Contents 1 April 1.1 1st 1.2 12th 1.3 15th 1.4 22th 1.5 23th 1.6 28th 1.7 29th 1.8 30th 2 May 2.1 1st 2.2 5th 2.3 8th 2.4 14th 2.5 19th 2.6 20th 2.7 21th 2.8 23rd 3 June 3.1 3rd 3.2 4th 3.3 5th 3.4 6th 3.5 14th 3.6 17th 3.7 20th 3.8 23th 3.9 25th 3.10 26th 3.11 27th 3.12 30th 4 July 4.1 3rd 4.2 9th 4.3 16th 4.4 22nd 4.5 23rd 4.6 24th 4.7 25th 4.8 28th 4.9 29th 4.10 30th 5 August 5.1 1st 5.2 2nd 5.3 3rd 5.4 4th 5.5 5th 5.6 6th 5.7 13th 5.8 19th 5.9 25th 5.10 26th 5.11 27th 6 September 6.1 3rd 6.2 4th 6.3 5th 6.4 6th 6.5 7th 6.6 15th 6.7 16th 6.8 17th 6.9 18th 6.10 19th 6.11 20th 6.12 22nd 6.13 26th 6.13.1 Gradient PCR to test new primers 6.14 27th 6.15 28th 6.16 29th 6.17 30th 7 October 7.1 1st 7.2 2nd 7.3 3rd 7.4 4th 7.5 5th	In order to detect the pathogens fast, specifically and inexpensively we are building sensor cells to detect these pathogens. These sensor cells can identify pathogens in very low concentration by responsing to specific extracellular molecules either secreted by or displayed on the pathogens. These molecules trigger a fast fluorescence response by our immobilized sensor cells which will be measured by our device.

More information will be available soon!

April

1st

Organisation

Where we can get:

• Key cards and keys for the lab
• Cooled centifuge
• Space in -80°C
• Bottles for 70% Ethanol
• ... (problems of a first year team ^^)

12th

• Make chemical competent NEB Top 10, DH5α, BL21

15th

• 800 ml LB for plates with 1,5% agar and kanamycin (50 µg/l) (Stefan)
• Test the efficiency of our competent cells (Anna)

Colonies on the agar plates were counted after transformation with 147 ng/µl DNA and afterwards incubated in SOC or LB medium

• BL21 all cells were down centrifuged and plated. Only 128 colonies were grown in total...very bad efficiency ~482.11...

With the formula: Efficiency = (CFU /µg DNA) / dilution

• for DH5α: medial efficiency in SOC: 1864.36 and in LB: 440.68
• for NEB: medial efficiency in SOC: 6779.66 and in LB: 4698.30

With SOC the efficiency is much better!

22th

Pcq lab PCR advanced primus 25, 96

Programm name IGEM.cyk

1. RFC25_F RFC25_R
2. RFC25_F REACh1_R
3. REACh1_F RFC25_R
4. RFC25_F REACh2_R
5. REACh2_F RFC25_R

23th

• Get our PCR tubes and run 5 µl on a 1,5% agarose gel
• Purify them with High Pure Product Purification Kit. Full lenght ??? with REACh1

• SOE
• ca. 30 ng/µl

Anneling: 52°C

Elongation: 20 sec

• PCR with Phusion polymerase

• Digestion for restriction with NEB enzymes

• Ligation with NEB Kit

28th

• Anna measured DNA concentration of SOE2 after purification

1: 57 ng/µl

2: 69.5 ng/µl

29th

• PCR SOE1 and SOE2

30th

• Run SOE2 on agasose gel for checking

→ doesn't look good. only full length is tine

• Run SOE again

→ more template

→ hot start

→ faster

→ elongation: 15 min

→ 20 cycles

• SOE1

template A+B → 20 µl → 13.8 + 6.2 5.3 + 14.7

• SOE2

May

1st

• Gel with M - full -full - REACh1 SOE3.2 - REACH2 SOE3.2 - M

→ 120 V, 30 min → cut out the bands

5th

• Anna made chemical competent DH5α, BL21

8th

• Test the efficiency of our competent cells

→ BL21: 6.6 x 10⁴

→ DH5α: 2.59 x 10⁷

• SOE-PCR step 2 like on 30.04 ... → with template of SOE1 from 30.04
• Run SOE2 product on gel for checking (5 µl)

→ restriction, (dephosphorylation of vector)

→ purify on gel with high pure kit

14th

• Florian made some LB agar plates with chloramphenicol and some with ampicillin
• REACh2 purification on 1.2% agarose gel
• After that purification of the 778 bp fragment with High Pure PCR Product Purification Kit

