Difference between revisions of "Team:Newcastle"

 
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<canvas id='canvas'></canvas>
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     <!-- home
 
     <!-- home
 
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     <section id="world" class="s-home target-section" data-parallax="scroll" data-image-src="https://static.igem.org/mediawiki/2018/6/6a/T--Newcastle--plantpic.jpeg" data-natural-width=3000 data-natural-height=2000 data-position-y=center>
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     <section id="world" class="s-home target-section" data-parallax="scroll" data-image-src="https://static.igem.org/mediawiki/2018/a/a5/T--Newcastle--ROOT.COVER.PHOTO.jpg" data-natural-width=3000 data-natural-height=2000 data-position-y=center>
  
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        <div class="overlay"></div>
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             <div class="row home-content__main">
 
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                 <h3>Welcome to Alternative Roots</h3>
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                 <h3>Welcome to</h3>
  
 
                 <h1>
 
                 <h1>
 
                     Alternative Roots <br>
 
                     Alternative Roots <br>
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                     Newcastle iGEM <br>
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                     Newcastle iGEM 2018<br>
 
                    
 
                    
 
                 </h1>
 
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                         Our Project
 
                         Our Project
 
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                     <a href="#contact" class="smoothscroll btn btn--stroke">
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                     <a href="#sponsors" class="smoothscroll btn btn--stroke">
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                         Contact Us
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                         Our Sponsors
 
                     </a>
 
                     </a>
 
                 </div>
 
                 </div>
  
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            <div class="home-content__scroll">
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                <a href="#project" class="scroll-link smoothscroll">
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                    <span>Scroll Down</span>
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            </div>
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     </section> <!-- end s-home -->
 
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    <!-- about
 
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    <section id='project' class="s-about">
 
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        <div class="row section-header has-bottom-sep" data-aos="fade-up">
 
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            <div class="col-full">
 
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                <h3 class="subhead subhead--dark">Hello There</h3>
 
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                <h1 class="display-1 display-1--light">We are Alternative Roots</h1>
 
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            </div>
 
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        </div> <!-- end section-header
 
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        <div class="row about-desc" data-aos="fade-up">
 
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                <p class="about-para">Sustainability is a topic of increasing concern in the fields of agriculture, food security and rural development. There is a dire need for innovation in this field; primarily driven by predictions of substantial global population increase coupled with severe pressure on non-renewable resources. The result is a necessity to increase food production whilst reducing our impact on the environment. As such, our aim is to find sustainable solutions that address some of these issues. </p>
 
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                <p class="about-para">Nitrogen-fixation for fertilizer production is extremely energy-intensive, accounting for 80% of energy use in agriculture. This is due to the high temperatures and pressures involved in the Haber-Bosch process. Nitrogen is essential for plant growth but cannot be directly accessed from the atmosphere by plants despite its abundance. If an alternative to fertilizers could be developed to provide nitrogen for plant growth that is cheap, easy to use and sustainable, then energy use in the agriculture sector could be greatly reduced.</p>
 
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<p class="about-para">In 2018, Team Newcastle aim to engineer microbes for sustainable agriculture. The team shall build upon Newcastle University’s long and illustrious history in agriculture and food security research by engineering root colonising microbes. The microbes will attract bacteria that modify the soil's composition including nitrogen content, in a fashion that is suitable for uptake by plants via the roots.</p>
 
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            </div>
 
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        </div> <!-- end project-desc
 
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        <div class="row about-stats stats block-1-4 block-m-1-2 block-mob-full" data-aos="fade-up">
 
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            <div class="col-block stats__col ">
 
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                <div class="stats__count">10</div>
 
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                <h5>BILLION PEOPLE WILL</h5>
 
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                <h5>INHABIT EARTH BY 2050</h5>
 
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            </div>
 
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            <div class="col-block stats__col">
 
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                <div class="stats__count">83</div>
 
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                <h5>MILLION EXTRA PEOPLE</h5>
 
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                <h5>NEED TO BE FED EACH YEAR</h5>
 
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            </div>
 
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            <div class="col-block stats__col">
 
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                <div class="stats__count">842</div>
 
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                <h5>MILLION PEOPLE SUFFER</h5>
 
