Difference between revisions of "Team:Aalto-Helsinki/Attributions"

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<h2>Project support and advice</h2>
 
<h2>Project support and advice</h2>
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<p>Our project is in large part based on two publications about propane production in E. coli.</p>
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<p>Our project is in large part based on two publications about propane production in <i>E. coli</i>.</p>
  
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<p>Kallio P, Pásztor A, Thiel K, Akhtar MK, Jones PR. An engineered pathway for the biosynthesis of renewable propane. Nat Commun. 2014;5:4731. doi: 10.1038/ncomms5731.</p>
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<p><a href="http://www.nature.com/ncomms/2014/140902/ncomms5731/full/ncomms5731.html target="_blank">Kallio <i>et al.</i> An engineered pathway for the biosynthesis of renewable propane.</a></p>
  
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<p>Menon N, Pásztor A, Menon BR, <i>et al.</i> A microbial platform for renewable propane synthesis based on a fermentative butanol pathway. Biotechnology for Biofuels. 2015;8:61. doi:10.1186/s13068-015-0231-1.</p>
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<p><a href ="http://www.biotechnologyforbiofuels.com/content/8/1/61" target="_blank">Menon <i>et al.</i> A microbial platform for renewable propane synthesis based on a fermentative butanol pathway.</a></p>
  
 
<p>Professor <b>Pauli Kallio</b> and Dr. <b>András Pásztor</b> have provided us with valuable advice about the propane pathway and its construction.</p>
 
<p>Professor <b>Pauli Kallio</b> and Dr. <b>András Pásztor</b> have provided us with valuable advice about the propane pathway and its construction.</p>
  
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<p>Our amphiphilic proteins are derived from the study by Huber et al.</p>
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<p>Our amphiphilic proteins are derived from the study</p>
  
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<p>Huber, Matthias C., <i>et al.</i> "Designer amphiphilic proteins as building blocks for the intracellular formation of organelle-like compartments." Nature materials 2014; 15. doi: 10.1038/NMAT4118.</p>
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<p><a href="http://www.nature.com/nmat/journal/v14/n1/full/nmat4118.html" target="_blank">Huber <i>et al.</i> Designer amphiphilic proteins as building blocks for the intracellular formation of organelle-like compartments.</a></p>
  
 
<p>Our advisor professor <b>Markus Linder</b> has given us valuable feedback on our ideas and general input on our development. Doctor <b>Jussi Jäntti</b> and other researchers from VTT gave help with expanding our idea and building our story.</p>  
 
<p>Our advisor professor <b>Markus Linder</b> has given us valuable feedback on our ideas and general input on our development. Doctor <b>Jussi Jäntti</b> and other researchers from VTT gave help with expanding our idea and building our story.</p>  
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<p><b>Jussi Jäntti</b> from VTT helped us with choosing a linker sequence and told us about the amphiphilic proteins.</p>
 
<p><b>Jussi Jäntti</b> from VTT helped us with choosing a linker sequence and told us about the amphiphilic proteins.</p>
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<p><b>Ritva Heinonen</b> from VTT helped us to analyze micelle formation with confocal microscopy.</p>
  
 
<p><b>Dominik Mojzita</b> from VTT introduced us to the Gibson Assembly method.</p>
 
<p><b>Dominik Mojzita</b> from VTT introduced us to the Gibson Assembly method.</p>
  
 
<p><b>Anja Martinez</b> from Thermo Fisher helped us optimize our genes for synthesis.</p>
 
<p><b>Anja Martinez</b> from Thermo Fisher helped us optimize our genes for synthesis.</p>
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<p><b>Jorg de Ruijter</b> from Markus' group helped with practicalities in the lab during the summer and teached us how to do an SDS-PAGE.</p>
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<p><b>Sami Havukainen</b> helped with Gibson assembly and continuous production measurements</p>
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<p><b>Christopher Jonkergouw</b> from Markus' group helped us to confirm GFP transformation with fluorescence microscopy.</p>
  
