The team meets for the first time.

The project is chosen - Bacto-Aid!.

The first project description is submitted to the advisors.

The project is presented for the advisors.

We learned to orientate in the "new" lab settings, and tried to perform basic experiments as a rehearsal. On the photo is Joel "learning" how to pipet.

The transformation is validated by cPCR.

The following program is used.

The protocol.

Ratio: 1:0, 1:2 and 1:5

The protocol.

The transformation is validated by cPCR.

The following program is used.

The protocol

This year the faculty of Biochemistry and Molecular Biology had a big workshop area with the theme “The Good, the Bad and the Ugly”: the probiotic bacteria, the pathogenic bacteria and the multiresistant bacteria.

See Protocol.

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we have done with the BioBrick K2018043 can be read in the protocol: Cloning Basic part K2018043 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we have done with the BioBrick K2018044 can be read in the protocol: Cloning Basic part K2018044 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we had done with the BioBrick K1763002 can be read in the protocol: Cloning Basic part K1763002 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we had done with the BioBrick K1763003 can be read in the protocol: Cloning Basic part K1763003 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we had done with the BioBrick K1763004 can be read in the protocol: Cloning Basic part K1763004 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we had done with the BioBrick K1763009 can be read in the protocol: Cloning Basic part K1763009 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we had done with the BioBrick K1763010 can be read in the protocol: Cloning Basic part K1763010 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we had done with the BioBrick K1763011 can be read in the protocol: Cloning Basic part K1763011 into pSB1C3

The brick was ordered from IDT and received: The received gblock had a weight of 200 ng. and was resuspended in dH2O. 5 µl diluted gblock and 95 µl ddH2O to make a 20X dilution.

What we had done with the BioBrick K1763012 can be read in the protocol: Cloning Basic part K1763012 into pSB1C3

The BioBircks are from the iGEM kit.

The protocol.

The protocol.

the ratio: 1:0, 1:2 and 1:5

J23104:K934001 (K2018038) and J23106:K934001 (K2018039)

The protocol.

The BioBrick was ordered from IDT in a plasmid pUCIDT-AMP and after receiving it, it was resuspended to a final concentration of 0.1 µg/µl.

After the resuspension, the plasmid was transformed into Top10 E. coli by following SOP0023_v01 Ca2+ Transformation , with the following remarks:

2.5 µl plasmid was used instead of the normal 1 µl.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The BioBrick is in an amp resistance plasmid.

The protocol

Thursday concert in Odense.

The BioBrick was ordered from IDT in a plasmid pUCIDT-AMP and after receiving it, it was resuspended to a final concentration of 0.1 µg/µl.

After the resuspension, the plasmid was transformed into Top10 E. coli by following SOP0023_v01 Ca2+ Transformation , with the following remarks:

2.5 µl plasmid was used instead of the normal 1 µl.

What we had done with the BioBrick K2018010 can be read in the protocols: Cloning composite part K2018010 into pSB1C3 and IMPACT Purification of K2018010

The BioBrick containing the gene K2018011 was digested with PstI and XbaI overnight by using SOP0017 .

After digesting, the sample was ligated by following SOP0015 with the standard iGEM plasmid, pSB1C3, overnight, and transformed into E.coli Top10.

cPCR program used:

After a colony PCR, SOP0021 , was run and verified on a gel, the following result was given: Our part is 259 bp and primer overhangs are 150 X 2 bp, which is, in total, 559 bp: A gel electrophoresis from cPCR showed a band around 600 bp, so we assumed that we had the correct part inserted into the iGEM standard plasmid.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The BioBrick was ordered from IDT in a plasmid pUCIDT-AMP and after receiving it, it was resuspended to a final concentration of 0.1 µg/µl.

After the resuspension, the plasmid was transformed into Top10 E. coli by following SOP0023_v01 Ca2+ Transformation , with the following remarks:

2.5 µl plasmid was used instead of the normal 1 µl.

