Team:Heidelberg/Team/Acknoledgements

From 2013.igem.org

(Difference between revisions)
(Created page with "{{:Team:Heidelberg/Templates/Navigation}} <html> <style type="text/css"> h1, h2, h3, h4, h5, h6, body { font-family:Arial, sans-serif; } h3 { font-size:21px; fo...")
m
 
(16 intermediate revisions not shown)
Line 11: Line 11:
     font-weight: 400;
     font-weight: 400;
}
}
-
.jumbotron {
+
.jumbotron li {
     font-size:14px;
     font-size:14px;
}
}
Line 20: Line 20:
                 <div class="col-sm-12">
                 <div class="col-sm-12">
                 <!--Project Description-->
                 <!--Project Description-->
-
                     <div style="position:absolute; top:110px;">
+
                     <div top:110px;">
-
                                 <h1><span style="font-size:180%;color:#9e90a3;">Safety.</span><span class="text-muted" style="font-size:100%"> We take good care of you!</span></h1>
+
                                 <h1><span style="font-size:180%;color:#9e90a3;">External Support.</span><span class="text-muted" style="font-size:100%"> Thank you very much!</span></h1>
                               <div class="jumbotron">
                               <div class="jumbotron">
-
                                 <p style="text-align:justify">The uttermost anxiety of those who do not work with genetically modified organisms is concerning safety. We face this critical issue with a tripartite approach. Safety precautions concerning our project can be broken down to the following three topics: Firstly, safety considerations about the wet-lab project, secondly, the general lab safety and thirdly, software safety.
+
                                  
