1. A mixture of different sized DNA fragments was separated on an agarose gel (from 0.7 to 2% agarose in 1x TAE buffer and 0.1 µg/ml ethidium bromide) at a constant voltage of 100 V.
2. UV light (λ = 254 nm) was used to visualize DNA with intercalated ethidium bromide

FRAGMENT ISOLATION from agarose gel

Restriction digest

1. Set up a restriction mixture:
   for analysis of cloned DNA
   • 1X optimized Restriction buffer (10X)
   • 0.5 µL restriction enzyme (10 U/µL)
   • Bring volume to 20 µL with nuclease-free water.
   or
   for isolation of specific DNA
   • 1X optimized Restriction buffer 10X
   • up to 2 µL restriction enzyme 10 U/µL
   • Bring volume to 50 µL with nuclease-free water.
2. The sample was incubated at optimal temperature for the restriction enzyme(s)
3. Analysis of fragmented DNA was done by gel electrophoreses (loading dye was added to the samples before loaded on a agarose gel)
4. Results were documented with
5. Desired DNA fragment was excised and purified using suitable DNA purification kit.

PCR

1. For Phusion polymerase: master mix contained
   • DNA (1-10 ng)
   • both primers (0,4 pmol/µl )
   • 1x Phusion HF buffer
   • 0,2 µM dNTPs
   • Phusion polymerase (0,02 U/ µl) and
   • MQ up to final volume of 25 µl
2. vAccuPrime reaction contained:
   • DNA (10 ng),
   • both primers (0,4 pmol/µl ),
   • 1xRnx mix,
   • enzyme (0,05 U/ µl) and
   • MQ up to final volume of 50 µl.
3. Taq polymerase mix contained:
   • both primers (0,4 pmol/µl),
   • 1x Taq PCR buffer II,
   • 0,2 µM dNTPs,
   • 5mM MgSO4,
   • enzyme (0,125 U/ µl) and
   • MQ up to total volume of 20 µl.
   • Then the bacterial colony was added to the reaction mix.
4. All temperature programs were designed according to manufacturer protocol, primers melting temperature and length of desired PCR products. Reactions were preformed in Applied Biosystems Veriti 96 well thermal cycler.

Gibson Assembly

1. 50 ng of each PCR product were added to Gibson assembly master mix and incubated at 50 °C.
2. After incubation, the transformation in bacteria was preformed.

Ligation

1. Estimate the vector and insert concentrations and set molar ratio of insert to vector 3:1 (100-150ng Vector DNA).
2. Set up a ligation mixture:
   1X ligase buffer (10X)
   1 µL T4 ligase (3 U/µL)
   Bring volume to 10 or 20 µL with nuclease-free water.
3. Incubate sample for sticky-end ligation reactions at room temperature for 3 hours (or at 4 to 8 °C, overnight).
   or
   Incubate blunt-end ligation reactions at 17 °C for 4 to 18 hours.
4. After incubation part of the ligation mixture is used for transformation of bacterial cells (see: transformation of bacteria)

Culturing clones

• 10 g/L tryptone
• 5 g/L yeast extract
• 10 g/L NaCl
• media is supplemented with suitable antibiotics depending on selection marker on transfected plasmid: ampicilin 100 mg/L or kanamycin 50 mg/L

• LB with 1.5% agar
• media is supplemented with suitable antibiotics depending on selection marker on transfected plasmid

Transformation of bacteria

1. 100 µL of competent cells were thawed on ice.
2. 50 – 400 ng DNA solution was added to competent bacterial cells (depending on the concentration of the DNA solution).
3. A mixture of cells and DNA solution was incubated on ice for 30-60 minutes.
4. Than the mixture was heat-shocked for 45 seconds at 42 °C.
5. Cooled down for 3 minute on ice.
6. The mixture were than rescued by adding 500 µL preheated antibiotic free LB-medium and incubated for one hour at 37 °C while shaking for induction of the antibiotic resistance.
7. The selection for plasmid containing and therefore antibiotic resistant bacteria was conducted by plating them on antibiotic containing LB-agar plates.

Glycerol stock for long term storage of bacteria

1. 1 mL of an overnight culture was added to 150 µL of 80% glycerol into a cryo-tube.
2. Mixed and incubated at room temperature for 30 min.
3. Afterwards the glycerol stock was stored at -80 °C.

Cell cultures

Eucaryotic cell lines and cultivation

HEK293 is a human cell line derived from kidney cells and grows in a monolayer culture. Cells were grown in DMEM medium supplemented with 10% FBS.