19th

• Transformation of K131026 in DH5α and NEB
• Transformation of K731520 in DH5α

20th

• Stefan made master plates on chloramphenicol (cam) → at least 6 clones on each plate
• Stefan prepared 2x 5 ml LB + cam
• Anna made sterile 50% glycerol

21th

• Cryo stock of clones 1 & 2 of each BioBrick/ host
• 15 ml cultures in 250 ,l flasks, inoculated with 1,5 ml preculture (3 cultures A B C from clones 1; 1 + 2; 2)
• Add 35 mg/ml cam from stock
• Grow until OD₆₀₀= 0.6, than induce one with IPTG

→ no negativ control without plasmid

23rd

• Transformation of some BioBricks
• Colony PCR (s. picture below)

→ K131026: 1807 bp

→ K731520: 2123 bp

→ full length EYFP: 778 bp

Colony PCR todo

June

3rd

• Transformation of 34 BioBricks

4th

• Make new 50% glycerol
• Make new LB plates with cam and with kanamycin (kan)
• Make master plates (6 clones per BioBrick)
• Make 60 steril glas tubes
• Make 2l LB^-
• Make 100ml steril glas beads

5th

• Make colony PCRs on all transformed BioBricks

→ pick 2 clones from each master plate

• Make 5 ml LB + cam over night cultures (make 250 ml LB + cam)

→ 1 culture per BioBrick

6th

• Make 2 glycerol stocks for each BioBrick

14th

PCR of E0030 to K1319000

• Q5 and Phusion polymerase are used

→ 30 cycles

17th

20th

• Colony PCR of K325108, K325218, C0062

→ 30 cycles

• Results 30 min on 1,2% gel at 110V

→ weak bands in K325108 a & b: 4.5kb, 9kb

23th

• Repeat the colony PCR of yesterday
• Preculture for plasmid prep
  • K1319000 → sequencing
  • K592100 → BFP
  • S01022 → CFP
  • J23101.E0240 → sequencing
  • J23115.E0240 → sequencing
• Plate K516132 and J23101.E0240 on LB + cam plates

25th

• Prepared a preculture for competent NEB10β cells
• Submitted samples for sequencing
• Made master plates of transformed BioBricks
• Centrifuged and froze overnight expression culture of J23101.E0240 and K516132

26th

• Made competent NEB10β cells, however, several things went wrong. (For future reference: pre-cool centrifuge, always check if it's indeed spinning, frequently check OD of the culture)
• Colony PCR on the transformed clones looked awful; there were too many cells in the 10 µL reaction volume. Some tubes were not fully sealed during the PCR. Basically only primers and smear, except for the positive control which contained a plasmid template instead of cells.
• 2x 500 mL of fresh LB and three sterile flasks were prepared and autoclaved.

27th

30th

July

3rd

• Anna made Chips with K1319042 and K731520 in NA and M9 medium

9th

• Anna made Chips with K1319042 in M9, M9 + casamino acids, Hartmann medium (HM)

16th

• Did plasmid preps
• Transformation of different reporter strains
  • NEB
    • pSEVE641_BsFbFP
    • pSEVA234_LasR
    • pSEVE641_BsFbFP pSEVA234_LasR
    • pSEVE641_BsFbFP pSB1C3_C0179
  • BL21
    • pSEVE641_BsFbFP pSEVA234_LasR
    • pSEVE641_BsFbFP pSB1C3_C0179
• Anna made Chips with K1319042 in Hartmann, Hartman + 20% glycerol, M9 medium

22nd

• Philipp and Michael made 100x stocks for Hartmans minimal medium.
• Michael and Vera made about 25 HM+C plates without glucose.
• K731520 iLOV was plated on a HM+C plate

23rd

• Michael made 25 new HM+C plates with 1 % agar and 4 g/L glucose
• He also added 170 µL of the glucose stock (500 g/L) to the glucose-free HM+C-plates
• 1 L of sterile HM+glucose was prepared
• K731520 iLOV was plated on HM+C+Glucose and HM+C+Glucose drops, 3x 5 mL HM+C+Glucose precultures were inoculated (17:00)

24th

• K731520 iLOV did not grow, neither on the plates, nor on in the liquid media. The most probable cause is that the E. coli is missing some vitamins
• Based on the [http://openwetware.org/wiki/M9_medium/supplemented M9 recipes by the Knight and Endy labs on OpenWetWare], we made a 20 mL supplement stock solution that can be added to 1x HM media

The powders for 1 L of 1x HM were dissolved in 20 mL of a 10 % w/v Casamino acid stock solution and filter-sterilized (.22 µm PES). To make agar chips, we can add 1 mL to the hot agar mixture, together with the three 500 µL 100x stocks for the HM.

