf Intestine Phosphate]
 
This treatment is given to only the vector of Lysis (Process will take 1.5 hour)
 
This is done so that the vector doesn't self ligate.
 
 
 
This enzyme will then be inactivated at 65 degree C.
 
 
 
This vector needs to be purified using column or chloroform
 
 
 
'''June 12th'''
 
 
 
Please look up this link before Monday. Special attention to restriction enzymes while you are at it!
 
http://partsregistry.org/Assembly:Standard_assembly
 
 
 
===Other ===
 
  
 
http://www.historyforkids.org/scienceforkids/biology/cells/doing/dna.htm
 
http://www.historyforkids.org/scienceforkids/biology/cells/doing/dna.htm
Line 359: Line 68:
 
http://igem.uwaterloo.ca/The_UW_iGEM_Team
 
http://igem.uwaterloo.ca/The_UW_iGEM_Team
  
== Readings ==
+
The IBB Pune Team's wiki
 +
[http://2009.igem.org/Team:IBB_Pune#]
  
 +
[http://2008.igem.org/Team:NYMU-Taipei NYMU-Taipei's 2008 Wiki]
  
 +
== Readings ==
  
'''Art and Politics'''
+
'''[[Art and Politics]]'''
 
 
Claire Pentecost::Beyond Face[http://www.clairepentecost.org/beyond_face.htm]
 
 
 
Claire Pentecost::Outfitting the Laboratory of the Symbolic: Towards a Critical Inventory of BioArt[http://www.clairepentecost.org/lab%20of%20symbolic_text.htm]
 
 
 
Donna Haraway::Speculative Fabulations for Technoculture's Generations[http://www.patriciapiccinini.net/essay.php?id=30]
 
 
 
Oron Catts, Ionat Zurr::The ethics of experiential engagement with the manipulation of life
 
 
 
'''Art'''
 
 
 
GeneAeshetics, The Art of Joe Davis[http://www.clondiag.com/frame.php?page=/art/joe.davis/index.php?docid=0]
 
 
 
Adam Zaretsky[http://www.emutagen.com/]
 
 
 
Patricia Piccinini[http://www.patriciapiccinini.net/]
 
 
 
Designer Bodies: Towards a Posthuman Condition[http://www.a-r-c.org.uk/db/about.html]
 
 
 
'''Science'''
 
 
 
What are bacteria?[http://www.disknet.com/indiana_biolab/b004.htm]
 
 
 
Planet of the Bacteria[http://www.stephenjaygould.org/library/gould_bacteria.html]
 
 
 
Introductory Video Lectures in Biology[http://videolectures.net/mit7012f04_introduction_biology/
 
 
 
DNA from the beginning[http://www.dnaftb.org/22/concept/index.html]
 
 
 
"'Ethics"'
 
 
 
Playing God for Fun and Profit[http://radar.oreilly.com/2008/02/play-god-for-fun-and-profit-mo.html]
 
 
 
 
 
 
 
'''Design & Technology'''
 
 
 
Urban BioGeography[http://www.tuurvanbalen.com/projects/urbanbiogeography]
 
 
 
Designer Bacteria may have a future in Fashion[http://www.nytimes.com/2001/08/19/style/designer-bacteria-may-have-a-future-in-fashion.html]
 
 
 
Sunlight to Oil via Designer Bacteria[http://www.thinkgene.com/light-oil-with-bacteria/]
 
 
 
Loop.ph-Design Research Studio[http://loop.ph/bin/view/Loop/WebHome]
 
 
 
Laughing in a sine curve- Abhishek Hazra[[http://abhishekhazra.blogspot.com/2009/04/laughing-in-sine-curve.html]
 
 
 
Some interesting bio-design stuff by Brandon Ballangee and the likes. [[http://io9.com/photogallery/biotechnique/1000502846]]
 
 
 
'''Synthetic Biology:
 
'''
 
 
 
Student Book from IGEM [http://openwetware.org/images/f/f9/IGEM_Student_Book.pdf]
 
 
 
Gel Electrophoresis [http://en.wikipedia.org/wiki/Gel_electrophoresis]
 
 
 
Extracting DNA at home [http://nature.ca/genome/05/051/pdfs/DNAextract_e.pdf]
 
 
 
Harvard 2006: Explaining their process[[http://parts2.mit.edu/wiki/index.php/Harvard_2006]]
 
 
 
