Talk:CH391L/S13/Biologically Inspired Materials

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  • Kevin Baldridge 17:25, 8 April 2013 (EDT):I remember reading about a self-healing carbon fiber-based material a few years ago. There were small pockets of the raw materials which would self assemble to heal a macro-scale break when the pockets were opened with the macro-scale break. I'll see if I can figure out what exactly it was
    • Kevin Baldridge 17:34, 8 April 2013 (EDT):I think this is the original material I was thinking of, but in looking for it I found a more synthetic-bio related material that incorporates bacteria here
    • Gabriel Wu 17:58, 14 April 2013 (EDT): Here's an example of a polymer based biologically inspired material that is supposed to mimic the structural and electrical properties of skin.
      • Kevin Baldridge 17:49, 8 April 2013 (EDT):Maybe that's the iGem thing you mentioned...
        • Gabriel Wu 02:56, 14 April 2013 (EDT): The iGEM idea is the same, but the implementation is different. The iGEM Newcastle team suggested upregulation of urease genes; whereas, the paper you cite uses calcium lactate as part of a two component "self-healing" concrete strategy (see response to Jeff's comment for details).
  • Kevin Baldridge 17:36, 8 April 2013 (EDT):You mention spider silk for use in sutures, would immunogenicity be a problem?
    • Gabriel Wu 18:00, 14 April 2013 (EDT): So while silk worm silk has known immunogenicity problems and needs to be treated prior to use in vivo, spider silk was implanted in pigs and shown to elicit immune responses similar to gauze, a well-established wound covering [1].
  • Aurko Dasgupta 17:51, 8 April 2013 (EDT):How is omniphobicity chemically achieved?
    • Max E. Rubinson 18:26, 10 April 2013 (EDT): There is a difference between the lotus effect and how the SLIPS work. I'm not sure I fully understand, but it sounds like the SLIPS are composed of structures that lock in an intermediary liquid that repels other liquids. I think the lotus effect is depends on the ability of a surface to form contact angles with liquids that result in increased hydrophobicity. Here is the paper describing SLIPS. And here is a link to the Wikipedia page describing contact angles and hydrophobicity.
      • Max E. Rubinson 18:28, 10 April 2013 (EDT): The first link is the same paper Gabe referenced (reference number 15).
        • Gabriel Wu 18:18, 14 April 2013 (EDT): Thanks, Max. A very good explanation. I'll add that the surface property of lotus leaves is due to "micro roughness." So, what happens is water sits on top of these little bumps on the surface of the plant without sticking because there isn't a enough surface area for the water droplets to stick to the plant. Instead, the water just sticks to itself and beads. The general phenomenon is known as the "lotus effect" [2].
        • Gabriel Wu 18:28, 14 April 2013 (EDT): As for "omniphobicity," that is determined by the properties of the "locked in" liquid (as Max puts it). In this case, the researchers chose perfluorinated liquids with low surface tension, and were non-volatile, and non-soluble with both aqueous and hydrocarbon liquids. An example of a perfluorinated compound is teflon, used to make cookware nonstick.
  • Dwight Tyler Fields 17:52, 8 April 2013 (EDT): Spiders for iGEM!!!
  • Aurko Dasgupta 17:53, 8 April 2013 (EDT): Was goat made silk expected to be more economical than microbially produced spider silk?
    • Catherine I. Mortensen 00:16, 12 April 2013 (EDT):I think Gabe mentioned that spiders are just generally difficult to deal with.
      • Gabriel Wu 03:33, 14 April 2013 (EDT): So, typically, to harness a large amount of material, the first attempt is to farm the native organism. Spiders are aggressive and territorial and will eat each other if put in small spaces together (typically necessary when farming anything). Next, the second attempt will be in a microbe, like E. coli or yeast. Spider silk proteins are highly repetitive and poorly matched in codon usage to these microbes. This resulted in small yields and lots of truncated products as recombination becomes a problem in these organisms when there are repetitive sequences present. So, the next step becomes more difficult. Production ideas turn to higher eukaryotes like tissue culture, plants, or transgenic animals. All of these are complicated, expensive, and hard to scale. The advantage of goat's milk is that it's easy to obtain in large amounts and the animal does not need to be killed in the process. So, the short answer, is yes, goat milk silk was "expected" to be economical. The company never actually released a viable silk product and eventually went bankrupt, so maybe it wasn't a great expectation. However, even though the company is gone, spider goats still live on beyond just the museum and are still in development in academic envrionments [3]. So, maybe the spider goat is still expected to be economical at some point.
  • Jeffrey E. Barrick 17:59, 8 April 2013 (EDT):How does the carbonate producing Bacillus work? What's the "part" for this?
    • Gabriel Wu 19:27, 14 April 2013 (EDT): So, there are two strategies that I know of:
      • The one that the 2010 Newcastle iGEM took was to increase urease production in B. subtilis. Urease catalyses the hydrolysis of urea into ammonium and carbonate through carbamate and bicarbonate intermediates. B. subtilis pulls cations from the environment onto their cell walls. These cations include calcium cations, which can react with carbonate ions and can use the cell surface as a nucleation site, which results in calcium carbonate precipitation [4]. Turns out up-regulation of ureA, ureB, and ureC, the B. subtilis urease genes, does not increase urease production. So, the 2010 Newcastle iGEM team used an alternate strategy. They planned on increasing arginine and arginase production. The logic was that increasing arginase, which converts arginine to ornithine and urea, would increase the total amount of urea and indirectly increase the production of urease. They designed an arginine part, which uses SR1, a small RNA that down regulates ahrC, which is a repressor of the arginine catabolic pathway and an arginase part, which uses rocF, the arginase gene. As far as I can tell, no parts where actually ever made.
      • The other method from Jonkers, et al. utilizes the metabolic conversion of calcium lactate to calcium carbonate. The authors cite the lack of ammonia has being a benefit of this method of mineralization.
  • Evan Weaver 13:54, 11 April 2013 (EDT): Why is it so hard to synthesize spider silk?
    • Benjamin Gilman 16:38, 11 April 2013 (EDT): You talked about it in class, but it's worth mentioning on the page why the spider silk projects haven't worked out, even though they can express the protein in transgenic animals. Aligning the strands, which they've mostly tried to do with an extrusion process, wasn't consistent enough to make strong fibers.
  • Alvaro E. Rodriguez M. 00:08, 12 April 2013 (EDT):Hey Gabe, do you know anything about the famous Speedo suits used by Olympic athletes, I remember at some point there was some talk about them improving the athlete's speeds as they resemble the smooth skin of a shark.
    • Catherine I. Mortensen 01:25, 12 April 2013 (EDT):I believe it's called FastSkin by Speedo. I found a bunch of articles on it. Here's one that talks about the suit and other bio inspired stuff. [5]
      • Gabriel Wu 19:44, 14 April 2013 (EDT): Thanks, Catherine. As far as I can tell, the FastSkinTM swimsuits utilize vortex generators [6]. Basically, the geometric pattern and spatial position of grooves on a surface can cause sufficient flow manipulation to reduce drag across the body. (Search for "vane vortex" in the reference to see some examples.)
    • Catherine I. Mortensen 01:25, 12 April 2013 (EDT):They should make a FastSkin suit out of spider silk.
      • Gabriel Wu 19:44, 14 April 2013 (EDT): Not sure what the overall properties of spider silk are compared to the nylon/elastane composite that Fastskin is made out of. The main advantages of spider silk is strength, which I'm not sure is a clear benefit in this situation [7].
  • Catherine I. Mortensen 00:20, 12 April 2013 (EDT):Here is an article about spider silk used in the regeneration of nerves. [8]
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