BerkiGEM2007 WikiPlaying2

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   <p><a href="https://2007.igem.org/Berkeley_UC">&lt;&lt;&lt; Return to UC Berkeley iGEM 2007 </a></p>
   <p><a href="https://2007.igem.org/Berkeley_UC">&lt;&lt;&lt; Return to UC Berkeley iGEM 2007 </a></p>
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   <p> <a href="https://2007.igem.org/BerkiGEM2007Present1">&lt;&lt;Previous Section: Oxygen Transport</a> | <a href="https://2007.igem.org/BerkiGEM2007Present3">Next Section: Controller&gt;&gt;</a></p>
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   <p><a href="https://2007.igem.org/Berkeley_Individual_Contributions">&lt;&lt;Previous Section: Individual Contributions</a> | <a href="https://2007.igem.org/BerkiGEM2007_Resources">Next Section: Team Resources&gt;&gt;</a></p>
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<h1 align="center">The Chassis</h1>
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<h1 align="center">Team Notebooks</h1>
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<p align="justify">There are several core issues associated with introducing <em>E. coli</em> into the bloodstream of human beings or other animals.  First is the issue of sepsis. <em>E. coli</em> possesses a species called lipid X, or endotoxin, in its outer membrane  which causes the release of TNFalpha in humans. This is an essential  process of the innate immune system, but high doses of lipid X can be  lethal. Bactoblood must have some ability to avoid this series of  events. Similarly, there are a variety of additional features in <em>E. coli</em> that can elicit strong adaptive immune responses including the pili and  flagella. From the bacterium's perspective, the interaction with the  bloodstream is no more desirable. The complement system, another core  component of the innate immune response, can kill bacteria directly.  Additionally, phagocytic cells including macrophages and neutrophils,  can engulf and kill <em>E. coli</em>.  Fortunately for our purposes, there are a variety of modifications we can make to circumvent these problems.</p>
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  <h3>Team Notebooks</h3>
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<h2 align="center">The <em>E. coli</em> Outer Surface</h2>
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<p align="justify"><img src="https://static.igem.org/mediawiki/2007/e/e4/BerkiGEM2007-ColiOuterSurface.gif" alt="" width="699" height="475" align="right">To understand these modifications, we must first understand what features are present in <em>E. coli</em> strain MC1061, our starting point for Bactoblood.  Like most strains of <em>E. coli</em> used in the lab, MC1061 comes from the MG1655 lineage and is a "rough"  strain. Unlike other "smooth" strains, MC1061 lacks surface-displayed  capsular polysaccharides known as K capsules and O antigens. It retains  the general 2-membrane architecture present in gram-negative bacteria.  In between these membranes is the periplasmic space which is composed  of a gel-like carbohydrate-rich polymer called peptidoglycan. The inner  membrane is composed of a lipid bilayer and a variety of proteins. The  outer membrane similarly is a lipid bilayer, and the lipid component of  it is called lipopolysaccharide, or LPS. The structure of LPS at it's  core is a 6 fatty acid lipid called lipid X. When O antigen polymer  chains are present, they are covalently attached to the outer leaf of  LPS. K capsules are similarly embedded in the outer leaf of the outer  membrane, but they are not directly attached to LPS. Other components  of the outer membrane include a structural protein, LPP, and a variety  of other proteins. This outer surface is the critical region of the  bacterium for understanding how it interacts physically with the  outside world. When the bloodstream "looks" at E. coli, what it "sees"  is the outer membrane because everything else is stuck inside.  Modifications such as O antigens and K capsules therefore have dramatic  effects on the bacterium's interactions with the outside world.</p>
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<p align="justify">&nbsp;</p>
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<p align="justify">&nbsp;</p>
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<h2 align="center">Capsular Polysaccharides</h2>
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<p align="center"><img src="https://static.igem.org/mediawiki/2007/e/e4/BerkiGEM2007_O16andK1Clusters.jpg" width="893" height="117" alt=""></p>
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<p align="justify"> The carbohydrates embedded in the outer membrane are extremely diverse within the <em>E. coli</em> species. Both K capsules and O antiens are linear carbohydrates  polymer, but at least 150 chemically-distinct O antigens exist in one <em>E. coli</em> strain or another. Similarly, at least 100 chemically-distinct K  capsules have been described. Almost all pathogenic strains of <em>E. coli</em> have some sort of capsular polysaccharide and are referred to as  "smooth" strains. The rough vs. smooth distinction refers to a visibly  discernible quality of their colonies. The particular choice of  carbohydrate present in a bacterium is essential to its ability to  survive in its living environment. For pathogenic and commensal  bacteria, specific O or K carbohydrates are appropriate for distinct  areas of the body (blood stream, urinary tract, intestines) and