What we had done with the BioBrick K2018014 can be read in the protocols: Cloning composite part K2018014 into pSB1C3 and IMPACT Purification of K2018014

The BioBrick was ordered from IDT in a plasmid pUCIDT-AMP and after receiving it, it was resuspended to a final concentration of 0.1 µg/µl.

After the resuspension, the plasmid was transformed into Top10 E. coli by following SOP0023_v01 Ca2+ Transformation , with the following remarks:

2.5 µl plasmid was used instead of the normal 1 µl.

What we had done with the BioBrick K2018019 can be read in the protocol: Cloning composite part K2018019 into pSB1C3

The BioBrick was first amplified by phusion PCR, SOP0010 , thereafter digested with restrictions enzymes, following SOP0017 . The restriction enzymes were: PstI for 2 h and EcoRI for 30 min. After digesting, the sample was verified by running a gel electrophoresis.

pPCR program used:

In the next step, the vector was ligated with the insert, SG47, overnight by following SOP0015 , and thereafter it was transformed, following SOP0009, into E.coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp which gives a total of DNA length of 419 bp. From this gel, the ligation of the gen incorporated into psB1C3 can be observed .

Picture of cPCR of different colonies on the same plate (each gene had its own plate). All the colony PCR shows a band near the 4-500 bp band, which was desired.

The second gel photo shows cutting of SB71 with Pst1 at 2 hours with 37 °C and EcoR1 at 30 minutes. Every second well had added restriction enzymes.If a band of approximately 160 bp could be seen on the gel, it was concluded as being successful and sent to sequencing.

What we had done with the BioBrick K1763002 can be read in the protocol: Cloning Basic part K1763002 into pSB1C3

The BioBrick was first amplified by phusion PCR, SOP0010 , and thereafter digested with restrictions enzymes, following SOP0017 . The restriction enzymes were: PstI for 2 h and EcoRI for 30 min. After digesting, the sample was verified by running a gel electrophoresis.

pPCR program used:

In the next step, the vector was ligated with the insert, SG48, overnight by following SOP0015 , and thereafter it was transformed, following SOP0009, into E.coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp which gives a total of DNA length of 419 bp. From this gel, the ligation of the gen incorporated into psB1C3 can be observed .

Picture of cPCR of different colonies on the same plate (each gene had its own plate). All the colony PCR shows a band near the 4-500 bp band.

The second gel photo shows cutting of SB73 with Pst1 at 2 hours with 37 °C and EcoR1 at 30 minutes. Every second well had added restriction enzymes.If a band of approximately 160 bp could be seen on the gel, it was concluded as being successful and sent to sequencing.

What we had done with the BioBrick K1763003 can be read in the protocol: Cloning Basic part K1763003 into pSB1C3

The BioBrick was first amplified by phusion PCR, SOP0010 , and thereafter digested with restrictions enzymes, following SOP0017 . The restriction enzymes were: PstI for 2 h and EcoRI for 30 min. After digesting, the sample was verified by running a gel electrophoresis.

pPCR program used:

In the next step, the vector was ligated with the insert, SG49, overnight by following SOP0015 , and thereafter it was transformed, following SOP0009, into E.coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp which gives a total of DNA length of 419 bp. From this gel, the ligation of the gen incorporated into psB1C3 can be seen.

Picture of cPCR of different colonies on the same plate (each gene had its own plate). All the colony PCR shows a band near the 4-500 bp band.

The second gel photo shows cutting of SB75 with Pst1 at 2 hours with 37 °C and EcoR1 at 30 minutes. Every second well had added restriction enzymes.If a band of approximately 160 bp could be seen on the gel, it was concluded as being successful and sent to sequencing.

What we had done with the BioBrick K1763004 can be read in the protocol: Cloning Basic part K1763004 into pSB1C3

The BioBrick was first amplified by phusion PCR, SOP0010 , and thereafter digested with restrictions enzymes, following SOP0017 . The restriction enzymes were: PstI for 2 h and EcoRI for 30 min. After digesting, the sample was verified by running a gel electrophoresis.

pPCR program used:

In the next step, the vector was ligated with the insert, SG56, overnight by following SOP0015 , and thereafter it was transformed, following SOP0009, into E.coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp which gives a total of DNA length of 419 bp. From this gel, the ligation of the gen incorporated into psB1C3 can be observed .