HEK293T cell line is derived form HEK293 cells. HEK293T cells express the SV40 large T-antigen that enables episomal replication of plasmids containing the SV40 origin of replication in transfected cells. Cells were grown in DMEM medium supplemented with 10% FBS.

NK-92 is an interleukin-2 (IL-2) dependent natural killer cell line derived from peripheral blood mononuclear cells from patient with non-Hodgkin's lymphoma. The cell line is cytotoxic to a wide range of malignant cells. Cells were grown in RPMI medium supplemented with 20% FBS and 100 U/ml IL-2.

Cultivation

1. Remove and discard culture medium from a T-75 flask containing a monolayer of HEK293 or HEK293T cells.
2. Rinse the T-75 flask with 10 ml of PBS buffer to remove all traces of growth medium (DMEM + 10% FBS) which otherwise inhibits trypsin function. Remove and discard the PBS buffer.
3. Add 2-3 ml of trypsine solution and gently tilt the flask to ensure the trypsine solution covers all the cells. Incubate the cells in trypsin for 0,5 - 3 min.
4. When the cells start to detach from the surface, add 7 ml of growth medium to the trypsin solution. Resuspend all remaining cells from the bottom of the T-75 flask by pipetting.
5. Transfer the cell suspension to a 15 ml centrifuge tube.
6. Centrifuge the cell suspension for 5 min at 1200 rpm.
7. Remove the trypsin-containing medium from the centrifuge tube.
8. Resuspend the cell pellet in fresh medium.
9. Take as much cells as you need and add fresh medium to a total volume of 10 ml.
10. Return the cells in a T-75 flask to the incubator (37 °C, 5 % CO2).

1. Count cells.
2. Calculate the desired number of cells per well. Dilute cells in DMEM with 10% FBS.
3. Transfer the cells into an appropriate plate and place in a cell culture incubator.

• 1 % L-Glutamine (GlutaMax)
• 10 % FBS
• Optionally: 1% Pen/Strep

• 1 % L-Glutamine (GlutaMax)
• 20 % FBS

Transfection

1. Dilute plasmid DNA to desired concentration in 150 mM NaCl, vortex gently and spin down briefly.
2. Dilute jetPEI (PolyPlus) in 150mM NaCl, vortex gently and spin down briefly.
3. Add the jetPEI solution to the DNA solution.
4. Vortex the solution immediately and spin down briefly.
5. Incubate for 15 to 30 minutes at room temperature.
6. Add the jetPEI/DNA mix to the cells in and gently swirl the plate.
7. Return the plate to a cell culture incubator.

Induction systems

Induction of cells

1. Transfect HEK293 or HEK293T cells with plasmids using JetPei transfection reagent (Polyplus transfection), following the manufacturers protocol (see cell culturing for details).
2. 2 hours post transfection change media and stimulate the cells by adding dilutions of appropriate inductors to the medium in a 1:10 (v:v).
3. After 2-3 days of incubation, replace cell medium with fresh medium and stimulate again appropriately.

Effectors

Biological assay

1. HEK293T cells, seeded in 6-well plate, were transfected with anakinra downstream of constitutive promoter.
2. Transfected cells were incubated for 48 h.
3. To detect anakinra's effect on NF-κB signalling pathway, other HEK293T cells were transfected with plasmid coding for Renilla luciferase and plasmid reporter with NF-κB-inducible firefly luciferase expression. HEK293T cells express IL-1R, so additional transfection with receptor gene wasn't needed.
4. After 24 h, medium was removed from cells transfected with reporter plasmids and 90 μL of anakinra-producing cells' supernatant was added to these wells.
5. After 24 h of stimulation, cells were lysed and NF-κB activation was assessed using dual luciferase assay.

1. HEK293T cells transfected with either the IFN-alpha encoding plasmid or an empty vector, and HEK293T cells transfected with the reporter vector were co-cultivated.
2. Additionally, we performed a co-transfection experiment, where HEK293T cells were transfected with both the reporter and the IFN-alpha encoding plasmids.
3. Day after transcfection cells were cultivated into 96-well plate at density 5x104 cells per well
4. After 24 hours of incubation, dual luciferase reporter assay was preformed.

1. HEK293T cells where plated on 6 well plates and transfected with a plasmid coding for human IFN-alpha or a control plasmid (pcDNA3).
2. Supernatants were collected after 16h and serial dilutions were measured for IFN-alpha levels by Human IFN-alpha Instant Elisa (eBioscience).

