FCCT Biochemistry Lab:iGEM-HS-2015:Group Meetings

11th September 2014
Location (institution): National Institute of Chemistry
Lecturer: dr. Ilija Gasan Osojnik Črnivec
Topics: General organisation of the team, general overwiev of work troughout the year, timeframe of work, ways of reaching to sponsors
Duration: 2 hours

29th October 2014
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturers: dr. Marko Dolinar, dr. Marina Klemenčič
Topics: Introduction to Synthetic Biology (dr. Dolinar)
Duration: 3 hours

12th November 2014
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturers: dr. Marko Dolinar, dr. Marina Klemenčič
Topics: Molecular cloning, Bacterial transformation and Registry of Standard Biological Parts by dr. Dolinar and Restriction sites by dr. Klemenčič
Duration: 3 hours

25th November 2014
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturers: dr. Marko Dolinar, dr. Marina Klemenčič
Topics: Design and organisation of our wiki page (dr. Dolinar) and Methods of molecular cloning (dr. Klemenčič)
Duration: 3 hours

26th November 2014
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturers: dr. Marko Dolinar, dr. Marina Klemenčič
Topics: How to use OpenWetWare (dr. Dolinar) and Basics of cloning and expression vectors (dr. Klemenčič)
Duration: 2 hours

4th December 2014
Location (institution): National Institute of Chemistry
Lecturer: dr. Ilija Gasan Osojnik Črnivec
Topics: Biotechnological basics of anaerobic microbial digestion and What is Escherichia coli
Duration: 2 hours

11th December 2014
Location (institution): National Institute of Chemistry
Lecturer: dr. Ilija Gasan Osojnik Črnivec
Topics: Production of butanoic acid and Optimal growth conditions for Esherichia coli DH5-Alpha
Duration: 2 hours

17th December 2014
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Revision and primers
Duration: 3 hours

7th January 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturers: dr. Marko Dolinar, dr. Marina Klemenčič
Topics: Lab safety (dr. Dolinar) and Laboratory exercise – restriction of plasmid and electrophoresis (dr. Klemenčič)
Duration: 4 hours

15th January 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Introduction to bioinformatics (SnapGene, Blast, NCBI base, ExPASy)
Duration: 3 hours

21st January 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marko Dolinar
Topics: Revision of homework (search and analysis of nucleotide sequence)
Duration: 2 hours

28th January 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturers: dr. Marko Dolinar, dr. Marina Klemenčič
Topics: Previous work on Clostridium genes
Duration: 3 hours

11th February 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Methods of gene isolation
Duration: 2 hours

12th February 2015
Location (institution): National Institute of Chemistry
Lecturer: dr. Petra Muri
Topics: Influence of operational conditions on final product
Duration: 1 hour

19th February 2015
Location (institution): National Institute of Chemistry
Lecturer: dr. Gasan Ilja Osojnik Črnivec
Topics: E. coli and Enterobacteriacteae, bioreactors, a tour of the lab
Duration: 3 hours

5th March 2015
Location (institution): National Institute of Chemistry
Lecturers: dr. Petra Muri, dr. Gasan Ilja Osojnik Črnivec
Topics: Cultivation of microorganisms in solid and liquid media
Duration: 2 hours

11th March 2015
Location (institution): National Institute of Chemistry
Lecturer: team meeting
Topics: Application and Wiki
Duration: 2 hours

12th March 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Methods of gene isolation
Duration: 3 hours

18th March 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Revision of previous work on Clostridium genes isolation
Duration: 3 hours

23th March 2015
Location (institution): National Institute of Chemistry
Supervisors: dr. Gasan Ilja Osojnik Črnivec, dr. Petra Muri
Topics: How to prepare a bioreactor and lab work
Duration: 5 hours

24th March 2015
Location (institution): National Institute of Chemistry
Supervisors: dr. Gasan Ilja Osojnik Črnivec, dr. Petra Muri
Topics: lab work
Duration: 4 hours