Picture of cPCR of different colonies on the same plate (each gene had its own plate). All the colony PCR shows a band near the 4-500 bp band.

The second gel photo shows cutting of SB77 with Pst1 at 2 hours with 37 °C and EcoR1 at 30 minutes. Every second well had added restriction enzymes.If a band of approximately 160 bp could be seen on the gel, it was concluded as being successful and sent to sequencing.

What we had done with the BioBrick K1763009 can be read in the protocol: Cloning Basic part K1763009 into pSB1C3

The BioBrick was first amplified by phusion PCR, SOP0010 , and thereafter digested with restrictions enzymes, following SOP0017 . The restriction enzymes were: PstI for 2 h and EcoRI for 30 min. After digesting, the sample was verified by running a gel electrophoresis.

pPCR program used:

In the next step, the vector was ligated with the insert, SG43, overnight by following SOP0015 , and thereafter it was transformed, following SOP0009, into E.coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp which gives a total of DNA length of 419 bp. From this gel, the ligation of the gen incorporated into psB1C3 can be observed.

Picture of cPCR of different colonies on the same plate (each gene had its own plate). All the colony PCR shows a band near the 4-500 bp band.

The second gel photo shows cutting of SB63 with Pst1 at 2 hours with 37 °C and EcoR1 at 30 minutes. Every second well had added restriction enzymes.If a band of approximately 160 bp could be seen on the gel, it was concluded as being successful and sent to sequencing.

What we had done with the BioBrick K1763010 can be read in the protocol: Cloning Basic part K1763010 into pSB1C3

The BioBrick was first amplified by phusion PCR, SOP0010 , and thereafter digested with restrictions enzymes, following SOP0017 . The restriction enzymes were: PstI for 2 h and EcoRI for 30 min. After digesting, the sample was verified by running a gel electrophoresis.

pPCR program used:

In the next step, the vector was ligated with the insert, SG44, overnight by following SOP0015 , and thereafter it was transformed, following SOP0009, into E.coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp which gives a total of DNA length of 419 bp. From this gel, the ligation of the gen incorporated into psB1C3 can be observed .

Picture of cPCR of different colonies on the same plate (each gene had its own plate). All the colony PCR shows a band near the 4-500 bp band.

The second gel photo shows cutting of SB65 with Pst1 at 2 hours with 37 °C and EcoR1 at 30 minutes. Every second well had added restriction enzymes.If a band of approximately 160 bp could be seen on the gel, it was concluded as being successful and sent to sequencing.

What we had done with the BioBrick K1763011 can be read in the protocol: Cloning Basic part K1763011 into pSB1C3

The BioBrick was first amplified by phusion PCR, SOP0010 , and thereafter digested with restrictions enzymes, following SOP0017 . The restriction enzymes were: PstI for 2 h and EcoRI for 30 min. After digesting, the sample was verified by running a gel electrophoresis.

pPCR program used:

In the next step, the vector was ligated with the insert, SG45, overnight by following SOP0015 , and thereafter it was transformed, following SOP0009, into E.coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp which gives a total of DNA length of 419 bp. From this gel, the ligation of the gen incorporated into psB1C3 can be observed .

Picture of cPCR of different colonies on the same plate (each gene had its own plate). All the colony PCR shows a band near the 4-500 bp band.

The second gel photo shows cutting of SB67 with Pst1 at 2 hours with 37 °C and EcoR1 at 30 minutes. Every second well had added restriction enzymes.If a band of approximately 160 bp could be seen on the gel, it was concluded as being successful and sent to sequencing.

What we had done with the BioBrick K1763012 can be read in the protocol: Cloning Basic part K1763012 into pSB1C3

The BioBrick containing the gene K2018010 was digested with PstI overnight and with EcoRI the day after by using SOP0017 .

