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Latest revision as of 22:47, 26 October 2012

Experimental methods

Cloning
Cell cultures
Induction systems
Effectors
Microscopy
Flow cytometry
Microencapsulation
Protein detection

Figure 1. Schematic presentation of methods used for cloning and culturing eukaryotic cells.

Figure 2. Schematic presentation of methods used for characterizing the switch, safety mechanisms, microencapsulation and effectors.

Cloning

Plasmid DNA isolation

MINI PREPs for analysis and sequencing

A single colony was picked from a LB-agar plate or glycerol stock and inoculated in 10 mL of LB-medium with the appropriate antibiotic for selection (100 mg/L ampicillin, 50 mg/L kanamycin, 35 mg/L chloramphenicol).
Bacteria were grown over night at 37 °C with agitation.
Plasmid DNA was isolated from 6-10 mL of over-night culture with GeneJET plasmid miniprep kit according to the manufacturer's protocol.
Amounts ranging from 6-10 µg of plasmid DNA were obtained.
The purity and concentration of the isolated DNA was analysed using NanoDrop.

Fragment DNA isolation from agarose gel

AGAROSE ELECTROPHORESIS

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.
UV light (λ = 254 nm) was used to visualize DNA with intercalated ethidium bromide

FRAGMENT ISOLATION from agarose gel

The band with the desired DNA fragment was excised from the gel, using a clean scalpel.
DNA was isolated from the gel slice with GeneJet Gel Extraction Kit according to the manufacturer’s protocol.
Purity and amount of DNA was determined using NanoDrop.

Restriction digest

To digest the desired DNA restriction reactions were prepared as follows:

for analysis of cloned DNA

2µl of the appropriate restriction buffer (10X)
0.5 µL restriction enzyme
Bring volume to 20 µL with nuclease-free water.

or

for isolation of specific DNA

2µl of the appropriate restriction buffer (10X)
up to 2 µL restriction enzyme
Bring volume to 50 µL with nuclease-free water.

The sample was incubated at optimal temperature for the restriction enzymes.
Analysis of fragmented DNA was done by gel electrophoreses.
Desired DNA fragment was excised and purified using suitable DNA purification kit.

PCR reaction

AccuPrime and Phusion DNA polymerase were used for DNA amplification. Colony PCR was performed with Taq DNA polymerase.

The master mix for reactions with Phusion DNA polymerase 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
The master mix for reactions with AccuPrime DNA polymerase 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.
The master mix for reactions with Taq DNA polymerase 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.
All temperature profiles were optimized according to manufacturer’s protocol,the melting temperature of primers, and the length of the desired PCR products. Reactions were performed in the Applied Biosystems Veriti 96 well thermal cycler.

PCR product purification. Desired PCR products were purified by GeneJet Gel Extraction Kit according to the manufacturer's protocol.

DNA concentration. An aliquot of the isolated DNA was analyzed using NanoDrop.

Gibson assembly

Gibson assembly master mix was prepared according to the protocol published in Gibson et al., 2009.

50 ng of each PCR product was added to the Gibson assembly master mix and incubated at 50 °C 1h.
After incubation, the entire master mix volume was transformed into competent bacterial cells.

Ligation

T4 ligase ligates the 5' phosphate and the 3'-hydroxyl groups of DNA.

Vector and insert concentrations were estimated and insert and vector fragments joined in a molar ratio of 3:1 (100-150ng Vector DNA).
A ligation mixture was prepared:

or

Blunt-end ligation reactions were incubated at 17 °C for 4 to 18 hours.
After incubation part of the ligation mixture was used for the transformation of bacterial cells (see: transformation of bacteria).

Culturing bacteria

For plasmid DNA propagation two bacterial strains were used: DH5alpha [fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80 Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17] and TOP10 [mcrA, Δ(mrr-hsdRMS-mcrBC), Phi80lacZ(del)M15, ΔlacX74, deoR, recA1, araD139, Δ(ara-leu)7697, galU, galK, rpsL(SmR), endA1,nupG].

Growth media for bacteria

Luria Broth (LB) : 10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, media is supplemented with suitable antibiotics depending on the selection marker on the transfected plasmid: ampicilin 100 mg/L or kanamycin 50 mg/L.

LB agar plates: LB with 1.5% agar, media is supplemented with suitable antibiotics depending on the selection marker on the transfected plasmid.

Transformation of bacteria

E. coli DH5alpha and TOP10 competent cells were used for the propagation of plasmid DNA.

100 µL of competent cells were thawed on ice.
50 – 400 ng DNA solution was added to competent bacterial cells (depending on the concentration of the DNA solution).
A mixture of cells and DNA solution was incubated on ice for 30-60 minutes.
The mixture was heat-shocked for 3 minutes at 42 °C.
Cooled for 3 minutes on ice.
500 µL of preheated antibiotic free LB-medium was added and incubated for one hour at 37 °C with agitation for the purpose of inducing antibiotic resistance.
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 mL of an overnight culture was added to 150 µL of 80% glycerol into a cryo-tube.
Mixed and incubated at room temperature for 30 minutes.
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 from 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.

Subculturing monolayer cell cultures

Remove and discard culture medium from a T-75 flask containing a monolayer of HEK293 or HEK293T cells.
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.
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 minutes.
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.
Transfer the cell suspension to a 15 ml centrifuge tube.
Centrifuge the cell suspension for 5 minutes at 1200 rpm.
Remove the trypsin-containing medium from the centrifuge tube.
Resuspend the cell pellet in fresh medium.
Take as much cells as you need and add fresh medium to a total volume of 10 ml.
Return the cells in a T-75 flask to the incubator (37 °C, 5 % CO2).

Cell plating

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

Media and buffers

DMEM supplemented with: 1 % L-Glutamine (GlutaMax), 10 % FBS, Optionally: 1% Pen/Strep.
RPMI supplemented with: 1 % L-Glutamine (GlutaMax), 20 % FBS.

Transfection

TABLE: Transfection mixtures for different culture format

Culture format	jetPEI reagent per µg of DNA (µL)	Typical amount of DNA (ng)	Volume of 150 mM NaCl solution for DNA and jetPEI (µL)	Total transfection mixture volume (µL)
96-well	2	200	10	20
24-well and 8-well microscope chamber	2	500	50	100
12-well	2	1000	50	100
6-well	2	2000	100	200
10 cm	2	15000	250	500

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

Induction systems

To control our switch we needed a way to affect it from the outside. For this purpose we chose several inducible transcription systems where the controlled gene is expressed when a small molecule inducer (such as tetracycline) is present and is not expressed when the inducer is absent. We chose specific systems which do not cross react and whose inducers are orally bioavailable and safe for human use (Clackson, 2000). We decided for the systems based on tetracycline, pristinamycin, erythromycin and rapamycin analogs, as inducers. We then adapted these systems by cloning TAL regulators under their control to make them compatible with our genetic circuits.

Tetracycline, erythromycin and pristinamycin systems

The tetracycline, erythromycin and pristinamycin system all function in a similar manner. They are composed of a DNA binding protein (such as TetR) fused to a KRAB domain which reversibly binds a specific DNA sequence (TRE for example) and silences transcription from nearby promoters. The addition of an inducer causes the DNA binding domain to dissociate from the DNA and allows transcription to start. (Deuschle et al., 1995; Kramer et al., 2004)

Figure 1: Induced expression of TAL.

TABLE

System	Tetracycline	Erythromycin	Pristinamycin
Regulating protein	TetR:KRAB	E:KRAB	PIP:KRAB
DNA sequence	TRE	ETR	PIR
Inducer	Tetracycline or doxycycline	Erythromycin	Pristinamycin
Constructs	pCMV_TRE_TAL-A:KRAB	pCMV_ETR_TAL-A:KRAB	pCMV_PIR_TAL-B:KRAB
	pCMV_TRE_TAL-B:VP16	pCMV_ETR_TAL-B:VP16	pCMV_PIR_TAL-A:VP16
	TRE_CMV_TAL-A:KRAB	pCMV_ETR_TAL-B:KRAB	pSV40_PIR_TAL-B:KRAB
	TRE_CMV_PEST-CL1:TAL-A:KRAB	pCMV_ETR_TAL-A:VP16	PIR_CMV_TAL-B:KRAB
	TRE_CMV_TAL-B:VP16	pSV40_ETR_TAL-B:KRAB	PIR_CMV_PEST-CL1:TAL-B:KRAB
	TRE_CMV_PEST-CL1:TAL-B:VP16	ETR_CMV_TAL-A:KRAB	TRE_CMV_TAL-A:VP16
		ETR_CMV_PEST-CL1:TAL-A:KRAB	TRE_CMV_PEST-CL1:TAL-A:VP16
		ETR_CMV_TAL-B:VP16
		ETR_CMV_PEST-CL1:TAL-B:VP16

Rapamycin system

In the rapamycin system the gene of interest is under the control of a minimal promoter. The gene's transcription rate is regulated by two proteins that consist of a drug binding domain and either a DNA binding domain or an activation domain. When rapamycin is added both drug binding domains bind to it, consequently joining the activation domain with the DNA binding domain, resulting in a functional transcription factor, which activates the gene of interest. Instead of rapamycin a rapamycin analogue (rapalogue), which is a 1000-fold less imunosupressive than rapamycin, but activates the inducible system like rapamycin, is usually used as the inducer. (Pollock et al., 2002)

Regulating vector	HetAct
DNA sequence	ZFHD
Constructs	ZFHD_pMIN_TAL-A:KRAB
	ZFHD_pMIN_TAL-B:VP16

Induction of cells

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

Inductor	Stock solution (solvent)	Dilution (solvent)	Concentration in cell medium (% solvent)
Rapalogue (AP21967)	1 mM (100% ethanol)	10 µM (1% ethanol)	1 µM (0,1% ethanol)
Doxycyclin	1 g/L (MQ)	10 mg/L (MQ)	1 mg/L (MQ)
Pristinamycin	50 g/L (100% DMSO)	20 mg/L (1% DMSO)	2 mg/L (0,1% DMSO)
Erythromycin	50 g/L (100% ethanol)	20 mg/L (1% ethanol)	2 mg/L (0,1% ethanol)

Effectors

Biological assay-anakinra

HEK293T cells, seeded in 6-well plate, were transfected with anakinra downstream of constitutive promoter.
Transfected cells were incubated for 48 h.
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 a receptor gene was notneeded.
After 24 h, the medium was removed from cells transfected with reporter plasmids and 90 μL of anakinra-producing cells' supernatant was added to these wells.
After 24 h of stimulation, cells were lysed and NF-κB activation was assessed using dual luciferase assay.

Biological assay-IFN-alpha

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

ELISA for IFN-alpha

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

Plate reader-fluorescence(The Switch)

HEK293T cells were seeded in black 96-well plates and transfected with plasmids encoding the switch. Plasmids and amounts used for transfection are listed in Figure legends.
Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.
Media supplemented with inducer or without inducer were changed after two or three days of cultivation.
After a maximum of 6 days after transfection, cells were lysed with 25 µL of 1x Passive lysis buffer (Promega ) per well.
Fluorescence was measured using an automated plate reader.