 
<p>Rest of Markus' lab group helped us with practicalities in the lab.</p>
 
<p>Rest of Markus' lab group helped us with practicalities in the lab.</p>
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<p><b>Pekka Heino</b> and <b>Tapio Palva</b> gave us some insights on cellulose degradation and pointed out some possible flaws in our system so we were able to do more research and fix them. Pekka Heino also gave some suggestions on the practicalities regarding wet lab work.</p>
 
<p><b>Pekka Heino</b> and <b>Tapio Palva</b> gave us some insights on cellulose degradation and pointed out some possible flaws in our system so we were able to do more research and fix them. Pekka Heino also gave some suggestions on the practicalities regarding wet lab work.</p>
  
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<p><b>Auli Murrola</b> ran our liquid chromatography analysis for all the glucose samples, evaluated the values and created standards for them.</p>
  
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<p><b>Janne Wallenius</b> helped us set up our continuous production and gave advice and estimates on good parameters to use for it.</p>
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<p><b>Janne Wallenius</b> helped us set up and maintain our continuous production, and gave advice and estimates on good parameters to use for it.</p>
 
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<p><b>Elena Czeizler</b> from Aalto University gave us insights on what to use for modeling and how to proceed with it.</p>
 
<p><b>Elena Czeizler</b> from Aalto University gave us insights on what to use for modeling and how to proceed with it.</p>
  
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<p><b>Anna-Liisa Ruskeepää</b> from VTT ran our GC-analysis for all the propane samples and created standards for them. Furthermore, she gave some advice for analysis.</p>
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<p><b>Marja Ilmen</b> from VTT made arrangements for GC-analysis.</p>
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<p><b>Anna-Liisa Ruskeepää</b> from VTT ran our GC-analysis for all the propane samples, evaluated the values and created standards for them. Furthermore, she gave some advice for analysis.</p>
  
 
<p><b>Antti Rantasalo</b> from VTT and our avisor <b>Heli Viskari</b> helped us with our construct design.</p>
 
<p><b>Antti Rantasalo</b> from VTT and our avisor <b>Heli Viskari</b> helped us with our construct design.</p>
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<p><b>Tuulikki Seppänen-Laakso</b> from VTT made arrangements for GC-analysis.</p>
  
 
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     <p><a href="https://www.helsinki.fi/en" target="_blank">The University of Helsinki</a> is the oldest and largest university in Finland and one of the leading multidisciplinary universities in the world. They concentrate on high quality scientific research and research education which form the basis of their teaching. The University of Helsinki also supports education and scholarship in the community with its wide contact network.</p>
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     <p><a href="https://www.helsinki.fi/en" target="_blank" style="padding:0">The University of Helsinki</a> is the oldest and largest university in Finland and one of the leading multidisciplinary universities in the world. They concentrate on high quality scientific research and research education which form the basis of their teaching. The University of Helsinki also supports education and scholarship in the community with its wide contact network.</p>
 
     <p>University of Helsinki supported us financially and offered group work spaces for us.</p>
 
     <p>University of Helsinki supported us financially and offered group work spaces for us.</p>
 
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    <a href="http://neb.com/" target="_blank"><img src="https://static.igem.org/mediawiki/2015/f/f5/Aalto-Helsinki_neb_logo.png" style = "max-width:100%;
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    <p><a href="https://neb.com/" target="_blank" style="padding:0">New England Biolabs (NEB)</a> is a major provider of native and recombinant enzymes for life science research. NEB is also a long-standing supporter of iGEM teams. Currently supplying over 276 restriction enzymes, NEB product catalog also includes products related to PCR, gene expression, cellular analysis, RNA analysis and epigenetics. </p>
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    <p>NEB donated our team laboratory materials, significantly helping us with our efforts in the laboratory. </p>
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     <p><a href="https://www.idtdna.com/" target="_blank">Integrated DNA Technologies</a> mainly provides DNA and oligonucleotide synthesis services. They are the largest custom oligo producer in the US with customers ranging from small research groups to big pharmaceutical companies. </p>
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     <p><a href="https://www.idtdna.com/" target="_blank" style="padding:0">Integrated DNA Technologies</a> mainly provides DNA and oligonucleotide synthesis services. They are the largest custom oligo producer in the US with customers ranging from small research groups to big pharmaceutical companies. </p>
 