-
In all of the three strands, we deliberated useful approaches and searched communication with safety advisors. Herewith, we wanted to get additional input which we could use for building up our opinion on which parts of the project could be critical or which measures would have to be taken.
+
                                <h2>External Support</h2>
-
                                </p>
+
                        <p style="font-size:20px">
-
                              </div>
+
                            <ul style="font-size:18px">
-
                    </div>
+
<li>Thanks to <b>Marika Ziesack, M.sc.</b> for giving us an introduction to Gibson Cloning.</li>
-
                </div>
+
<li>We recieved valuable advice from <b>Matthew Mattozzi, Ph.D.</b> from the Harvard Wyss Institute for Biologically Inspired Engineering, Center for Life Sciences in Boston on genomic homologous recombination. Dr. Mattozzi also kindly provided the pET21c-pcc-acc-mmce plasmid.</li>
-
            </div>
+
<li><b>Prof. Dr. Herzig</b> and his group at the German Cancer Research Center, Heidelberg for offering the possibility to use their electroporator.</li>
-
            <div class="row" style="margin-top:35%">
+
<li>We also would like to thank <b>PD Dirk M. Nettelbeck, Ph.D.</b> and his group at the German Cancer Research Center for his input on homologous recombination.</li>
-
                <div class="col-sm-6" id="generalSave">
+
<li><b>Lei Fang</b> from the <b>Pfeifer Lab</b> at the Department of Chemical and Biological Engineering, University of Buffalo, for providing the BAP1 strain and the pLF03 and pKD46 plasmids.</li>
-
                <h3 style="text-align:left"> General lab safety</h3>
+
<li>The <b>Gruss Lab</b> at the Center for Molecular Biology at the University Heidelberg who kindly provided us with the <i>E. coli</i> BL21(DE3) (pLys) strain.</li>
-
                <p style="text-align:justify">
+
<li><b>Prof. Russel</b>s group for supporting us with a vial of real <i>E. coli</i> BL21(DE3) cells.</li>
-
                  The solid basis of safety in the wetlab is good laboratory practice. The best starting point for this purpose are personal safety precautions, such as gloves, safety goggles and lab coats. Besides this, a division of the lab into different areas is crucial, as we were 12 people working in our lab most of the time. We designated separate areas for documentation, which of course did not happen on the benches, for lab-work, where we also worked with genetically modified bacteria and an ethidiumbromide-area where we could perform gel-electrophoresis and gel-analysis.<br>
+
<li>Special thanks to <b>Prof. Dr. Marahiel</b> at the Philipps-University Marburg, for providing us with the <i>Brevibacillus parabrevis</i> ATCC 8185 strain.</li>
-
Furthermore, we shifted working steps with β-mercaptoethanol, organic solvents and corrosives to the available fume cupboard. Naturally, we differentiated regular waste from S1-waste which, of course, is to be autoclaved. This should prevent any contamination of the environment with our bioactive material. We have received basic safety training for S1-work by the safety coordinator Mrs. Dr. Angret Joester before starting our work in the lab.
+
<li><b>Prof. Dr. Thomas Höfer</b>s Group at the BioQuant, Heidelberg for providing a sample of <i>E. coli</i> BL21 pLys. </li>
 +
<li><b>Prof. Fussenegger</b> for providing us with the expression plasmids for bpsA and svp, codon optimized for mammalian cells</li>
 +
<li>Thanks to <b>Prof. Groß</b> at the mass spectrometry facility (institute of organic chemistry, University of Heidelberg) for providing his HR-ESI MS.</li>
 +
<li><b>Dr. Oliver Wichmann</b> at the BioQuant, Heidelberg for supporting us with materials including his lyophilizer.</li>
 +
<li>For measurements with Mass Spectrometry we would like to thank <b>Dr. Ruppert</b> and <b>Dr. Hessling</b> of the Centre for molecular biology Heidelberg (ZMBH)</li>
 +
<li>Many thanks to <b>Dr. Dirk Kohlmüller</b> and <b>Dr. Kathrin Schmidt</b> at the neonate screening, University Medical Center Heidelberg for their support in amino acid level detection by mass spectrometry.</li>
 +
<li>Special thanks to <b>Dr. Holger Schäfer</b> from the Institute of Pharmacology and Molecular Biotechnology for scientific and moral support during cloning of Del constructs.</li>
 +
<li>We thank <b>Prof. Dr. Zawatzky</b> for his valuable feedback on safety considerations and ethical concerns.</li>
 +
<li>Thanks to <b>Prof. Dr. Klein</b>s lab at the Institute of Pharmacology and Molecular Biotechnology for giving us the possibility to use their Micro-TOF and especially <b>Lena Weigel</b> for her great support.</li>
 +
<li><b>Dr. Paul Oldham</b> from the Lancaster University and United Nations University, Yokohama for supporting us with his expertise in information processing, interpretation of the social aspects of synthetic biology and for sharing his collection of synthetic biology terms with us.</li>
 +
<li>Special thanks to <b>Dr. Wombacher</b>'s group at the Institute of Pharmacology and Molecular Biotechnology, especially <b> Marcel Best</b> for last minute supply of a rotary evaporator!</li>
 +
<li>We also thank <b>Dr. Rackwitz from Peptide Specialties Laboratories GmbH</b> at Heidelberg for insights in chemical peptide synthesis and valuable input on our project.</li>
 +
<li>Thanks to <b>Dorothea van Aaken</b> for opening up new ethical perspectives on synthetic biology.</li>
 +
<li>We also wish to thank <b>Stafan Dewald</b> and <b>Rolf Kickuth</b> from the <b>Sekular Humansists Rhein Neckar</b> for the lifely discussion on ethical implications of synthetic biology in general and our project in particular and their participation in our talk evening.</li>
 +
<li>Thanks to <b>Dr. Raoul Haschke</b> of the Heidelberg Technology Park UniTT Start-Up Centre for opening up new economical perspectives on possible industrial scale NRP production and the possibility to start our own company.</li>
 +
<li>We wish to thank <b>Paul Kroll</b> from the Institute of Chemical Engineering, Vienna, for scientific input on modelling industrial scale Delftibactin production in <i>E. coli</i>.</li>
 +
<li>And last but not least special thanks to Thi Bach <b>Nga Ly-Hartig</b> who put us in touch with several research groups that work with mass spectrometry and bringing us cupcakes.</li>
 +
                            </ul>
 +
                        </p>
-
                </p>
 