25th March 2015
Location (institution): National Institute of Chemistry
Supervisors: dr. Gasan Ilja Osojnik Črnivec, dr. Petra Muri
Topics: lab work
Duration: 5 hours

26th March 2015
Location (institution): National Institute of Chemistry
Supervisors: dr. Gasan Ilja Osojnik Črnivec, dr. Petra Muri
Topics: lab work
Duration: 4 hours

1st April 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Topics: lab work
Duration: 3 hours

2nd April 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marko Dolinar
Supervisor: dr. Marina Klemenčič
Topics: Introduction to OpenWetWare, lab work
Duration: 3 hours

2nd April 2015
Location (institution): National Institute of Chemistry
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Topics: lab work
Duration: 4 hours

3rd April 2015
Location (institution): National Institute of Chemistry
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Topics: lab work
Duration: 4 hours

8th April 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Topics: lab work
Duration: 3 hours

9th April 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Topics: lab work
Duration: 3 hours

15th April 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturers: dr. Marina Klemenčič, dr. Thorsten Heidorn
Topics: Revisiting primer creation, Production of Biofuels with Microalgae Utilising a Synthetic Biology Approach
Duration: 3 hours

22th April 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Topics: lab work
Duration: 3 hours

28th April 2015
Location (institution): National Institute of Chemistry
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Topics: lab work
Duration: 6 hours

6th May 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marko Dolinar
Supervisor: dr. Marina Klemenčič
Topics: Introduction to iGEM lab safety rules and lab work
Duration: 4 hours

8th May 2015
Location (institution): National Institute of Chemistry
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Topics: lab work
Duration: 5 hours

11th May 2015
Location (institution): National Institute of Chemistry
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Lab work: preparation of Luria-Bertani broth, sterilization with autoclave and data analysis
Duration: 7 hours

12th May 2015
Location (institution): National Institute of Chemistry
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Lab work: preparation of two new microbial growth mediums and sterilization with autoclave
Duration: 7 hours

13th May 2015
Location (institution): National Institute of Chemistry
Lab work:
data analysis, HPLC of microbial growth mediums
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Group meeting:
Location (institution): National Institute of Chemistry
Supervisors: dr. Ilija Gasan Osojnik Črnivec, dr. Marko Dolinar, dr. Marina Klemenčič
Topics: presentation of results and analysis of results, funding strategy
Duration: 5 hours

20th May 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: testing iGem Transformation Efficiency Kit
Duration: 3 hours

27th May 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Meeting of the whole group Duration: 1 hour

27th May 2015
Location (institution): Cleaning plant of gaswork KOTO (Ljubljana Zalog)
Excursion to cleaning plant, guided by Marjeta Resnik
Duration: 1 hour

28th May 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: preparation of transformed E.coli cells for negative controls
Duration: 2 hours

22th June 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: Ligation with pJET 1.2 VECTOR, overnight incubation, PCR
Duration: 2 hours

24th June 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: Plasmid DNA purification using centrifuges, Transformation using Heat Shock
Other: Wiki Duration: 9 hours

26th June 2015
Location (institution): National Institute of Chemistry
Supervisor: dr. Ilija Gasan Osojnik Črnivec
Topics: General organisation of the team, timeframe of work, ways of reaching to sponsors, brainstorming for our crowfunding campagin short movie and discussion with the photograoher
Duration: 1 hour

30th June 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: inoculation of the negative controls into liquid LB media, DNA purification (AdhE1 and AdhE2), preparation of cloning vectors (with inserts BdhA, CtfA, CtfB) and their transformation into E. coli
Duration: 9 hours

1st July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: colony PCR (transformed cells with BdhA, CtfA, CtfB)
Other: searching for sponsors and teams for collaboration, developing ideas for our crowfunding movie
Duration: 9 hours

