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          <td width="39%"><span class="headline"><a href="http://www.hku.hk">The University of Hong Kong</a> | <a href="http://www.hku.hk/facmed/">Li Ka Shing Faculty of Medicine</a></span></td>
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                        <td width="80%" align="left"><h1 class="style7"><a name="device" id="p0">Novel Devices</a></h1>
                          <h2><span class="style16"><a href="#p1">A. Movie Taker</a></span></h2>
                          <p><a href="#p2">Version A:</a></p>
                          <p><a href="#p3">Version B:</a></p>
                          <p><a href="#p4">Version C:</a></p>
                          <p><a href="#p5">Version D:</a></p>
                          <h2 align="left" class="style16"><a href="#p6">B. Reflection  spectrophotometer</a></h2>

                          <h2><span class="style16"><a name="device" id="p1"></a>A. Movie Taker</span></h2>
                          <p class="special">As the ring of  void pattern was repetitively obtained, we get more and more concerned about  the detailed formation process of this novel pattern. Several questions were  arisen in our experiment: 1) How soon will this ring pattern be formed? 2) Was  the ring formed once the bacteria get there or formed later on when cells have  grow evenly on the plate? 3) What is the difference of the process when our  programmed cells are compared to the wild type?</p>
                          <p>Therefore we  tried to take pictures periodically after dropping the cell on the plates. It  is a nontrivial process since we have to strictly control the quality of the  photos as well as the time points on which the photo has been taken. These data  are all crucial for a precise mathematical modeling. We have gone all the way  through five versions of the picture capturing apparatuses. One thing worth  noting is that, this procedure itself is exploration and creation in an unknown  area for us. We have solved two major problems we encountered during this  development, 1) How to capture high-quality pictures with appropriate light  source and a clear back ground. 2) How to do the automated capturing without  human interfering, since it usually take 15 to 20 hours for the pattern to be  developed.</p>
                          <p>4 versions of devices</p>
                          <p><a name="device" id="p2"></a>Version A:<br />
                            As we want to  have the plate photos with the same standards in order to compare patterns from  different plates and to observe single plate cell growth, the way we take plate  photos must be fixed, and that is the original motivation for designing such a  camera holder. As shown in the picture, a tripod is fixed on an empty cuvette  box with tapes, and a black sheet is attached at the bottom of the whole  device(not shown). The foam directly below the tripod is removed from the box  so the plate can be fixed there. In this way we are able to take plate photos  under identical conditions each time (same distance between the camera lens and  the plates, and same position of the plates each time we take photos).</p>
                          <p align="center"><img src="https://static.igem.org/mediawiki/2008/b/bc/Device_pic1.JPG" width="306" height="222" /></p>
                          <p><strong>Advantage:</strong> after all, a standard for taking plate photos is developed, and it  is better than nothing.</p>
                          <p><strong>Disadvantage: </strong>the device is very simple and crude. Since the  tapes doesn’t always make the tripod firmly fixed on the foam base, slight  differences are observed each time we take photos.</p>
                          <p align="right"><a href="#p0">[Back to top]</a></p>
                          <p>&nbsp;</p>
                          <p><a name="device" id="p3"></a>Version B:<br />
Having recognized that in the previous version, the camera is not  fixed firmly on the holder, we took an umbrella holder with two sets of  parallel tapes. In this way we eliminate the infirmity between the tripod and  the cuvette box, and both plate size and plate position has not changed after  this version of holder had been developed.</p>
                          <p align="center"><img src="https://static.igem.org/mediawiki/2008/3/31/Device_pic2.JPG" width="308" height="231" /></p>
                          <p><strong>Advantage:</strong> the camera is fixed firmly on the holder, so the differences  between plate positions and sizes from different photos are minimized.</p>
                          <p><strong>Disadvantage:</strong> environmental light change is the main factor that has great  influence on the brightness of the plates. Sometimes it is difficult for us to  compare the colors and densities of the pattern from the photo source.</p>
                          <p align="right"><a href="#p0">[Back to top]</a></p>
                          <p>&nbsp;</p>
                          <p><a name="device" id="p4"></a>Version C:<br />
Because light  change has become the main enemy for taking plate photos, we made another  holder from a big solid box. A hole is drilled on the top of the box for  digital camera connected to a computer, and a single constant light source is  provided from a fixed direction so the effects of light change are minimized. </p>
                          <p align="center"><img src="https://static.igem.org/mediawiki/2008/7/72/Device_pic3.JPG" width="252" height="244" /></p>
