Team:HKUST-Hong Kong/data.html

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<h3><b>Data Page</b></h3>
 
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<h4 align=left><a name=constructing></a>1. Constructing EX – the bacterial strain that allows selection without use of antibiotics</h4>
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<br>Data Page<br></p>
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To study the population dynamics and behavior of a certain antibiotics sensitive strain of <i>E. coli</i> in a medium of antibiotic, our <i>E. Trojan</i> that is introduced into the culture medium must not process a wide spectrum of antibiotic resistance that impose a selective advantage. At the same time, <i>E. Trojan</i> needs to be transformed with the T4MO gene to carry out its job of signal disruption. <br><br>
 
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Summarizing the above criteria, a solution where the bacteria can be transform with the gene of interest while remaining sensitive to antibiotics is needed. Therefore the requisite is to construct a new bacterial strain that can perform plasmid selection without the use of antibiotics, and contains as little antibiotics resistance gene as possible.
 
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<h4 align=left><a name=method></a>2. How to select against EX without the vector plasmid? Our alternative selection method</h4>
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<p><b>Abstract</b></p>
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Our EX will have one of its essential genes (genes that are required for viability) removed from its genome, and relocated onto an engineered plasmid pDummy. As illustrated, in order to survive, EX must rely on those extra-chromosomal copies of the essential gene; therefore, EX is addicted to pDummy. By having direct control over the replication of pDummy, we dictate the life and death of EX (and hence the name pDummy).
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Regardless the heated discussion atmosphere around the synthetic biology, few systematic surveys in this field has been conducted, especially in Asia. In this case, the iGEM2011 HKUST Team with the help of their Austrian partners, Markus Schmidt and Lei Pei, of IDC <http://www.idialog.eu/> and Biofaction <http://www.biofaction.com/?page_id=10>, launched this survey, treating Hong Kong as a starting point, trying to get the public perception of synthetic biology, especially in Asia, and the key factors influencing this impression. This report is treated as a snapshot of the response got so far to see if this online survey system can work well.
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Here, we introduce a heat-sensitive origin of replication as the only origin of pDummy. When we intend to switch off the replication of pDummy, we can incubate EX at above 30°C. This origin would then cease to function, and pDummy cannot be maintained. Deprived of the essential gene and the corresponding vital product, EX cannot propagate, unless, it receives an alternative but heat insensitive analog of pDummy. <br><br>
 
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This analog, named pCarrier, is the essentially our vector in cloning. Under an unfavorably high temperature, only those EX that are transformed with the insert-bearing pCarrier will be able to propagate and survive, while the others cannot undergo division and are virtually eliminated from the population. Eventually, the pDummy can be considered to be "shuffled out" by pCarrier. Our designed selection system, in short, bases itself on plasmid shuffling, and thus eliminates involvement of antibiotic resistance genes in any of the cloning steps.<a href=#top>[Top]</a><br>
 
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<h4 align=left><a name=assembly></a>3. Stepping in the heart of construction - methods of assembly</h4>
 
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<b>3.1 Construction and maintenance of an antibiotic-resistance-gene-free plasmid through antibiotic selection – the unavoidable evil two plasmid system</b><br>
 
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Our ultimate goal is to construct our EX without conferring it any new antibiotic resistance. For this reason no resistance gene should be found in our dummy plasmid pDummy. <br><br>
 
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Yet, such a plasmid would not be maintained by itself unless the host bacterium develops an addiction to it (i.e. losses the essential gene in its genome and depends on extra-chromosomal copies on pDummy), and inconveniently, the addiction can only be achieved after the introduction of the plasmid.<br><br>
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The solution is to develop a mutualistic relation between two plasmids and we planned to exploit positively regulated origin of replications. <br><br>
 
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Well studied examples are those in pSC101 and R6K origins of replication, where the origins of replication (OR) appear together with a constitutive gene (G). Initiation of replication happens if and only if the trans element of the gene is provided.<br></p>
 
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Let’s consider the following scenario: <br>
 
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i.  G is placed on pDummy with no selection marker but with a normal replication origin<br>
 