After digesting, the sample was verified by gel electrophoresis. The result gave the following: The Gel Photo below shows BG51 (At the photo named; 51). The composite part is 395 bp long. It is possible from the Gel photo to assume that the DNA is cut correctly. From this gel, is the BG51 band of approximately 400 bp purified and thereafter ligated into the standard iGEM plasmid.

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and transformed into E.coli Top10.

cPCR program used:

Hereafter a colony PCR was runned and verified on a gel, the result is given below:

The Gel Photo below shows to the left the GeneRulerTM 1 kb DNA ladder were used ThermoFisher scientific. . The following bands are BB54, 1, 2 and 4 which are the ligation of the vector PR17 and the insert BG51. From the photo, it can be seen that sample 54.1 and 54.3 are the vector with the insert, and 54.2 is a religation.

What we had done with the BioBrick K2018010 can be read in the protocols: Cloning composite part K2018010 into pSB1C3 and IMPACT Purification of K2018010

The BioBrick containing the gene K2018014 was digested with PstI overnight and with EcoRI the day after by using SOP0017 .

After digesting, the sample was verified by gel electrophoresis. The result gave the following: The Gel Photo below shows BG52 (At the photo named; 52).The composite part is 458 bp long. It is possible, from the Gel photo, to assume that the DNA is cut correctly. From this gel, the BG52 band of approximately 400 bp purified and thereafter ligated into the standard iGEM plasmid.

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and transformed into E.coli Top10.

cPCR program used:

Hereafter a colony PCR was runned and verified on a gel, the result is given below:

The Gel Photo below shows to the left, the GeneRulerTM 1 kb DNA ladder were used ThermoFisher scientific. . The following bands are BB55, 1, 2 and 4 are the ligation of the vector PR17 and the insert BG52. From the photo, it can be assumed that all 3 samples in BB55 are the vector with insert.

What we had done with the BioBrick K2018014 can be read in the protocols: Cloning composite part K2018014 into pSB1C3 and IMPACT Purification of K2018014

The BioBrick was ordered from IDT in a plasmid pUCIDT-AMP. When received, it was resuspended to a final concentration at 0.1 µg/µl.

After the resuspension, the plasmid is transformed into Top10 E. coli by following SOP0023_v01 Ca2+ Transformation with the following remarks:

2.5 µl plasmid were used instead of the normal 1 µl.

What we had done with the BioBrick K2018012 can be read in the protocols: Cloning composite part K2018012 into pSB1C3 and IMPACT Purification of K2018012

The BioBrick was ordered from IDT in a plasmid pUCIDT-AMP. When received, it was resuspended to a final concentration at 0.1 µg/µl.

After the resuspension, the plasmid is transformed into Top10 E. coli by following SOP0023_v01 Ca2+ Transformation with the following remarks:

2.5 µl plasmid were used instead of the normal 1 µl.

What we had done with the BioBrick K2018015 can be read in the protocols: <Cloning composite part K2018015 into pSB1C3 and IMPACT Purification of K2018015

The BioBrick, that was ordered from IDT had a defected promoter, and therefore we replaced the promoter region with a functional one. This was done by a phusion PCR, SOP0010 . The primer was; k2018015_IDT.

pPCR program used:

The Gel photo below shows the result from the pPCR. This was done to replace a defective promoter, with the correct one. This is done by using the Primer; k2018015_IDT. As it can be seen from the photo, is first the GeneRulerTM 1 kb DNA ladder were used ThermoFisher scientific. . and then sample BR74. The gene is 572 bp long. and it is therefore possible from the gel to assume that the pPCR is succeed.

Note: There is loaded 5 µl of each sample

What we had done with the BioBrick K2018015 can be read in the protocols: <Cloning composite part K2018015 into pSB1C3 and IMPACT Purification of K2018015

The BioBrick containing the gene K2018019 was digested with PstI for 2 hours and EcoRI for 30 min. by using SOP0017 .

After digesting, the sample was verified by gel electrophoresis. The result gave the following: The two Gel Photos below show the results for BG59 (At the photo named; 59). The composite part is 1739 bp long. It is possible from the Gel photo to assume that the DNA is cut correctly. From this gel, is the BG59 band of around 2000 bp purified and thereafter ligated into the standard iGEM plasmid.

