Difference between revisions of "Team:FAU Erlangen/Description"

 
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<div id="myquote" style="color:#fff; font-size:22px; padding: 15px; line-height:30px;"> <br/><br/><br/>"The best way to predict the future is to create it." <br/> <em>Abraham Lincoln</em></div>
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          <li><a class="hlight" href="https://2016.igem.org/Team:FAU_Erlangen/Description">Project</a><ul>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Description#Inspiration"><li>Inspiration</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Description#Biofilm"><li>Biofilm</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Description#BioSolar"><li>Grätzel Cell</li></a>
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          <li><a class="" href="https://2016.igem.org/Team:FAU_Erlangen/Results">Results</a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Results#Inspiration"><li>Growing Biofilms</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Results#Biofilm"><li>Binding of Heavy Metals</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Results#BioSolar"><li>ZnO Mineralization</li></a>
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                <a href="https://2016.igem.org/Team:FAU_Erlangen/Results#GCell"><li>Solar cell results</li></a>
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                <a href="https://2016.igem.org/Team:FAU_Erlangen/Results#Parts"><li>References</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Notebook#Inspiration"><li>Biology</li></a>
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                <a href="https://2016.igem.org/Team:FAU_Erlangen/Notebook#BioSolar"><li>References</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Human_Practices#Inspiration"><li>School laboratory</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Human_Practices#Biofilm"><li>Science Day</li></a>
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          </ul>
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          <li><a class="" href="https://2016.igem.org/Team:FAU_Erlangen/Collaborations">Collaborations</a>
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          <ul>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Collaborations#Inspiration"><li>iGEM Team Aachen</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Collaborations#Biofilm"><li>iGEM Team Munich</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Collaborations#BioSolar"><li>iGEM Team Marburg</li></a>
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          </ul></li>
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          <li><a class="" href="https://2016.igem.org/Team:FAU_Erlangen/Safety">Safety</a><ul>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Safety#Inspiration"><li>Killswitch</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Safety#Biofilm"><li>Binding of Heavy Metals</li></a>
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              <a href="https://2016.igem.org/Team:FAU_Erlangen/Safety#BioSolar"><li>References</li></a>
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          </ul></li>
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          <li><a class="" href="https://2016.igem.org/Team:FAU_Erlangen/Achievements">Achievements</a></li>
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          <li><a class="" href="https://2016.igem.org/Team:FAU_Erlangen/Team">Team</a></li>
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<a href="#BioSolar" id="cBioSolar"><li>Grätzel Cell</li></a>
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<a href="#GCell" id="cGCell"><li>Parts</li></a>
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<h5> Fabrication of Semiconducting Biofilms for Solar Cell Application </h5>
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<p class="cb" id="Inspiration"></p>
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<h1 id=""style="border-bottom: solid thin #aaa">Inspiration</h1>
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<p style="font-size:22px">
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The limitation of fossil fuels such as oil, coal and gas intensifies the need to find different sources to provide energy for a constantly rising world population. Renewable energy can be supplied by natural agents such as wind, water, plants or the sun. The conversion of solar energy in particular is a crucial issue as the sun presents an inexhaustible and easily accessible energy source for most inhabited regions of the Earth. Thus, optimizing the balance between efficient conversion of solar energy and the affordability and ease-of-manufacturing of solar cells is an important task for the future. In this regard, lower production costs will benefit manufacturer, customer, and the environment alike.  <br/><br/>
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Commercially available silicon solar cells provide a decent solar energy conversion rate in combination with moderate costs. As with most technologies, these factors may be improved by imitating natural processes, in this case photosynthesis. Upon absorption of a photon, a chlorophyll molecule is excited and donates its high energy electron into a redox cascade. This principle can be applied to solar cells by adding dyes that transfer electrons to a transparent semiconductor. Possible semiconductors are zinc oxide (ZnO) and titanium dioxide (TiO<sub>2</sub>), which are both produced in large quantities as ingredients of tooth paste, sun screen etc. <br/><br/>
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To reduce the production costs, a large area of the solar cell can be covered by autonomously working, living bacteria. Especially biofilms provide a promising approach because they can integrate metals into their structure and may be mineralized. Hence, the transparent semiconductor can be deposited by adding the initial salts to the bacteria solution. Mineralization may be performed either during the growth of the biofilm or after its growth. The electron donating dyes can also be provided by <i>Escherichia coli</i>, which was demonstrated by the iGEM team from <a href="https://2014.igem.org/Team:TU_Darmstadt">Darmstadt</a> in 2014. The only technical process is the deposition of the electrolyte and the sealing of the complete solar cell, which prevents the cell from drying out.  <br/>
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<h1 id="" style="border-bottom: solid thin #aaa">Biofilm</h1>
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<p style="font-size:22px">
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According to a IUPAC recommendation, a biofilm is an... “Aggregate of microorganisms in which cells that are frequently embedded within a self-produced matrix of extracellular polymeric substance (EPS) adhere to each other and/or to a surface. [...] A biofilm is a system that can be adapted internally to environmental conditions by its inhabitants. […] The self-produced matrix of EPS, which is also referred to as slime, is a polymeric conglomeration generally composed of extracellular <i>biopolymers</i> in various structural forms.” (Vert et al., 2012).
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<div style="margin: 0 auto" align="center">
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<img src="https://static.igem.org/mediawiki/2016/c/c5/Team_Erlangen_Bio1.png" width="80%" height="auto" alt=""style="display: block margin: auto"/>
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<p style="font-size:16px; color:#333; text-align:center">
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Figure 1: Steps of formation and maturation of a biofilm (Vlamakis et al., 2013).
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</p>
  