We made 250 mL of HM+C+Glucose+Supplements plates with 1.5 % agar.

Then we plated the following combinations:

We also prepared a 150 mL HM+C+Glucose+Supplements culture with K731520 iLOV to hopefully make agar chips on Friday, July 25th.

Six of last weeks J23115.E0240 clones were plated on LB+C, and 5 mL LB+C precultures were inoculated for plasmid preparation.

25th

The K731520 iLOV strain did not grow on the HM plate, while another strain with the J23101.E0240 construct did. Both have the pSB1C3 backbone. To confirm the plasmids and inserts, Michael set up a colony PCR:

Reaction volume per tube was 15 µL. GoTaq Green Mastermix and the VF2 and VR primers were used. You can find the durations and temperatures the table below:

Florian mini-prepped the 6 overnight cultures of J23115.E0240 clones. He used 3 mL instead of 1.5 mL culture medium and eluted twice with 25 µL nuclease-free water. Everything else was according to the protocol of the [http://www.gelifesciences.com/webapp/wcs/stores/servlet/productById/de/GELifeSciences/28904269 illustra plasmidPrep Mini-Spin Kit].

The resulting DNA concentrations are listed in this table:

In the evening, we plated some strains on the different media to investigate why the K731520 iLOV did not grow on the HM+suppl. plate. (Note: In the morning, Michael re-inoculated the HM+C+suppl. shake flask with cells from the LB-plate and by afternoon the culture did grow to a high cell density.)

Philipp inoculated J23101.E0240 in LB and HM+C+Glucose+supplements.

28th

29th

• ...

30th

• Anna made Chips with K1319042, K131026 in HM medium

August

1st

• Stefan and Vera made electrocompetent E.coli cells.
• Arne prepared cultures of Renés iLOV and K131026 for Saturday, August 2nd.

2nd

• Tested the OD measurement device and compared it to the spectrophotometer and the plate reader.
• Tested K131026 and K731520 iLOV for fluorescence in the plate reader
• Did a heat shock transformation of I746909 into NEB TOP 10 cells
• Did an electroshock transformation of pET17-Gal3 into E.coli rosetta

3rd

• OD measurements of the iGEM device in comparison to the spectrophotometer were taken.
• Cryo cultures of K131026 and K731520 iLOV were prepared

4th

• Arne and Michael made cryo stocks of K731520 iLOV and K131026 in NEB/BL21/DH5alpha, I746909 in BL21 and pET17-His-SNAP-YFP-Gal3 in E. coli rosetta (DE3), respectively.
• Michael did a plasmid prep, most of them using 1.5 mL culture medium, and eluted with 1x 50 µL of ddH₂O. The resulting DNA concentrations are shown below.

To confirm the quality of pET17-Gal3 transformations, the purified plasmids were tested by carrying out a digest. Results are shown in the below picture and table.

Test digest clones were test-digested

All pET17-Gal3 clones were positive and clone #1 was selected for further experiments.

5th

• Stefan, Arne and Michael assembled a V_R=2.5 L bioreactor for cultivation of a 1 L expression culture.
• Two precultures of 20 mL LB+A were inoculated at 19:00
• Anna transformed K746909 into BL21 cells and K1319000 into NEB10β cells.
• Anna made Chips with K1319042 in HM

6th

• Eshani and Arne transformed J04450 in pSB1K3 and pSB1A3 in NEB10β cells.
• They also did a plasmid prep of J04450 in pSB1C3 and Flo's vectors.
• Arne made precultures of NEB10βand DH5 alpha cells
• Arne and Michael inoculated the fermenter at 11:40, and induced the fermentation of pET17-Gal3. The fermentation is expected to run 24 h.

13th

• Anna made Chips with
  • K131026 and I746909 in LB and HM
  • K1319042 and Florians two plasmid construct in HM

19th

• Anna made Chips with K131026 and I746909 in HM

25th

• Did a plasmid restriction of I20260 (EcoRI,PstI), J23115 (EcoRI, SpeI), K516032 (XbaI,PstI), and J23101 (EcoRI, SpeI).
• Nina tested the growth of Pseudomonas fluorescens in different liquid media for high OD and strong fluorescence. She tested Standard I medium, Cetrimide medium and Pseudomonas-F medium, and Pseudomonas-F medium supplemented with 300 µL Fe3+ in 500 mL flasks with a filling volume of 30 mL. The flasks were inoculated with P. fluorescens cells on Standard I agar, and incubated at 30 °C at 250 rpm.

