SynthBioWorkshop2010

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<strong>Synthetic Biology for Artists and Designers 2</strong>

<strong>10th May 2010 </strong>

   •  Biology - individual understanding and definition.
   •  Brief History of Biology - Scientists/Microbiologists (Video)
                    ? Anton Von Leeuwenhoek
                    ? Gregor Mendel
                    ? Robert Hooke
                    ? Louis Pasteur
                    ? John Baptiste Van Helmont
                    ? Joseph Jackson Lister
                    ? Theodore Schwann
                    ? Rosalyn Franklin
                    ? Watson & Crick
   •  Evolution – Brief understanding and controversies
   •  DNA, Protein – Introduction
   •  Bacteria E.Coli
   •  Readings – PDF
                    ? Scientific America – Engineering Life
                    ? Synthesizing DNA of microorganisms for various purposes
                    ? Sequencing of DNA
                    ? Cost factors involved
                    ? Comparison to Moore’s Law
                    ? Human Genome
   •  Video – (BBC)-The Cell-The Hidden Kingdom

Homework - Reading (PDF)

   1. Life: What a concept!

<strong>11th May 2010</strong>

   •  Recap of yesterday’s learning
   •  Video lecture by David Sadava
           ? Expression of genes
           ? Phenotypes and Alleles
           ? The Nucleus
           ? Totipotent Cells
           ? Cloning
           ? Genes, chromosomes
           ? Human genetic information
           ? Cell processing
   •  Introduction to Synthetic Biology by Andrew Hessels
   •  Video – Darwin’s theory on evolution

Homework

      1.
      2.

<strong>12th May 2010</strong>

   •  Video Lecture by David Sadava
                   ? Epidemiology
                   ? Lung Cancer gene
                   ? Mutations
                   ? Requirements of a DNA
                   ? Responsibilities of a Protein
                   ? Variety in DNA
                   ? Somatic and Sex Cells
                   ? Virus
                   ? DNA & its properties
                   ? Structure of a DNA
                   ? Replication of DNA
   •  Video of Watson and his story of the discovery of the DNA model at TED.com
   •  Readings – Applying engineering to biology
   •  Reading – Adventures in Synthetic Biology

Homework

      1. Reading
      2. Online Research

<strong>13th May 2010</strong>

   1. Video Lecture by David Sadava
                   ? Spider web theory of protein
                   ? Protein production
                   ? Structure of protein
                   ? Synthesis of Protein
                   ? Human protein synthesis
                   ? Types of proteins
                   ? Expression of Proteins
                   ? Gene – Protein relationship
                   ? Metabolism
                   ? Thermodynamics
                   ? Mechanism, Cell Theory and Evolution
                   ? Ricin and its discovery
                   ? RNA and its role
                   ? Transcription and Translation
                   ? Nirenberg’s Experiment
                   ? Mutations and changes in base pairs
   • Video tutorial on DNA replication
   • Video tutorial on Protein synthesis

Homework

      1. Exercise – Make a piece of art form using any LIVING form that should have the
           capability to grow over a period of two months.

<strong>14th May 2010</strong>

   1. Video Lecture by David Sadava
      Genomes – further details
   ?
      Mutations & Mutagens
   ?
      Cancers caused by mutation of genes by radiation
   ?
      Genetic Damage
   ?
      Leukaemia
   ?
      Scientist Renato del Bucco’s work
   ?
      Hierarchical sequencing
   ?
      Shotgun sequencing – Craig Ventor
   ?
      Bioinformatics
   ?
      Information from a genetic sequence
   ?
      a. Coding sequence
      b. Protein amino acid sequence
      c. Gene control sequences
      Sequential Genomics
   ?
      First genome to be sequenced
   ?
      Hypothetical suggestion of 24000 genes in a human being
   ?
      Synthetic Biology - making artificial genes to bring about a desired result
   ?
      Scientist Werner Arber
   ?
      Restriction Endonuclease
   ?
      How a bacteria prevents Viral infections
   ?
      DNA Mapping
   ?
      Recombinant DNA
   ?
      Stanley Cohen & Herbert Boyer’s Experiment
   ?
      Goals for making rDNA
   ?
      Transgenic animals and plants
   ?
      Naked and Vector DNA
   ?