1. HEK293T cells were seeded in a black 96-well plate and transfected with plasmids for the switch. Plasmids and amount used for transfection are listed in Figure legends.
2. Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.
3. Media supplemented with inducer or without inducer were changed after two days cultivation.
4. 2 days after inductions and then 3 days after second media change cells were lysed with 25 µL of 1x Passive lysis buffer (Promega).
5. Fluorescence was then measured using an automated plate reader.

1. HEK293T cells were seeded in a white 96-well plate and transfected with plasmids for the switch. Plasmids and amount used for transfection are listed in Figure legends.
2. Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.
3. Media supplemented with inducer or without inducer were changed after two days cultivation.
4. 2 days after inductions and then 3 days after second media change cells were lysed with 25 µL of 1x Passive lysis buffer (Promega).
5. Luminescence of expressed reporter firefly luciferase was then measured with Orion (Berthold Technologies) using Luciferase buffer with luciferin as a substrate. For normalization Renilla luciferase activity was used. The Renilla luciferase was measured using Renilla buffer supplemented with colelenterazine.

Microscopy

Microscopy-cell viability with Hoechst and SytoxGreen514 (Safety mechanisms)

1. HEK293 cells were seeded in an 8-well microscope chamber and transfected with 100 ng CMV-mGMK_TK30 (pPCMV-mGMK_TK30).
2. Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures.
3. After 5 days of cultivation, a Hoechst dye (0.4 μg/mL) and a SytoxGreen514 dye (1 μM) were used to stain cells and discriminate between alive and dead cells.
4. Cells were incubated for approximately 10 minutes in dark at 37 °C before being imaged.
5. A 405-nm diode laser was used to excite Hoechst and a 514-nm line of 25 mW multi ion argon laser was used to excite SytoxGreen514. Successive images excited at 405 and 514 nm were captured. Fluorescence emission was detected at 450-500 nm and 520-560 nm for Hoechst and SytoxGreen respectively.

Microscopy-cell growth (Safety mechanisms)

1. HEK293 cells were seeded in an 8-well microscope chamber and transfected with 100 ng CMV-mGMK_TK30 (pPCMV-mGMK_TK30) and/or 20 ng mCitirne (pPCMV-mCitrine) (a transfection control).
2. Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures.
3. After 5 days of cultivation, a cell cultures were imaged.
4. A 514-nm line of 25 mW multi ion argon laser was used to excite mCitrine reporter protein. Fluorescence emission was detected at 520-560 nm for mCitrine. Bright field images were used to visualize number of cells.

Microscopy-cell count (Safety mechanisms)

1. HEK293 cells were seeded in 12-well plates and transfected with and transfected with 100 ng CMV-mGMK_TK30 (pPCMV-mGMK_TK30).
2. Cell cultures were treated with ganciclovir (GCV) in concentrations as indicated in figure legend.
3. After incubation the cells were resuspended by pipetting.
4. Cells suspension was then mixed with trypan blue.
5. Viable cell number was determined by counting the cells under a light microscope using Bürker-Türk counting chamber.

Microscopy-detection of reporter proteins (The Switch)

Reporters such as fluorescent proteins were used to detect expression of efektor in "The switch experiments". As reporters we used blue (tagBFP), yellow (mCitrine), orange (mCherry) and red fluorescent proteins (mNeptun). mCherry was used as transfection control, the others were used as reporters of "the switch".

1. HEK293T cells were seeded in an 8-well microscope chamber or 12-well plate and transfected with plasmids for the switch. Plasmids and amount used for transfection are listed in Figure legends.
2. Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.
3. Media supplemented with inducer or without inducer were changed after two days cultivation.
4. Images of cells expressing reporters were taken two days after transfection and inducers addition and then each day for 5 days.
5. A 405-nm diode laser was used to excite tagBFP, a 514-nm line of 25 mW multi-ion argon laser was used for mCitirne, a 543-nm HeNe laser was used for mCherry and a 633-nm HeNe laser was used to excite mNeptune. Successive images excited at 405, 514, 543 and 633 nm were captured. All intensities of laser and photomultipliers were kept unchanged during set of experiment to enable comparison of images. Fluorescence emission was detected at 450-500 nm, 520-560 nm, 560-600 nm and 640-700 nm for tagBFP, mCitrine, mCherry and mNeptune, SytoxGreen respectively.

Microscopy-alginate beads degradation (Microencapsulation)

To observe alginate beads degradation, 2000 kDa FITC-dexstran (Sigma) was added to 200 µL of culture medium containing alginate beads with immobilized HEK 293T cells. Because FITC-dexstran cannot penetrate into algnate beads, we can easily observe bead degradation uppon addition of alginate lyase from Sphingobacterium multivorum (Sigma).