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and thereafter transformed, SOP009_v01, into E.coli Top10.

The ratio of the ligation is shown hereunder:

cPCR program used:

Hereafter a colony PCR was runned and verified on a gel. The result is given in the following section: The Gel Photo below shows to the left the GeneRulerTM 1 kb DNA ladder were used ThermoFisher scientific. .. The following bands are BB59, 1 to 14, which represent the ligation of the vector BR60 with the insert BG59. From the photo it can be assumed that all the samples are perfectly ligated. One of the colonies can therefore, be used to make ON for the plasmid purification and Freeze stock.

What we had done with the BioBrick K2018019 can be read in the protocol: Cloning composite part K2018019 into pSB1C3

The BioBrick containing the gene K2018012 was digested with PstI and XbaI overnight by using SOP0017 .

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and thereafter transformed, SOP009_v01, into E.coli Top10.

The ratio of the ligation is shown hereunder:

cPCR program used:

Hereafter a colony PCR, SOP0021 , was runned and verified on a gel, The result is given below:

The following gel picture shows that we successfully cloned our part K2018012 into the standard iGEM plasmid, pSB1C3.

What we had done with the BioBrick K2018012 can be read in the protocols: Cloning composite part K2018012 into pSB1C3 and IMPACT Purification of K2018012

The BioBrick containing the gene K2018015 was digested with PstI and XbaI overnight by using SOP0017 .

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and thereafter transformed, SOP009_v01, into E.coli Top10.

The ratio of the ligation is shown hereunder:

cPCR program used:

After a colony PCR, SOP0021 , was runned and verified on a gel, the results were the following:

The Gel Photos below show the first Gel , to the left the GeneRulerTM 1 kb DNA ladder were used can be seen ThermoFisher scientific. . The following bands are BB79, 1 to 14. On the other gel can be seen first the GeneRulerTM 1 kb DNA ladder were used, and then BB79 sample 15 to 23ThermoFisher scientific. . BB79 is the ligation of the vector BG17 and the insert BG78. From the photo it can be assumed that all the samples, except; 2 and 6, are perfectly ligated. One of the colonies are therefore used to make ON for plasmid purification and Freeze stock.

What we had done with the BioBrick K2018015 can be read in the protocols: <Cloning composite part K2018015 into pSB1C3 and IMPACT Purification of K2018015

K2018011 in standard iGEM plasmid (pSB1C3) was used in a phusion PCR, SOP0010 . The primes have an overhang, which makes the gene compatible with the silk overhang, and thereby enabling us to make a hybrid silk fiber.

pPCR program:

The result is verified by Gel electrophoresis. The result is shown here:

Lane no. 5 is ThuricinS with DA-overhangs and is expected to be 217 bp long. We have used GeneRulerTM 50 bp DNA ladder were used, where the fourth band represents 200 bp ThermoFisher scientific. . Based on that, it can be assumed that we succeeded at getting silk-overhangs on ThuricinS.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

K2018011 in standard iGEM plasmid (pSB1C3) was used in a phusion PCR, SOP0010 . The primes have an overhang, which makes the gene compatible with the silk overhang, and thereby enabling us to make a hybrid silk fiber.

pPCR program:

The result is verified by Gel electrophoresis. The result is shown here:

The lane marked no. 2 is ThuricinS with DE-overhangs and it is assumed to be 217 bp long. We have used GeneRulerTM 50 bp DNA ladder were used, where the fourth band is 200 bp long ThermoFisher scientific. . Based on that, it can be assumed that we succeeded at getting silk-overhangs on ThuricinS.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

K2018011 in standard iGEM plasmid (pSB1C3) was used in a phusion PCR, SOP0010 . The primes have an overhang, which makes the gene compatible with the silk overhang, and thereby enabling us to make a hybrid silk fiber.

pPCR program:

The result is verified by Gel electrophoresis. The result is shown here:

