====== Synthetic development biology======

** 2nd of November - Nina Tandon (Epibone) nina@epibone.com **

[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/2016_11_02_HTGAA_Slides.pdf|class slides]]
Videos:
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/HTGAA%20Video%20Files/3Hz%202.AVI|Slide 11]]
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/HTGAA%20Video%20Files/Video%202.mov|Slide 16]]
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/HTGAA%20Video%20Files/080716%20movie.avi|Slide 49]]
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/HTGAA%20Video%20Files/Video%201.m4v|Slide 64]]
[[http://connectmedia.waag.org/AcadeMany/bio-2016/11/02/index.html|Recordings]]
{{vimeo>189940571?medium}}
{{vimeo>189959220?medium}}

We will discuss the biomimetic paradigm for tissue engineering (i.e. how to mimic developmental biology so as to grow tissues in the laboratory). For this lecture, we will focus on bioreactors (i.e. advanced cell culture systems that recapitulate living cellular environment in the laboratory). We will explore examples of bioreactors used to grow different tissue types, as well as a fun application of bioreactors for a different purpose: building biotic video games!
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===== Background reading  =====
(you'll need these for reference for the design and lab HWs)\\
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/papers/BioreactorsForTissueEngineering.pdf| Bioreactors for Tissue Engineering]]\\
[[http://www.stanford.edu/group/riedel-kruse/publications/Riedel_2011_LabChip.pdf|Design, engineering and utility of biotic games]]\\
[[http://chimera.labs.oreilly.com/books/1234000001995/ch09.html|Pac-Man of the Microscopic World]]\\
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/papers/Tandon%20et%20al%20IEEE%202009.pdf|Alignment and elongation of Human Adipose-derived stem cells in reponse to direct-current electrical stimulation]]\\
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/papers/Nature%20Prot%20El%20stim.pdf|Electrical stimulation systems for cardiac tissue engineering]]\\
[[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/papers/PNAS%20Grayson%20et%20al%202009.pdf|Engineering Anatomically Shaped Human Bone Grafts]]\\
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===== Design homework assignment: =====
Exploring bioreactor design elements.\\

  * [[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/2016_11_02_Design_HW.pdf|design homework]]
  * [[https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/Q2PicsHTGAA.zip|images for Q2 ]]
===== Lab homework assignment: =====
Build a Paramecium/Arduino interface.  \\
Measure how fast the paramecia (a) swim and (b) change direction in response to electrical stimulation.
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__Components__ (based off: http://making.do/paramecium/build.html)\\
IMPORTANT: Purchase these paramecia well in advance of class (link: http://www.carolina.com/protozoa/paramecium-caudatum-living/131554.pr -- you can state the expected use date. If you require international shipping, try: https://www.wardsci.com/store/catalog/product.jsp?catalog_number=871310 -- Let me know if you have any issues. nina@epibone.com)!)\\
NOTE: The interface described in the above setup is only an example -- Leave out the brain sensor unless you are feeling very ambitious! And don't feel tied to the laser-cut setup either -- The essential idea is that you are placing paramecia in between electrodes in a setup that facilitates imaging. I built a setup at home with the following components:\\
(1) toy microscope (4x works fine): http://www.amazon.com/gp/product/B000NOU54O/ref=ask_ql_qh_dp_hza\\
(2) eyepiece imager: http://www.amazon.com/gp/product/B003DVP7CE/? \\
(3) electrode setup: glued 0.9mm pencil leads to a microscope slide at 1cm spacing (and only used two leads instead of four). You can clip aligator clips to the parts of the pencil lead extending past the edge of the slide: https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/IMG_5224.JPG\\
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__Equipment__\\
multimeter\\
laser cutter\\
laptop or desktop computer\\
standard toolbox tools: wrenches, wirecutters, screwdrivers\\
standard lab equipment: pipetors, tubes\\
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__This is what the setup looks like through my toy microscope imager at 4x__: https://dl.dropboxusercontent.com/u/7293800/2016%2011%2002%20HTGAA/HTGAA%20Video%20Files/Movie%20on%2010-12-15%20at%208.17%20PM.mov

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