                          <p><strong>Advantage: </strong>very slight effects from the light source change  are observed. Also, with the help of computer, we are able to take cell growth  movie for a single plate automatically.</p>
                          <p><strong>Disadvantage:</strong> only one plate can be placed in the box for movie taking, so the  efficiency is very low as we have a comparatively great amount of plates movies  to take in a relatively short time.</p>
                          <p align="right"><a href="#p0">[Back to top]</a></p>
                          <p>&nbsp;</p>
                          <p><a name="device" id="p5"></a>Version D:<br />
Multiple  holes have been drilled on the top of the box, and multiple cameras are fixed  firmly in the holes. Plate movies as many as four can be taken simultaneously,  with minimum light source changes, minimum position changes and highly  automation. This device answers for our needs perfectly, and as you can see, the  best films and photos are taken in it.</p>
                          <p align="center"><img src="https://static.igem.org/mediawiki/2008/2/26/Device_pic4.JPG" width="308" height="231" /></p>
                          <p align="right"><a href="#p0">[Back to top]</a></p>
                          <h2 align="left" class="style16"><a name="device" id="p6"></a>B. Reflection  spectrophotometer</h2>
                          <p class="special" "align="left">This part of  data analysis is trying to analyze the relationship between plate brightness,  cell concentration, and OD. Furthermore, we want to try out if plate brightness  can be directly related to growth curve measurement.<br />
The traditional  OD test is the measurement of the amount of light absorbed by a suspension of  bacterial cells or a solution of an organic molecule with the use of a  colorimeter or spectrophotometer. The higher the optical density, the lower the  transmittance. In microbiology, the values can be used to measure turbidity,  which in turn is used to estimate the number of bacteria. The formula of OD  (Optical Density):</p>
                          <p align="center"><img src="https://static.igem.org/mediawiki/2008/7/75/Device_pic5.gif" width="217" height="33" /></p>
                          <p align="left"><em>O</em></br> = the opacity per-unit<br />
                              <em>T</em> = the transmittance per-unit<br />
                              <em>I0</em> = the intensity of the  incident light beam<br />
                              <em>I</em> = the intensity of the transmitted  light beam<br />
                            (Reference:  http://en.wikipedia.org/wiki/Optical_density)</p>
                          <p align="left"><br />
                            Our design is  hoped to be an alternation of the traditional OD test in a more easy and  convenient way. The method is that by imposing a unified, consistent light  source to plates with cells migrating (swim or swarm), cells with different  concentration will emit different light intensity which will be recorded and  measured. We’re hoping to come up with a relation between the light intensity  with cell concentration, and furthermore, relate light intensity directly to OD  value. A formula representing the relationship is deducted.<br />
                            Measuring  bacteria growth curve has been a frustrating experiment for our lab work,  especially for those cells with large doubling time (and we believe thousands  of people have experiencing the same problem). During our experiment of  measuring migration speed of cells, we come up with the idea that the total  cell number may have some relationship with total brightness of the plate with  static light source. By impose the unified, consistent light source to a single  plate at different time point and record the light intensity of whole plate,  the growth curve can be plot. As a result, we are hoping to implement our  “automatic OD machine” to accomplish the task of growth curve measurement.<br />
                            The design of  plate picture taking is being progressively improved and optimized. During the  design and setup phase, we have invented up to 5 version of “black room”, (Need to provide photos of each version) <br />
                            Along with the  version evolved, the problems solved/unsolved are as following:</p>
                          <ol>
                          <div align="left">
                            <p align="left">Background light noise  (solved): use black curtain as plate background. Also, black box is used to  block other light source in order to keep consistent and unified light source.  </p>
                          <p align="left">Static light intensity  (solved): firm light source intensity and distance to the plate each time.</p>
                          <p align="left">Reflection, Refraction problem  (need more work): The problem is that the brightness level we measured is from  the light collected now is the reflection from light source not vertical to the  plate. This method may relate more to the reflection of the surface cell, but  less to the brightness of the cells inside Agar gel. We are planning to change  the light source go in vertically from the other side of the plate, and the  diascoptic light is more accurately related to the total cell number on the  plate.</p>
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