Difference between revisions of "Team:Leiden/RPM"

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  <body id="myPage" data-spy="scroll" data-target=".navbar" data-offset="60">
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   <h1>
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   <div id="body-wrapper">
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   RPM Labjournal
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   <div id="nav-background" style="position: fixed; top: 15px;">
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  </h1>
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  </div>
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  <h2>
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   <div id="header_html" data-source="https://2016.igem.org/Team:Leiden/navbar?action=raw">
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   Experimental setup
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  </div>
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  </h2>
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   <div id="header-background" style="background-image: url('https://static.igem.org/mediawiki/2016/b/bf/Team-Leiden-images-headers-image15.jpg');">
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  <p>
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   </div>
−
   The Random Positioning Machine is a device that can simulate microgravity and partial gravity, designed by Airbus Defence and Space. By constantly rotating, it averages out effective gravity on longer time scales, as for bacterial growth are involved. In this way, we can study the effects of lower gravitational levels on bacteria in our labs on earth.
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   <div class="jumbotron text-center">
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  <br />
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     <p style="font-size: 100px; color: white; text-align: center; font-family: Montserrat, sans-serif; font-weight: normal;">
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  Four strains were studied this experiment:
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     RPM
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   <br />
+
     </p>
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   <ul>
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  </div>
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     <li>
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  <div id="Science behind the project" style="margin-top: -120px;" class="container-fluid bg-white">
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     <i>
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     <div class="row">
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      E. coli
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     <div class="col-sm-2">
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    </i>
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     </div>
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    DH5&alpha;
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     <div class="col-sm-8" style="text-align: justify;">
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     </li>
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      <h2 style="margin-bottom: 20px;">
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    <li>
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      Random Positioning Machine
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    <i>
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       </h2>
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      E. coli
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      <p>
−
    </i>
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      In space, many conditions are vastly different from what life is exposed to here on Earth. Though we can protect ourselves and bacteria to some of these conditions passively (e.g. through temperature and radiation shielding), changes in gravity cannot be evaded.
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    TOP10
+
      </p>
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    </li>
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      <p>
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     <li>
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      This led us to pose the question: “What are the effects of microgravity and Martian gravity on gene expression in
−
     <i>
+
      <i>
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      E. coli
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        E. coli
−
     </i>
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      </i>
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     BW25113
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      , compared to gene expression under Terran gravity?” But how on Earth can we study reduced gravity… on Earth? To this end we used the random positioning machine (RPM) by Airbus Defence and Space Netherlands, which allows us to simulate partial and microgravity.
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    </li>
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      <sup>
−
    <li>
+
        <a href="https://2016.igem.org/Team:Leiden/#references">
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    <i>
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        1
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       Pseudomonas putida
+
        </a>
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    </i>
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      </sup>
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    S12