<p>Since common energy resources such as oil and gas become rare and rare, the importance of renewable and sustainable energy resources rises continuously. Considering sustainability, nature provides a vast field for future power supply reaching from wind and water to solar energy. Further the production of biomass and the formation of biogas (methane) by bacteria should also be considered. The iGEM Team of the University Erlangen-Nuremberg aims to integrate current research in the preparation of conducting and semiconducting biofilms [1] to fabricate a series of novel highly absorbing layers in a bottom-up approach from the initial salts. We focus on the control of electron transport through the biofilms as it is crucial for optimization of the system. The result of our research can pave the way to a novel class of solar cells mainly fabricated by living cells. 
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<p style="font-size:22px">
In a first set of experiments, we will combine chemically and biologically synthesized zinc oxide (ZnO) as a wide band gap semiconductor with organic dye molecules and fluorescing proteins to inspect the charge transfer through a biofilm matrix. The emphasis lies on the layer thickness and the morphology of the biofilm, as well as the size of the ZnO colloids, which will affect the electron transport.
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Bacteria form the three-dimensional structures shown in Figure 1 to survive in the face of environmental stress. To assemble these aggregates, the bacteria have to specialize themselves to attach to the surface and to communicate with other microorganisms. In the process, they will lose their flagella, produce proteins for quorum sensing and induce expression of extracellular polymeric substances usually called slime.
In the second part, we will address the integration of chemically synthesized, strongly absorbing nanoscale semiconductors into biofilms to analyze the film morphology and the affinity of the different types of nanoparticles to the biofilms.  
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</p>
In the third stage we plan to replace the chemical route by biological fabrication of the nanoparticles. Both biofilms (ZnO/Absorber) will be deposited on a substrate, yielding the basic structure of a solar cell, which can be expanded to a complete device using physical or chemical deposition techniques. This primary device will be characterized regarding its photoinduced electron transfer and efficiency. </p>
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<p><i>State of the Art </i></p>
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<h2>The importance of curli fibers for our project</h2>
<p>The rising field of nanoparticular systems is attributed to their unique properties in terms of reactivity and spectroscopic behavior.[2, 3] Thus, biologic routes towards different types of nanoparticles are of current interest, as their “biosynthesis” avoids toxic stabilizing ligands and solvents, which is a crucial aspect of sustainable synthesis.[4] The formation of metal clusters exploits the natural defense mechanism of microorganisms against high metal concentrations.[5] With this strategy, a broad variety of colloids have already been realized, from metallic [6] to semiconducting nanoparticles, also called quantum dots.[4] In the field of semiconducting nanoparticles, metal sulfides are promising absorber materials, being easy to fabricate using bacteria and achieving good yields and morphology.[7] Additionally, Zinc oxide, which can serve as transparent top layer for solar cells, can also be fabricated by bacteria that can tolerate high amounts of zinc in solution.[8] </p>
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<p style="font-size:22px">
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Curli fibers, or simply curli, are thin, extracellular, proteinaceous structures produced by E.coli and other bacteria. Next to influencing community behavior and host cell adhesion, these amyloid fibers play a role in surface contacts and cell aggregation and mediate the formation of biofilms (Barnhart and Chapman, 2006). <br/><br/>
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Curli-related proteins are the products of two operons containing seven genes in total: csgBAC and csgDEFG. Of the seven proteins, CsgD is the transcriptional regulator and CsgE/F are responsible for the processing of CsgA. CsgC mediates the secretion of CsgA through the translocator CsgG. CsgB serves as the origin of nucleation and anchors CsgA, which makes up the majority of curli fibers, to the outer membrane (Nguyen et al., 2014; Hobley et al., 2015). The production of curli is demonstrated in Figure 2.
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</p>
  