     <p>IDT provided us with 20k base pairs of free DNA synthesis services.</p>
 
     <p>IDT provided us with 20k base pairs of free DNA synthesis services.</p>
 
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     <p><a href="https://www.flowdock.com/" target="_blank">Flowdock</a> is a team collaboration app for desktop, mobile & web. Work on things that matter, be transparent and solve problems across tools, teams & time zones.</p>
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     <p><a href="https://www.flowdock.com/" target="_blank" style="padding:0">Flowdock</a> is a team collaboration app for desktop, mobile & web. Work on things that matter, be transparent and solve problems across tools, teams & time zones.</p>
 
     <p>Flowdock provided us with licenses to their software, which we used as our main communication platform. It combines file sharing, chats for different areas and integration of team email and Twitter and much more. Notifications make sure you can reach all the people needed and not bother others!</p>
 
     <p>Flowdock provided us with licenses to their software, which we used as our main communication platform. It combines file sharing, chats for different areas and integration of team email and Twitter and much more. Notifications make sure you can reach all the people needed and not bother others!</p>
 
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Latest revision as of 04:49, 29 October 2015

Attributions

All the work not mentioned here was done by the students in the team. Most of the modeling and wet lab work was completed by the students, with help and guidance from people mentioned below. Wiki and website were created by the students with their previous knowledge and new skills learned during the summer. Aalto-Helsinki logo base was created by the previous year's team.

Our Supporters

Project support and advice

Our project is in large part based on two publications about propane production in E. coli.

Kallio et al. An engineered pathway for the biosynthesis of renewable propane.

Menon et al. A microbial platform for renewable propane synthesis based on a fermentative butanol pathway.

Professor Pauli Kallio and Dr. András Pásztor have provided us with valuable advice about the propane pathway and its construction.

Our amphiphilic proteins are derived from the study

Huber et al. Designer amphiphilic proteins as building blocks for the intracellular formation of organelle-like compartments.

Our advisor professor Markus Linder has given us valuable feedback on our ideas and general input on our development. Doctor Jussi Jäntti and other researchers from VTT gave help with expanding our idea and building our story.

Fundraising help and advice

Aalto-Helsinki 2014 helped us on how to approach possible sponsors and also provided us with a list of companies that they had contacted and where they had found funding.

Merja Penttilä from VTT and Markus Linder helped us with finding contacts in companies and gave suggestions on how to approach sponsors.

Lab support

Aalto University and our advisor Markus Linder provided us with lab spaces, equipment and resources for lab work. Also the rest of his group has given us good advice while working in the lab this summer. Martina Ikonen and Minttu Salmela from last year’s team gave us good tips on lab work and helped us design our primers.

Heli Viskari helped us with practicalities in the lab and took care of our orders. She also helped us with designing primers.

Pauli Kallio sent us plasmid maps, plasmids and strains from his research.

Anssi Rantasalo from VTT helped us design our assembly constructs.

Jussi Jäntti from VTT helped us with choosing a linker sequence and told us about the amphiphilic proteins.

Ritva Heinonen from VTT helped us to analyze micelle formation with confocal microscopy.

Dominik Mojzita from VTT introduced us to the Gibson Assembly method.

Anja Martinez from Thermo Fisher helped us optimize our genes for synthesis.

Jorg de Ruijter from Markus' group helped with practicalities in the lab during the summer and teached us how to do an SDS-PAGE.