+
      </p>
−
    </li>
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      <p>
−
  </ul>
+
      We decided to take on an ambitious approach and sequence E. coli’s entire transcriptome, using state-of-the-art RNAseq. This allows us to see every RNA inside
−
  First the time needed to get OD of around 0.4 is determined for each strain. Next different dilution are tested to obtain the desired number of colonies on each plate. Finally this knowledge is used to grow around 50 colonies on a plate both in and next to the RPM to monitor differences in morphology.
+
      <i>
−
  <h2>
+
        E. coli
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    Inoculating strains from plates
+
      </i>
−
  </h2>
+
      at a given time, providing a helicopter view of the changes occurring inside the bacteria. Though microgravity has been studied many times before, we are the first to study the effects of Martian gravity in
−
  </p>
+
      <i>
−
  <p>
+
        E. coli
−
  <i>
+
      </i>
−
    Day1: 2016/07/11
+
      . Moreover, many previous microgravity experiments involved microarrays, which can only detect changes in RNAs which are already known.
−
  </i>
+
      <a href="https://2016.igem.org/Team:Leiden/RNASeq">
−
  <br />
+
        RNAseq
−
  <b>
+
      </a>
−
    Investigator(s): Valentijn Broeken
+
      on the other hand, sequences RNAs indiscriminately. Following our RPM experiment,
−
  </b>
+
      <a href="https://2016.igem.org/Team:Leiden/RNASeq">
−
  <br />
+
        RNAseq
−
  <b>
+
      </a>
−
    Procedure
+
      was performed by BaseClear and subsequent analyses were performed by us.
−
  </b>
+
      </p>
−
  :
+
      <p>
−
After the strains were taken from the freezer and grown on solid LB medium, colonies were transferred to liquid LB medium. By making a dilution series of this culture, the optimal bacterial density (i.e. preferred dilution series) to be used on the plates in the RPM will be determined.
+
      The eventual goal of this experiment is to verify that our perchlorate reduction system will be expressed under Martian gravity. Furthermore, we will search for highly expressed genes that react in a gravity dependent manner and use the accompanied regulatory sequences to develop a biobrick for gravity dependent gene expression.
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  <ul>
+
      </p>
−
    <li>
+
      <img src="https://static.igem.org/mediawiki/2016/b/b3/Team-Leiden-images-rpm-1.png" style="width: 100%;" />
−
    For each strain, a 100 mL erlenmeyer was filled with 20 mL LB medium.
+
      <p>
−
    </li>
+
      <b>
−
    <li>
+
        The effects of low orbit gravity
−
    Seven colonies per strain were transferred from the plates to the flask using an &ouml;se.
+
      </b>
−
    </li>
+
      <br />
−
    <li>
+
      Multiple studies in the International Space Station (ISS) showed that in many cases bacteria grow faster, show increased virulence, and can even be less susceptible to antibiotics when growing in the microgravity of Lower Earth Orbit (LEO).
−
    These were grown overnight at 30 &deg;C and 200 rpm, starting at 17:00.
+
      <sup>
−
    </li>
+
        <a href="https://2016.igem.org/Team:Leiden/#references">
−
  </ul>
+
        2,3
−
  </p>
+
        </a>
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  <h2>
+
      </sup>
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  Colonies on plate
+
      We are keen to find out whether the effect of Martian gravity resembles that of microgravity, or if Mars is more reminiscent of Earth with respect to bacterial growth. Before conducting costly and time-consuming RNAseq, we characterized
−
  </h2>
+
      <i>
−
  <p>
+
        E. coli
−
  <i>
+
      </i>
−
    Day2: 2016/07/12
+
      (BW25113) growth through visual inspection of colonies in three conditions:
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  </i>
+
      <ul>
−
  <br />
+
        <li>
−
  <b>
+
        Gravity on Earth: 1g
−
    Investigator(s): Wouter Liefting
+
        </li>
−
  </b>
+
        <li>
−
  <br />
+
        Martian gravity: 0.38g
−
  <b>
+
        </li>
−
    Procedure
+
        <li>
−
  </b>
+
        Microgravity: 0g
−
  :
+
        </li>
−
In the mean time some experiments have been done and from these experiments the following results follow:
+
      </ul>
−
  <br />
+
      </p>
−
  <br />
+
      <img src="https://static.igem.org/mediawiki/2016/3/39/Team-Leiden-images-rpm-2.png" style="width: 100%;" />
−
  <b>
+
       <i>
−
    Getting the right OD
+
      Source: http://mars.nasa.gov/allaboutmars/facts/#?c=inspace&s;=distance
−
  </b>
+
      </i>
−
  <br />
+
      <p>
−
  <br />
+
      Of course, we cannot actually travel to Mars to experience its gravity, but instead, we used the Random Positioning Machine (RPM 2.0) by Airbus Defence and Space Netherlands. This machine constantly rotates the samples over three axes, averaging gravity out on longer timescales. By reprogramming the motion pattern of the RPM so that it will stay longer in the bottom part, the sample experiences (simulated) partial gravity.
−
  Grown in 20 mL LB in 100 mL erlenmeyer in shaker at 30 &amp;degC.;
+
      </p>
−
  </p>
+
      <p>
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  <table id="t01">
+
      <b>
−
  <tr>
+
        Results: visual inspection (0g vs. 1g)
−
    <th>
+
      </b>
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    </th>
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      <br />
−
    <th>
+