Plate reader-luminescence (The Switch)

HEK293T cells were seeded in white 96-well plates and transfected with plasmids encoding the switch. Plasmids and amounts used for transfection are listed in Figure legends.
Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.
Media supplemented with inducer or without inducer were changed after two to three days of cultivation.
After a maximum of 6 days after transfection, cells were lysed with 25 µL of 1x Passive lysis buffer (Promega).
Luminescence of expressed reporter firefly luciferase was 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 coelenterazine.

Plate reader-absorbance (The Switch)

HEK293T cells were seeded in white 24-well plates and transfected with plasmids encoding the positive feedback loop switch and 10x[TALB + TALC] operator_CMV promoter_fLuciferase reporter plasmid and 10x[TALA + TALC]operator_CMV promoter_SEAP plasmid. Plasmids and amounts used for transfection are listed in Figure legends.
Media supplemented with inducer or without inducer were changed after two days of cultivation.
Two and seven days after transfection the growth medium was collected and SEAP QUANTIBlue substrate was added. After 15 minutes incubation at 37°C the absorbance was measured at 630 nm.

Microscopy

For spatial and temporal imaging of samples a Leica TCS SP5 laser scanning microscope mounted on a Leica DMI 6000 CS inverted microscope (Leica Microsystems, Germany) with a 10× and 20× dry objective and an HCX plan apo 63× oil (NA 1.4) oil immersion objective was used. For image analysis we used ImageJ (Image Processing and Analysis in Java) software (http://rsbweb.nih.gov/ij/) measuring the mean grey values of each cell containing the promoter of interest.

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

Hoechst dye is a membrane permeable dye and stains all cells in a culture. On the other hand a SytoxGreen514 dye is a membrane impermeable dye staining only dead cells. Both dyes, blue fluorescent Hoechst and green fluorescent SytoxGreen514, bind to nucleic acids causing emission of fluorescent light.

HEK293 cells were seeded in an 8-well microscope chamber and transfected with 200 ng CMV-mGMK_TK30 (pPCMV_mGMK:TK30).
Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures.
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 live and dead cells.
Cells were incubated for approximately 10 minutes in the dark at 37 °C before imaging.
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 nm 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)

HEK293 cells were seeded in an 8-well microscope chamber and transfected with 100 ng mGMK:TK30 (pPCMV_mGMK:TK30) and/or 20 ng GFP (pPCMV-GFP) (for transfection control).
Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures.
After 5 days of cultivation, a cell cultures were imaged.
A 514-nm line of 25 mW multi ion argon laser was used to excite GFP reporter protein. Fluorescence emission was detected at 520-560 nm for GFP. Bright field images were used to visualize the number of cells.

Microscopy-cell count (Safety mechanisms)

HEK293 cells were seeded in 12-well plates and transfected with different amounts of mGMK:TK30 (pPCMV_mGMK:TK30) as indicated in Figure legend.
Cell cultures were treated with ganciclovir (GCV) in concentrations as indicated in the Figure legend.
After incubation the cells were resuspended by pipetting.
Cells suspensions were then mixed with trypan blue.
Viable cell number was determined by counting the cells under a light microscope using a Bürker-Türk counting chamber.

Microscopy-detection of reporter proteins (The Switch)

Fluorescent proteins were used as reporters in "The switch experiments". The fluorescent proteins used were blue (tagBFP), yellow (mCitrine), orange (mCherry) and red (mNeptun) fluorescent proteins. mCherry was used as transfection control while the others were used as reporters of "the switch".

HEK293T cells were seeded in an 8-well microscope chamber or 12-well plate and transfected with plasmids encoding the switch. Plasmids and amounts used for transfection are listed in Figure legends.
Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.
Media supplemented with inducer or without inducer were changed after two or three days of cultivation.
Images of cells expressing reporters were taken two days after transfection and then each day for 5 days.
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 one set of experiments 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 degradation (Microencapsulation)

To observe the degradation of alginate beads, 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 the alginate beads, we can easily observe bead degradation upon addition of alginate lyase from Sphingobacterium multivorum (Sigma).

Alginate beads suspended in culture medium were seeded in an 8-well microscope chamber (200 µL).
20 µL of 1 mg/mL FITC-dextran were added into well.
After the dye was evenly distributed throughout the suspension, 8 µL of Sphingobacterium multivorum alginate lyase were added.
The microscope was set to capture images every 20 seconds.
Screenshots were collected for at least 15 minutes.
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-secreted alginate lyase enzymatic activity (Microencapsulation)

HEK293T cells were seeded 1×10⁶ on 10 cm cell culture dish and grown in DMEM medium supplemented with 10 % FBS.
After reaching 50 – 70 % confluency, cells were transfected with 15 μg of DNA per culture dish with jetPEI transfection reagent (Polyplus Transfection).
Protein production lasted for 72 hours.
Cell supernatants were collected and concentrated 50-times using Sartorius Vivaspin 6 concentrators (5 kDa MWCO PES).
Alginate beads were produced with Büchi BIOTECH Encapsulator (see Microencapsulation: Encapsulation procedure 1.-6.).
Beads were incubated with concentrated supernatants for 72 hours in an 8-well microscope chamber.
20 µL of 1 mg/mL FITC-dextran were added into wells.
A 488-nm line of 25 mW multi-ion argon laser was used for FITC detection. Fluorescence emission was detected at 520-560 nm.
Beads' diameters were assessed using Leica LAS Image Analysis software.

Microscopy-encapsulated cell viability (Microencapsulation)

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

Encapsulated cells were grown in DMEM culture medium supplemented with 10% FBS.
200 µL of the microcapsule suspension was collected and alginate-PLL capsules were seeded into an 8-well microscope chamber.
5 µL of 7-AAD and 1 µL of Hoechst stain were added to one well.
Encapsulated cells were protected from direct light and stained for 30 minutes at 37 °C.
A 405-nm diode laser was used to excite Hoechst and a 543-nm line of HeNe laser was used to excite 7-AAD.
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 colors 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 labeled cells with Annexin V conjugated with phycoerythrin (PE). Annexin V is a Ca2+ dependent phospholipid-binding protein that has a high affinity for the phospholipid phosphatidylserine and therefore binds to apoptotic cells with phosphatidylserine exposed on their surface.

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

HEK293T cells seeded in 12-well plates were transfected with plasmids expressing MICA (pPCMV-MICA_pcDNA3).
Two days after transfection with CMV-MICA_pcDNA3, cells were resuspended in PBS at final concentration 1x10⁶ cells/mL, stained with CFSE (0,6μM) and incubated for 10 minutes at 37°C. Staining was quenched by the addition of 5 volumes of ice-cold culture media (RPMI+ 20% FBS) to the cells. After 5 minutes incubation on ice, cells were pelleted by centrifugation and then washed by resuspending the pellet in fresh media (RPMI+ 20% FBS) a further two times for a total of three washes. CFSE was used to discriminate between HEK293T and NK-92 cells or between NK target cells K562, which were used as a positive control, and NK-92 cells.
HEK293T cells or K562 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).
After incubation of HEK293T or K562 cells with NK-92 cells, cells were treated with propidium iodide.
Along with site and forward scatter the signal in the FL1 channel (530-580 nm) was also recorded.

Flow cytometry - detection of reporter proteins (The Switch)

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

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

Microencapsulation

Cell preparation for encapsulation

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

Encapsulation

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

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

SDS-PAGE

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

Immunodetection

All proteins to be detected had a Myc tag at the C-terminus.
The membrane was incubated with primary antibodies (rabbit anti-Myc diluted 1:500) overnight at 4 °C and 150 rpm. Membrane was washed.
Washing in wash buffer three times for 5 minutes each.
Membrane was incubated with secondary antibodies (anti-rabbit secondary antibodies, conjugated with HRP, diluted 1:3000) for 45 minutes at room temperature and 150 rpm.
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.

Buffers and solutions

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

References

Clackson, T. (2000) Regulated gene expression systems. Gene ther. 7, 120–125.

Deuschle, U., Meyer, W.K. and Thiesen, R. (1995) Tetracycline-reversible silencing of eukaryotic promoters. Mol. Cell. Biol. 15, 1907–1914.

Kramer, B.P., Fischer, C. and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells. Biotech. Bioeng. 87, 478–484.

Pollock, R. and Clackson, T. (2002) Dimerizer-regulated gene expression. Curr. Opin. Biotech. 13, 459–467.

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.