-
               
 
-
                </div>
 
-
                <div class="col-sm-6">
 
-
                <div id="myCarousel" class="carousel slide" style=" margin-bottom:0px;margin-top:42px" >
 
-
                        <!-- Indicators-->
 
-
                        <ol class="carousel-indicators">
 
-
                            <li data-target="#myCarousel" data-slide-to="0" class="active"></li>
 
-
                            <li data-target="#myCarousel" data-slide-to="1"></li>
 
-
                            <li data-target="#myCarousel" data-slide-to="2"></li>
 
-
                            <li data-target="#myCarousel" data-slide-to="3"></li>
 
-
                            <li data-target="#myCarousel" data-slide-to="4"></li>
 
-
                        </ol>
 
-
                        <div class="carousel-inner">
 
-
                            <div class="item active">
+
 
-
                                <img src="https://static.igem.org/mediawiki/2013/c/ce/Heidelberg_IMG_4775.JPG"> 
+
 
-
                                <div class="container">
+
                                  
-
                                    <div class="carousel-caption" data-offset="0">
+
-
                                      <p style="font-size:18px; color:#fff;text-align:center">Protection gloves</p>
+
-
                                    </div>
+
-
                                </div>
+
-
                            </div>
+
-
                            <div class="item">
+
-
                              <img src="https://static.igem.org/mediawiki/2013/1/1f/Heidelberg_IMG_4769.JPG">
+
-
                              <div class="container">
+
-
                                <div class="carousel-caption" data-offset="0">
+
-
                                  <p style="font-size:18px; color:#fff;text-align:center">Plate with <i>UV mask</i> </p>
+
-
                                 </div>
+
                               </div>
                               </div>
-
                            </div>
 
-
                            <div class="item">
 
-
                              <img src="https://static.igem.org/mediawiki/2013/e/e3/Heidelberg_IMG_4782.JPG">
 
-
                              <div class="container">
 
-
                                <div class="carousel-caption" data-offset="0">
 
-
                                  <p style="font-size:18px; color:#fff;text-align:center">Lab coats</p>
 
-
                                </div>
 
-
                              </div>
 
-
                            </div>
 
-
                            <div class="item">
 
-
                                <img src="https://static.igem.org/mediawiki/2013/f/f7/Heidelberg_IMG_4768.JPG"> 
 
-
                                <div class="container">
 
-
                                    <div class="carousel-caption" data-offset="0">
 
-
                                      <p style="font-size:18px; color:#fff;text-align:center">Ethidiumbromide-area</p>
 
-
                                    </div>
 
-
                                </div>
 
-
                            </div>
 
-
                            <div class="item">
 
-
                                <img src="https://static.igem.org/mediawiki/2013/4/44/Heidelberg_IMG_4776.JPG"> 
 
-
                                <div class="container">
 
-
                                    <div class="carousel-caption" data-offset="0">
 
-
                                      <p style="font-size:18px; color:#fff;text-align:center">Fume cupboard</p>
 
-
                                    </div>
 
-
                                </div>
 
-
                            </div>
 
-
                        </div>
 
-
                        <a class="left carousel-control" href="#myCarousel" data-slide="prev"><span class="glyphicon glyphicon-chevron-left"></span></a>
 
-
                        <a class="right carousel-control" href="#myCarousel" data-slide="next"><span class="glyphicon glyphicon-chevron-right"></span></a>
 