The lane marked no. 7 and 8 are ThuricinS with EA-overhangs and it are expected to be 217 bp long. We have used GeneRulerTM 50 bp DNA ladder were used, where the fourth band is 200 bp long ThermoFisher scientific. . Based on that, it can be expected that we succeeded at getting silk-overhangs on ThuricinS.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

K2018011 in standard iGEM plasmid (pSB1C3) was used in a phusion PCR, SOP0010 . The primes have an overhang, which makes the gene compatible with the silk overhang, and thereby enabling us to make a hybrid silk fiber.

pPCR program:

The result is verified by Gel electrophoresis. The result is shown here:

The lane marked no. 4 and 8 are ThuricinS with ED-overhangs and is expected to be 217 bp long. We have used GeneRulerTM 50 bp DNA ladder were used, where the fourth band is 200 bp ThermoFisher scientific. . Based on that it can be assumed that we succeeded at getting silk-overhangs on ThuricinS.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

We prepared an entire theme day for the biotech student on KOLD College where we had "designed" a experiment in the lab with some of our own BioBricks. The student got to perform a FastDigest following gel electrophoresis to verify their results. Thus we helped the students in the laboratory and entertained them in between with details of our project.

For using the IMPACT method for purification of bacteriocins, some specific restrictions sites are necessary. Therefore a Phusion PCR was made by following SOP0010 .

pPCR program:

What we had done with the BioBrick K2018010 can be read in the protocols: Cloning composite part K2018010 into pSB1C3 and IMPACT Purification of K2018010

For using the IMPACT method for purification of bacteriocins, some specific restrictions sites are necessary. Therefore a Phusion PCR was made by following SOP0010 .

pPCR program:

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The BioBrick was digested with with SpeI for 2h and EcoRI for 30 min, by following SOP0017 .

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and thereafter transformed into E. coli Top10, by following SOP0009. The ratio of the ligation is shown hereunder:

cPCR program used:

The samples 11-17 are from colonies containing plasmids with ThuricinS with DA overhang

ThuricinS with silk overhangs, together with primer overhangs (VF2 and VR), is 517 bp long. GeneRulerTM 1 kb DNA ladder were used was used, so from these pictures it can verified that ThuricinS with DA overhangs have the right length ThermoFisher scientific. .

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The BioBrick was digested with with SpeI for 2h and EcoRI for 30 min, by following SOP0017 .

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and thereafter transformed into E. coli Top10, by following SOP0009. The ratio of the ligation is shown hereunder:

cPCR program used:

The samples 25- 28 are from colonies containing plasmids with ThuricinS with DE overhang

ThuricinS with silk overhangs, together with primer overhangs (VF2 and VR), is 517 bp long. GeneRulerTM 1 kb DNA ladder were used was used, so from these pictures it can verified that ThuricinS with DE overhangs have the right length ThermoFisher scientific. .

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The BioBrick was digested with with SpeI for 2h and EcoRI for 30 min, by following SOP0017 .

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and thereafter transformed into E. coli Top10, by following SOP0009. The ratio of the ligation is shown hereunder:

cPCR program used:

The samples 18-24 are from colonies containing plasmids with ThuricinS with EA overhang

ThuricinS with silk overhangs, together with primer overhangs (VF2 and VR), is 517 bp long. GeneRulerTM 1 kb DNA ladder were used was used, so from these pictures it can verified that ThuricinS with EA overhangs have the right length ThermoFisher scientific. .

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The BioBrick was digested with with SpeI for 2h and EcoRI for 30 min, by following SOP0017 .

After digesting, the sample was ligated by following SOP0015 , with the standard iGEM plasmid, pSB1C3, overnight, and thereafter transformed into E. coli Top10, by following SOP0009. The ratio of the ligation is shown hereunder:

cPCR program used:

The samples 1-10 are from colonies containing plasmids with ThuricinS with ED overhang

ThuricinS with silk overhangs, together with primer overhangs (VF2 and VR), is 517 bp long. GeneRulerTM 1 kb DNA ladder were used was used, so from these pictures it can verified that ThuricinS with ED overhangs have the right length ThermoFisher scientific. .