Next: Lablog >>

@@ Line 2: / Line 2: @@
 <head>
 <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+<!-- back to top -->
+<div style="position:fixed; bottom:45px; right:30px; width:100px; height:66px; background-color:transparent;">
+<a href="#topofthepage">
+<table style="background-color:transparent;" onclick="window.location = '#topofthepage'" class="invisible" style="height:100%;">
+<tr class="invisible" style="background-color:transparent;">
+<td class="invisible" style="background-color:transparent;" valign="center">
+<img width="100px" src ="https://static.igem.org/mediawiki/2012/1/14/Svn12_hp_btt.png"></img>
+</td></tr></table>
+</a>
+</div>
 <style type="text/css">
@@ Line 13: / Line 22: @@
-p {line-height:1.5em; margin:0 0 15px; text-align:left;}
+p {line-height:1.5em; margin:0 0 15px; text-align:justify;}
 h2 {font-size:1.8em; font-weight:400; margin:0 0 12px;}
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+#cssmenu ul li > ul li a table tr td span{ outline:none; display:block; position:relative; margin:0; padding:0px 0px; font:10pt Arial, Helvetica, sans-serif; color:#fff; text-decoration:none; text-shadow:1px 1px 0 rgba(0,0,0, 0.5); }
 #cssmenu, #cssmenu > ul > li > ul > li a:hover
 { 	background:#043A6B;
@@ Line 216: / Line 226: @@
 #cssmenu > ul > li > a:hover{background:#0C5DA5;}
 /* end CSS navigation menu (blue) */
+/*new table start*/
+table.newtable {background-color:transparent;}
+td.newtable, th.newtable {background-color:transparent;}
+thead.newtable{ }
+tbody .newtable{}
+/*new table*/
@@ Line 292: / Line 310: @@
 <body>
+<a name="topofthepage" style="background-color:transparent;"></a>
 <div id="banner">
 </div>
@@ Line 301: / Line 319: @@
 <!-- start main menu -->
+	<!-- start main menu -->
 	<div id='cssmenu'>
 	<ul>
@@ Line 316: / Line 335: @@
 		<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchDesignedTALregulators'><span>Designed TAL regulators</span></a></li>
 		<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>
-		<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchPositiveFeedbackLoopSwitch'><span>Positive feedback loop switch</span></a></li>
+		<li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchPositiveFeedbackLoopSwitch'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/TheSwitchPositiveFeedbackLoopSwitch';" class="newtable"><tr class="newtable"><td class="newtable"><span>Positive feedback loop switch</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
+    <li><a href='https://2012.igem.org/Team:Slovenia/TheSwitchControls'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/TheSwitchControls';" class="newtable"><tr class="newtable"><td class="newtable"><span>Controls</span></td><td class="newtable"><img style="margin-right:-81px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 	  </ul>
 	</li>
@@ Line 324: / Line 344: @@
 		 <li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsEscapeTag'><span>Escape tag</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsTermination'><span>Termination</span></a></li>
-		 <li><a href='https://2012.igem.org/Team:Slovenia/SafetyMechanismsMicrocapsuleDegradation'><span>Microcapsule degradation</span></a></li>
+     <li><a href="https://2012.igem.org/Team:Slovenia/SafetyMechanismsMicrocapsuleDegradation"><table  onclick="window.location = 'https://2012.igem.org/Team:Slovenia/SafetyMechanismsMicrocapsuleDegradation';" class="newtable"><tr class="newtable"><td class="newtable"><span>Microcapsule degradation</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 	  </ul>
 	</li>
@@ Line 332: / Line 352: @@
 		 <li><a href='https://2012.igem.org/Team:Slovenia/ImplementationHepatitisC'><span>Hepatitis C</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/ImplementationIschaemicHeartDisease'><span>Ischaemic heart disease</span></a></li>
+     <li><a href='https://2012.igem.org/Team:Slovenia/ImplementationImpact'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ImplementationImpact';" class="newtable"><tr class="newtable"><td class="newtable"><span>Impact</span></td><td class="newtable"><img style="margin-right:-86px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 	  </ul>
@@ Line 339: / Line 360: @@
 	  <ul>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/Modeling'><span>Overview</span></a></li>
-		 <li><a href='https://2012.igem.org/Team:Slovenia/ModelingPK'><span>Pharmacokinetics</span></a></li>
+     <li><a href='https://2012.igem.org/Team:Slovenia/ModelingPK'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ModelingPK';" class="newtable"><tr class="newtable"><td class="newtable"><span>Pharmacokinetics</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/ModelingMethods'><span>Modeling methods</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/ModelingMutualRepressorSwitch'><span>Mutual repressor switch</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/ModelingPositiveFeedbackLoopSwitch'><span>Positive feedback loop switch</span></a></li>
-		 <li><a href='https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel'><span>Quantitative and stability model</span></a></li>
+		 <li><a href='https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ModelingQuantitativeModel';" class="newtable"><tr class="newtable"><td class="newtable"><span>Experimental model</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
+     <li><a href='https://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulations'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/ModelingInteractiveSimulations';" class="newtable"><tr class="newtable"><td class="newtable"><span>Interactive simulations</span></td><td class="newtable"><img style="margin-right:-15px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 	  </ul>
 	</li>
@@ Line 354: / Line 376: @@
 	  <ul>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/Notebook'><span>Experimental methods</span></a></li>
-		 <li><a href='https://2012.igem.org/Team:Slovenia/NotebookLablog'><span>Lablog</span></a></li>
+     <li><a href='https://2012.igem.org/Team:Slovenia/NotebookLablog'><table onclick="window.location = 'https://2012.igem.org/Team:Slovenia/NotebookLablog';" class="newtable"><tr class="newtable"><td class="newtable"><span>Lablog</span></td><td class="newtable"><img style="margin-right:-90px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/NotebookLabSafety'><span>Lab safety</span></a></li>
 	  </ul>
@@ Line 363: / Line 385: @@
 		 <li><a href='https://2012.igem.org/Team:Slovenia/Society'><span>Human practice</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyScientists'><span>Scientists</span></a></li>
-		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyMedicalDoctors'><span>Medical doctors</span></a></li>
+		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyMedicalDoctors'><span>Physicians</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyEthics'><span>Ethics, safety and regulations</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyPatients'><span>Patients</span></a></li>
-		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyMedia'><span>Media and general public</span></a></li>
+		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyMedia'><span>Journalists and general public</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyOutreach'><span>Outreach</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/SocietyQuestionnaire'><span>Questionnaire</span></a></li>
@@ Line 377: / Line 399: @@
 		 <li><a href='https://2012.igem.org/Team:Slovenia/Team'><span>Team members</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/TeamAttributions'><span>Attributions</span></a></li>
+		 <li><a href='https://2012.igem.org/Team:Slovenia/TeamCollaborations'><table  onclick="window.location = 'https://2012.igem.org/Team:Slovenia/TeamCollaborations';" class="newtable"><tr class="newtable"><td class="newtable"><span>Collaborations</span></td><td class="newtable"><img style="margin-right:-20px;" width="25px" src="https://static.igem.org/mediawiki/2012/e/ee/Svn12_hp_new.png"></img></td></tr></table></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/TeamGallery'><span>Gallery</span></a></li>
 		 <li><a href='https://2012.igem.org/Team:Slovenia/TeamSponsors'><span>Sponsors</span></a></li>
@@ Line 384: / Line 407: @@
 	</div>
 <!-- end main menu -->
+</div>
-</div> <!-- end menu -->
 <div id="main">
+<!-- dummy link na bannerju -->
+<a href="https://2012.igem.org/Main_Page">
+<div id="dummy" style="background-color:transparent; position:absolute; left:870px; top:25px; width:115px; height:80px; z-index:100; opacity:0.0;">
+</div>
+</a>
 <br/>
-<h1>Experimental methods</h1>
+<h1><a name="naslov"></a>Experimental methods</h1>
+<p>
+<ul style="margin-left:15px;">
+<li><a href="#cloning">Cloning</a><br/></li>
+<li><a href="#cellcultures">Cell cultures</a></li>
+<li><a href="#inductionsystems">Induction systems</a></li>
+<li><a href="#effectors">Effectors</a></li>
+<li><a href="#microscopy">Microscopy</a></li>
+<li><a href="#flowcytometry">Flow cytometry</a></li>
+<li><a href="#microencapsulation">Microencapsulation</a></li>
+<li><a href="#proteindetection">Protein detection</a></li>
+</ul>
+</p>
@@ Line 396: / Line 438: @@
 <!-- figure 1 -->
 <p>
-<table class="normal" style="width:80%;">
+<table class="invisible" style="width:80%;">
-<tbody  class="normal">
+<tbody  class="invisible">
-<tr class="normal">
+<tr class="invisible">
-<td class="normal">
+<td class="invisible">
-<img style="float:left;" src="https://static.igem.org/mediawiki/2012/a/a7/SVN12_7_notebook_cloning.png"/>
+<!--<img style="float:left; margin-right:0px;" src="https://static.igem.org/mediawiki/2012/a/a7/SVN12_7_notebook_cloning.png"/>
 <img src="https://static.igem.org/mediawiki/2012/8/8e/SVN12_7_notebook_cell_cultures.png"/>
-<div style="clear:both"></div>
+<div style="clear:both"></div>-->
+<img src="https://static.igem.org/mediawiki/2012/2/2f/Svn12_methods_fig1.PNG"/>
 </td>
 </tr>
-<tr class="normal">
+<tr class="invisible">
-<td class="normal"><b>Figure 1.</b> Schematic presentation of methods used for cloning and culturing eukaryotic cells.
+<td class="invisible"><b>Figure 1.</b> Schematic presentation of methods used for cloning and culturing eukaryotic cells.
 </td>
 </tr>
@@ Line 419: / Line 462: @@
 <!-- figure 2 -->
 <p>
-<table class="normal" style="width:50%;">
+<table class="invisible" style="width:77%;">
-<tbody  class="normal">
+<tbody  class="invisible">
-<tr class="normal">
+<tr class="invisible">
-<td class="normal">
+<td style="width:50%" class="invisible"><img style="width:100%"  src="https://static.igem.org/mediawiki/2012/8/84/SVN12_7_notebook_switch.png"/></td>
-<img src="https://static.igem.org/mediawiki/2012/8/84/SVN12_7_notebook_switch.png"/><br/>
+<td style="width:50%" class="invisible"><img style="width:100%" src="https://static.igem.org/mediawiki/2012/e/e7/SVN12_7_notebook_safety_mech.png"/></td>
-<img src="https://static.igem.org/mediawiki/2012/e/e7/SVN12_7_notebook_safety_mech.png"/><br/>
+</tr>
-<img src="https://static.igem.org/mediawiki/2012/9/91/SVN12_7_notebook_encapsulation.png"/><br/>
+<tr>
-<img src="https://static.igem.org/mediawiki/2012/c/c8/SVN12_7_notebook_effectors.png"/>