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ii.  OR is the sole origin of replication of another plasmid (here we introduce a new plasmid pToolkit) with a selection marker<br>
 
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iii. pDummy and pToolkit are co-transformed to a bacterium which is under selection stress</p>
 
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We would obtain three possible outcomes:<br>
 
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<b>1. only pDummy is uptaken</b><br>
 
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- since pDummy has no selection marker, the host bacteria die under selection pressure and cannot propagate<br><br>
 
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<b>2. only pToolkit is uptaken</b><br>
 
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- the host bacterium that uptakes pToolkit survives. Yet during propagation, pToolkit is not replicated because proteins of G are absent. Therefore daughter cells of the host bacterium will not receive copies of the pToolkit and die under selection pressure.<br><br>
 
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<b>3. both pDummy and pToolkit are uptaken</b><br>
 
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- in presence of pDummy, pToolkit is maintained and confers the host bacterium with stress resistance. Daughters that receive copies of both plasmids will survive and eventually develop into a colony.<br><br></p>
 
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The result shows that this online survey system can be adaptable, but should be spread more widely on the Internet and supported with more distributed hard copies to make the data more valid and reliable. And two major hypotheses have been obtained from this snapshot analysis. The first is that the public in HK tend to have a positive but close to natural perception of the synthetic biology, showing relatively conservative attitudes. Second, the general publics are very likely to know little about the synthetic biology, which probably has a positive correlation with their overall impression about this new technology. However, notwithstanding this lack of knowledge, the general awareness of the possible risks is nearly at the same level, and the opinions on the future development of this technology are similar. Finding Three is that the public are more inclined to accept the synthetic biology product when it has a big price advantage over the ordinary product.
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Using this mutualistic relation, the desired pDummy can be maintained once the host bacterium develops an addiction it, and pToolkit can be lost in bacteria propagation if the expression of G can be shut off manually. Eventually, the bacteria not obtain any new antibiotic resistance genes but keep pDummy.
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<b>3.2 Development of addiction – use of the lambda RED recombination system</b><br>
 
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To develop the addiction in the host bacterium to pDummy, an essential gene for survival is to be deleted from the bacteria genome, provided that the bacteria can survive on extra-chromosomal copies after the deletion.<br><br>
 
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The deletion here is mediated through the lambda RED recombination system<br><br>
 
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[Nat is still writing...z.z]<br><br>
 
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The lambda RED recombination cassette is located on the pToolkit (and hence the name of the plasmid). Once the recombination is successful, it can be eliminated from the host bacterium together with the antibiotic resistance gene. <br><br>
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Therefore, once the co-transformation of pDummy and pToolkit is successful, linear dsDNAs having a reporter gene flanked by homologous sequences to the essential gene can be introduced into the bacteria. <br><br>
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When the recombination is kicked started, the essential gene will be swapped out and the reporter gene will be incorporated into the bacteria genome.<br><br>
 
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Since the linear dsDNAs do not have origin of replications, they are not inherited in daughters unless they are swapped into the genomes. Thus, any observable signals from the reporter would allow identification of successful recombination. Identified colonies can then be further treated to induce loss of pToolkit, which afterwards would be the completed strain of EX.<br><br>
 
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<b>3.3 Complementation between reporter genes – manifesting completion of EX engineering</b><br>
 
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To ensure that the final strain of EX has: 1. successfully had its essential gene deleted from genome, 2. maintained the pDummy, a complementation reporter system between the pDummy and swapped gene is preferred over a single reporter at the swapped site.<br><br>
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<p><b>Discussion</b></p>
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Different methods can achieve the above aim:<br>
 
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i. Alpha complementation can be used in <i>E. coli</i> strains where the lacZ gene is completely removed. The larger fragment ω can be swapped for the essential gene while the smaller α fragment can stay on pDummy. In a X-gal rich medium, blue colonies suggest the desired engineered strains.<br><br>
 