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

We presented our project in front of the Academy of Talented Youth and also worked as their instructors in a brief lab course.

Before purifying the bacteriocin by IMPACT, the bacteriocin must first be transformed into the IMPACT vector bacteria, E. Coli:ER2566. To do this, we incorporated the pPCR product into the IMPACT plasmid, pTXB1. Thereafter the products are digested by following the SOP0025. step. 8.1.1. and afterwards ligated by following step 8.1.3 → 8.1.4 in the same SOP.

The following gel image were used to verify that K2018010 were successfully cloned into pTXB1 (the IMPACT vector). Lane 4-6 is K2018010/pTXB1. Lane 4 and 6 showed the correct sized band. Lane 5 is a negative.

What we had done with the BioBrick K2018010 can be read in the protocols: Cloning composite part K2018010 into pSB1C3 and IMPACT Purification of K2018010

Before purifying the bacteriocin by IMPACT, the bacteriocin must first be transformed into the IMPACT vector bacteria, E. Coli:ER2566. To do this, we incorporated the pPCR product into the IMPACT plasmid, pTXB1. Thereafter the products are digested by following the SOP0025. step. 8.1.1. and afterwards ligated by following step 8.1.3 → 8.1.4 in the same SOP.

The following gel image were used to verify that K2018011 were successfully cloned into pTXB1 (the IMPACT vector). Lane 4-6 is K2018010/pTXB1. Lane 1-3 is K2018011/pTXB1 and all showed the correct sized band.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

Before purifying the bacteriocin by IMPACT, the bacteriocin must first be transformed into the IMPACT vector bacteria, E. Coli:ER2566. To do this, we incorporated the pPCR product into the IMPACT plasmid, pTXB1. Thereafter the products are digested by following the SOP0025. step. 8.1.1. and afterwards ligated by following step 8.1.3 → 8.1.4 in the same SOP.

The following gel image were used to verify that K2018012 were successfully cloned into pTXB1 (the IMPACT vector). Lane 9-12 is K2018012/pTXB1 and they all showed the correct sized band.

What we had done with the BioBrick K2018012 can be read in the protocols: Cloning composite part K2018012 into pSB1C3 and IMPACT Purification of K2018012

Before purifying the bacteriocin by IMPACT, the bacteriocin must first be transformed into the IMPACT vector bacteria, E. Coli:ER2566. To do this, we incorporated the pPCR product into the IMPACT plasmid, pTXB1. Thereafter the products are digested by following the SOP0025. step. 8.1.1. and afterwards ligated by following step 8.1.3 → 8.1.4 in the same SOP.

The following gel image were used to verify that K2018014 were successfully cloned into pTXB1 (the IMPACT vector). The three first lanes is K2018014/pTXB1, where lane 1 and 3 showed the correct sized band but lane 2 was negative..

What we had done with the BioBrick K2018014 can be read in the protocols: Cloning composite part K2018014 into pSB1C3 and IMPACT Purification of K2018014

Before purifying the bacteriocin by IMPACT, the bacteriocin must first be transformed into the IMPACT vector bacteria, E. Coli:ER2566. To do this, we incorporated the pPCR product into the IMPACT plasmid, pTXB1. Thereafter the products are digested by following the SOP0025. step. 8.1.1. and afterwards ligated by following step 8.1.3 → 8.1.4 in the same SOP.

The following gel image were used to verify that K2018015 were successfully cloned into pTXB1 (the IMPACT vector). We used three different primers to ‘cross amplify’ the gene and a part of the vector plasmid, getting 2 different DNA bands. All of the given results were, as expected, at 330 bp and 494 bp.

What we had done with the BioBrick K2018015 can be read in the protocols: <Cloning composite part K2018015 into pSB1C3 and IMPACT Purification of K2018015

The BioBrick was first digested with restrictions enzymes by following SOP0017 . The restriction enzymes were: PstI and XbaI for 2h. After digesting, the sample was verified by Gel electrophoresis.

pPCR program used:

In the next step the vector was ligated with the insert overnight by following SOP0015 , and thereafter it was transformed, SOP0009, into E. coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp, which gives a total DNA length of 419 bp. From this gel the ligation of the gen incorporated into psB1C3 can be observed.

