Difference between revisions of "Team:Newcastle/Results"

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<p>Here you can describe the results of your project and your future plans. </p>
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<h2>Bacterial Chemotactic Response to Naringenin</h2>
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  <title>Alternative Roots/Results</title>
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<p>The Alternative Root project revolves around the idea of chemical signals which alter the soil microbiome with the main goal of aiding the nitrogen nourishment of plants. As such, it was important to be able to measure how our selected nitrogen fixers (<i>Azospirillum brasilense</i>, <i>Herbaspirillum seropedicae</i> and <i>Azorhizobium caulinodans</i>), <i>Pseudomonas fluorescens</i>, our root endophyte, and <i>Escherichia coli</i> interact with different concentrations of naringenin. Without observing these interactions, the potential that the transformed <i>E. coli</i> and eventually the <i>P. fluorescens</i> may produce too much naringenin, which is known to possess antimicrobial properties (<b>find reference from onedrive</b>), and potential kill the bacteria. Additionally, it is important to know the minimum concentration to elicit a response and whether naringenin elicits the expected response. Therefore, chemotaxis assays were integral to ensuring that concept of the project works</p>
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<h3>What should this page contain?</h3>
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<li> Clearly and objectively describe the results of your work.</li>
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    <section id="home" class="s-home target-section" data-parallax="scroll" data-image-src="https://static.igem.org/mediawiki/2018/thumb/0/06/T--Newcastle--Hardware11.jpg/800px-T--Newcastle--Hardware11.jpg" data-natural-width=3000 data-natural-height=2000 data-position-y=center>
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<li> Future plans for the project. </li>
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<li> Considerations for replicating the experiments. </li>
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                <h3>Alternative Roots</h3>
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<h3>Describe what your results mean </h3>
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<li> Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for. </li>
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<li> Show data, but remember all measurement and characterization data must be on part pages in the Registry. </li>
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<li> Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project. </li>
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                <h1>
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                    Results
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                        Gallery
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<h3> Project Achievements </h3>
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<p>You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.</p>
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<li>A list of linked bullet points of the successful results during your project</li>
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<li>A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.</li>
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                <h3 class="subhead subhead--dark">Stage One</h3>
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                <h1 class="display-1 display-1--light">Powering</h1>
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                <p class="about-para">Once the project idea was finalised, the team began looking for cheap, efficient and standardised methods for growing plants in iGEM. The hope was that such an item existed that would meet these specifications as well as being a closed container to prevent contamination and also providing a high throughput of plants. It was soon established that such an item did not exist to meet our specifications. Therefore, to combat this issue, it was decided that the best way forward would be to design our own hydroponics system. This would allow us to grow large amounts of Arabidopsis in a controlled setting for the purposes of our project. Several team members were assigned to this “sub-project”.</p>
 +
                <p class="about-para">Before getting hands-on in building the system, the team as a whole established a few design parameters. For example, the system needed to be cheap and easy to build from scratch. This is so future iGEM teams are able to construct the system for their own needs and even build upon our design, as necessary. Additionally, the system must be versatile, open-source and easily adapted for various conditions such as light intensity and wavelength. By adopting such an open and adaptable design the intention is that the end-user is able to effortlessly match the system to their needs, without getting entangled in streams of code.</p>
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                <p class="about-para">Several weeks were spent modifying the design until a design was found that met all the above criteria, the specifications of the design can be seen below.</p>
  
