Team:TU-Munich/Team/Attributions

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====Fluorescense Microscopy====
====Fluorescense Microscopy====
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====Transformation of ''Physcomitrella patens''====
== Laboratory of Prof. Dr. Skerra ==
== Laboratory of Prof. Dr. Skerra ==

Revision as of 09:50, 19 October 2013


iGEM Team TU-Munich 2013

Experimental measurements

All measurements were conducted by student members of the iGEM Team TU-Munich 2013. For the first usage of instruments they obtained a introduction to the technique and the instrument which was given by an instructor or someone from the laboratory. Measurements itself and the evaluation of the obtained data were done by student members.

LC-MS Measurements

ESI-TOF Measurements

Fluorescense Microscopy

Transformation of Physcomitrella patens

Laboratory of Prof. Dr. Skerra

The research group at the Chair of Biological Chemistry at TUM works in the biochemical field of protein engineering and design with a focus on therpeutic proteins and their application. The three main fields of research are (1) thee development of Anticalin which are alternative binding scaffolds and are a promising alterntive for conventinal antibodies (2) the extension of the plasma half-life of therapeutic proteins using a poly peptide polymer and (3) the site-specific conjugation of therapeutic proteins. Thus the focus of our hosting laboratory is biomedical engineering whereas our iGEM topic shows no intersection with this topic.
The single nigligible exception is that we used a higher engineered Anticalin (<partinfo>BBa_K1159003</partinfo>) to bind fluorescein in our BioAccumulation subproject compared to the conventional BioBrick (<partinfo>BBa_K157004</partinfo>). This higher engineered version has three additional amino acid exchanges and exhibits a 75-fold higher affinity for its binding partner (fluorescein). It was not essential to have this higher engineered version for our project but we wanted to supply the registry with this improved part.
Beside this plasmid we also obtained a plasmid for the TEV protease from the chair which we have used to generate the Split-TEV protease (<partinfo>BBa_K1159100</partinfo>, <partinfo>BBa_K1159101</partinfo> and <partinfo>BBa_K1159102</partinfo>).


Prof. Skerra kindly provided us with space in his laboratory, and generously advanced us money to pay for team registration, travel expenses and laboratory resources. Moreover he participated approximately one a month in our team meetings and advised us on our project.

Technical University Munich

Laboratory of Prof. Dr. Helmreich

Sanitary Environmental Engineering is a horizontal discipline comprised of civil engineering, process engineering and chemistry/biology. Research and teaching include the fields of water suppy, sewage and rain water treatment, water quality and the modelling of aquatic systems.

In our interview with Prof. Helmreich, she explained us several characterization techniques to assess water quality. Furthermore she kindly provided us with water samples from sewage treatment plants.

Laboratory of Prof. Dr. Langosch

The Chair for Chemistry of Biopolymers focuses on the structural biochemistry of integral membrane proteins. Core themes are molecular interactions between membrane proteins, strucural dynamics of membrane bound protein helices, membrane protein/lipid interactions and structure/function relationships of integral membrane protein complexes.

During the planning phase of our project we asked Prof. Langosch for advice concerning the design of the transmembrane domain of our constructs.

Laboratory of Prof. Dr. Rost

Prof. Rost works in the field of bioinformatics and computer-based biology, focussing on the prediction of structure and function of proteins and genes. His team's specialty is the use of artificial intelligence and machine learning algorithms to predict structure and function of proteins.

After developing an early version of our AutoAnnotator, we presented our work to Prof. Rost and his group. He gave us some very helpful advice on features we could add and provided us with access to his PredictProtein server. A special "thank you" goes to Manfred Roos for tailoring the access point of the server to our needs.

Laboratory of Prof. Dr. Schneitz

The Chair for Plant Developmental Biology is interested in the genetic and molecular basis of the regulatory pathways controlling organ development and tissue morphogenesis in plants.

The chair gave us great access to their microscopes and excellent support in how to use them. Many thanks therefore especially to Prasad Vaddepalli for his introduction to fluorescence microscopy.