                     </div>
                     </div>
-
 
 
-
            </div>
 
-
            </div>
 
-
<div class="row" style="margin-top:3%">
 
-
                <div class="col-sm-12">
 
-
                <h3 style="text-align:left"> Wet-Lab-Project Safety</h3>
 
-
                <p style="text-align:justify">
 
-
                  In addition to the general lab safety, we talked to the safety advisor on our campus, Dr. Willi Siller, with whom we double checked the feasibility of the project concerning its safety. One of his first questions was, which biosafety-level our donor- and chassis-organisms were ranked in. For the chassis-organism, this question was easy to answer, as we only used different strains of E. coli K12 and hence they all are ranked S1. As far as the donor organisms are concerned, the list is longer. However, all of them are categorized as S1, except for D. acidovorans, which is ranked S2 in Germany if used as a chassis-organism.<br>
 
-
This classification is due to the fact that D. acidovorans is capable of causing inflammatory diseases such as endocarditis. Still, we can well justify the work with D. acidovorans on the strength of two aspects: Firstly, we never use D. acidovorans as chassis-organism and secondly, upon research, we spotted that the pathogenicity of D. acidovorans is based on proteins belonging to the Omp-family. The genes, that encode for those proteins are on a different locus than our genes of interest – the Del-cluster. <br>
 
-
Consecutively, we can conclude that the work with either of the organisms we use for our project carries any risks for neither the experimentalist, nor for non-participants, if good laboratory practice is adhered to. As far as the peptides is concerned, we can state confidently that none of the peptides that we synthesize in our project are toxic or in any way hazardous. Tyrocidine is harmful to human blood and reproductive cells, but will never be used as entire peptide (i.e. only several amino acids) and was, besides that, publically available as antibiotic.<br>
 
-
Within our project, we however intend to share knowledge with the broad scientific community and introduce a new and efficient way of in vivo production of short peptides via NRPSs. The framework of NRPS of course allows production of various peptides, and hence it is imaginable that this system is accidently or intendedly used for the synthesis of perilous products. There is however a straight-forward justification for either of the aforementioned dangers: Firstly, to avert unintended production of hazardous substances, we intend to include several precautions within our software, which is elaborated on in the according section. Secondly, someone contemplating malicious abuse of our proposed framework, would also have the chance to produce the dangerous substances by chemical synthesis.<br>
 
-
As we, in our project intend to offer a more efficient way of recycling gold from electronic waste, we consider the implications of our projects for the environment a central point in our safety considerations. This reaches from the basic avoidance of contamination, which we ensure by good laboratory practice, to learning from and discussing with professionals about biosafety and precautions for the environment during an ABC-defense training (atomic, biological and chemical weapons) at the German Armed Forces. Please refer to our <a rel='prev' href="https://2013.igem.org/Team:Heidelberg/Outreach">Scientific Outreach</a>, for further details on that.
 
-
                </p>
 
-
                <p style="text-align:justify"><a class="btn btn-lg btn-default" href="https://static.igem.org/mediawiki/2013/d/da/Heidelberg_Safety_form.pdf" style="position:absoluite; vertical-align: middle;">Download Safety Form</a></p><p style="text-align:justify"><a class="btn btn-lg btn-default" href=https://static.igem.org/mediawiki/2013/9/9a/Heidelberg_Safety_form_appendix.pdf style="position:absoluite; vertical-align: middle;">Download Appendix</a></p>
 
-
                </div>
 
-
 
 
-
            </div>
 
-
<div class="row" style="margin-top:3%">
 
-
                <div class="col-sm-12">
 
-
                <h3 style="text-align:left"> Software-Safety</h3>
 
-
                <p style="text-align:justify">
 
-
                  Our software team developed the NRPSDesigner, a web application capable of suggesting cloning strategies for the creation of artificial NRP-synthetases, which can synthesize a peptide of choice. This software is built upon a database of domains, origins and products. The very nature of this project meant that we were confronted with safety issues all web developers face, as well as by issues specific to the biological underpinnings of our software. The latter overlapped in many cases with our considerations throughout the wetlab projects. <br>
 