also  for distinct animal types (birds, pigs, humans, cows, etc.). Over 90%  of human cases of <em>E. coli</em> bacteremia (the clinical word for  having bacteria in the bloodstream) are caused by strains that have a  specific type of K capsule called K1. K1 is a long linear polymer of  sialic acid that extends about half the diameter of the bacterium  beyond its surface. Because polysialic acid is a frequent coating on  mammalian cells, the human immune system does not recognize K1 as  foreign. Bacteria with a K1 capsule are therefore resistant to both  innate and adaptive immune responses. Proper display of a K1 capsule  requires the concomitant expression of any of several O antigens. For  our studies, we have chosen O16. Genetically, the K1 capsule requires  14 genes encoded within a 20kb cassette. The O16 antigen requires 11  genes encoded within a 12kb cassette. Together, these surface  modifications allow the bacterium to avoid detection by the immune  system and should extend the serum half-life of Bactoblood to several  hours rather than the less-than-5 minutes observed with rough strains.  Both of these gene clusters have been installed into the genome of  MC1061 in the course of preparing our chassis strain, MC828U.</p>
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<h2 align="center">Lipid X and Its Variants</h2>
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<div align="justify">The lipid X component of the LPS in <em>E. coli</em> contains 6 acyl  chains. Mammalian blood contains a protein called LBP that scavenges  this molecule from both live and lysed bacteria and transfers it to  toll-like receptor 4 present on mammalian cells. These events initiate  a signal transduction cascade resulting in the release of a protein  called TNFalpha. The inflammatory response to these events at low doses  helps your body fight off bacterial infections. At higher doses, it can  result in organ failure and even death. The lipid X moiety present in a  variety of other bacteria do not initiate this cascade of events.  Similarly, a pentaacylated variant of the <em>E. coli</em> lipid X is  1000x less agonistic of this response. Our bacteria synthesize this  pentaacylated variant due to the deletion of the gene responsible for  attaching the sixth acyl chain, <em>msbB</em>.
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<h2 align="center">Additional Cell-Surface Epitopes</h2>
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<div align="justify">Essentially any component on the surface of the bacteria has the  potential to elicit either innate or adaptive immune responses. Of  those present on MC1061's surface, type I pili and flagella are known  to elicit such responses. Each of these features is encoded within  multi-gene operons encoding protein assemblies that extend out from the  bacteral surface. Type I pili allow bacteria to adhere to the surface  of mammalian cells. Flagella are the "propellers" that allow the  bacteria to swim during chemotaxis. Bactoblood does not require either  of these activities, so these genes were deleted in the chassis strain. </div>
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<h2 align="center">Growth Control by Iron Restriction</h2>
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    <a href="https://2007.igem.org/John_Dueber_Notebook" title="John Dueber Notebook"> John Dueber's Notebook</a><br>
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<div align="justify">A critical challenge in the development of Bactoblood is the ability to  safely inject a large quantity of bacteria into the bloodstream. It is  essential that these bacteria do not grow for a safe administration. We  have adopted a two-tier strategy for eliminating the possibility of  growth. First, we make our bacteria unable to grow in the bloodstream  due to their inability to acquire a specific nutrient, iron. Secondly,  we introduce a genetic kill switch device that destroys the bacterium's DNA once it has produced all the necessary biochemical components  needed to carry oxygen. <em>E. coli</em> can acquire iron by either  high-affinity or low-affinity iron transport. When they grow in LB  media, they use low-affinity transport which involves specific  membrane-embedded transporters that can pump in free iron ions. In  animal body fluids, the concentration of these ions is less than 10-15  molar. The iron is sequestered in small molecule chelators such as heme  or proteins like transferrin and ferritin. Acquiring iron in such an  environment requires more elaborate processes involving secreted  chelators that can grab the iron from these proteins. These processes,  collectively referred to as high-affinity iron transport, all require  the function of <em>tonB</em>. By deleting <em>tonB</em> in our chassis  organism, we obtain a strain that retains its ability to grow normally  in LB media but is unable to grow in mammalian body fluids.
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    <a href="https://2007.igem.org/Christopher_Anderson_Notebook" title="Christopher Anderson Notebook"> Christopher Anderson's Notebook</a><br>
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    <a href="https://2007.igem.org/Farnaz_Nowroozi_Notebook" title="Farnaz Nowroozi Notebook"> Farnaz Nowroozi's Notebook</a><br>
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<h2 align="center">Characterization of the Chassis, MC828U</h2>