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ii. Complementation between split fluorescent proteins (sFP). 2010 iGEM Slovenia team has demonstrated the principle that N-terminal and C-terminal fragments of sFPS are able to complement in vivo and two sets of sfFPS are able to undergo Forster resonance energy transfer (FRET). This idea is adopted but an alternative set of candidate, split superfolder GFPs (sfGFP), was developed.</p>
 
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<b>3.4 Summary of construction flow:</b><br>
 
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1. Assembly pDummy and pToolkit<br>
 
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2. Co-transform both plasmid into <i>E. coli</i> and maintain stable strains<br>
 
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3. Introduce linear dsDNAs and induce recombination<br>
 
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4. Isolate recombinants<br>
 
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5. Induce loss of pToolkit
 
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<a href=#top>[Top]</a>
 
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<ul><li><b>Effectiveness and Feasibility for Further Spreading</b></li></ul>
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<ul><li>The Form of the Survey</li></ul>
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<h4 align=left><a name=component></a>4. Details of the components – a closer look to the molecular basis of assembly</h4>
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To get more effective and valid results, a more widely distributed online survey should be launched and more hard copies should be distributed randomly to the general public. Originally, the form thought to be adapted for this survey is the online version for the easiness to collect mass responses and unlimited access to the Internet. But the results here show that the online form has a strong inherent bias in the respondents, especially in fields like education and age when the distribution range is relatively small. So a solution for this is to still use the online version as a data input agent, but the link should be spread more widely on the Internet, accompanying with bigger range of field surveys.</p>  
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<b>4.1 Temperature-sensitive origin of replication_oriR101 & repA101-ts (BBa_K524000)</b><br>
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oriR101 & repA101-ts is a set of low copy origin of replication derived from the pSC101 origin of replication. The repA101-ts gene codes for a heat-labile protein that is required in trans for the initiation of replication at oriR101. In our construct, our characterization has shown that plasmids with this origin of replication can only be maintained below than 300°C, and partial maintenance of plasmid was observed within temperature range from 290°C to 330°C. This part was cloned out from pKD46 plasmid (courtesy of The Coli Genetic Stock Center), and standardized by a nucleotide mutation.<br>
 
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<b>4.2 split superfolder green fluroscent protein_split sfGFP<br>
 
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sfGFP1-10 (BBa_K524001) [Twins: BBa_K524006]<br>
 
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sfGFP11 (BBa_K524002) [Twins: BBa_K524007]</b><br>
 