+<td class="invisible"><img style="width:100%" src="https://static.igem.org/mediawiki/2012/9/91/SVN12_7_notebook_encapsulation.png"/></td>
-</td>
+<td class="invisible"><img style="width:100%" src="https://static.igem.org/mediawiki/2012/c/c8/SVN12_7_notebook_effectors.png"/></td>
 </tr>
-<tr class="normal">
-<td class="normal"><b>Figure 2.</b> Schematic presentation of methods used for characterizing the switch, safety mechanisms, microencapsulation and effectors.
-</td>
-</tr>
 </tbody>
 </table>
@@ Line 439: / Line 479: @@
-<h2>Cloning</h2>
+<table class="invisible" style="width:80%;">
+<tbody>
+<tr class="invisible">
+<td  class="invisible"><b>Figure 2.</b> Schematic presentation of methods used for characterizing the switch, safety mechanisms, microencapsulation and effectors.</td>
+</tr>
+</tbody>
+</table>
+<h2><a name="cloning"> Cloning </a></h2>
 <h3>Plasmid DNA isolation</h3>
-<b>A. MINI PREPs for analysis and sequencing</b>
+<p><b>MINI PREPs for analysis and sequencing</b></p>
 <ol>
-<li>A single colony was picked from a LB-agar plate or glycerol stock and inoculated 10 mL LB-medium with appropriate antibiotic for selection (100 mg/L ampicillin, 50 mg/L kanamycin, 35 mg/L chloramphenicol).</li>
+<li>A single colony was picked from a LB-agar plate or glycerol stock and inoculated in 10 mL of LB-medium with the appropriate antibiotic for selection (100 mg/L ampicillin, 50 mg/L kanamycin, 35 mg/L chloramphenicol). </li>
+<li>Bacteria were grown over night at 37 °C with agitation. </li>
-<li>Bacteria were grown over night at 37 °C while shaking.</li>
+<li>Plasmid DNA was isolated from 6-10 mL of over-night culture with GeneJET plasmid miniprep kit according to the manufacturer's protocol. </li>
-<li>Plasmid DNA was isolated from 2-6 mL of over-night culture with GeneJET plasmid miniprep kit according to manufacturer's protocol.</li>
+<li>Amounts ranging from 6-10 µg of plasmid DNA were obtained. </li>
-<li>Around 6-10 µg plasmid DNA was obtained.</li>
+<li>The purity and concentration of the isolated DNA was analysed using NanoDrop. </li>
-<li>Purity and amount of DNA was analysed using a NanoDrop.</li>
 </ol>
+</br>
 <h3>Fragment DNA isolation from agarose gel</h3>
-<b>A. AGAROSE ELECTROPHORESIS</b>
+<p><b>AGAROSE ELECTROPHORESIS</b></p>
 <ol>
-<li>A mixture of DNA fragments with different sizes were separated with agarose gel (0.7 and 2% agarose in 0.5x TAE buffer and 0.1 µg/ml ethidium bromide) at constant voltage of 100 V.</li>
+<li>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. </li>
-<li>UV light (λ = 254 nm) was used to visualize ethidium bromide intercalated into DNA.</li>
+<li>UV light (λ = 254 nm) was used to visualize DNA with intercalated ethidium bromide </li>
-<li>Position of DNA fragments are documented and cut out from agarose.</li>
 </ol>
-<br/>
+</br>
+<p><b>FRAGMENT ISOLATION from agarose gel </b></p>
-<b>B. FRAGMENT ISOLATION from agarose gel</b>
 <ol>
-<li>The band with the desired DNA fragment was excised from the gel, using a clean scalpel.</li>
+<li>The band with the desired DNA fragment was excised from the gel, using a clean scalpel. </li>
-<li>DNA was isolated from the gel slice with GeneJet Gel Extraction Kit according to manufacturers protocol.</li>
+<li>DNA was isolated from the gel slice with GeneJet Gel Extraction Kit according to the manufacturer’s protocol. </li>
-<li>Purity and amount of DNA was determined using a NanoDrop.</li>
+<li>Purity and amount of DNA was determined using NanoDrop. </li>
 </ol>
-<br/>
+</br>
 <h3>Restriction digest</h3>
 <ol>
-<li>Set up a restriction mixture:
+<li>To digest the desired DNA restriction reactions were prepared as follows: </li>
 <ul style="margin-left:15px;"> <b>for analysis of cloned DNA</b>
-           <li>1X optimized Restriction buffer (10X)</li>
+           <li>2µl of the appropriate restriction buffer (10X)</li>
-           <li>0.5 µL restriction enzyme (10 U/µL)</li>
+           <li>0.5 µL restriction enzyme</li>
            <li>Bring volume to 20 µL with nuclease-free water.</li>
@@ Line 482: / Line 524: @@
 <i>or</i>
 <ul style="margin-left:15px;"> <b>for isolation of specific DNA</b>
-           <li>1X optimized Restriction buffer 10X</li>
+           <li>2µl of the appropriate restriction buffer (10X)</li>
-           <li>up to 2 µL restriction enzyme 10 U/µL</li>
+           <li>up to 2 µL restriction enzyme </li>
            <li>Bring volume to 50 µL with nuclease-free water.</li>
 </ul>
 </li>
-<li>The sample was incubated at optimal temperature for the restriction enzyme(s)</li>
+<li>The sample was incubated at optimal temperature for the restriction enzymes.</li>
-<li> Analysis of fragmented DNA was done by gel electrophoreses (loading dye was added to the samples before loaded on a agarose gel)</li>
+<li>Analysis of fragmented DNA was done by gel electrophoreses. </li>
-<li>Results were documented with</li>
+<li>Desired DNA fragment was excised and purified using suitable DNA purification kit. </li>
-<li>Desired DNA fragment was excised and purified using suitable DNA purification kit.</li>
 </ol>
 <br/>
-<h3>PCR</h3>
+<h3>PCR reaction</h3>
-<b>A. PCR REACTION</b><br/>
+<p>AccuPrime and Phusion DNA polymerase were used for DNA amplification. Colony PCR was performed with Taq DNA polymerase. </p>
-AccuPrime and Phusion polymerase were used for DNA amplification. Colony PCR was preformed with Taq polymerase.
 <ol>
-<li>For Phusion polymerase: master mix contained
+<li>The master mix for reactions with Phusion  DNA polymerase contained:
 <ul style="margin-left:15px;">
            <li>DNA (1-10 ng)</li>
@@ Line 517: / Line 559: @@
 <li>
-vAccuPrime reaction contained:
+The master mix for reactions with AccuPrime DNA polymerase contained:
 <ul style="margin-left:15px;">
            <li>DNA (10 ng),</li>
@@ Line 532: / Line 574: @@
 <li>
-Taq polymerase mix contained:
+The master mix for reactions with Taq DNA polymerase contained:
 <ul style="margin-left:15px;">
           <li>both primers (0,4 pmol/µl),</li>
@@ Line 550: / Line 592: @@
 </li>
-<li>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.</li>
+<li>All temperature profiles were optimized according to manufacturer’s protocol,the melting temperature of primers, and the length of the desired PCR products. Reactions were performed in the Applied Biosystems Veriti 96 well thermal cycler. </li>
 </ol>
+</br>
-<br/>
+<p><b>PCR product purification</b>. Desired PCR products were purified by GeneJet Gel Extraction Kit according to the manufacturer's protocol. </p>
-<b>B. PCR product purification </b><br/>
+<p><b>DNA concentration. </b> An aliquot of the isolated DNA was analyzed using NanoDrop. </p>
-Desired PCR product was purified by GeneJet Gel Extraction Kit according to manufacturer's protocol.
+ <h3>Gibson assembly </h3>
+<p>Gibson assembly master mix was prepared according to the protocol published in Gibson et al., 2009. </p>
-<br/><br/>
-<b>DNA concentration.</b> An aliquot of DNA isolation was analyzed using a NanoDrop.
-<br/>
-<br/>
-<h3>Gibson Assembly</h3>
-Gibson assembly master mix was prepared as by Gibson at al., 2009.
 <ol>
-<li>50 ng of each PCR product were added to Gibson assembly master mix and incubated at 50 °C.</li>
+<li>50 ng of each PCR product was added to the Gibson assembly master mix and incubated at 50 °C 1h. </li>
-<li>After incubation, the transformation in bacteria was preformed.</li>
+<li>After incubation, the entire master mix volume was transformed into competent bacterial cells. </li>
 </ol>
+</br>
-<br/>
 <h3>Ligation</h3>
-T4 ligase joins the 5' phosphate and the 3'-hydroxyl groups of DNA.
+<p>T4 ligase ligates the 5' phosphate and the 3'-hydroxyl groups of DNA. </p>
 <ol>
-<li>Estimate the vector and insert concentrations and set molar ratio of insert to vector 3:1 (100-150ng Vector DNA).
+<li>Vector and insert concentrations were estimated and insert and vector fragments joined in a molar ratio of 3:1 (100-150ng Vector DNA). </li>
-</li>
+<li>A ligation mixture was prepared: </li>
-<li>Set up a ligation mixture:
 <br/>
 X ligase buffer (10X)
@@ Line 582: / Line 616: @@
 <br/>
            Bring volume to 10 or 20 µL with nuclease-free water.
-</li>
+</li></br>
-<li>Incubate sample for sticky-end ligation reactions at room temperature for 3 hours (or at 4 to 8 °C, overnight).
+<i>or</i>
-<br/>
-          <i>or</i>
+<li>Blunt-end ligation reactions were incubated at 17 °C for 4 to 18 hours. </li>
-<br/>Incubate blunt-end ligation reactions at 17 °C for 4 to 18 hours.
+<li>After incubation part of the ligation mixture was used for the transformation of bacterial cells (see: transformation of bacteria). </li>
-</li>
-<li>After incubation part of the ligation mixture is used for transformation of bacterial cells (see: transformation of bacteria)</li>
 </ol>
+</br>
+<h3> Culturing bacteria</h3>
+<p>For plasmid DNA propagation two bacterial strains were used: <b>DH5alpha</b> [<i>fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80 Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17</i>] and <b>TOP10</b> [<i>mcrA, Δ(mrr-hsdRMS-mcrBC), Phi80lacZ(del)M15, ΔlacX74, deoR, recA1, araD139, Δ(ara-leu)7697, galU, galK, rpsL(SmR), endA1,nupG</i>]. </p>
+<p><b> Growth media for bacteria</b></p>
+<p><b> Luria Broth (LB) </b>: 10 g/L tryptone,    5 g/L yeast extract,    10 g/L NaCl,    media is supplemented with suitable antibiotics depending on the selection marker on the transfected plasmid: ampicilin 100 mg/L or kanamycin 50 mg/L.<p>
+<p><b> LB agar plates</b>: LB with 1.5% agar, media is supplemented with suitable antibiotics depending on the selection marker on the transfected plasmid.</p>
+</br>
-<br/>
+ <h3>Transformation of bacteria</h3>
-<h3>Culturing clones</h3>
+<p>  E. coli DH5alpha and TOP10 competent cells were used for the propagation of plasmid DNA. </p>
-<b>A. BACTERIA</b><br/>
-For plasmid DNA propagation two bacterial strains were used: <b>DH5alpha</b> [fhuA2Δ(argF-lacZ)U169 phoA glnV44 Φ80 Δ(lacZ)M15 gyrA96 recA1 relA1 endA1 thi-1 hsdR17] and <b>TOP10</b> [mcrA, Δ(mrr-hsdRMS-mcrBC), Phi80lacZ(del)M15, ΔlacX74, deoR, recA1, araD139, Δ(ara-leu)7697, galU, galK, rpsL(SmR), endA1,nupG].
-<br/>
-<br/>
-<b>B. GROWTH MEDIA for BACTERIA</b><br/>
-<b>Luria Broth (LB)</b>
-<ul style="margin-left:15px;">
-   <li>10 g/L tryptone</li>
-   <li>5 g/L yeast extract</li>
-   <li>10 g/L NaCl</li>
-   <li>media is supplemented with suitable antibiotics depending on selection marker on transfected plasmid: ampicilin 100 mg/L or kanamycin 50 mg/L</li>
-</ul>
-<b>LB agar plates</b><br/>
-<ul style="margin-left:15px;">
-   <li>LB with 1.5% agar</li>
-   <li>media is supplemented with suitable antibiotics depending on selection marker on transfected plasmid</li>
-</ul>
-<br/>
-<h3>Transformation of bacteria</h3>
-For enrichment of vectors E. coli DH5alpha and TOP10 were used.
 <ol>
-<li>100 µL of competent cells were thawed on ice.</li>
+<li>100 µL of competent cells were thawed on ice. </li>
+<li>50 – 400 ng DNA solution was added to competent bacterial cells (depending on the concentration of the DNA solution). </li>
-<li>50 – 400 ng DNA solution was added to competent bacterial cells (depending on the concentration of the DNA solution).</li>
+<li>A mixture of cells and DNA solution was incubated on ice for 30-60 minutes. </li>