26th

• Ligation of J23115 and K516032 to J23115.K516032, and J23101 and K516032 to J23101.K516032, respectively.
• Plasmid prep of I20260, K516032 and B0034
• Restriction of plasmids I20260, K516032, B0034 with EcoRI and PstI
• A gel with restricted the I20260, K516032 and B0034 was run.
• Purification of vector backbones pSB1A2, pSB3K3 and pSB1C3
• Restriciton of synthesized TEV protease with EcoRI and PstI
• Nina qualitatively tested the Pseudomonas fluorescens that had grown over night for OD and fluorescence. She determined that Pseudomonas-F medium is the most adequate for the cultivation of the strain we use, since both OD and fluorescence were best in the flask containing the respective medium. Growth in the Pseudomonas-F medium supplemented with 300 µg/L Fe3+ was weaker, however, fluorescence was also successfully suppressed.

27th

• Ligation of J23101.K516032 into pSB3K3 and J23115.K516032 into pSB3K3 and K1319004 into pSB1C3
• Transformation of K1319004 into pUC and pSB1C3, and J04450 into pSB1K3 and pSB1A3, respectively

September

3rd

Michael, Vera and Eshani prepared 50 mL LB+antibiotic overnight-cultures of pSBX-vectors that were sent in by team Heidelberg.

4th

• In the morning, at 10:15, Anna inoculated the precultures for the interlab study experiment.
• Michael prepared cryo stocks of the pSBX-carrying E. coli from the overnight cultures. He also purified each pSBX-vector, eluting with 15+30 µL water, and resulting in the following DNA concentrations:

• Anna did PCRs for Gibson assembly of K1319003 into pET17. Duplicates of 25 µL reaction volume (12.5 µL Q5 2x Master Mix, 1.25 µL per primer, 2 µL template)

The PCR conditions:

• Finally, Florian did the Gibson assembly and a heat shock transformation into NEB10β cells.

• At 10:15, Arne inoculated the primary cultures of the interlab study experiment and began with regular fluorescence measurements.

5th

• Anna made master plates of yesterday's transformed cells.

6th

• Anna made precultures of 3 clones from each prepared master palte and inoculated precultures for OD/F measurements as well as chip production on the 7th.

7th

• Anna made cryos stocks of the precultures.
• Michael and Arne purified the following plasmids:

Elution was performed twice with 15 µL of nuclease free water each time.

15th

Arne and Michael were able to analyze the sequencing data from the clones of GFP_Reach 1, GFP_Reach 2 and K1319008.

GFP_Reach 2 clone #3 and #5 were fine, including the Leu to Ile mutation. GFP_Reach 1 clone #4 and #5 were fine and did not contain the Leu to Ile mutation. Clone #6 was fine but contained the Leu to Ile mutation from the Reach 1 quick change mutations.

For future experiments, we will use the GFP_Reach 1 clone #4 and the GFP_Reach 2 clone #4.

Transformation of GFP_Reach 1 clone #3 and GFP_Reach 2 clones #3 and #5 were performed together with the TEV protease to create two plasmid construct.

The GFP_Reach 1 and GFP_Reach 2 constructs were also restricted and ligated into the pSB1C3 vector from the pSB3K3 vector.

16th

• Vera made master plates of the transformation from the day before.

• Also PCRs were made from pSBXA3, I20260 and K131900 for a Gibson assembly. The PCRs were checked with a gel electrophoresis.

17th

• Nina prepped and autoclaved 33 500 mL shake flasks.

18th

• Nina tested Pseudomonas fluoresence if they are suitable for a growth experiment that is planned for our collaboration with the NEAnderLab next week. Therefore, she filled 2 500 mL flasks with 30 mL LB Pseudomonas-F medium, and inoculated each one with 1 mL culture medium of the overnight preculture. Flasks were inoculated at 30 °C at 250 rpm. However, after 5 hours no exponential growth could be shown (s. plot below). Thus, it was decided to use a E. coli K12 derivate strain in TB medium instead, and 30 mL of TB medium in a 500 mL flask were inoculated with E. coli DH5alpha cells and incubated at 37 °C at 300 rpm over night. According to the DSMZ E . coli K12 strain derivates, such as DH5alpha, are adequate for the kind of school experiment we are planning with the NEAnderLab.

Growth Curves Unfortunately, P. fluorescens did not show a nice exponential growth curve over the observed 5 hours.

19th

• René, Arne and Philipp made flask cultures of K1319013, K1319013 + K1319008, K1319013 + K1319008 + iPTG, K1319014, K1319014 + K1319008, K1319014 + K1319008 + iPTG, B0015 (negative control) and I20260 (positive control). iPTG was added at an OD of ~0.5. Inoculation was done via precultures in 500 ml shake flasks (50 ml filling volume). Media was always LB. Cultivation was done at 37°C and 300 rpm. The starting OD was aimed to be 0.1. Inoculation occured directly from the precultures. Samples were taken every hour and checked for OD and fluorescence using a spectrophotometer and plate reader, respectively.