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The sfGFPs are mutated variants of GFPs that has improved folding kinetics and resistance to chemical denaturants. Split sfGFPs at amino acid residues 214 and 215 have been reported to undergo spontaneous complementation to give green fluorescence. The two split constructs were produced from an existing biobrick – pBAD driven sfGFP BBa_I746908. CDS of sfGFP amino acid residues 1-214 were copied out for sfGFP1-10 using PCR and stop codon was added to the end. The sfGFP11 was produced in a similar fashion, with a start codon added to the front of the CDS of amino acid residues 215 to 238.
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<ul><li>The Effectiveness of the Parameters in Part Two</li></ul>
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The variances in the personal background in this set of data do not show significant difference. The inherent problems of the online survey may contribute a lot, but the effectiveness of the parameters is also in doubt. However, this should be further checked with the results from the more widely spread survey</p>
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<ul><li><b>Major Hypotheses from the Snapshot Results</b></li></ul>
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Although the influence of the parameters about the personal information cannot be counted a lot in the analysis due to the relatively big bias, the interaction between the targets of the questions can still give some meaningful hypotheses regarding the factors influencing the general public’s perception about the synthetic biology. To sum up, there are three major findings or possible hypotheses from this snapshot.<br><br>
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First of all, the overall impression about the synthetic biology in HK is more likely to be positive according to the data, but close to neutral. This probably shows a general conservative attitude towards the synthetic biology among the general public in Hong Kong since the variance for each parameter is small regardless the bias.<br><br>
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<b>4.3 Essential gene <i>nadE</i> (BBa_K524003)</b><br>
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Secondly, the general publics in HK tend to know little about the synthetic biology and that possibly affects their perception of the synthetic biology, but does not have much impact on their foresight for its potential risks and future development. Although the overall responses for heard of the term “synthetic biology” is nearly 50%, seldom actually know what the synthetic biology is and spare special concerns (measured as the frequency respondents talked or searched about the synthetic biology) in this this field. The tiny difference of the scores in Q12 between the groups, who have heard of the synthetic biology and the groups not is a kind of effective support for that. <br><br>
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<i>nadE</i> is a vital gene in <i>E. coli</i>. It codes for NAD+ synthetase. In principle, removal of such gene from the genome would cause addiction of bacteria to a plasmid that has a copy of the gene. CyaR (a sRNA) regulates the expression of <i>nadE</i> post-transcriptionally. This feature is retained in our construct. Transcription of <i>nadE</i> operon requires the sigma-70 factor and is terminated by downstream extragenic sites. The <i>nadE</i> gene was cloned out from the genome of strain BL21(DE3), and was completed the <i>nadE</i> by having B0015 terminator assembled to its end.
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However, the mean score of Q12 is significantly higher in groups who frequently confronted the information about the synthetic biology (F+ group) than others. Also, this “F+ group” show higher confidence towards the potential benefits brought by the synthetic biology (Q5) and fewer tendencies to the tight regulation of the synthetic biology (Q10). And according to the analysis, these two features are very closely related to the higher overall impression score of the synthetic biology (Q11). Then, that should be modestly surprising to see that this “F+ group” holds more positive attitudes towards the synthetic biology.<br><br>
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This tendency is somehow contrary to the familiarity hypothesis (Kahan et al. 2008a; Macoubrie 2006) and the conclusion from the US synthetic biology survey (Pauwels E. et.al. 2009). One possible explanation for this is that the spreading of the idea of the synthetic biology is so low in HK that the major problem faced by the public is the lack of information about the synthetic biology. The mysterious feeling towards this new technology outweighs the tradeoff effects between the benefits and risks when asking for its perception. In this case, the clearness of the mysteries will help to increase the support a bit. The highest concerns and curiosity about the “scientific processes and techniques of the synthetic biology” in Q4 can also be a side support for the relative blankness of the public’s knowledge for the synthetic biology.
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Despite the obvious difference in the responses for Q5, Q10, Q11 and Q12 between the “F+ group” and the other groups, there is no differential pattern for their opinions on the possible risks and the future development. All respondents are more inclined to trust the experts and scientific evidence rather than base on the social concerns about the thoughts of the majority when deciding the future development of the synthetic biology, and “uncontrollable results may be generated” and “the abuse of the technology by the terrorists” are the top worries for most people. This may prove that the public’s imagination of these two factors are similar regardless their different familiarity with the synthetic biology. The finding from the US synthetic biology survey (Pauwels E. et.al. 2009) that people tend to use the other biological technologies like stem cell technology and genetic engineering as references when dealing with some issues about the synthetic biology may be a possible explanation for this.<br><br>
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The third finding is about the price influence on the acceptance of the synthetic biology product (Q7). The public turns out to be more acceptable to the synthetic biology product if an enough strong price advantage of the synthetic biology product is shown. Although more than 80% respondents choose the ordinary product when the two products are of the same price, only one-third stick to their choice when a more favorable is introduced to the synthetic biology product. And this pattern is independent of the other questions in Part One according to the quantitative testing, but the influence of the parameters in unknown due to the biases.
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<b>4.4 Replication initiator pi protein encoded by pir gene (BBa_K524004) and ori-gamma from R6K plasmid</b><br>
 
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ori-gamma is one of three replication origins (the other two being alpha and beta) of the R6K origin. Initiation of replication at ori-gamma requires the pi protein in trans, which is encoded by the pir gene. Yet doubling the concentration of pi protein would effectively shut down the replication as well. Expression of pi protein is autogenously regulated. The pir construct was cloned out from the genome of strain BW25141 (courtesy of The Coli Genetic Stock Center) and standardized. The ori-gamma was adopted from the R6K origin of replication BBa_J61001.
 