Laboratory of Prof. Dr. Schwechheimer

The Chair for Systems Biology of Plants investigates a range of queries concerning the ubiquitin proteasome system of plants applying a combination of genetics, molecular biology and cell biology with both genomic and proteomic approaches.

Together with Prof. Schwechheimer we discussed several different signal transduction pathways that could be utilised for our kill-switch. Moreover he kindly granted us access to a fluorescence microscope.

Laboratory of Prof. Dr. Scherer

The Chair for microbial ecology conducts basic research in the field of molecular genetics and ecology of pathogenic microorganisms. Projects include the microbial characterization of food and microbial diagnostics and consulting in the food industry for prevention and clearance of contaminations.

The team kindly provided us with a culture of Micrococcus luteus for the Kirby-Bauer assay and also helped out with a tube of restriction enzyme during an unexpected shortage.

Other Universities

Laboratory of Prof. Dr. Reski at Freiburg University

The team at the Chair for Plant Biotechnology is working on gene expression in the bryophyte model plant Physcomitrella patens (Hedw.) B.S.G. at different levels in correlation with phenotype analysis and additionally employs comparative genomics approaches.

The Reski team kindly supported us by supervising our moss transformations at their lab and by allwoing us to use some of their equipment and materials for the process. Our special thanks go to Dr. Gertrud Wiedemann.

Laboratory of Prof. Dr. Fussenegger at ETH Zurich

The research group at the Chair for Biotechnology and Bioengineering is implementing progress in basic research to achieve generic and prototypic advances in human therapy by focusing on mammalian cells and capitalizing on an integrated interdisciplinary systems approach. Their current research initiatives include several programs interfacing with biopharmaceutical manufacturing, gene therapy and tissue engineering.

They kindly provided us with the pSH21 (IRES) plasmid.

Laboratory of Dr. G.D. Wright at McMaster University

The Wright Lab is trying to understand fundamental aspects of how antibiotics work, their sources and how bacteria become resistant to them.

They kindly provided us with the plasmids pDEST14_ereA and pDEST14_ereB.

Laboratory of Prof. Dr. Arndt at Potsdam University

The team at the Chair for Molecular Biotechnology investigates the factors that mediate interactions in coiled-coil proteins in order to target coiled-coil domains of proteins e.g. involved in tumorigenesis, tumor proliferation and metastasis.

Sven Hagen kindly provided us with the pBad-mVenus (RFC 25) plasmid.

Webdesign

The webdesign was entirely done by Florian Albrecht who has programmed different websites before. He also wrote the webdesign tutorial we have put online to explain other teems how they can use code developed by our team. The grafic elements used on the website were created by several different student members (such as Ingmar Polte, Katrin Fischer, Jeffery Truong, Rosario Ciccone and others) using the oper source vector software Inkscape. The only component that was bought are the two direction signs used in the header (obtained from http://vector-images.de/clipart/clp217632).

normalize.css

Normalize.css was used to reset the wiki style (version used: 2.1.3).

jQuery

jQuery is a powerful JavaScript extension used by many Webdesigners (version used: 1.10.2).

jQuery UI

jQuery UI is a GUI extension of jQuery and was used for the datepicker on the arduino data page (version used: 1.10.3).

Slimbox 2

Slimbox 2 was used as a picture viewer (version used: 2.05). The code had to be adapted to work with the wiki and bxSlider and we added a feature that fits the viewer to the browser size.

bxSlider

bxSlider is a JavaScript content slider and powers the slideshows and picture galleries on our wiki (version used: 4.1.1). The code was modified so all the images are scaled to the same height in gallery mode.

NVD3

NVD3 is a JavaScript chart library and was used for the interactive chart of the arduino data (version used: 1.1.13).

Software

jQuery

Powerful extension of JavaScript

James Padolsey

We used James Padolsey´s jQuery extension for Cross-domain AJAX requests in the AutoAnnotator.

FlotChart

Plotting Charts

Excanvas

Extend <canvas>-tag to IE 8.0 and earlier.

Paul Johnston

MD5 generator

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