+<li>The mixture was heat-shocked for 3 minutes at 42 °C. </li>
-<li>A mixture of cells and DNA solution was incubated on ice for 30-60 minutes.</li>
+<li>Cooled for 3 minutes on ice. </li>
+<li> 500 µL  of preheated antibiotic free LB-medium was added and incubated for one hour at 37 °C with agitation for the purpose of inducing antibiotic resistance. </li>
-<li>Than the mixture was heat-shocked for 45 seconds at 42 °C.</li>
+<li>The selection for plasmid containing and therefore antibiotic resistant bacteria was conducted by plating them on antibiotic containing LB-agar plates. </li>
-<li>Cooled down for 3 minute on ice.</li>
-<li>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.</li>
-<li>The selection for plasmid containing and therefore antibiotic resistant bacteria was conducted by plating them on antibiotic containing LB-agar plates.</li>
 </ol>
+</br>
+ <h3>Glycerol stock for long term storage of bacteria</h3>
-<br/>
-<h3>Glycerol stock for long term storage of bacteria</h3>
 <ol>
-<li>1 mL of an overnight culture was added to 150 µL of 80% glycerol into a cryo-tube.</li>
+<li>1 mL of an overnight culture was added to 150 µL of 80% glycerol into a cryo-tube. </li>
+<li>Mixed and incubated at room temperature for 30 minutes. </li>
-<li>Mixed and incubated at room temperature for 30 min.</li>
+<li>Afterwards the glycerol stock was stored at -80 °C. </li>
-<li>Afterwards the glycerol stock was stored at -80 °C.</li>
 </ol>
+<br/>
+ <h2><a name="cellcultures"> Cell cultures </a></h2>
-<!-- ------------------------------------------------------------------- -->
-<br/>
-<h2>Cell cultures</h2>
 <h3>Eucaryotic cell lines and cultivation</h3>
-<p><b>HEK293</b> 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.
+<p><b>HEK293</b> 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. </p>
-</p><p>
+<p><b>HEK293T</b> cell line is derived from 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. </p>
-<b>HEK293T</b> 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.
+<p><b>NK-92</b> 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.</p>
-</p><p>
+</br>
-<b>NK-92</b> 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.
-</p>
+<h3>Subculturing monolayer cell cultures</h3>
-<br/>
-<h3>Cultivation</h3>
-<b>A. SUBCULTURING MONOLAYER CELL CULTURES</b>
 <ol>
-<li>Remove and discard culture medium from a T-75 flask containing a monolayer of HEK293 or HEK293T cells.</li>
+<li>Remove and discard culture medium from a T-75 flask containing a monolayer of HEK293 or HEK293T cells. </li>
+<li>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. </li>
-<li>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.</li>
+<li>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 minutes. </li>
+<li>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. </li>
-<li>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.</li>
+<li>Transfer the cell suspension to a 15 ml centrifuge tube. </li>
+<li>Centrifuge the cell suspension for 5 minutes at 1200 rpm. </li>
-<li>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.</li>
+<li>Remove the trypsin-containing medium from the centrifuge tube. </li>
+<li>Resuspend the cell pellet in fresh medium. </li>
-<li>Transfer the cell suspension to a 15 ml centrifuge tube.</li>
+<li>Take as much cells as you need and add fresh medium to a total volume of 10 ml. </li>
+<li>Return the cells in a T-75 flask to the incubator (37 °C, 5 % CO2). </li>
-<li>Centrifuge the cell suspension for 5 min at 1200 rpm.</li>
-<li>Remove the trypsin-containing medium from the centrifuge tube.</li>
-<li>Resuspend the cell pellet in fresh medium.</li>
-<li>Take as much cells as you need and add fresh medium to a total volume of 10 ml.</li>
-<li>Return the cells in a T-75 flask to the incubator (37 °C, 5 % CO2).</li>
 </ol>
+</br>
+<h3>Cell plating</h3>
-<br/>
-<b>B. CELL PLATING</b>
 <ol>
-<li>Count cells.</li>
+<li>Count cells. </li>
+<li>Calculate the desired number of cells per well. Dilute cells in DMEM with 10% FBS. </li>
-<li>Calculate the desired number of cells per well. Dilute cells in DMEM with 10% FBS.</li>
+<li>Transfer the cells into an appropriate plate and place in a cell culture incubator. </li>
-<li>Transfer the cells into an appropriate plate and place in a cell culture incubator.</li>
 </ol>
 <br/>
-<b>MEDIA and BUFFERS</b>
+<p><b>Media and buffers</b>
 <br/>
-<b>DMEM</b> supplemented with
+<br><b>DMEM</b> supplemented with:    1 % L-Glutamine (GlutaMax),    10 % FBS,    Optionally: 1% Pen/Strep.
-<ul style="margin-left:15px">
+<br><b>RPMI</b> supplemented with:    1 % L-Glutamine (GlutaMax),    20 % FBS.</p>
-    <li>1 % L-Glutamine (GlutaMax)</li>
-    <li>10 % FBS</li>
-    <li>Optionally: 1% Pen/Strep</li>
-</ul>
-<br/>
-<b>RPMI</b>   supplemented with
-<ul style="margin-left:15px">
-    <li>1 % L-Glutamine (GlutaMax)</li>
-    <li>20 % FBS</li>
-</ul>
 <br/>
 <h3>Transfection</h3>
@@ Line 769: / Line 739: @@
 </tbody>
 </table>
 <ol>
-<li>Dilute plasmid DNA to desired concentration in 150 mM NaCl, vortex gently and spin down briefly.</li>
+<li>Dilute plasmid DNA to desired concentration in 150 mM NaCl, vortex gently and spin down briefly.  </li>
+<li>Dilute jetPEI (PolyPlus) in 150mM NaCl, vortex gently and spin down briefly. </li>
+<li>Add the jetPEI solution to the DNA solution. </li>
+<li>Vortex the solution immediately and spin down briefly. </li>
+<li>Incubate for 15 to 30 minutes at room temperature. </li>
+<li>Add the jetPEI/DNA mix to the cells in and gently swirl the plate. </li>
+<li>Return the plate to a cell culture incubator. </li>
+</ol>
-<li>Dilute jetPEI (PolyPlus) in 150mM NaCl, vortex gently and spin down briefly.</li>
-<li>Add the jetPEI solution to the DNA solution.</li>
+<br/>
-<li>Vortex the solution immediately and spin down briefly.</li>
+<h2><a name="inductionsystems"> Induction systems </a></h2>
-<li>Incubate for 15 to 30 minutes at room temperature.</li>
+<h3>Induction systems</h3>
+<p>To control our switch we needed a way to affect it from the outside. For this purpose we chose several inducible transcription systems where the controlled gene is expressed when a small molecule inducer (such as tetracycline) is present and is not expressed when the inducer is absent. We chose specific systems which do not cross react and whose inducers are orally bioavailable and safe for human use (Clackson, 2000). We decided for the systems based on tetracycline, pristinamycin, erythromycin and rapamycin analogs, as inducers. We then adapted these systems by cloning TAL regulators under their control to make them compatible with our genetic circuits. </p>
+<h3>Tetracycline, erythromycin and pristinamycin systems</h3>
+<p>The tetracycline, erythromycin and pristinamycin system all function in a similar manner. They are composed of a DNA binding protein (such as TetR) fused to a KRAB domain which reversibly binds a specific DNA sequence (TRE for example) and silences transcription from nearby promoters. The addition of an inducer causes the DNA binding domain to dissociate from the DNA and allows transcription to start. (Deuschle et al., 1995; Kramer et al., 2004) </p>
+<img src="https://static.igem.org/mediawiki/2012/c/c4/Svn12_parts_inducibilni.png"></img>
+<center><p><b> Figure 1: Induced expression of TAL</b>.</p></center>
+ <p>TABLE</p>
-<li>Add the jetPEI/DNA mix to the cells in and gently swirl the plate.</li>
-<li>Return the plate to a cell culture incubator.</li>
+<!-- table -->
-</ol>
+<table class="normal" style="font-size:90%; width:90%; text-align:center;">
+<thead class="normal">
+<tr class="normal">
+<th> System </th>
+<th> Tetracycline </th>
+<th> Erythromycin</th>
-<!-- ------------------------------------------------------------ -->
+<th> Pristinamycin </th>
-<br/>
-<h2>Induction systems</h2>
-The induction systems are described <a href="https://2012.igem.org/Team:Slovenia/Parts">here</a>.
-<br/>
+</tr>
-<h3>Induction of cells</h3>
+</thead>
-<ol>
-<li>Transfect HEK293 or HEK293T cells with plasmids using JetPei transfection reagent (Polyplus transfection), following the manufacturers protocol (see cell culturing for details).</li>
-<li>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).</li>
-<li>After 2-3 days of incubation, replace cell medium with fresh medium and stimulate again appropriately.</li>
+<tbody  class="normal">
-</ol>
+		<tr class="normal"><td class="normal"> Regulating protein </td>
+                                   <td class="normal"> TetR:KRAB </td>
+                                   <td class="normal"> E:KRAB </td>
+                                   <td class="normal"> PIP:KRAB </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> DNA sequence </td>
+                                   <td class="normal"> TRE </td>
+                                   <td class="normal"> ETR </td>
+                                   <td class="normal"> PIR </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> Inducer </td>
+                                   <td class="normal"> Tetracycline or doxycycline </td>
+                                   <td class="normal"> Erythromycin </td>
+                                   <td class="normal"> Pristinamycin </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> Constructs </td>
+                                   <td class="normal"> pCMV_TRE_TAL-A:KRAB </td>
+                                   <td class="normal"> pCMV_ETR_TAL-A:KRAB </td>
+                                   <td class="normal"> pCMV_PIR_TAL-B:KRAB </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> </td>
+                                   <td class="normal"> pCMV_TRE_TAL-B:VP16</td>
+                                   <td class="normal"> pCMV_ETR_TAL-B:VP16</td>
+                                   <td class="normal"> pCMV_PIR_TAL-A:VP16</td>
+                  </tr>
+		<tr class="normal"><td class="normal"> </td>
+                                   <td class="normal"> TRE_CMV_TAL-A:KRAB</td>
+                                   <td class="normal"> pCMV_ETR_TAL-B:KRAB</td>
+                                   <td class="normal"> pSV40_PIR_TAL-B:KRAB</td>
+                  </tr>
+		<tr class="normal">
+				<td class="normal">  </td>
+				<td class="normal"> TRE_CMV_PEST-CL1:TAL-A:KRAB</td>
+                                   <td class="normal"> pCMV_ETR_TAL-A:VP16</td>
+                                   <td class="normal"> PIR_CMV_TAL-B:KRAB </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> </td>
+                                   <td class="normal">TRE_CMV_TAL-B:VP16 </td>
+                                   <td class="normal">pSV40_ETR_TAL-B:KRAB  </td>
+                                   <td class="normal">PIR_CMV_PEST-CL1:TAL-B:KRAB</td>
+                  </tr>
+		<tr class="normal"><td class="normal"> </td>
+                                   <td class="normal">TRE_CMV_PEST-CL1:TAL-B:VP16 </td>
+                                   <td class="normal">ETR_CMV_TAL-A:KRAB  </td>
+                                   <td class="normal"> TRE_CMV_TAL-A:VP16 </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> </td>
+                                   <td class="normal"> </td>
+                                   <td class="normal"> ETR_CMV_PEST-CL1:TAL-A:KRAB </td>