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<p><b>Acknowledgement
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For successfully completing this snapshot survey report, the heartfelt thanks should give to the people below for their continuous support and guidance to this synthetic biology survey:
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<b>4.5 iGEM 2010 Slovenia Split/FRET constructs</b><br>
 
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The split CFP and YFP from the biobricks of Slovenia team last year were used as alternative reporters. The idea is to put one of the terminal fragments of a split fluorescence protein into the pDummy, and swap out the essential <i>nadE</i> gene from the genome with the other terminal fragment. Driven by pLac R0010, both fragments should express simultaneously when induced by IPTG and fluorescence signal would be observed as an indicator of successful recombination. <a href=#top>[Top]</a>
 
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Dr Markus SCHMIDT and Dr Lei PEI, from <a href=http://www.idialog.eu/><b>IDC</b></a> and
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<a href=http://www.biofaction.com/?page_id=10><b>Biofaction</b></a>
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The Hong Kong University of Science and Technology (HKUST)
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Professor King L. CHOW, from the Department of Life Science in HKUST
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Professor Michelle YIK, from the Department of Social Science in HKUST
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Mr Jin ZENG, Teaching Assistant from the Department of Social Science in HKUST
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The Hong Kong Institute of Engineers (HKIE)
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The Hong Kong Teachers’ Association (HKTA)
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Members and Advisors of the iGEM2011 HKUST Team
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<h2>Data Page</h2>
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For a complete survery report, please click <a href=><b>here</b></a> to download the PDF file.
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<a href=#constructing>1. Constructing EX</a> <br>
 
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<a href=#method>2. How to Select? </a><br>
 
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Our Project</font></b></p>
Our Project</font></b></p>
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<a href="overview.html" target=_top>Overview</a> |  
<a href="overview.html" target=_top>Overview</a> |  
<a href="data.html" target=_top>Data Page</a><br>
<a href="data.html" target=_top>Data Page</a><br>
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Human Practice</font></b></p>
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Revision as of 09:00, 5 October 2011


Data Page



Abstract

Regardless the heated discussion atmosphere around the synthetic biology, few systematic surveys in this field has been conducted, especially in Asia. In this case, the iGEM2011 HKUST Team with the help of their Austrian partners, Markus Schmidt and Lei Pei, of IDC and Biofaction , launched this survey, treating Hong Kong as a starting point, trying to get the public perception of synthetic biology, especially in Asia, and the key factors influencing this impression. This report is treated as a snapshot of the response got so far to see if this online survey system can work well.

The result shows that this online survey system can be adaptable, but should be spread more widely on the Internet and supported with more distributed hard copies to make the data more valid and reliable. And two major hypotheses have been obtained from this snapshot analysis. The first is that the public in HK tend to have a positive but close to natural perception of the synthetic biology, showing relatively conservative attitudes. Second, the general publics are very likely to know little about the synthetic biology, which probably has a positive correlation with their overall impression about this new technology. However, notwithstanding this lack of knowledge, the general awareness of the possible risks is nearly at the same level, and the opinions on the future development of this technology are similar. Finding Three is that the public are more inclined to accept the synthetic biology product when it has a big price advantage over the ordinary product.

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Discussion

  • Effectiveness and Feasibility for Further Spreading
  • The Form of the Survey

To get more effective and valid results, a more widely distributed online survey should be launched and more hard copies should be distributed randomly to the general public. Originally, the form thought to be adapted for this survey is the online version for the easiness to collect mass responses and unlimited access to the Internet. But the results here show that the online form has a strong inherent bias in the respondents, especially in fields like education and age when the distribution range is relatively small. So a solution for this is to still use the online version as a data input agent, but the link should be spread more widely on the Internet, accompanying with bigger range of field surveys.

  • The Effectiveness of the Parameters in Part Two

The variances in the personal background in this set of data do not show significant difference. The inherent problems of the online survey may contribute a lot, but the effectiveness of the parameters is also in doubt. However, this should be further checked with the results from the more widely spread survey

  • Major Hypotheses from the Snapshot Results

Although the influence of the parameters about the personal information cannot be counted a lot in the analysis due to the relatively big bias, the interaction between the targets of the questions can still give some meaningful hypotheses regarding the factors influencing the general public’s perception about the synthetic biology. To sum up, there are three major findings or possible hypotheses from this snapshot.