Sami Havukainen helped with Gibson assembly and continuous production measurements

Christopher Jonkergouw from Markus' group helped us to confirm GFP transformation with fluorescence microscopy.

Rest of Markus' lab group helped us with practicalities in the lab.

András Pásztor gave us many ideas and insights on producing propane. He also helped us with the methods to detect propane and designing the constructs.

Pekka Heino and Tapio Palva gave us some insights on cellulose degradation and pointed out some possible flaws in our system so we were able to do more research and fix them. Pekka Heino also gave some suggestions on the practicalities regarding wet lab work.

Auli Murrola ran our liquid chromatography analysis for all the glucose samples, evaluated the values and created standards for them.

Janne Wallenius helped us set up and maintain our continuous production, and gave advice and estimates on good parameters to use for it.

Difficult technique support

Merja Aho from VTT gave us some tips on places to get started and advice on the tools we could use for modeling.

Elena Czeizler from Aalto University gave us insights on what to use for modeling and how to proceed with it.

Marja Ilmen from VTT made arrangements for GC-analysis.

Anna-Liisa Ruskeepää from VTT ran our GC-analysis for all the propane samples, evaluated the values and created standards for them. Furthermore, she gave some advice for analysis.

Antti Rantasalo from VTT and our avisor Heli Viskari helped us with our construct design.

Tuulikki Seppänen-Laakso from VTT made arrangements for GC-analysis.

Project advisor support

Markus Linder advised us throughout the project starting from ideation to presenting at the Giant Jamboree. He helped us get in contact with researchers who helped us in defining our project idea and gave us tips on labwork, modeling and funding. He also gave us feedback on our project throughout the summer and helped us refine our presentation and poster.

Heli Viskari helped us with practicalities in the lab and with lab orders. She also followed our project closely throughout the summer and gave feedback on our approaches and our presentations.

Human practices support

Tarja Knuuttila and her associates including Leena Tulkki, Rami Koskinen, Miles MacLeod, Tero Ijäs and Anita Välikangas from the University of Helsinki helped us create our idea and gave feedback and suggestions on the questions we chose for our human practices questionnaire. They also helped us analyze and gather our results as well as gave feedback on our report.

Our Sponsors

The Aalto University School of Science aims to change the world for the better through its internationally-acclaimed and high-level research and by making a significant impact on society in a variety of ways. They have high level research with wide connections to international networks with focus to address the increasingly complex challenges faced by society; namely, those associated with energy, the environment, well-being, and decision-making.

The Aalto University School of Science was very enthusiastic about our project and funded us financially to make it possible.

The Aalto University School of Chemical Technology combines natural sciences and engineering in a unique way. The school aims for high co-operation with the business world and Finnish industry.

Aalto University School of Chemical Technology has been a very important partner in our project. They provided us with lab space, required reagents and equipment to test propane production. Additionally, we got valuable knowledge from professors and the lab team around us whenever we ran into problems. The School of Chemical Technology also supported us financially.

The University of Helsinki is the oldest and largest university in Finland and one of the leading multidisciplinary universities in the world. They concentrate on high quality scientific research and research education which form the basis of their teaching. The University of Helsinki also supports education and scholarship in the community with its wide contact network.

University of Helsinki supported us financially and offered group work spaces for us.

The University of Helsinki Faculty of Science focuses on high quality basic research aiming for more sustainable future and better quality of life. Their research is highly multi-disciplinary with co-operations between different research facilities in the faculty. Kumpula Science Campus is the most versatile cluster of scientific competence in the Nordic countries with several national Centers of Excellence.

They offered us both monetary support and visibility in their magazine as well as aid in modelling questions.

Together with the other units at the Viikki Campus, the Faculty of Biological and Environmental Sciences forms Finland’s most prominent and, by volume, largest cluster in research and education in the biosciences. They focus in high-level international research and creating functional framework for teaching and research in the fields of biosciences and the environment and for their societal influence and interaction.