+                                   <td class="normal"> TRE_CMV_PEST-CL1:TAL-A:VP16</td>
+                  </tr>
+                 <tr class="normal"><td class="normal"> </td>
+                                   <td class="normal"> </td>
+                                   <td class="normal"> ETR_CMV_TAL-B:VP16 </td>
+                                   <td class="normal">  </td>
+                  </tr>
+                 <tr class="normal"><td class="normal"> </td>
+                                   <td class="normal"> </td>
+                                   <td class="normal">  ETR_CMV_PEST-CL1:TAL-B:VP16</td>
+                                   <td class="normal">  </td>
+                  </tr>
+</tbody>
+</table>
+<h3>Rapamycin system</h3>
+<p>In the rapamycin system the gene of interest is under the control of a minimal promoter. The gene's transcription rate is regulated by two proteins that consist of a drug binding domain and either a DNA binding domain or an activation domain. When rapamycin is added both drug binding domains bind to it, consequently joining the activation domain with the DNA binding domain, resulting in a functional transcription factor, which activates the gene of interest. Instead of rapamycin a rapamycin analogue (rapalogue), which is a 1000-fold less imunosupressive than rapamycin, but activates the inducible system like rapamycin, is usually used as the inducer. (Pollock et al., 2002) </p>
+ <!-- table -->
+<table class="normal" style="font-size:90%; width:90%; text-align:center;">
+<thead class="normal">
+<tr class="normal">
+<th> Regulating vector </th>
+<th> HetAct </th>
+</tr>
+</thead>
+<tbody  class="normal">
+		<tr class="normal"><td class="normal"> DNA sequence </td>
+                                   <td class="normal"> ZFHD </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> Constructs </td>
+                                   <td class="normal"> ZFHD_pMIN_TAL-A:KRAB </td>
+                  </tr>
+		<tr class="normal"><td class="normal"> </td>
+                                   <td class="normal"> ZFHD_pMIN_TAL-B:VP16</td>
+                  </tr>
+</tbody>
+</table>
+</br>
+<h3>Induction of cells</h3>
+<ol>
+<li>Transfect HEK293 or HEK293T cells with plasmids using JetPei transfection reagent (Polyplus transfection), following the manufacturers protocol (see cell culturing for details). </li>
+<li>Two hours post transfection change media and stimulate the cells by adding dilutions of appropriate inductors to the medium in a 1:10 (v:v). </li>
+</ol>
+</br>
 <table class="normal" style="font-size:90%; width:90%; text-align:center;">
@@ Line 816: / Line 929: @@
 </thead>
 <tbody  class="normal">
-		<tr class="normal"><td class="normal">Rapalogue (AP21967</td>
+		<tr class="normal"><td class="normal">Rapalogue (AP21967)</td>
                                     <td class="normal">1 mM (100% ethanol)</td>
                                     <td class="normal">10 µM (1% ethanol)</td>
@@ Line 845: / Line 958: @@
 <!-- ----------------------------------------------------------------- -->
-<br/>
+</br><br/>
-<h2>Effectors</h2>
-<h3>Biological assay</h3>
-<b>DETECTION OF THE ACTIVITY OF ANAKINRA, produced in HEK293T cells</b>
+<h2><a name="effectors"> Effectors </a></h2>
+<h3>Biological assay-anakinra </h3>
 <ol>
-<li>HEK293T cells, seeded in 6-well plate, were transfected with anakinra downstream of constitutive promoter.</li>
+<li>HEK293T cells, seeded in 6-well plate, were transfected with anakinra downstream of constitutive promoter. </li>
+<li>Transfected cells were incubated for 48 h. </li>
-<li>Transfected cells were incubated for 48 h.</li>
+<li>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 a receptor gene was notneeded. </li>
+<li>After 24 h, the medium was removed from cells transfected with reporter plasmids and 90 μL of anakinra-producing cells' supernatant was added to these wells. </li>
-<li>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.</li>
+<li>After 24 h of stimulation, cells were lysed and NF-κB activation was assessed using dual luciferase assay. </li>
-<li>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.</li>
-<li>After 24 h of stimulation, cells were lysed and NF-κB activation was assessed using dual luciferase assay.</li>
 </ol>
+</br>
-<br/>
+<h3> Biological assay-IFN-alpha </h3>
-<b>DETECTION OF IFN-ALPHA, produced in HEK293T cells</b>
 <ol>
-<li>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.</li>
+<li>HEK293T cells transfected with eithera  plasmid encoding IFN-alpha under the control of a constitutive promoter or an empty vector, and HEK293T cells transfected with the reporter vector were co-cultivated . </li>
+<li>Additionally, we performed a co-transfection experiment, where HEK293T cells were transfected with both the reporter and the IFN-alpha encoding plasmids. </li>
-<li>Additionally, we performed a co-transfection experiment, where HEK293T cells were transfected with both the reporter and the IFN-alpha encoding plasmids.</li>
+<li>Day after transcfection cells were cultivated into 96-well plate at density 5x104 cells per well.</li>
+<li>After 24 hours of incubation, dual luciferase reporter assay was performed. </li>
-<li>Day after transcfection cells were cultivated into 96-well plate at density 5x104 cells per well</li>
-<li>After 24 hours of incubation, dual luciferase reporter assay was preformed.</li>
 </ol>
+</br>
+<h3>ELISA for IFN-alpha</h3>
-<br/>
-<b>ELISA for IFN-alpha</b>
 <ol>
-<li>
+<li>HEK293T cells where plated on 6 well plates and transfected with a plasmid coding for human IFN-alpha under the control of a constitutive promoter or a control plasmid (pcDNA3). </li>
-HEK293T cells where plated on 6 well plates and transfected with a plasmid coding for human IFN-alpha or a control plasmid (pcDNA3).</li>
+<li>Supernatants were collected after 16h and serial dilutions were measured for IFN-alpha levels by Human IFN-alpha Instant Elisa (eBioscience). </li>
-<li>Supernatants were collected after 16h and serial dilutions were measured for IFN-alpha levels by Human IFN-alpha Instant Elisa (eBioscience).</li>
 </ol>
+</br>
+<h3>Plate reader-fluorescence(The Switch) </h3>
-<br/>
-<b>PLATE READER-FLUORESCENCE (The Switch)</b>
 <ol>
-<li>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.</li>
+<li>HEK293T cells were seeded in black 96-well plates and transfected with plasmids encoding the switch. Plasmids and amounts used for transfection are listed in Figure legends. </li>
+<li>Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends. </li>
-<li>Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.</li>
+<li>Media supplemented with inducer or without inducer were changed after two  or three days of cultivation. </li>
+<li>After a maximum of 6 days after transfection,  cells were lysed with 25 µL of 1x Passive lysis buffer (Promega ) per well. </li>
-<li>Media supplemented with inducer or without inducer were changed after two days cultivation.</li>
+<li>Fluorescence was measured using an automated plate reader. </li>
-<li>2 days after inductions and then 3 days after second media change cells were lysed with 25 µL of 1x Passive lysis buffer (Promega).</li>
-<li>Fluorescence was then measured using an automated plate reader.</li>
 </ol>
+</br>
+<h3>Plate reader-luminescence  (The Switch) </h3>
-<br/>
-<b>PLATE READER-LUMINESCENCE (The Switch)</b>
 <ol>
-<li>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.</li>
+<li>HEK293T cells were seeded in white 96-well plates and transfected with plasmids encoding the switch. Plasmids and amounts used for transfection are listed in Figure legends. </li>
+<li>Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends. </li>
-<li>Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.</li>
+<li>Media supplemented with inducer or without inducer were changed after two to three days of cultivation. </li>
+<li>After a maximum of 6 days after transfection, cells were lysed with 25 µL of 1x Passive lysis buffer (Promega). </li>
-<li>Media supplemented with inducer or without inducer were changed after two days cultivation.</li>
+<li>Luminescence of expressed reporter firefly luciferase was 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 coelenterazine. </li>
-<li>2 days after inductions and then 3 days after second media change cells were lysed with 25 µL of 1x Passive lysis buffer (Promega).</li>
-<li>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.</li>
 </ol>
+</br>
-<!-- -------------------------------------------------------- -->
+<h3>Plate reader-absorbance  (The Switch) </h3>
-<br/>
-<h2>Microscopy</h2>
-For spatial and temporal imaging of samples a Leica TCS SP5 laser scanning microscope mounted on a Leica DMI 6000 CS inverted microscope (Leica Microsystems, Germany) with a 10× and 20× dry objective and an HCX plan apo 63× oil (NA 1.4) oil immersion objective was used. For image analysis we used the ImageJ (Image Processing and Analysis in Java) software (<a href="http://rsbweb.nih.gov/ij/">http://rsbweb.nih.gov/ij/</a>) measuring the mean grey values of each cell containing the promoter of interest.
-<br/>
-<h3>Microscopy-cell viability with Hoechst and SytoxGreen514 (Safety mechanisms)</h3>
-<b>Hoechst</b> dye is membrane permeable dye and stains all cells in a culture. On the other hand a <b>SytoxGreen514</b> dye is membrane impermeable dye staining only dead cells. Both dyes blue fluorescent Hoechst and green fluorescent binds SytoxGreen514 bind to nucleic acids to fluoresce.
 <ol>
-<li>HEK293 cells were seeded in an 8-well microscope chamber and transfected with 100 ng CMV-mGMK_TK30 (pPCMV-mGMK_TK30).</li>
+<li>HEK293T cells were seeded in white 24-well plates and transfected with plasmids encoding the positive feedback loop switch and 10x[TALB + TALC] operator_CMV promoter_fLuciferase reporter plasmid and 10x[TALA + TALC]operator_CMV promoter_SEAP plasmid. Plasmids and amounts used for transfection are listed in Figure legends.</li>
+<li>Media supplemented with inducer or without inducer were changed after two days of cultivation.</li>
+<li>Two and seven days after transfection the growth medium was collected and SEAP QUANTIBlue substrate was added. After 15 minutes incubation at 37°C  the absorbance was measured at 630 nm. </li>
+</ol>
+</br>
-<li>Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures.</li>
-<li>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.</li>
-<li>Cells were incubated for approximately 10 minutes in dark at 37 °C before being imaged.</li>
+<h2><a name="microscopy"> Microscopy </a></h2>
+<p>For spatial and temporal imaging of samples a Leica TCS SP5 laser scanning microscope mounted on a Leica DMI 6000 CS inverted microscope (Leica Microsystems, Germany) with a 10× and 20× dry objective and an HCX plan apo 63× oil (NA 1.4) oil immersion objective was used. For image analysis we used ImageJ (Image Processing and Analysis in Java) software (http://rsbweb.nih.gov/ij/) measuring the mean grey values of each cell containing the promoter of interest. </p>
+</br>
-<li>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.</li>
+<h3>Microscopy-cell viability with Hoechst and SytoxGreen514 (Safety mechanisms) </h3>