First of all, the overall impression about the synthetic biology in HK is more likely to be positive according to the data, but close to neutral. This probably shows a general conservative attitude towards the synthetic biology among the general public in Hong Kong since the variance for each parameter is small regardless the bias.

Secondly, the general publics in HK tend to know little about the synthetic biology and that possibly affects their perception of the synthetic biology, but does not have much impact on their foresight for its potential risks and future development. Although the overall responses for heard of the term “synthetic biology” is nearly 50%, seldom actually know what the synthetic biology is and spare special concerns (measured as the frequency respondents talked or searched about the synthetic biology) in this this field. The tiny difference of the scores in Q12 between the groups, who have heard of the synthetic biology and the groups not is a kind of effective support for that.

However, the mean score of Q12 is significantly higher in groups who frequently confronted the information about the synthetic biology (F+ group) than others. Also, this “F+ group” show higher confidence towards the potential benefits brought by the synthetic biology (Q5) and fewer tendencies to the tight regulation of the synthetic biology (Q10). And according to the analysis, these two features are very closely related to the higher overall impression score of the synthetic biology (Q11). Then, that should be modestly surprising to see that this “F+ group” holds more positive attitudes towards the synthetic biology.

This tendency is somehow contrary to the familiarity hypothesis (Kahan et al. 2008a; Macoubrie 2006) and the conclusion from the US synthetic biology survey (Pauwels E. et.al. 2009). One possible explanation for this is that the spreading of the idea of the synthetic biology is so low in HK that the major problem faced by the public is the lack of information about the synthetic biology. The mysterious feeling towards this new technology outweighs the tradeoff effects between the benefits and risks when asking for its perception. In this case, the clearness of the mysteries will help to increase the support a bit. The highest concerns and curiosity about the “scientific processes and techniques of the synthetic biology” in Q4 can also be a side support for the relative blankness of the public’s knowledge for the synthetic biology. Despite the obvious difference in the responses for Q5, Q10, Q11 and Q12 between the “F+ group” and the other groups, there is no differential pattern for their opinions on the possible risks and the future development. All respondents are more inclined to trust the experts and scientific evidence rather than base on the social concerns about the thoughts of the majority when deciding the future development of the synthetic biology, and “uncontrollable results may be generated” and “the abuse of the technology by the terrorists” are the top worries for most people. This may prove that the public’s imagination of these two factors are similar regardless their different familiarity with the synthetic biology. The finding from the US synthetic biology survey (Pauwels E. et.al. 2009) that people tend to use the other biological technologies like stem cell technology and genetic engineering as references when dealing with some issues about the synthetic biology may be a possible explanation for this.

The third finding is about the price influence on the acceptance of the synthetic biology product (Q7). The public turns out to be more acceptable to the synthetic biology product if an enough strong price advantage of the synthetic biology product is shown. Although more than 80% respondents choose the ordinary product when the two products are of the same price, only one-third stick to their choice when a more favorable is introduced to the synthetic biology product. And this pattern is independent of the other questions in Part One according to the quantitative testing, but the influence of the parameters in unknown due to the biases.

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Acknowledgement

For successfully completing this snapshot survey report, the heartfelt thanks should give to the people below for their continuous support and guidance to this synthetic biology survey:

Dr Markus SCHMIDT and Dr Lei PEI, from IDC and Biofaction
The Hong Kong University of Science and Technology (HKUST)
Professor King L. CHOW, from the Department of Life Science in HKUST
Professor Michelle YIK, from the Department of Social Science in HKUST
Mr Jin ZENG, Teaching Assistant from the Department of Social Science in HKUST
The Hong Kong Institute of Engineers (HKIE)
The Hong Kong Teachers’ Association (HKTA)
Members and Advisors of the iGEM2011 HKUST Team

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For a complete survery report, please click here to download the PDF file.


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