      E. coli BW25113 was plated on LB and in duplo exposed to microgravity in the Random Positioning Machine. Just besides the RPM, plates with the same dilutions were placed at ‘normal’ surface gravity of the Earth. After less than 22 hours, the difference between the plates (in and next to the RPM) were clearly visible: colonies are larger when grown in microgravity than when grown in 1g. Two plates are shown below as an example:
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    <i>
+
      </p>
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      E. coli
+
      <img src="https://static.igem.org/mediawiki/2016/5/5c/Team-Leiden-images-rpm-3.png" style="width: 100%;" />
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    </i>
+
       <p>
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    DH5&alpha;
+
      This reaffirms the expected change in growth and bacterial physiology under reduced gravity. Note that these bacteria were grown at room temperature for practical reasons. The subsequent RNAseq experiment was performed with the RPM enclosed in a stove at a constant 37ºC.
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    </th>
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      </p>
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    <th>
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      <p>
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    <i>
+
      <b>
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      E. coli
+
        Results:
−
    </i>
+
        <a href="https://2016.igem.org/Team:Leiden/RNAseq">
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    TOP10
+
        RNAseq
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    </th>
+
        </a>
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    <th>
+
        (0g vs. 0.38g vs. 1g)
−
    <i>
+
      </b>
−
      E. coli
+
      Below, you can read the abstract of the
−
    </i>
+
      <a href="https://2016.igem.org/Team:Leiden/RNAseq">
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    BW25113
+
        RNAseq
−
    </th>
+
      </a>
−
    <th>
+
      experiment. Click any of the links to the
−
    <i>
+
      <a href="https://2016.igem.org/Team:Leiden/RNAseq">
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      Pseudomonas putida
+
        RNAseq
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    </i>
+
      </a>
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    S12
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      page for the full report.
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    </th>
+
      <br />
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  </tr>
+
      <i>
−
  <tr>
+
        Abstract
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    <td>
+
      </i>
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    Growth time
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      We compared
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    </td>
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      <i>
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    <td>
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        E. coli
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    4.5h
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      </i>
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    </td>
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      BW25113 bacteria under three different conditions: controls (1g) simulating Martian (± 0.4g) and microgravity (± 0g). Subsequently, RNA isolation and state-of-the-art RNAseq were performed, revealing significant down regulation of a translation initiation factor (yciH, p_FDR &lt; 0.05) and increased expression of two membrane proteins (yceK, hdeD, p_FDR &lt; 0.1). Furthermore, under simulated Martian gravity, 56 antisense RNAs were found to be significantly differentially expressed, constituting 56% of differentially expressed RNAs. Genome annotation (GO) of the genes inhibited by the affected antisense RNAs in the 0.4g treatment shows that
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    <td>
+
      <i>
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    4h
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        E. coli
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    </td>
+
      </i>
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    <td>
+
      specifically appears to suffer from carbon-deprivation and acid stress. These results are intuitive, given the reduced or absent convection in partial and microgravity, respectively, leading to build-up of waste products. We conclude that
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    3h
+
      <i>
−
    </td>
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        E. coli
−
    <td>
+
      </i>
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    3h
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      primarily responds to perceived changes in gravity on a translational level.
−
    </td>
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      </p>
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  </tr>
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      <p>
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  <tr>
+
      <b>
−
    <td>
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        References
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    OD
+
      </b>
−
    </td>
+
      <br />
−
    <td>
+
      <ol id="references" style="font-size: 8pt">
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    0.26
+
        <li>
−
    </td>
+
        <a href="https://2016.igem.org/Team:Leiden/www_partialgravity_com">
−
    <td>
+
          www.partialgravity.com
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    0.42
+
        </a>
−
    </td>
+
        </li>
−
    <td>
+
        <li>
−
    0.45
+