+<p><b>Hoechst</b> dye is a membrane permeable dye and stains all cells in a culture. On the other hand a <b>SytoxGreen514</b> dye is a membrane impermeable dye staining only dead cells. Both dyes, blue fluorescent Hoechst and green fluorescent SytoxGreen514, bind to nucleic acids causing emission of fluorescent light. </p>
+<ol>
+<li>HEK293 cells were seeded in an 8-well microscope chamber and transfected with 200 ng CMV-mGMK_TK30 (pPCMV_mGMK:TK30). </li>
+<li>Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures. </li>
+<li>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 live and dead cells. </li>
+<li>Cells were incubated for approximately 10 minutes in the dark at 37 °C before imaging. </li>
+<li>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 nm and 514 nm were captured. Fluorescence emission was detected at 450-500 nm and 520-560 nm for Hoechst and SytoxGreen respectively. </li>
 </ol>
+</br>
+<h3>Microscopy-cell growth (Safety mechanisms) </h3>
-<br/>
-<h3>Microscopy-cell growth (Safety mechanisms)</h3>
 <ol>
-<li>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).</li>
+<li>HEK293 cells were seeded in an 8-well microscope chamber and transfected with 100 ng mGMK:TK30 (pPCMV_mGMK:TK30) and/or 20 ng GFP (pPCMV-GFP) (for transfection control). </li>
+<li>Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures. </li>
-<li>Ganciclovir (GCV) in concentrations 0, 10 and 100 μg/mL was added to the cell cultures.</li>
+<li>After 5 days of cultivation, a cell cultures were imaged. </li>
+<li>A 514-nm line of 25 mW multi ion argon laser was used to excite GFP reporter protein. Fluorescence emission was detected at 520-560 nm for GFP. Bright field images were used to visualize the number of cells. </li>
-<li>After 5 days of cultivation, a cell cultures were imaged.</li>
-<li>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.</li>
 </ol>
+</br>
-<br/>
+<h3>Microscopy-cell count (Safety mechanisms) </h3>
-<h3>Microscopy-cell count (Safety mechanisms)</h3>
 <ol>
-<li>HEK293 cells were seeded in 12-well plates and transfected with and transfected with 100 ng CMV-mGMK_TK30 (pPCMV-mGMK_TK30).</li>
+<li>HEK293 cells were seeded in 12-well plates and transfected with different amounts of mGMK:TK30 (pPCMV_mGMK:TK30) as indicated in Figure legend. </li>
+<li>Cell cultures were treated with ganciclovir (GCV) in concentrations as indicated in the Figure legend. </li>
-<li>Cell cultures were treated with ganciclovir (GCV) in concentrations as indicated in figure legend.</li>
+<li>After incubation the cells were resuspended by pipetting. </li>
+<li>Cells suspensions were then mixed with trypan blue. </li>
-<li>After incubation the cells were resuspended by pipetting.</li>
+<li>Viable cell number was determined by counting the cells under a light microscope using a Bürker-Türk counting chamber. </li>
-<li>Cells suspension was then mixed with trypan blue.</li>
-<li>Viable cell number was determined by counting the cells under a light microscope using Bürker-Türk counting chamber.</li>
 </ol>
+</br>
-<br/>
+<h3>Microscopy-detection of reporter proteins (The Switch) </h3>
-<h3>Microscopy-detection of reporter proteins (The Switch)</h3>
+<p>Fluorescent proteins were used as reporters in "The switch experiments". The fluorescent proteins used were blue (tagBFP), yellow (mCitrine), orange (mCherry) and red (mNeptun) fluorescent proteins. mCherry was used as transfection control while the others were used as reporters of "the switch".</p>
-<p>
-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".
-</p>
 <ol>
-<li>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.</li>
+<li>HEK293T cells were seeded in an 8-well microscope chamber or 12-well plate and transfected with plasmids encoding the switch. Plasmids and amounts used for transfection are listed in Figure legends. </li>
+<li>Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends. </li>
-<li>Two hours after transfection, media was changed and cells were stimulated with inducers. Inducers and their concentration are described in Figure legends.</li>
+<li>Media supplemented with inducer or without inducer were changed after two or three days of cultivation. </li>
+<li>Images of cells expressing reporters were taken two days after transfection and then each day for 5 days. </li>
-<li>Media supplemented with inducer or without inducer were changed after two days cultivation.</li>
+<li>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 one set of experiments 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. </li>
-<li>Images of cells expressing reporters were taken two days after transfection and inducers addition and then each day for 5 days.</li>
-<li>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.</li>
 </ol>
+</br>
-<br/>
+<h3>Microscopy-alginate degradation (Microencapsulation) </h3>
-<h3>Microscopy-alginate degradation (Microencapsulation)</h3>
+<p>To observe the degradation of alginate beads, 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 the alginate beads, we can easily observe bead degradation upon addition of alginate lyase from Sphingobacterium multivorum (Sigma).</p>
-<p>
-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 <i>Sphingobacterium multivorum</i> (Sigma).</p>
 <ol>
-<li>Alginate beads suspended in culture medium were seeded into an 8-well microscope chamber (200 µL).</li>
+<li>Alginate beads suspended in culture medium were seeded in an 8-well microscope chamber (200 µL). </li>
+<li>20 µL of 1 mg/mL FITC-dextran were added into well. </li>
+<li>After the dye was evenly distributed throughout the suspension, 8 µL of Sphingobacterium multivorum alginate lyase were added. </li>
+<li>The microscope was set to capture images every 20 seconds. </li>
+<li>Screenshots were collected for at least 15 minutes. </li>
+<li>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. </li>
+</ol>
+</br>
-<li>20 µL of 1 mg/mL FITC-dextran were added into well.</li>
-<li>After the dye has been evenly distributed throughout the suspension, 8 µL of Sphingobacterium multivorum alginate lyase were added.</li>
+<h3>Microscopy-secreted alginate lyase enzymatic activity (Microencapsulation)</h3>
+<ol>
-<li>Microscope was set to capture images every 20 seconds.</li>
+<li>HEK293T cells were seeded 1×10<sup>6</sup> on 10 cm cell culture dish and grown in DMEM medium supplemented with 10 % FBS.</li>
+<li>After reaching 50 – 70 % confluency, cells were transfected with 15 μg of DNA per culture dish with jetPEI transfection reagent (Polyplus Transfection).</li>
-<li>Screenshots were collected for at least 15 minutes.</li>
+<li>Protein production lasted for 72 hours.</li>
+<li>Cell supernatants were collected and concentrated 50-times using Sartorius Vivaspin 6 concentrators (5 kDa MWCO PES).</li>
-<li>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.</li>
+<li>Alginate beads were produced with Büchi BIOTECH Encapsulator (see Microencapsulation: Encapsulation procedure 1.-6.).</li>
+<li>Beads were incubated with concentrated supernatants for 72 hours in an 8-well microscope chamber.</li>
+<li>20 µL of 1 mg/mL FITC-dextran were added into wells.</li>
+<li>A 488-nm line of 25 mW multi-ion argon laser was used for  FITC detection. Fluorescence emission was detected at 520-560 nm.</li>
+<li>Beads' diameters were assessed using Leica LAS Image Analysis software.</li>
 </ol>
+</br>
-<br/>
+<h3>Microscopy-encapsulated cell viability (Microencapsulation) </h3>
-<h3>Microscopy-encapsulated cells viability (Microencapsulation)</h3>
+<p>To observe encapsulated cells' viability, HEK 293T cells were stained with Hoechst and 7-aminoactinomycin D (7-AAD) viability stains. Hoechst stains both live and dead cells, while 7-AAD stains dead cells only.</p>
-<p>
-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.</p>
 <ol>
-<li>Encapsulated cells were grown in DMEM culture medium supplemented with 10% FBS.</li>
+<li>Encapsulated cells were grown in DMEM culture medium supplemented with 10% FBS. </li>
+<li>200 µL of the microcapsule suspension was collected and alginate-PLL capsules were seeded into an 8-well microscope chamber. </li>
-<li>200 µL of microcapsule suspension were collected and alginate-PLL capsules were seeded into an 8-well microscope chamber.</li>
+<li>5 µL of 7-AAD and 1 µL of Hoechst stain were added to one well. </li>
+<li>Encapsulated cells were protected from direct light and stained for 30 minutes at 37 °C. </li>
-<li>5 µL of 7-AAD and 1 µL of Hoechst stain were added into well.</li>
+<li>A 405-nm diode laser was used to excite Hoechst and a 543-nm line of HeNe laser was used to excite 7-AAD. </li>
+<li>Fluorescence emission was detected at 450-500 nm and 600-700 nm for Hoechst and 7-AAD respectively. </li>
-<li>Encapsulated cells were protected from direct light and stained for 30 min at 37 °C.</li>
-<li>Microscope chamber was transfered to Leica confocal microscope.</li>
-<li>A 405-nm diode laser was used to excite Hoechst and a 543-nm line of HeNe laser was used to excite 7-AAD.</li>
-<li>Fluorescence emission was detected at 450-500 nm and 600-700 nm for Hoechst and 7-AAD respectively.</li>
 </ol>
+</br>
-<!-- ------------------------------------------------------- -->
-<br/>
-<h2>Flow cytometry</h2>
-<p>
-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.
-</p>
-<h3>Flow cytometry - the annexin assay (Safety mechanisms)</h3>
+<h2><a name="flowcytometry"> Flow cytometry </a></h2>
-<p>
+<p>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 colors of fluorescence.</p>
-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.
+</br>
-</p>
+<h3>Flow cytometry - the annexin assay (Safety mechanisms) </h3>
+<p>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 labeled cells with Annexin V conjugated with phycoerythrin (PE). Annexin V is a Ca2+ dependent phospholipid-binding protein that has a high affinity for the phospholipid phosphatidylserine and therefore binds to apoptotic cells with  phosphatidylserine exposed on their surface.</p>
 <ol>
-<li>HEK293 cells were seeded in 12-well plates.</li>
+<li>HEK293 cells were seeded in 12-well plates. </li>
+<li>Cells were transfected with pCMV-mGMK_TK30 and treated with ganciclovir. Concentrations of ganciclovir and plasmids are indicated in Figure legends. </li>
-<li>Cells were transfected with pCMV-mGMK_TK30 and treated with ganciclovir. Concentrations of ganciclovir and plasmid are indicated in figure legends.</li>
+<li>After incubation the cells were washed with PBS buffer and resuspended by pipetting. </li>
+<li>Cells were pelleted with centrifugation at 1200 rpm. </li>
-<li>After incubation the cells were washed with PBS buffer and resuspended by pipetting.</li>
+<li>The cell pellet was washed in 1x Annexin Binding Buffer (10 mM HEPES, 140 mM NaCl, and 2.5 mM CaCl2, pH 7.4). </li>
+<li>The pellet was then resuspended in 1x Annexin Binding Buffer and PE-Annexin V (5 µl per 100 μl cell suspension) was added. </li>
-<li>Cells were pelleted with centrifugation at 1200 rpm.</li>
+<li>Samples were incubated for 20 minutes in the dark at room temperature and then immediately analyzed with a flow cytometer. </li>
+<li>Along with site and forward scatter, the signal in the FL2 channel  (540-580 nm) was also recorded. </li>