2nd July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: AGE of yesterday's samples, colony PCR (transformed cells with BdhA, CtfA, CtfB)
Other: searching for sponsors and teams for collaboration, developing ideas for our crowfunding movie
Duration: 9 hours

3rd July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: AGE of yesterday's samples, DNA purification (CtfA), colony PCR (BdhA, CtfB)
Other: searching for sponsors and teams for collaboration, developing ideas for our crowfunding movie
Duration: 9 hours

6th July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: AGE of the last colony PCR samples, DNA purification (CtfB), colony PCR (BdhA), AGE of the samples (colony PCR of BdhA insert), BdhA ligation and transformation repeated
Other: searching for sponsors, developing ideas for our crowfunding movie
Duration: 10 hours

7th July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: AGE of the samples (colony PCR with BdhA insert of the yesterday's transformed cells). Colony PCR repeated with new primers and new master mix. Inoculation of the transformed cells (with BdhB, AdhE1, AdhE2, CtfB, CtfA inserts) into liquid LB media. Restriction of the purified DNA (plasmids with CtfA, CtfB, BdhB, AdhE1 and AdhE2 inserts).
Other: searching for sponsors, developing ideas for our crowfunding movie
Duration: 10 hours

8th July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: AGE of the samples (last colony PCR and restriction samples). DNA purification repeated (BdhB, AdhE1, AdhE2, CtfA, CtfB).
Other: filming our crowfunding movie, skype with Aalto-Helsinki
Duration: 10 hours

13th July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: Plasmid DNA purification using centrifuges, Absorbance of CtfA, CtfB, BdhB, Control restriction of genes.
Other: filming our crowfunding movie, skype with Aalto-Helsinki
Duration: 8 hours

20th July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: colony PCR of CtfB, BdhB and CtfA cells, AGE of the samples. Inoculation of E. coli with BdhB, CtfB, AdhE2, CtfA plasmids and an empty pSB1c vector in a liquid LB media
Other: designing wiki page
Duration: 10 hours

21th July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: Gene restrictions, PCR, Electrophoresis, Isolation from agarose gel, Ligation
Duration: 3 hours

22th July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: transformation of Ctfa, CtfB and BdhB plasmids into cells
Other: designing wiki page, skype call with iGem Team Aachen
Duration: 6 hours

23rd July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: colony PCR of the transformed cells, AGE of the samples, colony PCR and AGE repeated
Other: designing wiki page, skype call with iGem Team Aachen
Duration: 12 hours

23rd July 2015
Location (institution): Faculty of Chemistry and Chemical Technology, University of Ljubljana
Supervisor: dr. Marina Klemenčič
Lab work: colony PCR of the transformed cells, AGE of the samples, colony PCR and AGE repeated
Other: designing wiki page, skype call with iGem Team Aachen
Duration: 10 hours

4th August 2014
Location (institution):Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Plasmid isolation from liquid medium, inoculation of CtfA gene from plate into liquid medium, measuring absrobance of isolated plasmid, separatinon of proteins for each gene, restriction for pSB1C3+P+RBS+CtfB and pSB1C3+P+RBS+BdhB, overnight incubation
Duration: 12 hours

5th August 2014
Location (institution):Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Plasmid isolation from liquid medium, electrophoresis of restrictions, measuring of absorbance for CtfA, preparing gels for protein separation, colaboration work with Aachen iGEM team.
Duration: 8 hours

6th August 2014
Location (institution):Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič
Topics: Electrophoresis of PCR samples,inoculation of constructs CtfB and BdhB on the plate, transformation, spectrofotometry of samples colaboration work for Aachen iGEM team
Duration: 7 hours

7th August 2014
Location (institution):Faculty of Chemistry and Chemical Technology, University of Ljubljana
Lecturer: dr. Marina Klemenčič, dr. Ilja Gasan Osojnik Črnivec, dr. Albin Pintar
Topics: Team meeting, presentation of results and analysis of results, funding strategy, work organisation
Duration: 2 hours