Difference between revisions of "Team:UI Indonesia/InterLab"

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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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<h1>InterLab</h1>
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<h3>Bronze Medal Criterion #4</h3>
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<p><b>Standard Tracks:</b> Participate in the Interlab Measurement Study and/or obtain new, high quality experimental characterization data for an existing BioBrick Part or Device and enter this information on that part's Main Page in the Registry. The part that you are characterizing must NOT be from a 2018 part number range.
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<br><br>
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For teams participating in the <a href="https://2018.igem.org/Measurement/InterLab">InterLab study</a>, all work must be shown on this page.  
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  <a href="https://2018.igem.org/Team:UI_Indonesia">Home</a>
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      <a class="w3-bar-item w3-light-green" href="https://2018.igem.org/Team:UI_Indonesia/Project">Project ⯆</a>
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              <a href="https://2018.igem.org/Team:UI_Indonesia/Project#overview">Overview</a>
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              <a href="https://2018.igem.org/Team:UI_Indonesia/Project#ourproject">Our Project</a>
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              <a href="https://2018.igem.org/Team:UI_Indonesia/Project#resultsanddiscuccions">Results and Discussions</a>
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          </div>
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  <a href="https://2018.igem.org/Team:UI_Indonesia/Modeling">Modeling</a>
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  <a href="https://2018.igem.org/Team:UI_Indonesia/InterlabStudies">Interlab Studies</a>
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  <a href="https://2018.igem.org/Team:UI_Indonesia/HumanPractices">Human Practices</a>
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  <a href="https://2018.igem.org/Team:UI_Indonesia/Collaborations">Collaborations</a>
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  <a href="https://2018.igem.org/Team:UI_Indonesia/Team">Team</a>
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  <a href="https://2018.igem.org/Team:UI_Indonesia/Attributions">Attributions</a>
 
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<!-- Container (Overview Section) -->
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<div class="bgimg-3 w3-display-container w3-opacity-min" id="overview">
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    <span class="w3-center w3-padding-large w3-black w3-xlarge w3-wide w3-animate-opacity">InterLab Studies</span>
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  </div>
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</div>
  
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<div class="w3-content w3-container w3-padding-64">
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<h3><b>Introduction</u></h3>
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<h5>In the field of engineering, repeatable and reproducible measurements are important to obtain valid and reliable results. However, these have been proven difficult to achieve as there are differences in environmental condition of laboratories, individuals conducting the measurements, instruments being used, and other sources of variability. Eventually, this could lead to hindrance of advancements in engineering, including synthetic biology.
 +
<br></br>    For past several years, iGEM Measurement Committee has been working on this issue by encouraging registered iGEM 2018 teams to participate in annual InterLab study. Since its introduction in 2014, the study has been conducted four times, making this year’s study to be the fifth one. The goal of this study is to minimize possible sources of variability in laboratory measurements and thus allowing synthetic biology to attain its full potential as a tool for improving quality of life.
 +
<br></br>
 +
    InterLab study is mainly focused on fluorescence measurements as one of widely utilized protocols in synthetic biology studies. Data obtained from such measurements are often reported in different units, or processed in different methods, thereby hampering fluorescence data comparison. Hence, iGEM Measurement Committee introduces a standardized protocol for green fluorescence protein (GFP) expression level measurement. Previous studies showed that variability of the measurements can be significantly reduced by calibrating measured absolute fluorescence units of expressed GFP against known concentration of florescent molecule. However, when the procedure is carried out against a population of cells, the cell number in given sample makes great variability among measurements. This is due to the values of total cell number used to calculate mean expressed GFP per cell are obtained from optical density (OD), which is a subject to large variability. 
 +
<br></br>
 +
    Therefore, in this year’s InterLab study, participating 2018 iGEM teams are encouraged to help iGEM Measurement Committee in investigating whether more direct method in expressing total cell number for fluorescence calculation, such as absolute cell count or colony-forming units (CFUs), are better than OD to reduce variability in bulk measurement. We proudly announce our participation in 5th InterLab study for the first time ever, in the hope that our results may contribute to the improvements in synthetic biology. Our members contributing in this InterLab study are shown in Figure 1.</h5><br>
  
 +
  <h3><b>Pathogenesis of Diphtheria: How Does Corynebacterium diphtheriae Cause the Disease?<b></h3>
 +
  <h5>C. diphtheriae is a Gram-positive rod bacterium that causes diphtheria. It produces exotoxin with two fragments (AB toxin). Fragment B facilitates toxin internalization within host cell via endocytosis upon binding with HB-EGF receptor. Endosome internal environment allows catalytic process to split AB toxin into separate fragments, while fragment B forms a pore in endosome membrane, allowing fragment A to be transported into host cell cytoplasm. Fragment A then catalyzes modification of elongation factor 2 (EF-2), thereby attenuates protein synthesis and ultimately killing cell. This process underlies several complications found in patients with diphtheria, such as myocarditis, liver and kidney necrosis. In posterior pharynx, diphtheria infection leads to pseudomembrane formation, which is a local reaction and deposition of dead epithelial cells, bacteria, and immune cells enclosed within fibrin. Large formed pseudomembrane potentially causes respiratory tract obstruction and death.</h5><br>
  