• Vera did a plasmid preparation from the cultures of the day before (K1319013, K1319013 + K1319008, K1319013 + K1319008 + iPTG, K1319014, K1319014 + K1319008, K1319014 + K1319008 + iPTG, B0015 and I20260). The plasmid were then be cut with EcoRI and PstI, and the results were be put on an agarose gel in order to perform a restriction test. Also plasmids of K1319013 and K1319014 will be cut with EcoRi and SpeI. K1319008 will be cut with XbaI and PstI. These will then be ligated together and then ligated into a pSB1A3 vector via the 3A assembly (vector cut with EcoRI and PstI). These constructs will be transformed into BL21 (and NEB as a backup). The created construts will be known as K1319018 (K1319013.K1319008) and K1319019 (K1319014.K1319008).

• Florian made precultures of the master plates from the day before (K1319008, K1319013, K1319015 and pSBX1A3 with Gal3).

• Arne also inoculated 4 cultures for the further testing of the OD/F device (the F part). The cultures are 2 shake flasks of I20260 and 2 shake flasks of B0015.

• Furthermore, Nina did a growth experiment with DH5alpha for the NEAnderLab school experiment. 3 500mL shake flasks were filled with 50mL TB medium, and inoculated to an OD of 1.5 with the overnight preculture. Samples were taken every 30 minutes and tested for OD using our own device as well as the spectrophotometer. The resulting growth curve is shown below. Nina concluded that the growth was fast enough for these growth conditions to be used for the school experiment on the 24th.

Growth Curves Growth under these conditions was sufficient for the school experiment to be carried in 5 hours. And our device did a good job measuring, too!

• Anna also made chips with K1319013 + K1319008, K1319014 + K1319008, K1319013, K1319014, B0015 and K131026. These will be inocubated for an hour at 37 degress Celsius. Then they will be induced with iPTG/HSL and fotos will be made every 30 minutes to check for fluorescence (GFP).

• Florian tested our OD/F device with a dilution test. Samples were checked with the spectrophotometer (OD), our OD/F device (fluorescence) and platereader (fluorescence).

• Anna and Vera made SDS gels.

• Stefan inoculated a culture of K1319008, B0015 as well as I20260 to check whether the results from our construct are from a wrongly done Gibson assembly with a still functioning superfolded GFP (the TEV protease was inserted in a backbone that formely contained superfolded GFP.)

20th

22nd

• Nina poured several Pseudomonas-F agar plates with 0, 150 and 300 µg/L for the NEAnderLab school experiment. She also autoclaved 12 500 mL shake flasks, partly to be used for the school collaboration on Wednesday.

26th

• Michael did a check PCR on several cryo cultures. All samples with G00100_Alternative+K1319004_check_R combinations resulted in a strong band at ~2300 bp that we cannot explain. All G00100_Alternative+K1319004_check_R combinations resulted in a strong band at 900 bp that we cannot explain either. We concluded that the annealing temperatures were wrong and favored unspecific products. Therefore, we decided to do a gradient PCR to find out the optimal annealing temperatures for our new primers.

Gradient PCR to test new primers

Florian and Michael did gradient PCR with these new primers:

Three PCRs with different primer combinations were run. In all of them the templates were K1319004 in pSB1C3, K1319008 in pSB1C3 and I746909 in pSB1C3.

The first gradient PCR tested the G00100_Alternative + G00101_Alternative combination:

Gradient PCR 1 the primers were G00100_Alternative and G00101_Alternative and they worked well at all temperatures from 55-65 °C.

The second gradient PCR tested the G00100_Alternative + I746916_check_R combination:

Gradient PCR 2 the primers were G00100_Alternative and I746916_check_R and they worked well at all temperatures from 55-65 °C. Apparently the K1319008 template contained I746916.

The third gradient PCR tested the G00100_Alternative + K1319004_check_R combination:

Gradient PCR 3 The primers were G00100_Alternative and K1319004_check_R and they worked well at all temperatures from 60-68.1 °C. To our disappointment, the K1319008 template did not contain K1319004. It is unclear why the 5 bands of K1319008 and I746916 look different.

The results of these three PCRs are:

1. The KAPA2G Fast ReadyMix worked well
2. All three primers work well at >65 °C annealing temperature
3. The K1319008 template was contained I746916 instead of the intended K1319004 ORF

It was concluded that a similar check PCR with 65 °C annealing temperature will be done on all plasmids and cryos of K1319008.