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<h3>Inspiration</h3>
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        </div> <!-- end project-desc -->
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<p>See how other teams presented their results.</p>
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<ul>
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<li><a href="https://2014.igem.org/Team:TU_Darmstadt/Results/Pathway">2014 TU Darmstadt </a></li>
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<li><a href="https://2014.igem.org/Team:Imperial/Results">2014 Imperial </a></li>
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<li><a href="https://2014.igem.org/Team:Paris_Bettencourt/Results">2014 Paris Bettencourt </a></li>
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                <h5>UP TO</h5>
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                <div class="stats__count">1344</div>
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                <h5>SEEDS CAN BE GROWN</h5>
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                <h5>IN HYDROPONICS</h5>
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            </div>
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            <div class="col-block stats__col">
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                <h5>APPROXIMATELY</h5>
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                <div class="stats__count">70</div>
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                <h5>KWH OF POWER ANNUALLY</h5>
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                <h5>USED TO POWER SYSTEM</h5>
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            </div>
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            <div class="col-block stats__col">
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                <h5>PROVIDES UP TO</h5>
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                <div class="stats__count">1700</div>
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                <h5>LUX OF LIGHT</h5>
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                <h5>TO GROW SEEDS</h5>
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            </div>
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            <div class="col-block stats__col">
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                <h5>CONTAINS</h5>
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                <div class="stats__count">120</div>
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                <h5>INDIVIDUALLY ADDRESSABLE</h5>
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                <h5>LOW-POWER LED'S</h5>
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                            <h3 class="subhead">Stage Two</h3>
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                    <p style="font-size:100%">Having identified the design parameters for the system, the next stage was to begin ordering parts and putting it together. The system was divided into three independent, functional sub-systems to make the task of assembling the system more manageable and allowing team members to focus on the sub-system that most suited their specialty. These three sub-systems were hardware, software and biological aspects.</p>
 +
                    <p style="font-size:100%">The function of the hardware is to contain the electronics and organisms, power the LED’s/microcontroller and maximise the light available to the plants. Containment is through the use of a sealed box, with a detachable lid for access. This box is glued with tin foil and sprayed black to minimise exchange of light with the environment. Powering the LED’s proved to be more difficult, taking our engineers many days to find the optimal solution. You can find all the grizzly details on this process here. However, essentially the system is powered from a 5V 2.1A AC adapter that plugs straight in to your mains power supply. Alternatively, you can use 4 AA batteries to power the system for short periods of time if necessary. The LED’s are wired in parallel so the same light is provided along the length of the container. This can be seen from images in the Gallery.</p>
 +
                    <p style="font-size:100%">The purpose of the software is to control the LED’s, by allowing the user to easily adapt features such as light intensity, wavelength and also specify the length of the day/night cycle. For our design, we use the Arduino UNO microcontroller to control these characteristics as it offers a user-friendly interface and is well-suited to our design. You can find all the code laid bare and a guide to the Arduino here.</p>
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                    <p style="text-align:center"><br>The engineers, hard at work trying to troubleshoot issues with the system.</p>
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                    <img src="https://static.igem.org/mediawiki/2018/thumb/e/e5/T--Newcastle--Hydroponicssystem.jpeg/800px-T--Newcastle--Hydroponicssystem.jpeg">
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                    <p style="text-align:center"><br>The finished product, set to a rainbow function that cycles through various wavelengths of light</p>
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                    <h3 class="subhead">Stage Three</h3>
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                    <h1 class="display-2 display-2--light">LED Wiring</h1>
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                    <font size="4" font face="verdana" font color="green">Substantial time was spent carrying out extensive research, both inside and outside the lab, in order to optimise the system for the target audience. This included speaking with organisations and individuals in industry who are involved with hydroponics-based systems or those who may be interested in working with such a system in the future. Some of the individuals we liaised with include Chris Tapsell, the Research Director of KWS UK, one of the biggest seed companies in the world, and Richard Ballard, co-founder of Growing Underground in London where they hydroponically grow micro greens and salad leaves 33 metres below the ground. These potential clients helped us focus our product so that it can better meet the needs of our clients.</font><br><br>
 +
                    <font size="4" font face="verdana" font color="green">In addition to gathering external opinion on our system, we also did our own tests on system performance. This included tests to verify the optimal light intensity, wavelength and positioning. The graph below illustrates how the light intensity (measured in lux) varies over time (in seconds) when the system is operated under various wavelengths of light. The black line indicates the system running with the rainbow function loaded which cyclically varies the light wavelength. As the results showed that blue, red and purple light and provided the most lux we are currently using these in the system but plan to use the rainbow function too in future to see how this affects growth or the aesthetics of the plant.
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<img src="https://static.igem.org/mediawiki/2018/thumb/4/4f/T--Newcastle--Hardware14.jpg/450px-T--Newcastle--Hardware14.jpg">
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Revision as of 13:42, 11 September 2018