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    <a href="https://2007.igem.org/Amin_Hajimorad_Notebook" title="Amin Hajimorad Notebook"> Amin Hajimorad's Notebook</a><br>
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<p align="justify">The genotype of our chassis organism is: </p>
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    <a href="https://2007.igem.org/Rickey_Bonds_Notebook" title="Rickey Bonds Notebook"> Rickey Bonds' Notebook</a><br>
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  <pre><strong>MC828U</strong> delta(<em>araA</em>-<em>leu</em>)7697 <em>araD139</em> delta(<em>codB</em>-<em>lac</em>)=delta<em>lac74</em> <em>galK16</em>  <em>
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galE15</em> <em>mcrA0</em> <em>relA1</em> <em>rpsL150</em> <em>spoT1</em> <em>mcrB9999</em> <em>hsdR2</em> O16(delta<em>wbbL</em>
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    <em>Keep your wiki notebooks,  sequencing/construction logs, and the registry updated!</em> </p>
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K1(delta<em>neuS</em>) delta<em>msbB</em> delta<em>fim</em> delta<em>tonB</em> delta<em>flhCD</em>   <em>
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upp</em>::(Ptet-<em>wbbL</em>-<em>neuS</em></pre>
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    <a href="https://2007.igem.org/Arthur_Yu_Notebook" title="Arthur Yu Notebook"> Arthur Yu's 1337 Notebook</a><br>
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    <a href="https://2007.igem.org/Austin_Day_Notebook" title="Austin Day Notebook"> Austin Day's Notebook</a><br>
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<p align="justify">To illustrate the function of our chassis, here we show the function  of 2 critical features of chassis: its ability to survive in serum and  loss of chemotaxis due to the deletion of flagella. </p>
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    <a href="https://2007.igem.org/David_Tulga_Notebook" title="David Tulga Notebook"> David Tulga's Notebook</a><br>
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    <a href="https://2007.igem.org/Kristin_Doan_Notebook" title="Kristin Doan Notebook"> Kristin Doan's Notebook</a><br>
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  The serum assay shows the chassis' ability to survive in serum due to its K1:O16 additions and msbB deletion.</p>
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    <a href="https://2007.igem.org/Samantha_Liang_Notebook" title="Samantha Liang Notebook"> Samantha's Notebook (June - July 19, 2007</a><br>
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<p><img src="https://static.igem.org/mediawiki/2007/9/9c/Serumassaypic.jpg" alt="" width="835" height="685" align="middle"></p>
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    <a href="https://2007.igem.org/Samantha_Liang_Notebook2" title="Samantha Liang Notebook2"> Samantha's Notebook (July 20, 2007 - present)</a><br>
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    <a href="https://2007.igem.org/Vaibhavi_Umesh_Notebook" title="Vaibhavi Umesh Notebook"> Vaibhavi Umesh's Notebook</a><br>
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    <a href="https://2007.igem.org/Kristin_Fuller_Notebook" title="Kristin Fuller Notebook"> Kristin Fuller's Notebook</a><br>
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    <a href="https://2007.igem.org/Vincent_Parker_Notebook" title="Vincent Parker Notebook"> Vincent Parker's Notebook</a><br>
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    <a href="https://2007.igem.org/Nhu_Nguyen_Notebook" title="Nhu Nguyen Notebook"> Nhu Nguyen's Notebook</a><br>
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  <a href="https://2007.igem.org/Hannah_Cole_Notebook" title="Hannah Cole Notebook"> Hannah Cole's Notebook</a></p>
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<p>In a swarming assay done to demonstrate the effect of flagella  deletion, the wildtype MC1061 cells on the left plate were able to swim  out much farther than those of the MC828U chassis, shown on the right  plate.</p>
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    <img src="https://static.igem.org/mediawiki/2007/f/f3/SwarmingPic.jpg" alt="" width="492" height="272" align="absmiddle"></p>
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<p>&nbsp;</p>
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<p align="center"><a href="https://2007.igem.org/Berkeley_UC">&lt;&lt;&lt; Return to UC Berkeley iGEM 2007 </a></p>
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<p align="center"> <a href="https://2007.igem.org/BerkiGEM2007Present1">&lt;&lt;Previous Section: Oxygen Transport</a> | <a href="https://2007.igem.org/BerkiGEM2007Present3">Next Section: Controller&gt;&gt;</a></p>
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Latest revision as of 23:07, 26 October 2007

Untitled Document

<<< Return to UC Berkeley iGEM 2007

<<Previous Section: Individual Contributions | Next Section: Team Resources>>

Team Notebooks

Team Notebooks



John Dueber's Notebook
Christopher Anderson's Notebook
Farnaz Nowroozi's Notebook
Amin Hajimorad's Notebook
Rickey Bonds' Notebook


Keep your wiki notebooks, sequencing/construction logs, and the registry updated!


Arthur Yu's 1337 Notebook
Austin Day's Notebook
David Tulga's Notebook
Kristin Doan's Notebook
Samantha's Notebook (June - July 19, 2007
Samantha's Notebook (July 20, 2007 - present)
Vaibhavi Umesh's Notebook
Kristin Fuller's Notebook


Vincent Parker's Notebook
Nhu Nguyen's Notebook
Hannah Cole's Notebook