iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing...
Transcript of iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing...
![Page 1: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/1.jpg)
iGEM Measurement committee webinar seriesExisting part collections and measurement
René Inckemann 19.06.2020
![Page 2: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/2.jpg)
2
Overview
• Pre-existing part collections outside from iGEM
• Pre-existing iGEM part collection
• Importance of measurements
• Part documentation
![Page 3: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/3.jpg)
3
Pre-existing part collections outside from iGEM
![Page 4: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/4.jpg)
4
Pre-existing iGEM part collections
![Page 5: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/5.jpg)
5
Pre-existing iGEM part collections
Reporter collection
![Page 6: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/6.jpg)
6
Pre-existing iGEM part collections
iGEM Vilnius 2017: SynOri
![Page 7: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/7.jpg)
7
Pre-existing iGEM part collections
iGEM Marburg 2018: Vibrigens (Basic set of standard MoClo parts)
![Page 8: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/8.jpg)
8
Importance of measurements
Characterized parts are much morevaluable for future projects and iGEMteams, in order to facilitate more complexgenetic designs
Example: Promoter, RBS, terminator collections fordifferent chassis
Lee et al 2015
![Page 9: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/9.jpg)
9
Importance of measurements
Example: iGEM William Mary 2017
absolute units relative units
![Page 10: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/10.jpg)
10
Part documentation
• Create an entry for all of your parts in the registry with a description
• You should have confirmed yourparts by sequencing
• You should have all your data for a specific part on the correct registrypage (not just on the wiki)
![Page 11: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/11.jpg)
11
Part documentation
• Create an entry for all of your parts in the registry with a description
• You should have confirmed yourparts by sequencing
• You should have all your data for a specific part on the correct registrypage (not just on the wiki)
![Page 12: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/12.jpg)
12
practical part
![Page 13: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/13.jpg)
iGEM Measurement committee webinar seriesThe importance of Parts
René Inckemann 19.06.2020
![Page 14: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/14.jpg)
2
Overview
• Parts in engineering/Parts in sythetic biology
• Why is standardization important for synbio?
• The invention of the first part standard forSynbio: Biobrick assembly + Registry of parts
• The “new“ standard: Phytobricks and TypeIIS
![Page 15: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/15.jpg)
3
Parts in common engineering
• Building airplanes or complex circuit boardswithout standard parts impossible
• Well defined parts, with perfectly knownproperties and characteristics
• Parts can be reused for other engineeringefforts
• Parts are tested in different setups and conditions
![Page 16: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/16.jpg)
4
Parts in synthetic biology
Federici et al 2013
• Using engineering principles like standardization and abstraction forengineering biology
• DNA on the lowest level
• Parts could be definded by function, such as: promoters, RBS, CDS, terminator, UTR, tags
![Page 17: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/17.jpg)
5
Why is standardizationimportant for iGEM and Synbio?
• Parts can be exchanged with other labs/iGEMteams
• New teams can use already existing parts and combine them with their own parts
• Parts can be further characterized and testedin different setups and condtions to defineproperties and characteristics
→ parts get better via collective efforts
![Page 18: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/18.jpg)
6
The invention of the first part standard for Synbio: Biobrick assembly
![Page 19: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/19.jpg)
7
The invention of the first part standard for Synbio: Biobrick assembly
If you want to learn more about Biobrick assembly /3A assembly go to the following links:
https://www.youtube.com/watch?v=F1mXoy1-Vr0https://www.youtube.com/watch?v=Zrtdwvn4G6s
![Page 20: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/20.jpg)
8
Registry of parts
• Library of parts created by iGEMteams in all the years
• Every iGEM team sends biobricksand fills in data and description
• All parts are standardized and can beeasily combined
![Page 21: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/21.jpg)
9
The „new“ standard: Phytobricks and TypeIIS
![Page 22: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/22.jpg)
10
The „new“ standard: Phytobricks and TypeIIS
![Page 23: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/23.jpg)
11
The „new“ standard: Phytobricks and TypeIIS
Much more information next week in the Golden Gate and Modular Cloning webinar!
![Page 24: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/24.jpg)
12
The „new“ standard: Phytobricks and TypeIIS
practical part
![Page 25: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/25.jpg)
Basic Techniques in Molecular Biology
Tania Pozzo Ph.D.
June 23, 2020
![Page 26: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/26.jpg)
Polymerase Chain Reaction (PCR)
https://youtu.be/QwT-Tj89VLo
• PCR is the fundamental technique
used to make copies of gene
sequences.
• PCR products are commonly
referred to as amplicons.
• Metabolic engineering requires DNA
manipulation using PCR.
• Understanding how PCR works is
essential for developing new DNA
based technologies.
![Page 27: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/27.jpg)
Restriction DigestionsDigestion of DNA with Restriction Enzymes
• Polymers of dsDNA are cleaved
using restriction endonucleases that
recognize specific nucleotide
sequences (see video).
• Circular Plasmids (Vectors) used for
gene cloning are cleaved by
restriction enzymes in order to insert
PCR products such as protein
coding sequences into the plasmid. https://youtu.be/4CsLLcveIB0
![Page 28: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/28.jpg)
DNA Ligation with DNA Ligase
https://youtu.be/xMBC3q_CbTA
• Amplicons from PCR are inserted
into open vectors to form
recombinant plasmids.
• DNA ligase forms phosphodiester
linkages between the ends of the
amplicons and the open ends of the
plasmid (see video).
• A common DNA ligase used for
gene cloning is T4 DNA Ligase.
![Page 29: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/29.jpg)
Bacterial transformation
https://youtu.be/7Ul9RVYG5CM
• Bacterial cells are “transformed” by
taking recombinant plasmids into
the cell.
• Bacterial transformation occurs via
chemical transformation or
electroporation (see video).
• Transformed bacterial cells are
cultured on selective medium
corresponding to selection marker
gene expression (e.g. antibiotic
resistance).
![Page 30: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/30.jpg)
Thanks for listening!
![Page 31: iGEM Measurement committee webinar series · iGEM Measurement committee webinar series Existing part collections and measurement René Inckemann 19.06.2020. 2 Overview • Pre-existing](https://reader034.fdocuments.in/reader034/viewer/2022052014/602c0c80872aed5d266a932b/html5/thumbnails/31.jpg)
Upcoming webinars
• Week 3 - Tuesday June 30th - 7am EDT
- Modeling circuits with ODEs and
experimental data
• Week 3 - Tuesday June 30th - 10am EDT
- DNA assembly techniques