27th

• First Michael transformed K1319001, K1319002, K1319003 and K1319004 (all in pSB1C3) into NEB10β cells. He tested the PCR machine for semi-automated heat-shocking by splitting the 50 µL cells with the plasmid into 2x 25 µL. All 100 µL were plated for all construct/machine combinations.

• Vera transformed several constructs into chemically competent BL21(DE3) cells.

• Philipp and Michael did colony-PCR on all plasmids, cryos and colonies that should contain the K1319004 sequence.

• Vera also made check a PCR on galectin-constructs:

28th

• Michael made a restriction of BioBrick K1319020 and vector pSB1C3 with restriction enzymes EcoRI and PstI. Then Vera ligated the restricted parts and made a transformation using E. coli NEB 10ß cells.

29th

• Eshani made cryo cultures and plasmid preparation of K1319010, K1319011, K1319012, K1319021 and K1319042. Vera determined the contentration of plasmids and made did a restriction digest of K1319010, K1319011, K1319012, pSB1C3, K1319021, K1319013 and K1319014, followed by a ligation in K1319010.pSB1C3, K1319011.pSB1C3, K1319012.pSB1C3, K1319021.K1319013.pSB1A3 and K1319021.K1319013.pSB1A3. All constructs were transformed into E. coli NEB 10ß.

• Nina prepared 3 500 mL flasks with 30 mL LB medium which were inoculated with a Pseudomonas putida strain. The cells were cultured over night at 28 °C and ~300 rpm. The cultures are supposed to be used to test our OD device.

30th

• Sequencing samples were sent in for K1319020 clone #2, 3 & 5 (in pSB1C3), K1319017 clone #1 (in pSB1C3), K1319010 clone #2 (in pSB3K3), K1319011 clone #1 (in pSB3K3), K1319012 clone #2 (in pSB3K3), K1319013 clone #1 (in pSB1C3), K1319014 clone #1 (in pSB1C3), K1319001 (in pSB1C3) and K1319002 (in pSB1C3).

• A plasmid prep of K1319013 and K1319014 was run.

• A Gibson assembly with the K1319015 from the I20260 backbone and the K1319000 insert, forming K3139015, was conducted. The product was subsequently transformed into NEB10β cells.

• The pSB1C3 plasmid backbones were amplified via PCR and purified.

• Colony-PCRs of K1319008 and K1319012 master plates were made to confirm the colony's identity. Subsequently, pre-cultures were inoculated.

• A transformation of K1319010 and K1319010 in pSB1C3 was conducted.

• Another plasmid prep of K1319010 clone #2, K1319011 clone #1, K1319012 clone #2 (all in pSB3K3), K1319013 clone #4, K1319014 #3, K139020 #2, 3, 5 (all in pSB1C3) was run.

• The OD device was tested with a dilution series of a Pseudomonas putida culture.

October

1st

• Prepartations for sensor-chip manufacturing the following day (2014-10-02):
  • At 18:30 Patrick prepared over-night cultures from K1319042, B0015 and K131026 by inoculating 250 mL Erlenmeyer flasks each containing 50 mL LB medium . The flasks were incubated for ~12 hours at 37 °C on a shaker.

2nd

• At 8:30, Nina and Arne did a plasmid prep of dublicate samples of K1319011 clone #1 and #6. Florian measured the DNA yield, and the higher concentrated sample of clone #1 and #6, respectively, were sent in for sequencing.
• Nina made precultures and a master plate of 6 colonies of K3139008 in psB1C3 in NEB10β cells that had been plated at 5:30 this morning.

• Manufacturing of sensor-chips:
  • At 10:00 Patrick prepared 150 mL LB medium containing 1.5% (w/v) agarose, which will be referred to as LB+agarose hereafter. The LB+agarose solution was autoclaved and subsequently tempered to 45 °C. Precultures (50 mL each) of K1319042, B0015 and K131026 were spinned down at 3000 rpm (?check?) for 10 min at 21 °C and resuspended in 1 mL pretempered (21 °C) LB-medium. The resuspended cultures were mixed with 49 mL LB+agarose and poured onto three sensor-chip-templates (one template per culture). Sensor chips were cut out from the template and incubated at 37 °C for 1 h.
  • K1319042 and B0015 were induced with 0.2 µL IPTG (100 mM) subsequently to incubation and K131026 was induced with 0.2 µL homoserinlacton stock solution (50 µM) 30 minutes after induction of the K1319042 and B0015. The induced sensor-chips were read out evry 30 minutes for 180 minutes in total. An additional readout was conducted 285 minutes post induction. Readout was conducted at 450 nm and 480 nm wavelength.