 +
  <h3><b>Tar-mediated Chemotaxis System in Escherichia coli<b></h3>
 +
  <h5>Chemotaxis system allows motile living cells to sensitize chemical signals in the environment and moving towards or away from them. This involves signal transduction processes mediated by ligand binding to chemoreceptor. In E. coli, chemotaxis mediated by methyl-accepting chemotaxis proteins (MCPs) has been widely studied. MCPs are transmembrane chemoreceptors with periplasmic ligand binding domain and cytoplasmic signaling domain. To date, four different E. coli MCPs have been identified: Tar, Tsr, Trg and Tap chemoreceptors.</h5><br>
 +
  <h5>Tar chemoreceptor mediates E. coli movement away from nickel and cobalt (repellent molecules), and towards aspartate and maltose (attractant molecules). Its cytoplasmic domain is associated with two proteins, CheW and CheA. CheW mediates signal transduction from Tar chemoreceptor to CheA, while CheA has a kinase domain which autophosphorylates its own histidyl residue. Tar chemoreceptor undergoes conformational change upon repellent molecule binding, leading to CheA activation and thus transfers its phosphoryl group to CheY, a regulatory protein that phosphorylates FliM in basal body of bacterial flagellum. These processes eventually lead the bacterium to swim smoothly away from repellent substance. On the other hand, attractant molecule binding into Tar chemoreceptor inhibits CheA and thus phosphorylation of CheY and FliM will not happen. This causes the bacterial flagellum to rotate in opposite direction and facilitates the bacterium to swim towards attractant substance.</h5><br>
  
 +
  <h3><b>LuxAB-eYFP Fluorescence Resonance Energy Transfer (FRET) System<b></h3>
 +
  <h5>Basically, a molecule is excited to higher energy state when it absorbs a photon energy. This molecule relaxes back to ground state when the energy is emitted back to the environment or transferred into another molecule. FRET is a phenomenon in which non-radioactive energy is transferred from excited donor molecule to acceptor molecule via dipole-dipole interactions. Molecules involved in this phenomenon are called fluorophores as they emit fluorescence according to their respective emission spectrum after absorbing higher photon energy. The fluorescence emission spectrum of donor fluorophore must overlap with the absorption and emission spectrum of acceptor fluorophore for FRET to occur. Furthermore, the efficiency of energy transfer is highly influenced by the physical proximity of interacting fluorophores, being the most efficient at several nanometers. Hence, FRET can be applicated to study the distance of macromolecules such as proteins at molecular level.</h5><br>
 +
  <h5>LuxAB and eYFP are one of the most widely studied paired fluorophores. In this case, LuxAB is the donor fluorophore as it emits cyan colored light with relatively high energy (peak emission at 490 nm). eYFP serves as the acceptor fluorophore when in close contact with LuxAB, as it absorbs high energy from LuxAB that is overlapped with its own absorption spectrum and emits yellow colored light with lower energy (peak emission at 530 nm). To be utilized in macromolecules interaction studies, LuxAB and eYFP should be incorporated with the molecules of interest. When the molecules of interest are in contact, energy transfer between LuxAB and eYFP will happen and its efficiency can be measured with fluorescence-lifetime imaging microscopy method.</h5><br>
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    <span class="w3-center w3-padding-large w3-black w3-xlarge w3-wide w3-animate-opacity">OUR PROJECT</span>
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  <h5 class="w3-center">To be added</h5>
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<div class="bgimg-4 w3-display-container w3-opacity-min" id="resultsanddiscuccions">
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    <span class="w3-center w3-padding-large w3-black w3-xlarge w3-wide w3-animate-opacity">RESULTS AND DISCUSSIONS</span>
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Revision as of 07:56, 26 July 2018

Home
Project ⯆
Overview Our Project Results and Discussions
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InterLab Studies

Introduction

In the field of engineering, repeatable and reproducible measurements are important to obtain valid and reliable results. However, these have been proven difficult to achieve as there are differences in environmental condition of laboratories, individuals conducting the measurements, instruments being used, and other sources of variability. Eventually, this could lead to hindrance of advancements in engineering, including synthetic biology.

For past several years, iGEM Measurement Committee has been working on this issue by encouraging registered iGEM 2018 teams to participate in annual InterLab study. Since its introduction in 2014, the study has been conducted four times, making this year’s study to be the fifth one. The goal of this study is to minimize possible sources of variability in laboratory measurements and thus allowing synthetic biology to attain its full potential as a tool for improving quality of life.