<p>Biofilms are aggregates of microorganisms frequently embedded within an extracellular matrix promoting adherence of cells to each other and to surfaces.[9] Biofilms are dynamic structures, selforganizing and highly adaptive to their environment. As materials, biofilms and similar multicellular consortia such as bone or shells have various characteristics that are of interest for technological applications.[10]
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<div style="margin: 0 auto" align="center">
Recently, semiconducting nanoparticles such as CdTe, CdS and ZnS have been successfully integrated into biofilms.[1] This was accomplished by conjugating the nanoparticles with antibodies or appropriate peptide tags, which in turn were linked to amyloid fibrils (curli) produced by E. coli cells. This attempt was further expanded by integrating gold nanoparticles into the film to address electric conductivity in biofilms. A direct preparation of silver nanoparticles within the biofilm matrix has also been shown to facilitate conductivity.[11]
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<img src="https://static.igem.org/mediawiki/2016/e/ed/Team_Erlangen_Bio2.png" width="40%" height="auto" alt=""style="display: block margin: auto"/>
We intend to pick up this approach to program bacteria to build a scaffold for a solar cell, utilizing the unique ability of living materials to self-organize into nanoscale structures. </p>
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<p style="font-size:16px; color:#333; text-align:center">
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Figure 2: Biosynthetic pathway and formation of curli fibers from CsgA subunits (Hobley et al., 2015)
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</p>
  