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                <h5>FROM HUNGER WORLDWIDE</h5>
 
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            </div>
 
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            <div class="col-block stats__col">
 
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                <div class="stats__count">200</div>
 
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                <h5>MILLION TONNES OF</h5>
 
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                <h5>FERTILIZER USED ANNUALLY</h5>
 
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            </div>
 
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        <div class="about__line"></div>
 
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         <div class="row section-header has-bottom-sep" data-aos="fade-up">
 
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                 <div class="col-full">
 
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                             <h3 class="subhead">Alternative Roots</h3>
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                             <h3 class="subhead"></h3>
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                 <h1 class="display-2">PROJECT OVERVIEW</h1>
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                 <h1 class="display-2">Project Overview</h1>
 
             </div>
 
             </div>
 
         </div> <!-- end section-header -->
 
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                     <!-- Full-width images with number and caption text -->
 
                     <!-- Full-width images with number and caption text -->
 
                     <div class="mySlides fade">
 
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                         <div class="numbertext">1 / 15</div>
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                         <img src="https://static.igem.org/mediawiki/2018/thumb/f/fc/T--Newcastle--Slide1.png/800px-T--Newcastle--Slide1.png">
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                         <div class="text">All soils have a unique, diverse microbial community</div>
+
                         <div class="text">Soils contain diverse microbial communities.</div>
 
                     </div>
 
                     </div>
  
 
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                         <img src="https://static.igem.org/mediawiki/2018/thumb/b/bb/T--Newcastle--Slide4.png/800px-T--Newcastle--Slide4.png">
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                         <div class="text">Within each microbial community there are many microbes with useful abilities </div>
+
                         <div class="text">Within these communities are microbes with useful properties.</div>
 
                     </div>
 
                     </div>
  
 
                     <div class="mySlides fade">
 
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                         <div class="numbertext">3 / 15</div>
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                         <img src="https://static.igem.org/mediawiki/2018/thumb/3/34/T--Newcastle--Slide3.png/800px-T--Newcastle--Slide3.png">
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                         <div class="text">The bacterium Pseudomonas fluorescens lives in plant roots and helps them to grow</div>
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                         <div class="text">Endophytes are microbes that live harmlessly within plant tissues.</div>
 
                     </div>
 
                     </div>
  
 
                     <div class="mySlides fade">
 
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                         <div class="numbertext">4 / 15</div>
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                         <img src="https://static.igem.org/mediawiki/2018/thumb/5/56/T--Newcastle--Slide5.png/800px-T--Newcastle--Slide5.png">
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                         <div class="text">By introducing new genes for our Pseudomonas to express we can influence the microbial community</div>
+
                         <div class="text">Can we programme endophytes to influence the wider microbial community?</div>
 
                     </div>
 
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                         <img src="https://static.igem.org/mediawiki/2018/thumb/6/6f/T--Newcastle--Slide6.png/800px-T--Newcastle--Slide6.png">
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                         <div class="text">We can attract or repel certain species in any way desired </div>
+
                         <div class="text">Could they synthesise chemicals to attract beneficial soil microbes?</div>
 
                     </div>
 
                     </div>
  
 
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                         <div class="numbertext">6 / 15</div>
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                         <img src="https://static.igem.org/mediawiki/2018/thumb/e/eb/T--Newcastle--Slide7.png/800px-T--Newcastle--Slide7.png">
−
                         <div class="text">In our case, we use flavonoids to attract free-living nitrogen fixers, that convert nitrogen gas to nitrate for plant growth</div>
+
                         <div class="text">Attracting bacteria to fix nitrogen and reducing the need for chemical fertilisers.</div>
 
                     </div>
 
                     </div>
  
 
                     <div class="mySlides fade">
 
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                         <div class="numbertext">7 / 15</div>
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                         <div class="numbertext">7 / 8</div>
 
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                         <img src="https://static.igem.org/mediawiki/2018/thumb/5/5b/T--Newcastle--Slide10.png/800px-T--Newcastle--Slide10.png">
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                         <div class="text">P. fluorescens has many other abilities, including the ability to repel parasitic nematode worms [1], produce antifungals and insecticides [2] and induce plant stress tolerance [3]</div>
+
                         <div class="text">Or maybe the endophytes can synthesise chemicals that deter pests or pathogens?</div>
 