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Alternative Roots/Results

Alternative Roots

Results

Guide Gallery
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Stage One

Powering

Once the project idea was finalised, the team began looking for cheap, efficient and standardised methods for growing plants in iGEM. The hope was that such an item existed that would meet these specifications as well as being a closed container to prevent contamination and also providing a high throughput of plants. It was soon established that such an item did not exist to meet our specifications. Therefore, to combat this issue, it was decided that the best way forward would be to design our own hydroponics system. This would allow us to grow large amounts of Arabidopsis in a controlled setting for the purposes of our project. Several team members were assigned to this “sub-project”.

Before getting hands-on in building the system, the team as a whole established a few design parameters. For example, the system needed to be cheap and easy to build from scratch. This is so future iGEM teams are able to construct the system for their own needs and even build upon our design, as necessary. Additionally, the system must be versatile, open-source and easily adapted for various conditions such as light intensity and wavelength. By adopting such an open and adaptable design the intention is that the end-user is able to effortlessly match the system to their needs, without getting entangled in streams of code.

Several weeks were spent modifying the design until a design was found that met all the above criteria, the specifications of the design can be seen below.

UP TO
1344
SEEDS CAN BE GROWN
IN HYDROPONICS
APPROXIMATELY
70
KWH OF POWER ANNUALLY
USED TO POWER SYSTEM
PROVIDES UP TO
1700
LUX OF LIGHT
TO GROW SEEDS
CONTAINS
120
INDIVIDUALLY ADDRESSABLE
LOW-POWER LED'S
================================================== -->

Stage Two

Control

Having identified the design parameters for the system, the next stage was to begin ordering parts and putting it together. The system was divided into three independent, functional sub-systems to make the task of assembling the system more manageable and allowing team members to focus on the sub-system that most suited their specialty. These three sub-systems were hardware, software and biological aspects.

The function of the hardware is to contain the electronics and organisms, power the LED’s/microcontroller and maximise the light available to the plants. Containment is through the use of a sealed box, with a detachable lid for access. This box is glued with tin foil and sprayed black to minimise exchange of light with the environment. Powering the LED’s proved to be more difficult, taking our engineers many days to find the optimal solution. You can find all the grizzly details on this process here. However, essentially the system is powered from a 5V 2.1A AC adapter that plugs straight in to your mains power supply. Alternatively, you can use 4 AA batteries to power the system for short periods of time if necessary. The LED’s are wired in parallel so the same light is provided along the length of the container. This can be seen from images in the Gallery.

The purpose of the software is to control the LED’s, by allowing the user to easily adapt features such as light intensity, wavelength and also specify the length of the day/night cycle. For our design, we use the Arduino UNO microcontroller to control these characteristics as it offers a user-friendly interface and is well-suited to our design. You can find all the code laid bare and a guide to the Arduino here.


The engineers, hard at work trying to troubleshoot issues with the system.


The finished product, set to a rainbow function that cycles through various wavelengths of light

================================================== -->

Stage Three

LED Wiring

Substantial time was spent carrying out extensive research, both inside and outside the lab, in order to optimise the system for the target audience. This included speaking with organisations and individuals in industry who are involved with hydroponics-based systems or those who may be interested in working with such a system in the future. Some of the individuals we liaised with include Chris Tapsell, the Research Director of KWS UK, one of the biggest seed companies in the world, and Richard Ballard, co-founder of Growing Underground in London where they hydroponically grow micro greens and salad leaves 33 metres below the ground. These potential clients helped us focus our product so that it can better meet the needs of our clients.

In addition to gathering external opinion on our system, we also did our own tests on system performance. This included tests to verify the optimal light intensity, wavelength and positioning. The graph below illustrates how the light intensity (measured in lux) varies over time (in seconds) when the system is operated under various wavelengths of light. The black line indicates the system running with the rainbow function loaded which cyclically varies the light wavelength. As the results showed that blue, red and purple light and provided the most lux we are currently using these in the system but plan to use the rainbow function too in future to see how this affects growth or the aesthetics of the plant.