<p>Nanoscale semiconductors provide a powerful platform for the development of numerous classes of solution-processed optoelectronic devices such as photovoltaic cells, photodetectors and lightemission devices. In addition to enabling solution processing, a key advantage of quantum dots is the size confinement effect: optical and electrical properties can be adjusted by varying the size and shape of the nanoparticles. In photovoltaic devices, quantum dot films are combined with a metal (Schottky junction cells) or with another semiconductor (TiO2/ZnO) to form a functional device.[12, 13]
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<p style="font-size:22px">
Against the background of nanoparticle solar cells, thin film solar cells provide a powerful tool to reduce the amount of material required for fabrication of solar cells. Different highly absorbing metal sulfide and metal selenide materials present the opportunity to reduce the layer thickness of the absorption layer to less than 5 µm. [14] A crucial limitation in the field of thin film solar cells is the Shockley-Queisser limit [15], describing the compromise between charge separation and absorption quality of the film; charge separation accelerates with decreasing layer thickness, while light absorption rises with increasing layer thickness. </p>
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Up to 40% of the total biofilm volume can be occupied by curli (Nguyen et al., 2014). Since curli consist mostly of CsgA monomers that interact with each other and possibly with other substances in the biofilm, modifying these monomers provides a simple way to change the properties of the whole biofilm.
<p><i>References </i></p>
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</p>
<p>1 Lu T. et al. Nat. Mater. 2014, 13 (5), 515-523. </p>
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<p>2 Carey G.; Abdelhady L.; Ning Z.; Thon S.; Bakr O.; Sargent E. Chem. Rev. 2015, 115 (23), 1273212763. </p>
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<p>3 Yang Y.; Wu H.; Williams K.; Cao Y. Angew. Chem. 2005, 117 (41), 6870-6873.  </p>
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<p>4 Hosseini M.; Sarvi M. Mater. Sci. Semicond. Process. 2015, 40, 293-301. </p>
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<p>5 Ikuma K.; Decho A.; Lau B. Front. Microbiol. 2015, 6, 591.  </p>
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<p>6 Thakkar K.; Mhatre S.; Parikh R. Biol. Med. 2010, 6 (2), 257-262.  </p>
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<p>7 Jacob J.; Lens P.; Balakrishnan R. Microb. Biotechnol. 2016, 9 (1), 11-21.  </p>
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<p>8 Jayaseelan C.; Rahuman A.; Kirthi A.; Marimuthu S.; Santhoshkumar T.; Bagavan A.; Rao K. Spectrochim. Acta, Part A 2012, 90, 78-84. </p>
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<p>9 http://pac.iupac.org/publications/pac/pdf/2012/pdf/8402x0377.pdf (state: 03/27/2016) </p>
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<p>10 Rezwan K.; Chen Q.; Blaker J.; Boccachini A. Biomaterials 2006, 27 (18), 3413-3431. </p>
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<p>11 Kalathil S.; Lee J.; Cho M. Green Chem. 2011, 13 (6), 1482-1485.  </p>
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<p>12 Gur I.; Fromer N.; Geier M.; Alivisatos A. Science 2005, 310 (5747), 462-465. </p>
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<p>13 Carey G.; Abdelhady A.; Ning Z.; Thon S.; Bakr O.; Sargent E. Chem. Rev. 2015, 115 (23), 1273212763. </p>
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<p>14 Aberle A. Thin Solid Films 2009, 517 (17), 4706-4710. </p>
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<p>15 Shockley W.; Queisser H. J. Appl. Phys. 1961, 32 (3), 510-519. </p>
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<h1 style="border-bottom: solid thin #aaa">Grätzel Cell</h1>
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<h2>Setup of a Dye Sensitized Solar Cell</h2>
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<p style="font-size:22px">
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A dye sensitized solar cell (DSSC) does not require expensive material or complex working conditions. It can be literally built out of tooth paste or sun screen combined with a dye obtained from fruits or tea. The starting layer is a glass slide coated with a transparent conducting material. Commonly used coating materials are indium tin oxide (ITO) or fluorine doped tin oxide (FTO). The transparent semiconductors ZnO or TiO<sub>2</sub> can be deposited on the conducting slide and serve as the electron transporting layer, which is then soaked with a dye. Functional groups of the dye molecules direct and anchor them on the surface of the semiconductor. An electrolyte containing iodine and iodide is added onto this layer to provide electrons and facilitate current flow. The cell is completed with another glass slide coated with traditional conducting materials such as graphite or platinum.
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</p>
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<h2>Mechanism of a DSSC</h2>
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<p style="font-size:22px">
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Upon irradiation of the solar cell, the electrons in the organic dye are excited to a higher level, called the lowest unoccupied molecular orbital (LUMO). If the LUMO level is energetically high enough, the electron can be transferred to the conduction band of the transparent semiconductor and from there continue to the anode. The missing electron of the dye is restored by the electrolyte and the electrolyte regains its electron from the cathode. This results in a continuous current flow for the duration of the irradiation.
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<h1 style="border-bottom: solid thin #aaa">Parts</h1>
  