                     </div>
 
                     </div>
  
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                        <img src="https://static.igem.org/mediawiki/2018/thumb/2/22/T--Newcastle--RoundLogo.png/555px-T--Newcastle--RoundLogo.png">
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<br></br>
 +
                        <div class="text">Alternative Roots: engineering endophytes for smart agricultural solutions.</div>
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                    </div>
  
 
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                     <a class="prev" style="color:black;" onclick="plusSlides(-1)">&#10094;</a>
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                 </div>
 
                 <br>
 
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     </section> <!-- end s-services -->
 
     </section> <!-- end s-services -->
  
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<section id='team' class="s-services" style="padding-top:0">
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 +
 +
<div class="row section-header has-bottom-sep" data-aos="fade-up">
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                <div class="col-full">
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                            <h3 class="subhead"></h3>
 +
                <h1 class="display-2" style="margin-bottom:0px" >Abstract</h1>
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            </div>
 +
        </div> <!-- end section-header -->
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            <div class="row about-desc" data-aos="fade-up">
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                <div class="col-full">
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                    <p><font size="3"> The demand for food, fuel and materials is placing unprecedented pressure on agricultural production. To secure higher productivity, the sector relies upon synthetic fertilisers derived from energy intensive manufacturing methods. Here, we propose an alternative approach to support plant productivity. </font></p>
 +
 +
                    <p><font size="3">The Alternative Roots project developed an endophytic bacterium as a synthetic biology chassis organism. Endophytes are micro-organisms that live within plant tissues without detrimental impact on their host. In developing a benign plant-colonising chassis there is the possibility of developing novel mechanisms for beneficial soil microbiome manipulation without genetically modified crops.</font></p>
  
 +
                    <p><font size="3">Legal and social considerations of the project, combined with concepts borrowed from the Urban Farming movement, drove the development of NH-1 - a low-cost, small-scale and programmable hydroponic system - and plans for the deployment of smart agricultural developments beneath the streets of Newcastle. Taken as a whole, the Alternative Roots project supports a vision for enhancing crop production at a local and accessible level.</font></p>
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     <!-- clients
 
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−
    this.particles.push(particle);
 
−
  }
 
−
}
 
−
 
−
Canvas.prototype.findClosest = function() {
 
−
  var index = -1;
 
−
  var pointsLength = this.particles.length;
 
−
 
−
  while(++index < pointsLength) {
 
−
    var closestIndex = -1;
 
−
    this.particles[index].closest = [];
 
−
   
 
−
    while(++closestIndex < pointsLength) {
 
−
      var closest = this.particles[closestIndex];
 
−
      var distance = this.particles[index].position.distanceTo(closest.position);
 
−
      if(distance < this.options.maxDistance) {
 
−
        var vector = new Vector(closest.position.x, closest.position.y);
 
−
        vector.opacity = 1 - (distance / this.options.maxDistance);
 
−
        vector.distance = distance;
 
−
        this.particles[index].closest.push(vector);
 
−
      }
 
−
    }
 
−
  }
 
−
}
 
−
 
−
Canvas.prototype.loop = function() {
 
−
//  this.clear();
 
−
  if(isTouch || isSafari) {
 
−
  this.ghost();
 
−
  } else {
 
−
  this.ghostGradient();
 
−
  }   
 
−
  if(this.options.maxDistance > 0) {
 
−
  this.findClosest();
 
−
  }   
 
−
  this.draw();
 
−
 
 
−
  window.requestAnimationFrame(_.bind(this.loop, this));
 
−
}
 
−
 
−
Canvas.prototype.clear = function() {
 
−
  this.ctx.clearRect(0, 0 , this.width, this.height);
 
−
}
 
−
 
−
Canvas.prototype.ghost = function() {
 
−
  this.ctx.globalCompositeOperation = "source-over";
 
−
  this.ctx.rect(0, 0 , this.width, this.height);
 
−
  if(typeof this.options.background === 'string') {
 
−
  this.ctx.fillStyle = "rgb(" + this.options.background + ")";
 