The Synthetic Biology Comic[[http://www.nature.com/nature/comics/syntheticbiologycomic/]] The .pdf version is here:[http://mit.edu/endy/www/scraps/comic/AiSB.vol1.pdf]
 
 
 
Introduction to Biological Engineering Design [http://openwetware.org/wiki/20.20]
 
 
 
Introduction to Synthetic Biology[http://openwetware.org/wiki/Intertech:iSB2008:Materials]
 
 
 
Ibio Seminars [http://www.ibioseminars.org/]
 
 
 
Gel electrphoresis process[http://web.utk.edu/~khughes/GEL/sld008.htm]
 
 
 
Primer on Synthetic Biology[http://openwetware.org/images/3/3d/SB_Primer_100707.pdf]
 
 
 
DIY Synthetic Biology[http://www.scribd.com/doc/14663730/DIY-Synthetic-Biology]
 
 
 
[[File:Keiki-gel-1-225x300.jpg|150px|thumb|none|Drinking straw gel electrophoresis]]
 
Drinking straw gel electrophoresis[http://maradydd.livejournal.com/417631.html]
 
 
 
Open Gel Box [http://openwetware.org/wiki/DIYbio:Notebook/Open_Gel_Box_2.0]
 
 
 
BioBricks on Youtube [http://www.youtube.com/user/BioBricksFoundation]
 
  
[http://diybio.org/wp-content/uploads/2009/04/CodeCon09_SynthBio_tutorial_handout/appendix3%20-%20GinkgoBioworks%20guide%20to%20engineering%20biology.pdf Ginko BioWorks Guide to Synthetic Biology]
+
'''[[Art]]'''
  
[http://techtv.mit.edu/collections/mitmuseum/videos/1684-soap-box-do-it-yourself-biology DIY Biology Webcast]
+
'''[[Science]]'''
  
[http://groups.google.com/group/diybio/web/diybio-model-organisms DIYBio Model Organisms]
+
'''[[Ethics]]'''
  
'''General Design Links'''
+
'''[[Design &amp; Technology]]'''
  
http://psd.tutsplus.com/drawing/the-role-of-sketching-in-the-design-process/
+
'''[[Synthetic Biology]]'''
  
http://www.wallwisher.com/wall/iGemSrishti
+
'''[[General Design Links]]'''

Latest revision as of 18:01, 10 December 2010

Hackteria banner1.png

About

We consider ourselves amateurs/novices within the context of the IGEM competition. Our endeavor as “outsiders” is to bring our training in the arts and design to synthetic biology. Over this summer, we learnt the tools and techniques of synthetic biology and developed a piece of life which reflects our concerns, namely, the cultural, ethical and aesthetic implications of Synthetic Biology. Using a DIY approach and getting our hands “wet” was a critical element in the learning process. This approach allowed us to engage in constructive discussions with scientists working in the field. Our construct synthesizes Geosmin, an enzyme normally produced by cyanobacteria and actinobacteria. The biosynthesis of geosmin from farnesyl diphosphate is catalyzed by a single enzyme germacradienol/germacrene D synthase. E. coli, does not bear a gene that codes for germacradienol/germacrene D synthase. We have expressed this gene in different strains of E. coli, under control of the pTrc promoter present in the pTrc99a vector. Geosmin is responsible for producing the earthy smell that occurs in the air when rain falls after a dry spell of weather.

People

Akash Hirosh

Dhruv Nawani

Nikhil Patil

Upasana Simha

Sandeep Mathew

Sanya Rai Gupta

Avni Sethi

Neha Bhat

Gautam Vishwanath

Krupakar Dhinakaran

Ideas

Click for a closer look

Major Outcomes -

  • Facilitate a group of children to design their 'perfect creature' through visual/tactile media and then draw from these experiences and ideas to build another structure.
  • Basic information on micro biology-synthetic biology becomes accessible in the forms of brochures/charts/posters in the team's work space.

Workshop

Week One Week Two Week Three Week Four
Week Five Week Six Week Seven Week Eight

<br/>

Other

http://www.historyforkids.org/scienceforkids/biology/cells/doing/dna.htm

It is helpful to have an idea of how the other teams are progressing. So, if anyone comes across interesting iGEM team wikis/sites - please put up the links here.

http://igem.uwaterloo.ca/The_UW_iGEM_Team

The IBB Pune Team's wiki [1]

NYMU-Taipei's 2008 Wiki

Readings

Art and Politics

Art

Science

Ethics

Design & Technology

Synthetic Biology

General Design Links