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<table width="100%" border="1" style="margin-left:2%;">
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      <td>Zinc Oxide binding Peptide:</td>
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      <td>part:BBa_K2169137</td>
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      <td>Zinc Sulfide nucleation peptide:</td>
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      <td>part:BBa_K2169138</td>
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      <td>Zinc Oxide bindings CsgA:</td>
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      <td>part:BBa_K2169001</td>
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      <td>Metal sulfide binding CsgA:</td>
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      <td>part:BBa_K2169000</td>
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<p class="cb" id="Parts"></p>
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<h1 style="border-bottom: solid thin #aaa">References</h1>
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<ul style="list-style:none; line-height:20px; font-size:18px;">
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<li> Barnhart, M. M., & Chapman, M. R. (2006). Curli biogenesis and function. <i>Annual review of microbiology, 60</i>, 131. doi: 10.1146/annurev.micro.60.080805.142106</li><br/>
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<li>Hobley, L., Harkins, C., MacPhee, C. E., & Stanley-Wall, N. R. (2015). Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. <i>FEMS microbiology reviews, 39</i>(5), 649-669. doi: 10.1093/femsre/fuv015</li><br/>
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<li>Nguyen, P. Q., Botyanszki, Z., Tay, P. K. R., & Joshi, N. S. (2014). Programmable biofilm-based materials from engineered curli nanofibres. <i>Nature communications, 5</i>. doi: 10.1038/ncomms5945</li><br/>
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<li>Vert, M., Hellwich, K. H., Hess, M., Hodge, P., Kubisa, P., Rinaudo, M., & Schué, F. (2012). Terminology for biorelated polymers and applications (IUPAC Recommendations 2012). <i>Pure and Applied Chemistry, 84</i>(2), 377-410. doi: 10.1351/PAC-REC-10-12-04</li><br/>
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<li>Vlamakis, H., Chai, Y., Beauregard, P., Losick, R., & Kolter, R. (2013). Sticking together: building a biofilm the <i>Bacillus subtilis</i> way. <i>Nature Reviews Microbiology, 11</i>(3), 157-168. doi: 10.1038/nrmicro2960</li><br/>
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Latest revision as of 03:41, 20 October 2016

iGEM Erlangen


Inspiration

The limitation of fossil fuels such as oil, coal and gas intensifies the need to find different sources to provide energy for a constantly rising world population. Renewable energy can be supplied by natural agents such as wind, water, plants or the sun. The conversion of solar energy in particular is a crucial issue as the sun presents an inexhaustible and easily accessible energy source for most inhabited regions of the Earth. Thus, optimizing the balance between efficient conversion of solar energy and the affordability and ease-of-manufacturing of solar cells is an important task for the future. In this regard, lower production costs will benefit manufacturer, customer, and the environment alike.

Commercially available silicon solar cells provide a decent solar energy conversion rate in combination with moderate costs. As with most technologies, these factors may be improved by imitating natural processes, in this case photosynthesis. Upon absorption of a photon, a chlorophyll molecule is excited and donates its high energy electron into a redox cascade. This principle can be applied to solar cells by adding dyes that transfer electrons to a transparent semiconductor. Possible semiconductors are zinc oxide (ZnO) and titanium dioxide (TiO2), which are both produced in large quantities as ingredients of tooth paste, sun screen etc.

To reduce the production costs, a large area of the solar cell can be covered by autonomously working, living bacteria. Especially biofilms provide a promising approach because they can integrate metals into their structure and may be mineralized. Hence, the transparent semiconductor can be deposited by adding the initial salts to the bacteria solution. Mineralization may be performed either during the growth of the biofilm or after its growth. The electron donating dyes can also be provided by Escherichia coli, which was demonstrated by the iGEM team from Darmstadt in 2014. The only technical process is the deposition of the electrolyte and the sealing of the complete solar cell, which prevents the cell from drying out.


Biofilm

According to a IUPAC recommendation, a biofilm is an... “Aggregate of microorganisms in which cells that are frequently embedded within a self-produced matrix of extracellular polymeric substance (EPS) adhere to each other and/or to a surface. [...] A biofilm is a system that can be adapted internally to environmental conditions by its inhabitants. […] The self-produced matrix of EPS, which is also referred to as slime, is a polymeric conglomeration generally composed of extracellular biopolymers in various structural forms.” (Vert et al., 2012).

Figure 1: Steps of formation and maturation of a biofilm (Vlamakis et al., 2013).

Bacteria form the three-dimensional structures shown in Figure 1 to survive in the face of environmental stress. To assemble these aggregates, the bacteria have to specialize themselves to attach to the surface and to communicate with other microorganisms. In the process, they will lose their flagella, produce proteins for quorum sensing and induce expression of extracellular polymeric substances usually called slime.