−
  } else  {
 
−
    this.ctx.fillStyle = "rgb(" + this.options.background[0] + ")";
 
−
  }
 
−
   
 
−
  this.ctx.fill();
 
−
}
 
−
 
−
Canvas.prototype.ghostGradient = function() {
 
−
  var gradient;
 
−
 
 
−
  if(typeof this.options.background === 'string') {
 
−
    this.ctx.fillStyle = 'rgb(' + this.options.background + ')'; 
 
−
  } else {
 
−
var gradient = this.ctx.createRadialGradient(this.width/2, this.height/2, 0, this.width/2, this.height/2, Math.max(this.width, this.height)/2);
 
−
   
 
−
    var length = this.options.background.length;
 
−
    for(var i = 0; i < length; i++){
 
−
      gradient.addColorStop((i+1) / length, 'rgb(' + this.options.background[i] + ')');
 
−
    }
 
−
    this.ctx.fillStyle = gradient;
 
−
  }
 
−
 
 
−
  this.ctx.globalOpacity = 0.1;
 
−
  this.ctx.globalCompositeOperation = "darken";
 
−
  this.ctx.fillRect(0, 0 , this.width, this.height);
 
−
}
 
−
 
−
// Draw
 
−
Canvas.prototype.draw = function() {
 
−
  var index = -1;
 
−
  var length = this.particles.length;
 
−
  while(++index < length) {
 
−
    var point = this.particles[index];
 
−
    var color = point.color || this.options.color;
 
−
    point.update(this.target, index);
 
−
   
 
−
    this.ctx.globalAlpha = 0.3;
 
−
    this.ctx.globalCompositeOperation = "lighten";
 
−
    this.ctx.fillStyle = 'rgb(' + color + ')';
 
−
    this.ctx.beginPath();
 
−
    this.ctx.arc(point.position.x, point.position.y, point.size, 0, PI2, false);
 
−
    this.ctx.closePath();
 
−
    this.ctx.fill();
 
−
   
 
−
    if(this.options.maxDistance > 0) {
 
−
    this.drawLines(point, color);
 
−
    }
 
−
  } 
 
−
}
 
−
 
−
// Draw connecting lines
 
−
Canvas.prototype.drawLines = function (point, color) {
 
−
  color = color || this.options.color;
 
−
  var index = -1;
 
−
  var length = point.closest.length;
 
−
  this.ctx.globalAlpha = 0.2;
 
−
  this.ctx.globalCompositeOperation = "screen";
 
−
  this.ctx.lineCap = 'round';
 
−
  while(++index < length) {
 
−
    this.ctx.lineWidth = (point.size * 2) *  point.closest[index].opacity;
 
−
    this.ctx.strokeStyle = 'rgba(' + color + ', ' + point.closest[index].opacity + ')';
 
−
    this.ctx.beginPath();
 
−
    this.ctx.moveTo(point.position.x, point.position.y);
 
−
    this.ctx.lineTo(point.closest[index].x, point.closest[index].y);
 
−
    this.ctx.stroke();
 
−
  }
 
−
}
 
−
 
−
function Particle(options) {
 
−
  options = _.clone(options || {});
 
−
  this.options = _.defaults(options, this.options);
 
−
 
 
−
  this.position = this.shift = new Vector(this.options.x, this.options.y);
 
−
 
 
−
  this.speed = this.options.speed || 0.01 + Math.random() * 0.04;
 
−
 
 
−
  this.angle = this.options.angle || 0;
 
−
   
 
−
  if(this.options.color) {
 
−
    var color = this.options.color.split(',');
 
−
  var colorIndex = -1;
 
−
    while(++colorIndex < 3) {     
 
−
      color[colorIndex] = Math.round(parseInt(color[colorIndex], 10) + (Math.random()*100)-50);
 
−
     
 
−
      // Clamp
 
−
      color[colorIndex] = Math.min(color[colorIndex], 255);
 
−
      color[colorIndex] = Math.max(color[colorIndex], 0);
 
−
    }
 
−
    this.color = color.join(', ');
 
−
  }
 
−
 
 
−
  // Size
 
−
  this.options.size = this.options.size || 7;
 