1. Alginate beads suspended in culture medium were seeded into an 8-well microscope chamber (200 µL).
2. 20 µL of 1 mg/mL FITC-dextran was added into well.
3. After the dye has been evenly distributed throughout the suspension, 8 µL of Sphingobacterium multivorum alginate lyase were added.
4. Microscope was set to capture images every 20 seconds.
5. Screenshots were collected for at least 15 minutes.
6. A 488-nm line of 25 mW multi-ion argon laser was used for FITC. Fluorescence emission was detected at 520-560 nm. At the same time a bright field image was taken.

Microscopy-encapsulated cells viability (Microencapsulation)

To observe encapsulated cells' viability, HEK 293T cells were dyed with Hoechst and 7-aminoactinomycin D (7-AAD) viability stains. Hoechst stains both living and dead cells, while 7-AAD stains dead cells only.

1. Encapsulated cells were grown in DMEM culture medium supplemented with 10% FBS.
2. 200 µL of microcapsule suspension was collected and alginate-PLL capsules were seeded into an 8-well microscope chamber.
3. 5 µL of 7-AAD and 1 µL of Hoechst stain were added into well.
4. Encapsulated cells were protected from direct light and stained for 30 min at 37 °C.
5. Microscope chamber was transfered to Leica confocal microscope.
6. A 405-nm diode laser was used to excite Hoechst and a 543-nm line of HeNe laser was used to excite 7-AAD.
7. Fluorescence emission was detected at 450-500 nm and 600-700 nm for Hoechst and 7-AAD respectively.

Flow cytometry

Flow cytometry is a laser based technology employed in cell counting and biomarker detection. It allows simultaneous multiparametric analysis of the physical as well as biochemical and biological characteristics of particles. We used a CyFlow Space (Partec) flow cytometer equipped with three lasers (405, 488 and 633 nm). The CyFlow detects forward scatter and side scatter signals and up to 6 colours of fluorescence.

Flow cytometry - the annexin assay (Safety mechanisms)

To determine the percentage of cells undergoing apoptosis as a result of herpes simplex virus thymidine kinase (HSV-TK) (pCMV-mGMK_TK30) transfection and ganciclovir treatment we labelled cells with Annexin V conjugated with phycoerythrin (PE). Annexin V is Ca2+ dependent phospholipid-binding protein that has a high affinity for the phospholipid phosphatidylserine and therefore binds to apoptotic cells that have phosphatidylserine exposed on their surface.

1. HEK293 cells were seeded in 12-well plates.
2. Cells were transfected with pCMV-mGMK_TK30 and treated with ganciclovir. Concentrations of ganciclovir and plasmid are indicated in figure legends.
3. After incubation the cells were washed with PBS buffer and resuspended by pipetting.
4. Cells were pelleted with centrifugation at 1200 rpm.
5. The cell pellet was washed in 1x Annexin Binding Buffer (10 mM HEPES, 140 mM NaCl, and 2.5 mM CaCl2, pH 7.4).
6. The pellet was then resuspend in 1x Annexin Binding Buffer and PE-Annexin V (5 µl per 100 μl cell suspension) was added.
7. Samples were incubated for 20 minutes in dark at room temperature and then immediately analyzed with the flow cytometer.
8. Along with site and forward scatter also signal in FL2 channel (540-580 nm) was recorded.

Flow cytometry - the propidium iodide assay (Safety mechanisms)

To determine the percentage of dead cells due to cytotoxic activity of natural killer cells against HEK293T cells expressing MICA protein, cells were stained with propidium iodide dye, which intercalates into DNA and stains only dead cells, because it is membrane impermeant fluorescent molecule.

1. HEK293T cells seeded in 12-well plates were transfected with plasmid expressing MICA (pPCMV-MICA_pcDNA3) and/or blue fluorescent protein (BFP) (pPCMV-BFP). BFP was used to discriminate between HEK293T and NK-92 cells.
2. Two days after transfection cells were mixed with NK-92 cells in different ratios (1:1, 1:5, 1:10) and incubated for 4 hours at 37 °C in culture medium consisting of RPMI, 20% FBS and hIL-2 (100 U/ml).
3. After incubation of HEK293T with NK-92 cells, cells were treated with propidium iodide.
4. Along with site and forward scatter also signal in FL1 channel (530-580 nm) was recorded.

Flow cytometry - detection of reporter proteins (The Switch)

Reporters such as fluorescent proteins were used to detect expression of effectors in "The switch experiments". As reporters we used blue (tagBFP) and yellow (mCitrine) fluorescent proteins.