        <a href="http://www.nasa.gov/mission_pages/station/research/experiments/631.html">
−
    </td>
+
          http://www.nasa.gov/mission_pages/station/research/experiments/631.html
−
    <td>
+
        </a>
−
    0.43
+
        </li>
−
    </td>
+
        <li>
−
  </tr>
+
        <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524529/">
−
  </table>
+
          https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524529/
−
  <br />
+
        </a>
−
  <p>
+
        </li>
−
  <b>
+
      </ol>
−
    Getting the right number of colonies
+
      </p>
−
  </b>
+
    </div>
−
  <br />
+
    <div class="col-sm-2">
−
  <br />
+
    </div>
−
  Number of colonies from the OD given above (average of two plates):
+
     </div>
−
  </p>
+
   </div>
−
  <table id="t01">
+
  </div>
−
  <tr>
+
  <div id="footer_html" data-source="https://2016.igem.org/Team:Leiden/footer?action=raw">
−
    <th>
+
   </div>
−
    </th>
+
−
    <th>
+
−
    <i>
+
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      E. coli
+
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    </i>
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    DH5&alpha;
+
−
    </th>
+
−
    <th>
+
−
    <i>
+
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      E. coli
+
−
    </i>
+
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    TOP10
+
−
    </th>
+
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    <th>
+
−
    <i>
+
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      E. coli
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    </i>
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    BW25113
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    </th>
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    <th>
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    <i>
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      Pseudomonas putida
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    </i>
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    S12
+
−
    </th>
+
−
  </tr>
+
−
  <tr>
+
−
    <td>
+
−
    10
+
−
    <sup>
+
−
      -6
+
−
    </sup>
+
−
    </td>
+
−
    <td>
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−
    1
+
−
    </td>
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−
    <td>
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−
    45
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−
    </td>
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−
    <td>
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−
    144
+
−
    </td>
+
−
    <td>
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−
    170
+
−
    </td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td>
+
−
    10
+
−
    <sup>
+
−
      -6.5
+
−
    </sup>
+
−
    </td>
+
−
    <td>
+
−
    0
+
−
    </td>
+
−
    <td>
+
−
    10
+
−
    </td>
+
−
    <td>
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−
    45
+
−
    </td>
+
−
    <td>
+
−
    5
+
−
    </td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td>
+
−
    10
+
−
    <sup>
+
−
       -7
+
−
    </sup>
+
−
    </td>
+
−
    <td>
+
−
    10
+
−
    </td>
+
−
    <td>
+
−
    87
+
−
    </td>
+
−
    <td>
+
−
    25
+
−
    </td>
+
−
    <td>
+
−
    3
+
−
    </td>
+
−
  </tr>
+
−
  </table>
+
−
  <br />
+
−
  <p>
+
−
  From this we can conclude that we need to grow both
+
−
  <i>
+
−
    Pseudomonas putida
+
−
  </i>
+
−
  S12 and
+
−
  <i>
+
−
    E. coli
+
−
  </i>
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−
  BW25113 3 hours,
+
−
  <i>
+
−
    E. coli
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−
  </i>
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  TOP10 4 hours and
+
−
  <i>
+
−
    E. coli
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−
  </i>
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−
  DH5&alpha; 5 hours. Then we need to dilute them 10
+
−
  <sup>
+
−
    -6.5
+
−
  </sup>
+
−
  to get the desired number of colonies on each plate.
+
−
  </p>
+
−
  <h2>
+
−
  Inoculating strains for phenotype study in simulated microgravity
+
−
  </h2>
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−
  <p>
+
−
  <i>
+
−
    Day3: 2016/07/19
+
−
  </i>
+
−
  <br />
+
−
  <b>
+
−
    Investigator(s): Wouter Liefting
+
−
  </b>
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−
  <br />
+
−
  <b>
+
−
    Procedure
+
−
  </b>
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−
  :
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−
Strains were inoculated from the plates in the refrigerator (grown up from the -80 &degC; stock made at the beginning of these experiments &rarr; this has to be repeated when the experiment is started for the RNA-seq data!). One colony of each plate is put in 2.5 mL liquid LB in 10 mL tube. Overnight in the shaker at 30 &amp;degC.;
+
−
  </p>
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−
  <p>
+
−
  <i>
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−
    Day4: 2016/07/20
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−
  </i>
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−
  <br />
+
−
  <b>
+
−
    Investigator(s): Wouter Liefting, Valentijn Broeken
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−
  </b>
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−
  <br />
+
−
  <b>
+
−
    Procedure
+
−
  </b>
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−
  :
+
−
To get the desired OD of 0.4 around 20h30 in the evening, the strains were transferred to new medium at different time points:
+
−
  <ul>
+
−
    <li>
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−
    DH5&alpha; around 15:35
+
−
    </li>
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−
    <li>
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−
    TOP10 around 16:40