−
  this.size = 1 + Math.random() * this.options.size;
 
−
  this.targetSize = this.options.targetSize || this.options.size;
 
−
 
 
−
  this.orbit = this.options.radius * 0.5 + (this.options.radius * 0.5 * Math.random());
 
−
}
 
−
 
−
Particle.prototype.update = function(target, index) {
 
−
  this.angle += this.speed;
 
−
 
−
  this.shift.x += (target.x - this.shift.x) * this.speed;
 
−
  this.shift.y += (target.y - this.shift.y) * this.speed;
 
−
 
−
  this.position.x = this.shift.x + Math.cos(index + this.angle) * this.orbit;
 
−
  this.position.y = this.shift.y + Math.sin(index + this.angle) * this.orbit;
 
−
 
 
−
  if(!isSafari) {
 
−
    this.size += (this.targetSize - this.size) * 0.03;
 
−
 
−
    if(Math.round(this.size) === Math.round(this.targetSize)) {
 
−
      this.targetSize = 1 + Math.random() * this.options.size;
 
−
    }
 
−
  }
 
−
}
 
−
 
−
function Vector(x, y) {
 
−
  this.x = x || 0;
 
−
  this.y = y || 0;
 
−
}
 
−
 
−
Vector.prototype.distanceTo = function(vector, abs) {
 
−
  var distance = Math.sqrt(Math.pow(this.x - vector.x, 2) + Math.pow(this.y - vector.y, 2));
 
−
  return abs || false ? Math.abs(distance) : distance;
 
−
};
 
−
 
−
new Canvas({
 
−
  el: document.getElementById('canvas'),
 
−
 
−
  count: 25,
 
−
  speed: 0.3,
 
−
  radius: 6,
 
−
  width: function() { return window.innerWidth; },
 
−
  height: function() { return window.innerHeight; },
 
−
  size: 15,
 
−
  color: '30, 180, 1',
 
−
  maxDistance: 100,
 
−
  background: ['1, 62, 66', '1, 40, 60']
 
−
});
 
−
</script>
 
  
 
</body>
 
</body>

Latest revision as of 16:21, 17 October 2018

Alternative Roots

Welcome to

Alternative Roots
Newcastle iGEM 2018

Our Project Our Sponsors

Project Overview

1 / 8
Soils contain diverse microbial communities.
2 / 8
Within these communities are microbes with useful properties.
3 / 8
Endophytes are microbes that live harmlessly within plant tissues.
4 / 8
Can we programme endophytes to influence the wider microbial community?
5 / 8
Could they synthesise chemicals to attract beneficial soil microbes?
6 / 8
Attracting bacteria to fix nitrogen and reducing the need for chemical fertilisers.
7 / 8
Or maybe the endophytes can synthesise chemicals that deter pests or pathogens?
8 / 8


Alternative Roots: engineering endophytes for smart agricultural solutions.

Abstract

The demand for food, fuel and materials is placing unprecedented pressure on agricultural production. To secure higher productivity, the sector relies upon synthetic fertilisers derived from energy intensive manufacturing methods. Here, we propose an alternative approach to support plant productivity.

The Alternative Roots project developed an endophytic bacterium as a synthetic biology chassis organism. Endophytes are micro-organisms that live within plant tissues without detrimental impact on their host. In developing a benign plant-colonising chassis there is the possibility of developing novel mechanisms for beneficial soil microbiome manipulation without genetically modified crops.

Legal and social considerations of the project, combined with concepts borrowed from the Urban Farming movement, drove the development of NH-1 - a low-cost, small-scale and programmable hydroponic system - and plans for the deployment of smart agricultural developments beneath the streets of Newcastle. Taken as a whole, the Alternative Roots project supports a vision for enhancing crop production at a local and accessible level.





Our Sponsors

Newcastle iGEM is proud to be sponsored by:

The iGEM Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition, and the development of an open community and collaboration. This is done by fostering an open, cooperative community and friendly competition.

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iGEMers are building a better world by solving problems with the help of synthetic biology. We inspire responsible innovation through our efforts in biosafety, biosecurity and public outreach.

Author image

This global network is leading the field, taking what they learned in the competition and expanding it to continue to build a better world.

Author image