1. HEK293T cells were seeded in a 12 or 24-well plate and transfected with plasmids for the switch.
2. Two hours after transfection, media was changed and cells were stimulated with inducers.
3. Medium with inducer or without the inducer was changed after two days of cultivation.
4. Cells were collected at different time points (2 days after induction and than 3 days after second media change).
5. Cells were washed and then resuspended in PBS buffer
6. A 405 nm diode laser was used to excite tagBFP and a 488-nm diode laser was used for mCitirne.
7. Along with site and forward scatter also signals in FL1 (540-580 nm) channel (mCitrine) and FL5 (450-480 nm) channel (tagBFP) were recorded.

Microencapsulation

1. HEK 293T cells were seeded 5x10⁵ per 10 cm cell culture dish (3 per encapsulation) and grown in DMEM medium supplemented with 10 % FBS.
2. After reaching 50 – 70 % confluency, cells were transfected with 15 μg of DNA per culture dish with jetPEI transfection reagent (Polyplus Transfection).
3. On the next day, the medium was removed. Transfected cells were detached using 3 mL trypsin solution and centrifuged after the addition of fresh medium to inactivate the trypsin.
4. Supernatant was removed and cells were resuspended in 15 mL DMEM with 10% FBS.
5. Cells were counted using Countess automated cell counter (Invitrogen).
6. HEK 293T cells were again centrifuged and supernatant was removed.
7. Cells were resuspended in 2 mL of pre-warmed MOPS buffer.
8. 10 mL of pre-warmed alginate solution (1,5%) was added to cell suspension.

1. The encapsulator was equipped with a 200-µm nozzle.
2. The reactor vessel was filled with 225 mL 100 mM CaCl2.
3. Cell-alginate mixture was transferred into 20 mL syringe with a Luer lock.
4. The syringe was connected to bead producing unit (BPU).
5. Microcapsules were produced at flow rate of 12-14 units, vibration frequency 1030-1100 Hz and voltage for bead dispersion 900-1300 V.
6. Polymerisation lasted for 10 min.
7. The polymerisation solution was drained and 75 mL of 0,05% poly-L-lysine (PLL) solution was added.
8. Beads were incubated in PLL solution for 10 minutes.
9. The PLL solution was removed and beads were washed twice (for 1 and for 5 min) with 150 mL of MOPS buffer.
10. 100 mL of 0,03% alginate was added and beads were incubated for 10 min.
11. Alginate solution was drained and beads were washed once with 150 mL of MOPS buffer for 1 min.
12. 150 mL of depolymerization solution was added for 10 min.
13. Depolymerization solution was removed and capsules were resuspended in 150 mL MOPS and collected in bead collection flask.
14. MOPS was removed and microcapsules were transferred to T-75 with 10 mL DMEM, 10% FBS media supplemented with penicillin and streptomycin.

C. BUFFERS AND SOLUTIONS
10 mM MOPS buffer (pH = 7,2)
MOPS buffer with NaCl (pH = 7,2)
10 mM MOPS
0,85% NaCl

Polymerisation solution (pH = 7,2)
10 mM MOPS
100 mM CaCl2

Depolymerisation solution (pH = 7,2)
10 mM MOPS
50 mM Na3-citrate
0,45% NaCl

0,05% poly-L-lysine (15-30 kDa) in MOPS buffer (pH = 7,3)
0,03% alginate in MOPS buffer (pH = 7,2)
1,5% alginate (low viscosity) in MOPS buffer (pH = 7,2)

Protein detection

1. Samples were loaded on a 12% acrylamide gel and ran at a constant voltage (200 V) for 1 h.
2. Proteins were then blotted on a nitrocellulose membrane at a constant current (350 mA) for 1 h.
3. The membrane was washed with MQ and PBS and blocked for 1,5 h by incubation in I-Block blocking reagent at room temperature.

1. All proteins to be detected had a Myc tag at the C-terminus.
2. The membrane was incubated with primary antibodies (rabbit anti-Myc diluted 1:500) overnight at 4 °C and 150 rpm. Membrane was washed.
3. Washing in wash buffer three times for 5 min each
4. Membrane was incubated with secondary antibodies (anti-rabbit secondary antibodies, conjugated with HRP, diluted 1:3000) for 45 min at room temperature and 150 rpm.
5. HRP activity was detected by addition of SuperSignal West Femto or Pico Substrate (Thermo Scientific). Images were captured with Syngene G:Box chemiluminescent imaging system.

1x PBS
0,01% (v/v) Tween 20

References

Gibson, D.G., Young, L., Chuang, R., Venter J.C., Hutchison III, C. A. and Smith, H.O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases.Nature methods. 6, 343–345.