-
Any web application has to deal with diverse attacks of malicious intent. Dealing with these was simplified by using Django, a stable web framework. Such frameworks try to trivialize common tasks in the work of a web developer and of course safety issues fall into this category. For example, Django provides a mechanism for protection against cross site request forgery attempts, in which a malicious site can cause actions in the server by using the credentials of a logged-in user. The Django development team also uses a very strict process for dealing with new security issues in a timely and safe fashion by initially fixing these through private, confidential channels. Once the patches have been applied, the security issue is publicly disclosed, so that server maintainers can update to the latest Django version. As an example, this September a set of security releases were issued by the Django development team in order to remedy a problem with denial-of-service (DoS) attacks. Of course, after being informed of this release, we immediately updated the Django version running on our server to the latest one. <br>
 
-
A second issue arising during web development, is the safety of a user's confidential data. Again Django provides an in-built authentication system which encrypts the password of all registered users using PBKDF2 (Password-Based Key Derivation Function 2). Beyond the Django security features, we also used a password protected storage server for the MySQL NRPSDesigner database. <br>
 
-
In regards to the biological background of the NRPSDesigner software, we were particularly troubled about not leading a user astray with the organisms suggested for the cloning, especially in case they were not of the S1 safety level. This is particular important in the case of NRPS, because many interesting NRPS such as Pyoverdine, a fluorescent siderophore, are produced by pathogenic microorganisms (e.g. Pseudomonas aeruginosa). As of the European wiki freeze, the NRPSDesigner database includes only S1 organisms. Nevertheless, as in the future the database may be expanded with S2 organisms, we intend to handle such cases by issuing appropriate alert messages to the end-user and also allowing him to filter the domains available to his constructs based on the safety level. <br>
 
-
A second consideration arises from the extensibility of the NRPSDesigner database, which means that any user can enter new NRPS domain sequences. These in turn are fed into the algorithm for the design of synthetic NRPS constructs. Thus it is important to ensure that no malicious sequence can be entered, which could then be returned as the output of the NRPSDesigner to an unsuspecting user. This is achieved by ensuring the correct domains have been entered by use of the automated domain prediction pipeline using Hidden Markov Models. Additionally, a user that wants to be particularly safe, can filter the domains available to the NRPSDesigner algorithm according to curation status. (Curated domains have been entered or validated by an iGEM Heidelberg or Edinburgh 2013 team member or by another NRPS specialist in contrast to domains that have been entered by other end-users.) The other non-NRPS sequences, such as backbones, promoters etc., which can be added to the constructs after the domains have been determined by the software, are specific to the user that entered them (e.g. by the automated interface to the API of the Parts Registry) and hence pose no danger to other users. <br>
 
-
Another important safety issue arising from the theoretical underpinnings of the NRPSDesigner is its use for the malicious synthesis of toxic peptides. Thus in a future version we want to integrate information from databases on toxins in order disable the design of NRPS domains for toxic peptides. We also searched for peptide toxicity prediction tools which could be integrated with the NRPSDesigner. One such tool, called ToxinPred [gupta2013], uses machine learning methods and a dataset of 1805 toxic peptides in order to accomplish this very task. Unfortunately, the current implementation only considers peptides consisting of proteinogenic amino acids and not the variety of modified or D-amino acids available to NRP-synthetases.
 
-
                </p>
 
-
                <p style="text-align:justify"><a class="btn btn-lg btn-default" href=https://static.igem.org/mediawiki/2013/a/ae/Heidelberg_Software_Safety_form.pdf style="position:absoluite; vertical-align: middle;">Download Safety Form</a></p>
 
                 </div>
                 </div>
-
 
 
             </div>
             </div>
 +
         
         </div>
         </div>
   </body>
   </body>
</html>
</html>
{{:Team:Heidelberg/Templates/Footer-Nav}}
{{:Team:Heidelberg/Templates/Footer-Nav}}

Latest revision as of 15:41, 26 October 2013


External Support. Thank you very much!