+
−
    </li>
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−
    <li>
+
−
    <i>
+
−
       Pseudomonas
+
−
    </i>
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    and BW25113 around 17:30
+
−
    </li>
+
−
  </ul>
+
−
  200 &micro;L of each bacterial overnight culture was added to 20 mL of LB medium in a shake flask, and was then grown at 30&deg;C.
+
−
  <h2>
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    Incubating the strains in the RPM for phenotype study in simulated microgravity
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−
  </h2>
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−
  </p>
+
−
  <p>
+
−
  <i>
+
−
    Day4: 2016/07/20
+
−
  </i>
+
−
  <br />
+
−
  <b>
+
−
    Investigator(s): Valentijn Broeken, Vincent de Bakker
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−
  </b>
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−
  <br />
+
−
  <b>
+
−
    Procedure
+
−
  </b>
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−
  :
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−
At 20:30 the OD values of the cultures were measured. By accident, the OD was measured at 546nm, while the OD had to be measured at 600nm. The OD-values were:
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−
  </p>
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−
  <table id="t01">
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−
  <tr>
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−
    <th>
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−
    Strain
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−
    </th>
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−
    <th>
+
−
    OD
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−
    <sub>
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−
      546nm
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−
    </sub>
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−
    </th>
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−
  </tr>
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−
  <tr>
+
−
    <td>
+
−
    TOP10
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−
    </td>
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−
    <td>
+
−
    0.371
+
−
    </td>
+
−
  </tr>
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−
  <tr>
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−
    <td>
+
−
    BW25113
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−
    </td>
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−
    <td>
+
−
    0.420
+
−
    </td>
+
−
  </tr>
+
−
  <tr>
+
−
    <td>
+
−
    Pseudomonas
+
−
    </td>
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−
    <td>
+
−
    0.263
+
−
    </td>
+
−
  </tr>
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−
  <tr>
+
−
    <td>
+
−
    DH5&alpha;
+
−
    </td>
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−
    <td>
+
−
    0.263
+
−
    </td>
+
−
  </tr>
+
−
  </table>
+
−
  <p>
+
−
  The Pseudomonas was placed back in the incubater for another 45 minutes during the dilution steps of the other strains. After that, the OD was measured at 600nm and was found to be 0.750.
+
−
  <br />
+
−
  <br />
+
−
  The anticipated OD
+
−
  <sub>
+
−
    600
+
−
  </sub>
+
−
  at this time would be 0.4. The bacterial cultures were diluted 10
+
−
  <sup>
+
−
    -6.5
+
−
  </sup>
+
−
  (100x &gt; 100x &gt; 50x) and 10
+
−
  <sup>
+
−
    -7
+
−
  </sup>
+
−
  times (another 2x). Dilution steps were done in duplo and each of the two final dilutions per duplo were plated twice, one for 1g and one for 0g. There are thus four 10
+
−
  <sup>
+
−
    -6.5
+
−
  </sup>
+
−
  dilutions and four 10
+
−
  <sup>
+
−
    -7
+
−
  </sup>
+
−
  dilutions plated for each strain. Since the OD
+
−
  <sub>
+
−
    600
+
−
  </sub>
+
−
  was far too high for Pseudomonas, this culture was diluted 2x before the standard dilutions described above.
+
−
  <br />
+
−
  <br />
+
−
  At 22:45h the plates were put at 30&degC; besides (1g) or in the RPM (0g). It is however thought that the incubator's temperature is too low, because the next morning no colonies could be seen.
+
−
  <h2>
+
−
    Photographing colonies
+
−
  </h2>
+
−
  </p>
+
−
  <p>
+
−
  <i>
+
−
    Day5: 2016/07/21
+
−
  </i>
+
−
  <br />
+
−
  <b>
+
−
    Investigator(s): Valentijn Broeken, Wouter Liefting
+
−
  </b>
+
−
  <br />
+
−
  <b>
+
−
    Procedure
+
−
  </b>
+
−
  :
+
−
  <br />
+
−
  At 10:30: we looked at the plates but we didn't see any colonies yet. The plates were putted back.
+
−
  <br />
+
−
  At 17:00: this time colonies were present. We took photos of all plates and putted them back.
+
−
  <br />
+
−
  At 20:30: Unfortunately the tape we used wasn't strong enough so when we came back 4 hours later we found the plates had come loose and the RPM didn't rotate. We don't know how long it had been turning before this happened but we think it probably happened soon after we left. We still took photos and used duct-tape again to make sure the plates wouldn't come loose.
+
−
  </p>
+
−
  <p>
+
−
  <i>
+
−
    Day6: 2016/07/22
+
−
  </i>
+
−
  <br />
+
−
  <b>
+
−
    Investigator(s): Wouter liefting
+
−
  </b>
+
−
  <br />
+
−
  <b>
+
−
     Procedure
+
−
  </b>
+
−
  :
+
−
   <br />
+
−
  At 10:00: new photo's of the colonies. Last photo's will be taken at the end of this day.
+
−
  <br />
+
−
  At 15:00 new photo's of the colonies are taken. Again the tape (this time the duct-tape) got loose and the rotation stopt after max. 15 minutes. We need a construct to put our plates in to make it not only much easier to work with buth also more reliable.
+
−
  <br />
+
−
  The plates are stored in the refrigerator on the 1st floor after these last photo's.
+
−
   </p>
+
 