<strong>17th May 2010-05-17</strong>

   1. Video Lecture by David Sadava
           ? Isolation of genes
           ? PKU and dystrophy
           ? Methods of analyzing DNA
           ? Reverse Genetics
           ? Dystrophine Gene and Utrophine
           ? Gene Therapy
           ? Nucleic Acid Hybridization
           ? Genome Library
           ? DNA Microarray
           ? Metastasis
   2. Exercise - Think of your own creature. Design it. Explain detailed mechanisms using
      diagrams. This organism could be hypothetical. Name it.
   3. Make a scientific paper on your creature
   4. Demonstration of Gabriel’s current prototype of visually representing genetic sequenced
      data of a human mitochondria.

Homework – develop and complete creature.

<strong>18th May 2010</strong>

    1. Video Documentary – BBC – The Cell – Chemistry of Life
    2. Video Documentary – BBC – The Cell – The Spark of Life
    3. Discussion of Creatures, peer feedback and progress

<strong>19th May 2010</strong>

<object width="400" height="300"><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="movie" value="http://vimeo.com/moogaloop.swf?clip_id=12045337&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1%22 /><embed src="http://vimeo.com/moogaloop.swf?clip_id=12045337&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1%22 type="application/x-shockwave-flash" allowfullscreen="true" allowscriptaccess="always" width="400" height="300"></embed></object><a href="http://vimeo.com/12045337%22>Center for Genomic Gastronomy @ Srishti, Bangalore, India</a> from <a href="http://vimeo.com/user3901760%22>genomic gastronomy</a> on <a href="http://vimeo.com%22>Vimeo</a>.

    1. Presentation by Zac on The center for Genomic Gastronomy
           ? What is Biotechnolgy
           ? Perspective of food by all living things
           ? Geohackers, Biohackers, Geoengineers, Planetcrafters
           ? Agriculture Biodiversity
           ? Agrinformatics
           ? Metadata and food Genomes
           ? Food System Adaptation
           ? Agriculture Terrorism
           ? First world eating issues
           ? Cuisinformatics
    2. Extraction of DNA

<strong>20th May 2010</strong>

    1. Presentation of Abstracts of New Creatures
           ? The Booster Cell
           ? Supercule
           ? Thermo Cell
    2. Exercise – Create another new creature which does not necessarily have to be a
       microorganism or even possible to exist. Completely hypothetical, imaginary of fantastical is
       great!

<strong>21st May 2010</strong>

Minutes of the Class

    1. Discussion of ideation on creation of machines.

<strong>22nd May 2010</strong>

Minutes of the Class

   1. Video Documentary by Craig Ventor
           ? Scientific Breakthrough – First fully Synthetic Cell to be cultutred.
           ? Genome copied from Mycoplasma Genatalium
           ? Genome synthetically prepared in the lab
           ? Introduced into yeast cells to complete transformation
           ? Introduced into host bacterial cell which transforms to new organism
           ? Watermarked with 46 authors, web address and mail ID
           ? Significance – vaccine production and Oil Spill reduction
   2. Artist & other Research
           ? Stellarc
           ? Symbiotica
           ? Orlan

<strong>25th May 2010</strong>

   1. Visit to NCBS
           ? Tour of the Campus
           ? Meeting with PhD student Mehra and Navneet
           ? Introduction to the lab space
           ? Discussion over Science Institutes and their pros and cons
           ? Tour of other labs with various workflow instruments

<strong>26th May 2010</strong>

Minutes of the Class

   1. Video Tutorial by David Sadava
           ? Bioremediation – using organism to improve the environment
           ? Fluorescence in nature and different organisms
           ? TNT used as example
           ? Degraded by Psuedomonas Putida
           ? Integrated Pest Management
           ? Bacteria in decomposition
           ? Bacteria in Waste Water Treatment
           ? Extremophiles
           ? PCR and its significance
   2. List of materials required to build the art form made from a living organism
   3. Artist & other Research
           ? Institution of Applied Autonomy
           ? Center for Post Natural History
           ? George Gessert

<strong>27th May 2010</strong>

Minutes of the Class

   1. Video Documentary by Kary Mullis on the making of the PCR
   2. Artist & other Research
           ? Adam Zaretsky
           ? Eduardo Kac
           ? Patricia Piccinni
   3. Field work on material for art form construction.

<strong> 1st June </strong>

Yeast Growing http://www.disknet.com/indiana_biolab/b021.htm