InterLab study is mainly focused on fluorescence measurements as one of widely utilized protocols in synthetic biology studies. Data obtained from such measurements are often reported in different units, or processed in different methods, thereby hampering fluorescence data comparison. Hence, iGEM Measurement Committee introduces a standardized protocol for green fluorescence protein (GFP) expression level measurement. Previous studies showed that variability of the measurements can be significantly reduced by calibrating measured absolute fluorescence units of expressed GFP against known concentration of florescent molecule. However, when the procedure is carried out against a population of cells, the cell number in given sample makes great variability among measurements. This is due to the values of total cell number used to calculate mean expressed GFP per cell are obtained from optical density (OD), which is a subject to large variability.

Therefore, in this year’s InterLab study, participating 2018 iGEM teams are encouraged to help iGEM Measurement Committee in investigating whether more direct method in expressing total cell number for fluorescence calculation, such as absolute cell count or colony-forming units (CFUs), are better than OD to reduce variability in bulk measurement. We proudly announce our participation in 5th InterLab study for the first time ever, in the hope that our results may contribute to the improvements in synthetic biology. Our members contributing in this InterLab study are shown in Figure 1.

Pathogenesis of Diphtheria: How Does Corynebacterium diphtheriae Cause the Disease?

C. diphtheriae is a Gram-positive rod bacterium that causes diphtheria. It produces exotoxin with two fragments (AB toxin). Fragment B facilitates toxin internalization within host cell via endocytosis upon binding with HB-EGF receptor. Endosome internal environment allows catalytic process to split AB toxin into separate fragments, while fragment B forms a pore in endosome membrane, allowing fragment A to be transported into host cell cytoplasm. Fragment A then catalyzes modification of elongation factor 2 (EF-2), thereby attenuates protein synthesis and ultimately killing cell. This process underlies several complications found in patients with diphtheria, such as myocarditis, liver and kidney necrosis. In posterior pharynx, diphtheria infection leads to pseudomembrane formation, which is a local reaction and deposition of dead epithelial cells, bacteria, and immune cells enclosed within fibrin. Large formed pseudomembrane potentially causes respiratory tract obstruction and death.

Tar-mediated Chemotaxis System in Escherichia coli

Chemotaxis system allows motile living cells to sensitize chemical signals in the environment and moving towards or away from them. This involves signal transduction processes mediated by ligand binding to chemoreceptor. In E. coli, chemotaxis mediated by methyl-accepting chemotaxis proteins (MCPs) has been widely studied. MCPs are transmembrane chemoreceptors with periplasmic ligand binding domain and cytoplasmic signaling domain. To date, four different E. coli MCPs have been identified: Tar, Tsr, Trg and Tap chemoreceptors.

Tar chemoreceptor mediates E. coli movement away from nickel and cobalt (repellent molecules), and towards aspartate and maltose (attractant molecules). Its cytoplasmic domain is associated with two proteins, CheW and CheA. CheW mediates signal transduction from Tar chemoreceptor to CheA, while CheA has a kinase domain which autophosphorylates its own histidyl residue. Tar chemoreceptor undergoes conformational change upon repellent molecule binding, leading to CheA activation and thus transfers its phosphoryl group to CheY, a regulatory protein that phosphorylates FliM in basal body of bacterial flagellum. These processes eventually lead the bacterium to swim smoothly away from repellent substance. On the other hand, attractant molecule binding into Tar chemoreceptor inhibits CheA and thus phosphorylation of CheY and FliM will not happen. This causes the bacterial flagellum to rotate in opposite direction and facilitates the bacterium to swim towards attractant substance.

LuxAB-eYFP Fluorescence Resonance Energy Transfer (FRET) System

Basically, a molecule is excited to higher energy state when it absorbs a photon energy. This molecule relaxes back to ground state when the energy is emitted back to the environment or transferred into another molecule. FRET is a phenomenon in which non-radioactive energy is transferred from excited donor molecule to acceptor molecule via dipole-dipole interactions. Molecules involved in this phenomenon are called fluorophores as they emit fluorescence according to their respective emission spectrum after absorbing higher photon energy. The fluorescence emission spectrum of donor fluorophore must overlap with the absorption and emission spectrum of acceptor fluorophore for FRET to occur. Furthermore, the efficiency of energy transfer is highly influenced by the physical proximity of interacting fluorophores, being the most efficient at several nanometers. Hence, FRET can be applicated to study the distance of macromolecules such as proteins at molecular level.

LuxAB and eYFP are one of the most widely studied paired fluorophores. In this case, LuxAB is the donor fluorophore as it emits cyan colored light with relatively high energy (peak emission at 490 nm). eYFP serves as the acceptor fluorophore when in close contact with LuxAB, as it absorbs high energy from LuxAB that is overlapped with its own absorption spectrum and emits yellow colored light with lower energy (peak emission at 530 nm). To be utilized in macromolecules interaction studies, LuxAB and eYFP should be incorporated with the molecules of interest. When the molecules of interest are in contact, energy transfer between LuxAB and eYFP will happen and its efficiency can be measured with fluorescence-lifetime imaging microscopy method.

OUR PROJECT
To be added
RESULTS AND DISCUSSIONS
To be added
Team UI Indonesia
  igemui2018@gmail.com