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Revision as of 12:55, 16 October 2016

iGEM Leiden Wiki : RPM

RPM

Random Positioning Machine

In space, many conditions are vastly different from what life is exposed to here on Earth. Though we can protect ourselves and bacteria to some of these conditions passively (e.g. through temperature and radiation shielding), changes in gravity cannot be evaded.

This led us to pose the question: “What are the effects of microgravity and Martian gravity on gene expression in E. coli , compared to gene expression under Terran gravity?” But how on Earth can we study reduced gravity… on Earth? To this end we used the random positioning machine (RPM) by Airbus Defence and Space Netherlands, which allows us to simulate partial and microgravity. 1

We decided to take on an ambitious approach and sequence E. coli’s entire transcriptome, using state-of-the-art RNAseq. This allows us to see every RNA inside E. coli at a given time, providing a helicopter view of the changes occurring inside the bacteria. Though microgravity has been studied many times before, we are the first to study the effects of Martian gravity in E. coli . Moreover, many previous microgravity experiments involved microarrays, which can only detect changes in RNAs which are already known. RNAseq on the other hand, sequences RNAs indiscriminately. Following our RPM experiment, RNAseq was performed by BaseClear and subsequent analyses were performed by us.

The eventual goal of this experiment is to verify that our perchlorate reduction system will be expressed under Martian gravity. Furthermore, we will search for highly expressed genes that react in a gravity dependent manner and use the accompanied regulatory sequences to develop a biobrick for gravity dependent gene expression.

The effects of low orbit gravity
Multiple studies in the International Space Station (ISS) showed that in many cases bacteria grow faster, show increased virulence, and can even be less susceptible to antibiotics when growing in the microgravity of Lower Earth Orbit (LEO). 2,3 We are keen to find out whether the effect of Martian gravity resembles that of microgravity, or if Mars is more reminiscent of Earth with respect to bacterial growth. Before conducting costly and time-consuming RNAseq, we characterized E. coli (BW25113) growth through visual inspection of colonies in three conditions:

  • Gravity on Earth: 1g
  • Martian gravity: 0.38g
  • Microgravity: 0g

Source: http://mars.nasa.gov/allaboutmars/facts/#?c=inspace&s;=distance

Of course, we cannot actually travel to Mars to experience its gravity, but instead, we used the Random Positioning Machine (RPM 2.0) by Airbus Defence and Space Netherlands. This machine constantly rotates the samples over three axes, averaging gravity out on longer timescales. By reprogramming the motion pattern of the RPM so that it will stay longer in the bottom part, the sample experiences (simulated) partial gravity.

Results: visual inspection (0g vs. 1g)
E. coli BW25113 was plated on LB and in duplo exposed to microgravity in the Random Positioning Machine. Just besides the RPM, plates with the same dilutions were placed at ‘normal’ surface gravity of the Earth. After less than 22 hours, the difference between the plates (in and next to the RPM) were clearly visible: colonies are larger when grown in microgravity than when grown in 1g. Two plates are shown below as an example:

This reaffirms the expected change in growth and bacterial physiology under reduced gravity. Note that these bacteria were grown at room temperature for practical reasons. The subsequent RNAseq experiment was performed with the RPM enclosed in a stove at a constant 37ºC.

Results: RNAseq (0g vs. 0.38g vs. 1g) Below, you can read the abstract of the RNAseq experiment. Click any of the links to the RNAseq page for the full report.
Abstract We compared E. coli BW25113 bacteria under three different conditions: controls (1g) simulating Martian (± 0.4g) and microgravity (± 0g). Subsequently, RNA isolation and state-of-the-art RNAseq were performed, revealing significant down regulation of a translation initiation factor (yciH, p_FDR < 0.05) and increased expression of two membrane proteins (yceK, hdeD, p_FDR < 0.1). Furthermore, under simulated Martian gravity, 56 antisense RNAs were found to be significantly differentially expressed, constituting 56% of differentially expressed RNAs. Genome annotation (GO) of the genes inhibited by the affected antisense RNAs in the 0.4g treatment shows that E. coli specifically appears to suffer from carbon-deprivation and acid stress. These results are intuitive, given the reduced or absent convection in partial and microgravity, respectively, leading to build-up of waste products. We conclude that E. coli primarily responds to perceived changes in gravity on a translational level.

References

  1. www.partialgravity.com
  2. http://www.nasa.gov/mission_pages/station/research/experiments/631.html
  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524529/