• Gibson Assembly of K1319008
  • Template Backbone: I746909, Insert: K1319004
  • Transformation in E.coli NEB10β and BL21

• PCRs for Gibson Assembly of K1319010 and K1319015
  • Template Backbone: I20260 for K1319010 and K1319015
  • Template Insert: K1319000 for K1319010 and K1319015 (but different primer)

• preculture of K1319013 and K1319014 in pSB3K3

• K1319011 in pSB1C3 prepped for sequencing

• Gibson Assembly of K1319017 (PCRs, Gibson Assembly, Restriction with DnpI, Transformation into NEB10β)
  • Template Backbone: B0015
  • Template Insert 1: LasI synthesized gene
  • Template Insert 2: K660004

3rd

• Made master plates of K1319008 in NEB10β and BL21 and precultures

• Check PCR for K1319008 to validate the Gibson Assembly check for potential I746909 residues

Check PCR K1319008 K1319008 was checked with the Primers K1319008_Check_R and I746909_Check_R (both with G00100 Alternative as froward primer) for presence of K1319008 or I746909. All tested clones were positive for K1319008 and negative for I746909.

• Florian and Stefan did a plasmid prep and made cryo stocks of K1319008 in NEB (clones #1, #2, #3) and BL21 (clones #1, #2)

• Plasmid prep of K1319013 and K1319014 in pSB3K3

• Gibson assembly for K1319010 and transformation into NEB10β

• Cryo stocks of K1319011 clone #6

• Restriction of K1319012, k1319013 and K1319014 with EcoRI and PstI. Restriction of linearized plasmid backbone pSB1C3 with EcoRI and PstI. Ligation of K1319012, K1319013 and K1319014 into pSB1C3. Transformation into NEB10β.

• Gibson assembly of K1319015 and transformation into NEB10β

• Colony PCR of K1319017

colony PCR K1319017 K1319017 was checked with a colony PCR for the right insert length. Clones #2 and #4 were correct and used forthwith.

• Did plasmid prep and cryo of clones #2 and #4 of K1319017

• New plasmid backbone of pSB1C3 was made using the [http://parts.igem.org/Help:Protocols/Linearized_Plasmid_Backbones|standard protocol].

• Transformation of K1319008 clone #1 (from BL21) and K1319013 into BL21 (two plasmids in one cell).

• Transformation of K1319008 clone #1 (from BL21) and k1319014 into BL21 (two plasmids in one cell).

• OD measurements of three biological triplicates from E. coli BW21 113, P. putida and S. cerevisiae. Measurement as an analytic triplicate in the spectrophotometer (absorbance and transmission) and our own OD/F device.

• Gibson assembly of K1319021
  • Template Backbone: K1319008
  • Template Insert: LasI gene synthesis

• At 19:00 Patrick and Florian measured OD, Absorption (Spectrophotometer) and transmission for 19 diltuions in the range of 100-2.5% from yeast (saccharomyces cerevisiae) and p. putida liquid cultures. Measurements were conducted in biological as well as technical triplicates.

• Prepartations for sensor-chip manufacturing the following day (2014-10-04):
  • At 22:00 Patrick prepared over-night cultures from B0015, K1319017 and K131026 by inoculating 250 mL Erlenmeyer flasks each containing 50 mL LB medium for sensor-chip manufacturing th next day. The flasks were incubated for ~12 hours at 37 °C on a rotary shake

4th

• Colony PCR of K1319015 and Check PCR of K1319010
  • K1319010: clone #1 was positive
  • K1319015: in all clones the inserts were too short.

• New digestion of Gibson Mastermix of K1319015 with DnpI

• Transformation of new Gibson Mastermix into NEB 10 Beta

• Restriction of K1319010,K1319012, K1319013 and K1319014 (all in pSB3K3) with EcoRI and PstI, cutting of pSB1C3 with EcoRI and PstI, ant then ligation.

• Master plates and precultures of the transformations of K1319008 in BL21, K1319013 + K1319008 in BL21 and K1319014 + K1319008 in BL21

• Colony PCR of the master plates of the double plasmid constructs K1319013 + K1319008 and K1319014 + K1319008

• Sending the first biobricks to the iGEM headquarters:
  • K1319000
  • K1319001
  • K1319002
  • K1319003
  • K1319004
  • K1319008
  • K1319011
  • K1319017
  • K1319020
  • K1319042

• Shake flask expreriments with K1319008 (clone #1), K1319013 + K1319008 (clone #2) and K1319014 + K1319008 (clone #2) in LB (2 flasks each). Inoculation with 50 µl preculture and inducing with iPTG at OD of 1,5.