External Support

  • Thanks to Marika Ziesack, M.sc. for giving us an introduction to Gibson Cloning.
  • We recieved valuable advice from Matthew Mattozzi, Ph.D. from the Harvard Wyss Institute for Biologically Inspired Engineering, Center for Life Sciences in Boston on genomic homologous recombination. Dr. Mattozzi also kindly provided the pET21c-pcc-acc-mmce plasmid.
  • Prof. Dr. Herzig and his group at the German Cancer Research Center, Heidelberg for offering the possibility to use their electroporator.
  • We also would like to thank PD Dirk M. Nettelbeck, Ph.D. and his group at the German Cancer Research Center for his input on homologous recombination.
  • Lei Fang from the Pfeifer Lab at the Department of Chemical and Biological Engineering, University of Buffalo, for providing the BAP1 strain and the pLF03 and pKD46 plasmids.
  • The Gruss Lab at the Center for Molecular Biology at the University Heidelberg who kindly provided us with the E. coli BL21(DE3) (pLys) strain.
  • Prof. Russels group for supporting us with a vial of real E. coli BL21(DE3) cells.
  • Special thanks to Prof. Dr. Marahiel at the Philipps-University Marburg, for providing us with the Brevibacillus parabrevis ATCC 8185 strain.
  • Prof. Dr. Thomas Höfers Group at the BioQuant, Heidelberg for providing a sample of E. coli BL21 pLys.
  • Prof. Fussenegger for providing us with the expression plasmids for bpsA and svp, codon optimized for mammalian cells
  • Thanks to Prof. Groß at the mass spectrometry facility (institute of organic chemistry, University of Heidelberg) for providing his HR-ESI MS.
  • Dr. Oliver Wichmann at the BioQuant, Heidelberg for supporting us with materials including his lyophilizer.
  • For measurements with Mass Spectrometry we would like to thank Dr. Ruppert and Dr. Hessling of the Centre for molecular biology Heidelberg (ZMBH)
  • Many thanks to Dr. Dirk Kohlmüller and Dr. Kathrin Schmidt at the neonate screening, University Medical Center Heidelberg for their support in amino acid level detection by mass spectrometry.
  • Special thanks to Dr. Holger Schäfer from the Institute of Pharmacology and Molecular Biotechnology for scientific and moral support during cloning of Del constructs.
  • We thank Prof. Dr. Zawatzky for his valuable feedback on safety considerations and ethical concerns.
  • Thanks to Prof. Dr. Kleins lab at the Institute of Pharmacology and Molecular Biotechnology for giving us the possibility to use their Micro-TOF and especially Lena Weigel for her great support.
  • Dr. Paul Oldham from the Lancaster University and United Nations University, Yokohama for supporting us with his expertise in information processing, interpretation of the social aspects of synthetic biology and for sharing his collection of synthetic biology terms with us.
  • Special thanks to Dr. Wombacher's group at the Institute of Pharmacology and Molecular Biotechnology, especially Marcel Best for last minute supply of a rotary evaporator!
  • We also thank Dr. Rackwitz from Peptide Specialties Laboratories GmbH at Heidelberg for insights in chemical peptide synthesis and valuable input on our project.
  • Thanks to Dorothea van Aaken for opening up new ethical perspectives on synthetic biology.
  • We also wish to thank Stafan Dewald and Rolf Kickuth from the Sekular Humansists Rhein Neckar for the lifely discussion on ethical implications of synthetic biology in general and our project in particular and their participation in our talk evening.
  • Thanks to Dr. Raoul Haschke of the Heidelberg Technology Park UniTT Start-Up Centre for opening up new economical perspectives on possible industrial scale NRP production and the possibility to start our own company.
  • We wish to thank Paul Kroll from the Institute of Chemical Engineering, Vienna, for scientific input on modelling industrial scale Delftibactin production in E. coli.
  • And last but not least special thanks to Thi Bach Nga Ly-Hartig who put us in touch with several research groups that work with mass spectrometry and bringing us cupcakes.

Thanks to