The importance of curli fibers for our project

Curli fibers, or simply curli, are thin, extracellular, proteinaceous structures produced by E.coli and other bacteria. Next to influencing community behavior and host cell adhesion, these amyloid fibers play a role in surface contacts and cell aggregation and mediate the formation of biofilms (Barnhart and Chapman, 2006).

Curli-related proteins are the products of two operons containing seven genes in total: csgBAC and csgDEFG. Of the seven proteins, CsgD is the transcriptional regulator and CsgE/F are responsible for the processing of CsgA. CsgC mediates the secretion of CsgA through the translocator CsgG. CsgB serves as the origin of nucleation and anchors CsgA, which makes up the majority of curli fibers, to the outer membrane (Nguyen et al., 2014; Hobley et al., 2015). The production of curli is demonstrated in Figure 2.

Figure 2: Biosynthetic pathway and formation of curli fibers from CsgA subunits (Hobley et al., 2015)

Up to 40% of the total biofilm volume can be occupied by curli (Nguyen et al., 2014). Since curli consist mostly of CsgA monomers that interact with each other and possibly with other substances in the biofilm, modifying these monomers provides a simple way to change the properties of the whole biofilm.


Grätzel Cell

Setup of a Dye Sensitized Solar Cell

A dye sensitized solar cell (DSSC) does not require expensive material or complex working conditions. It can be literally built out of tooth paste or sun screen combined with a dye obtained from fruits or tea. The starting layer is a glass slide coated with a transparent conducting material. Commonly used coating materials are indium tin oxide (ITO) or fluorine doped tin oxide (FTO). The transparent semiconductors ZnO or TiO2 can be deposited on the conducting slide and serve as the electron transporting layer, which is then soaked with a dye. Functional groups of the dye molecules direct and anchor them on the surface of the semiconductor. An electrolyte containing iodine and iodide is added onto this layer to provide electrons and facilitate current flow. The cell is completed with another glass slide coated with traditional conducting materials such as graphite or platinum.

Mechanism of a DSSC

Upon irradiation of the solar cell, the electrons in the organic dye are excited to a higher level, called the lowest unoccupied molecular orbital (LUMO). If the LUMO level is energetically high enough, the electron can be transferred to the conduction band of the transparent semiconductor and from there continue to the anode. The missing electron of the dye is restored by the electrolyte and the electrolyte regains its electron from the cathode. This results in a continuous current flow for the duration of the irradiation.


Parts

Zinc Oxide binding Peptide: part:BBa_K2169137
Zinc Sulfide nucleation peptide: part:BBa_K2169138
Zinc Oxide bindings CsgA: part:BBa_K2169001
Metal sulfide binding CsgA: part:BBa_K2169000


References

  • Barnhart, M. M., & Chapman, M. R. (2006). Curli biogenesis and function. Annual review of microbiology, 60, 131. doi: 10.1146/annurev.micro.60.080805.142106

  • Hobley, L., Harkins, C., MacPhee, C. E., & Stanley-Wall, N. R. (2015). Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. FEMS microbiology reviews, 39(5), 649-669. doi: 10.1093/femsre/fuv015

  • Nguyen, P. Q., Botyanszki, Z., Tay, P. K. R., & Joshi, N. S. (2014). Programmable biofilm-based materials from engineered curli nanofibres. Nature communications, 5. doi: 10.1038/ncomms5945

  • Vert, M., Hellwich, K. H., Hess, M., Hodge, P., Kubisa, P., Rinaudo, M., & Schué, F. (2012). Terminology for biorelated polymers and applications (IUPAC Recommendations 2012). Pure and Applied Chemistry, 84(2), 377-410. doi: 10.1351/PAC-REC-10-12-04

  • Vlamakis, H., Chai, Y., Beauregard, P., Losick, R., & Kolter, R. (2013). Sticking together: building a biofilm the Bacillus subtilis way. Nature Reviews Microbiology, 11(3), 157-168. doi: 10.1038/nrmicro2960