• Manufacturing of sensor-chips:
  • At 13:30 Patrick prepared 150 ml LB+agarose medium (1.5% (w/v) agarose). The LB+agarose solution was autoclaved and subsequently tempered to 45 °C. Precultures (50 mL each) of B0015 and K1319017 and K131026 were spinned down at 3000 rpm (?check?) for 10 min at 21 °C and resuspended in 1 mL pretempered (21 °C) LB-medium. The resuspended cultures were mixed with 49 mL LB+agarose and poured onto three sensor-chip-templates (one template per culture). Sensor chips were cut out from the template and incubated at 37 °C for 1 h.
  • B0015,K1319017and K131026 were induced with 0.2 µL homoserinlacton stock solution (50 µM). The induced sensor-chips were read out evry 30 minutes for 240 minutes in total. Readout was conducted at 450 nm and 480 nm wavelength. An additional readout was conducted after 12 hours.

• At 17:00 Patrick prepared 4 liquid cultures from the K1319010_PsB3K3 master-plate (clone#1) in 5 mL LB-medium, each. The liquid cultures were prepared in order to create cryo-stocks from K1319010-PsB3K3. Kanamycin was added to the liquid cultures as antibiotic.

• At 18:00 Patrick prepared a master-plate (LB+C) and corresonding liquid cultures from 6 clones of E.coli NEB10B k1319021-psB1C3. Liquid cultures and master-plate were incubated at 37 °C.

• At 23:30 Patrick prepared liquid cultures from K1319025-psB3K3 clones #7, #8 and #9 in 5 mL LB-medium. Kanamycin was used as antibiotic and the cultures were incubated at 37 °C. Purpose of the cultures was cryo stock preparation and plasmid prep.

5th

• At 12:00 Patrick prepared liquid cultures from K139010-pSB3K3, K139011-pSB3K3, K139012-pSB3K3, K139013-pSB3K3, K139014-pSB3K3, K139015-pSB3K3 in 5 ml LB-medium each. Kanamycin was used as antibiotic. Purpose for the cultures was characterization of constituitive expression and additional plasmid prep in case of K139013-pSB3K3 and K139014-pSB3K3.

• At 11:45 Patrick and Anna prepred cryo stocks from NEB K1319010-pSB3k3 #1, K1319025-pSB3K3 #7, K1319025-pSB3K3 #8 and K1319025-pSB3K3 #9 by mixing 750 µl lquid culture with 750 µl 50% (v/v) Glycerol-solution in 26 ml EPPIs.
  • Plasmid prep was also done for the cultures mentioned above.

• Manufacturing of sensor-chips:
  • At 13:00 Patrick prepared 150 ml LB+agarose medium (1.5% (w/v) agarose). The LB+agarose solution was autoclaved and subsequently tempered to 45 °C. Precultures (50 mL each) of BL21 pSB1C3-K131900+pSB3K3-K1319014, BL21 pSB1C3-K1319008+pSB3K3-K1319013 and NEB pSB1C3-B0015 were spinned down at 3000 rpm (?check?) for 10 min at 21 °C and resuspended in 1 mL pretempered (21 °C) LB-medium. The resuspended cultures were mixed with 49 ml LB+agarose and poured onto three sensor-chip-templates (one template per culture). Sensor chips were cut out from the template and incubated at 37 °C for 1 h.
  • BL21 pSB1C3-K131900+pSB3K3-K1319014, BL21 pSB1C3-K1319008+pSB3K3-K1319013 and NEB pSB1C3-B0015 were induced with 0.2 µl IPTG. The induced sensor-chips were read out every 30 minutes for 360 minutes in total. K1319013 was induced earlier and thus measurements were taken for 450 min in total. Readout was conducted at 450 nm and 480 nm wavelength. An additional readout was conducted after XX hours.

At 15:30 Patrick prepared liquid cultures from i746909-pSB1C3, I20260-pspSB3K3, K731520-pSB1C3, K1319008-pSB1C3, K1319013-pSB3K3, K1319014-pSB3K3, B0015-pSB1C3,K1319013/08-pSB1C3-pspSB3K3 and B0015-pSB1C3, K1319014/08-pSB1C3-pspSB3K3. Purpose for the cultivation was characterization of ITPG inducible expression.

Florian and Patrick prepared a colony PCR from K1319014-pSB1C3 clones #3, #4, #5 and#6. H20 and K1319014-pSB3K3 were used as controls.

At 22:20 Michael and Vera prepared 1 L LB+C plates (2.5 g NaCl, 10 g Agar, 2.5 g yeast extract and 5 g Trypton). N-Z-amine (peptone from casein) was used instead of tryptone, because the tryptone stock was depleted.