University of Helsinki Faculty of Biological and Environmental Sciences supported us financially and provided us with assistance from their professors.

Stora Enso is Finnish forest industry company and one of the worlds largest pulp and paper manufacturer. They have long expertise with wood industry and are currently focusing on transforming from traditional paper production into renewable materials growth company. "Do good for the People and the Planet" is their new motto.

Stora Enso supported us financially and were very enthusiastic about our project.

The University of Helsinki department of Food and Environmental Sciences also resides in Viikki and is part of the Faculty of Agriculture and Forestry. They offer high quality and internationally respected research and teaching. They focus on food quality and raw materials, clean environment and utilization of microbes.

University of Helsinki Department of Food and Environmental Sciences supported us financially.

Aalto University Student Union gives students of the Aalto University housing, guidance services and represent student rights. They also host all kinds of events and fund student projects to keep the community innovative. The union was formed from the former student unions of Helsinki School of Economics, University of Art and Design Helsinki and Helsinki University of Technology

Aalto University Student Union supported our project financially.

LAL, the Finnish Union of Experts in Science is a union for people with higher degrees in different sciences. LAL has over 7900 members and aims to protect the financial, social and professional interests of it's members.

LAL helped us financially.

Industrial Biotechnology Cluster Finland promotes sustainability and bioeconomy in the Finnish industry. They both connect and start projects between companies and research institutes for creating new solutions and products in the field in Finland as well as abroad.

IBC Finland supported us financially.

New England Biolabs (NEB) is a major provider of native and recombinant enzymes for life science research. NEB is also a long-standing supporter of iGEM teams. Currently supplying over 276 restriction enzymes, NEB product catalog also includes products related to PCR, gene expression, cellular analysis, RNA analysis and epigenetics.

NEB donated our team laboratory materials, significantly helping us with our efforts in the laboratory.

Integrated DNA Technologies mainly provides DNA and oligonucleotide synthesis services. They are the largest custom oligo producer in the US with customers ranging from small research groups to big pharmaceutical companies.

IDT provided us with 20k base pairs of free DNA synthesis services.

The Student Union of the University of Helsinki provides the students of the University of Helsinki with guidance services and interest representation as well as great discounts. HYY is the oldest student union in Finland and had a big part in creating many of the present traditions.

The Student Union of the University of Helsinki supported us financially.

Flowdock is a team collaboration app for desktop, mobile & web. Work on things that matter, be transparent and solve problems across tools, teams & time zones.

Flowdock provided us with licenses to their software, which we used as our main communication platform. It combines file sharing, chats for different areas and integration of team email and Twitter and much more. Notifications make sure you can reach all the people needed and not bother others!

Geneious is the world’s leading bioinformatics software platform used by over 2500 universities and institutes, and commercial companies in more than 65 countries. It also supports user-made plugins to customize your user experience and speed up the workflow.

Geneious provided us with software licenses for the duration of the project.

The Chemical Industry Federation of Finland is a trade association for the chemical industry and its closely related sectors, covering various fields in the basic and production chemical industry. They actively promote the competitiveness and operational preconditions of its members in Finland.

While they are not actually related to biotechnology, they still supported us financially and invited us to their workshop.

Ratekoulutus is a Finnish service that provides high quality courses and seminars for customized needs in various fields. Their course emphasize life long learning and networking.

Ratekoulutus supported us financially.

Genscript provides innovative services and products to bypass the laborious steps of research. They provide gene synthesis, peptide, protein, antibody and discovery biology service capabilities and are internationally recognized as a leading Contract Research Organization (CRO) specializing in biological research and early-phase drug discovery services.

Genescript provided us with credit to use for their synthesis services, helping us create the constructs needed for our pathway.

Grano produces digi- and print services, products, marketing and solutions in three countries. They have a huge range of possibilities, from house sized banners to small stickers. Grano has extensive environment policy and aims to create sustainable products and services for everyone.

Grano is sponsoring our poster printing.