-<li>The cell pellet was washed in 1x Annexin Binding Buffer (10 mM HEPES, 140 mM NaCl, and 2.5 mM CaCl2, pH 7.4).</li>
-<li>The pellet was then resuspend in 1x Annexin Binding Buffer and PE-Annexin V (5 µl per 100 μl cell suspension) was added.</li>
-<li>Samples were incubated for 20 minutes in dark at room temperature and then immediately analyzed with the flow cytometer.</li>
-<li>Along with site and forward scatter also signal in FL2 channel (540-580 nm) was recorded.</li>
 </ol>
+</br>
+<h3>Flow cytometry - the propidium iodide assay (Safety mechanisms) </h3>
-<br/>
+<p>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 a membrane impermeant fluorescent molecule.</p>
-<h3>Flow cytometry - the propidium iodide assay (Safety mechanisms)</h3>
-<p>
-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.</p>
 <ol>
-<li>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.</li>
+<li>HEK293T cells seeded in 12-well plates were transfected with plasmids expressing MICA (pPCMV-MICA_pcDNA3).</li>
+<li>Two days after transfection with CMV-MICA_pcDNA3, cells were resuspended in PBS at final concentration 1x10<sup>6</sup> cells/mL, stained with CFSE (0,6μM) and incubated for 10 minutes at 37°C. Staining was quenched by the addition of 5 volumes of ice-cold culture media (RPMI+ 20% FBS) to the cells. After 5 minutes incubation on ice, cells were pelleted by centrifugation and then washed by resuspending the pellet in fresh media (RPMI+ 20% FBS) a further two times for a total of three washes. CFSE was used to discriminate between HEK293T and NK-92 cells or between NK target cells K562, which were used as a positive control, and NK-92 cells.</li>
-<li>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).</li>
+<li>HEK293T cells or K562 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).</li>
+<li>After incubation of HEK293T or K562 cells  with NK-92 cells, cells were treated with propidium iodide.</li>
-<li>After incubation of HEK293T with NK-92 cells, cells were treated with propidium iodide.</li>
+<li>Along with site and forward scatter the signal in the FL1 channel (530-580 nm) was also recorded.</li>
-<li>Along with site and forward scatter also signal in FL1 channel (530-580 nm) was recorded.</li>
 </ol>
+</br>
+<h3>Flow cytometry - detection of reporter proteins (The Switch) </h3>
-<br/>
+<p>Reporters such as fluorescent proteins were used to detect the expression of effectors in "The switch experiments". As reporters we used blue (tagBFP) and yellow (mCitrine) fluorescent proteins.</p>
-<h3>Flow cytometry - detection of reporter proteins (The Switch)</h3>
-<p>
-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.
-</p>
 <ol>
-<li>HEK293T cells were seeded in a 12 or 24-well plate and transfected with plasmids for the switch.</li>
+<li>HEK293T cells were seeded in a 12 or 24-well plate and transfected with plasmids encoding the switch. </li>
+<li>Two hours after transfection, media was changed and cells were stimulated with inducers. </li>
+<li>Medium with inducer or without the inducer was changed after two days of cultivation. </li>
+<li>Cells were collected at different time points (2 days after induction and then 3 days after the second media change). </li>
+<li>Cells were washed and resuspended in PBS buffer. </li>
+<li>A 405 nm diode laser was used to excite tagBFP and a 488-nm diode laser was used for mCitirne. </li>
+<li>Along with site and forward scatter signals in the FL1 (540-580 nm) channel (mCitrine) and the FL5 (450-480 nm) channel (tagBFP) were also recorded. </li>
+</ol>
+</br>
-<li>Two hours after transfection, media was changed and cells were stimulated with inducers.</li>
-<li>Medium with inducer or without the inducer was changed after two days of cultivation.</li>
-<li>Cells were collected at different time points (2 days after induction and than 3 days after second media change).</li>
-<li>Cells were washed and then resuspended in PBS buffer</li>
+<h2><a name="microencapsulation"> Microencapsulation </a></h2>
+<h3>Cell preparation for encapsulation</h3>
+<ol>
+<li>HEK 293T cells were seeded 5x10⁵ per 10 cm cell culture dish (3 per encapsulation) and grown in DMEM medium supplemented with 10 % FBS. </li>
+<li>After reaching 50 – 70 % confluency, cells were transfected with 15 μg of DNA per culture dish with jetPEI transfection reagent (Polyplus Transfection). </li>
+<li>The medium was removed the next day.. Transfected cells were detached using 3 mL of trypsin solution and centrifuged after the addition of fresh medium to inactivate the trypsin. </li>
+<li>Supernatant was removed and cells were resuspended in 15 mL DMEM with 10% FBS. </li>
+<li>Cells were counted using Countess automated cell counter (Invitrogen). </li>
+<li>HEK 293T cells were again centrifuged and supernatant was removed. </li>
+<li>Cells were resuspended in 2 mL of pre-warmed MOPS buffer. </li>
+<li>10 mL of pre-warmed alginate solution (1,5%) was added to cell suspension. </li>
+</ol>
+</br>
-<li>A 405 nm diode laser was used to excite tagBFP and a 488-nm diode laser was used for mCitirne.</li>
+<h3>Encapsulation</h3>
+<ol>
-<li>Along with site and forward scatter also signals in FL1 (540-580 nm) channel (mCitrine) and FL5 (450-480 nm) channel (tagBFP) were recorded.</li>
+<li>The encapsulator was equipped with a 200-µm nozzle. </li>
+<li>The reactor vessel was filled with 225 mL 100 mM CaCl2. </li>
+<li>Cell-alginate mixture was transferred to a 20 mL syringe with a Luer lock. </li>
+<li>The syringe was connected to the bead producing unit (BPU). </li>
+<li>Microcapsules were produced at a flow rate of 12-14 units, vibration frequency 1030-1100 Hz and voltage for bead dispersion 900-1300 V. </li>
+<li>Polymerization lasted for 10 minutes. </li>
+<li>The polymerization solution was drained and 75 mL of 0,05% poly-L-lysine (PLL) solution was added. </li>
+<li>Beads were incubated in PLL solution for 10 minutes. </li>
+<li>The PLL solution was removed and beads were washed twice (for 1 and for 5 minutes) with 150 mL of MOPS buffer. </li>
+<li>100 mL of 0,03% alginate was added and beads were incubated for 10 minutes. </li>
+<li>Alginate solution was drained and beads were washed once with 150 mL of MOPS buffer for 1 minute. </li>
+<li>150 mL of depolymerization solution was added for 10 minutes. </li>
+<li>Depolymerization solution was removed and capsules were resuspended in 150 mL MOPS and collected in a bead collection flask. </li>
+<li>MOPS was removed and microcapsules were transferred to T-75 with 10 mL DMEM, 10% FBS media supplemented with penicillin and streptomycin. </li>
 </ol>
-<!-- ------------------------------------- -->
 <br/>
-<h2>Microencapsulation</h2>
+<p><b>Buffers and solutions</b>
-<b>A. CELL PREPARATION FOR ENCAPSULATION</b>
+<br/>
-<ol>
+<br><b>10 mM MOPS buffer</b> (pH = 7,2)
-<li>HEK 293T cells were seeded 5x10⁵ per 10 cm cell culture dish (3 per encapsulation) and grown in DMEM medium supplemented with 10 % FBS.</li>
+<br><b>MOPS buffer with NaCl</b> (pH = 7,2):    10 mM MOPS,    0,85% NaCl
+<br><b>Polymerisation solution</b> (pH = 7,2):    10 mM MOPS,    100 mM CaCl2
+<br><b>Depolymerisation solution</b> (pH = 7,2):    10 mM MOPS,    50 mM Na3-citrate,    0,45% NaCl
+<br><b>0,05% poly-L-lysine</b> (15-30 kDa) in MOPS buffer (pH = 7,3)
+<br><b>0,03% alginate</b> in MOPS buffer (pH = 7,2)
+<br><b>1,5% alginate</b> (low viscosity) in MOPS buffer (pH = 7,2)</p>
+</br>
-<li>After reaching 50 – 70 % confluency, cells were transfected with 15 μg of DNA per culture dish with jetPEI transfection reagent (Polyplus Transfection).</li>
-<li>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.</li>
-<li>Supernatant was removed and cells were resuspended in 15 mL DMEM with 10% FBS.</li>
+<h2><a name="proteindetection"> Protein detection </a></h2>
+<h3>SDS-PAGE</h3>
-<li>Cells were counted using Countess automated cell counter (Invitrogen).</li>
+<ol>
+<li>Samples were loaded on a 12% acrylamide gel and ran at a constant voltage (200 V) for 1 h. </li>
-<li>HEK 293T cells were again centrifuged and supernatant was removed.</li>
+<li>Proteins were then blotted on a nitrocellulose membrane at a constant current (350 mA) for 1 h. </li>
+<li>The membrane was washed with MQ and PBS and blocked for 1,5 h by incubation in I-Block blocking reagent at room temperature. </li>
-<li>Cells were resuspended in 2 mL of pre-warmed MOPS buffer.</li>
-<li>10 mL of pre-warmed alginate solution (1,5%) was added to cell suspension.</li>
 </ol>
+</br>
+<h3>Immunodetection </h3>
-<br/>
-<b>B. ENCAPSULATION</b>
 <ol>
-<li>The encapsulator was equipped with a 200-µm nozzle.</li>
+<li>All proteins to be detected had a Myc tag at the C-terminus. </li>
+<li>The membrane was incubated with primary antibodies (rabbit anti-Myc diluted 1:500) overnight at 4 °C and 150 rpm. Membrane was washed. </li>
-<li>The reactor vessel was filled with 225 mL 100 mM CaCl2.</li>
+<li>Washing in wash buffer three times for 5 minutes each.</li>
+<li>Membrane was incubated with secondary antibodies (anti-rabbit secondary antibodies, conjugated with HRP, diluted 1:3000) for 45 minutes at room temperature and 150 rpm. </li>
-<li>Cell-alginate mixture was transferred into 20 mL syringe with a Luer lock.</li>
+<li>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. </li>
-<li>The syringe was connected to bead producing unit (BPU).</li>
-<li>Microcapsules were produced at flow rate of 12-14 units, vibration frequency 1030-1100 Hz and voltage for bead dispersion 900-1300 V.</li>
-<li>Polymerisation lasted for 10 min.</li>
-<li>The polymerisation solution was drained and 75 mL of 0,05% poly-L-lysine (PLL) solution was added.</li>
-<li>Beads were incubated in PLL solution for 10 minutes.</li>
-<li>The PLL solution was removed and beads were washed twice (for 1 and for 5 min) with 150 mL of MOPS buffer.</li>
-<li>100 mL of 0,03% alginate was added and beads were incubated for 10 min.</li>
-<li>Alginate solution was drained and beads were washed once with 150 mL of MOPS buffer for 1 min.</li>
-<li>150 mL of depolymerization solution was added for 10 min.</li>
-<li>Depolymerization solution was removed and capsules were resuspended in 150 mL MOPS and collected in bead collection flask.</li>
-<li>MOPS was removed and microcapsules were transferred to T-75 with 10 mL DMEM, 10% FBS media supplemented with penicillin and streptomycin.</li>
 </ol>
+<p><b>Buffers and solutions </b></p>
+<p><b>Wash buffer</b>:    1x PBS,    0,01% (v/v) Tween 20</p>
+</br>
+</p>
+<h2 style="color:grey;">References</h2>
+<p style="color:grey;">
+Clackson, T. (2000) Regulated gene expression systems. <i> Gene ther.</i> <b>7</b>, 120–125.<br/><br/>
+Deuschle, U., Meyer, W.K. and Thiesen, R. (1995) Tetracycline-reversible silencing of eukaryotic promoters. <i>Mol. Cell. Biol. </i> <b>15</b>, 1907–1914.<br/><br/>
+Kramer, B.P., Fischer, C. and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells. <i> Biotech. Bioeng.</i> <b>87</b>, 478–484.<br/><br/>
+Pollock, R. and Clackson, T. (2002) Dimerizer-regulated gene expression. <i> Curr. Opin. Biotech. </i> <b>13</b>, 459–467.<br/><br/>
+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. <i>Nature methods.</i> <b>6</b>, 343–345.
+</p>