This is the picture of the colony PCR where 1.2 to 1.6 are different colonies of the same plate for MaSp1 CD. 1.3 was used to purify plasmids.

The second gel photo shows cutting of SB100 with Xbal and PstI. Every second well had added restriction enzymes. If a band of 145 bp long was observed on the gel of ligation and transformation of SB100, it was concluded successful and sent to sequencing.

What we have done with the BioBrick K2018043 can be read in the protocol: >Cloning Basic part K2018043 into pSB1C3

The BioBrick was first digested with restrictions enzymes by following SOP0017 . The restriction enzymes were: PstI and XbaI for 2 h. After digesting, the sample was verified by Gel electrophoresis.

pPCR program used:

In the next step the vector was ligated with the insert overnight by following SOP0015 , and thereafter it was transformed, SOP0009, into E. coli Top10. The ratio of the ligation is shown hereunder:

To verify that the transformation and ligation succeeded, a colony PCR was run, SOP0021 .

cPCR program used:

The Gel Photo below shows the cPCR results. VR and VF2 primers adds a total of 300 bp, the gene is 119 bp long, which gives a total DNA length of 419 bp. From this gel the ligation of the gen incorporated into psB1C3 can be indicated .

This is the picture of the colony PCR where 2.1 to 2.3 are different colonies of the same plate for MaSp2 CD. 2.1 was used to purify plasmids

The second gel photo shows cutting of SB101 with Xbal and PstI. Every second well had added restriction enzymes. From this gel, the ligation and transformation of SB101, a band around 145 bp after digestion, was concluded as being successful and sent to sequencing.

What we have done with the BioBrick K2018044 can be read in the protocol: Cloning Basic part K2018044 into pSB1C3

The IMPACT purification is done by following the SOP0025 step. 8.1.6→ 8.4.3. and the purity is determined by Bradford Protein Concentration determination.

In the Bradford assay, we measured OD595= 0.09400, and together with the BSA standard curve (see appendix) we calculated the final protein concentration as being 67.1 µg/ml.

What we had done with the BioBrick K2018010 can be read in the protocols: Cloning composite part K2018010 into pSB1C3 and IMPACT Purification of K2018010

The IMPACT purification is done by following the SOP0025 step. 8.1.6→ 8.4.3. and the purity is determined by Bradford Protein Concentration determination.

In the Bradford assay we measured OD595= 0.05700, and together with the BSA standard curve (see appendix) we calculated a final protein concentration as being 33.5 µg/ml.

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The IMPACT purification is done by following the SOP0025 step. 8.1.6→ 8.4.3. and the purity is determined by Bradford Protein Concentration determination.

In the Bradford assy, we measured an OD595= 0.06900, and together with the BSA standard curve (see appendix) we calculated a final protein concentration as being 44.4 µg/ml.

What we had done with the BioBrick K2018012 can be read in the protocols: Cloning composite part K2018012 into pSB1C3 and IMPACT Purification of K2018012

The IMPACT purification is done by following the SOP0025 step. 8.1.6→ 8.4.3. and the purity is determined by Bradford Protein Concentration determination.

In the Bradford assay we measured an OD595= 0.05360, and together with the BSA standard curve (see appendix) we calculated a final protein concentration as being 30.4 µg/ml.

What we had done with the BioBrick K2018014 can be read in the protocols: Cloning composite part K2018014 into pSB1C3 and IMPACT Purification of K2018014

The IMPACT purification is done by following the SOP0025 step. 8.1.6→ 8.4.3. and the purity is determined by Bradford Protein Concentration determination.

In the Bradford assay we measured OD595= 0.07800, and together with the BSA standard curve (see appendix) we calculated a final protein concentration as being 52.5 µg/ml.

What we had done with the BioBrick K2018015 can be read in the protocols: <Cloning composite part K2018015 into pSB1C3 and IMPACT Purification of K2018015

The effect of the bacteriocins is validated by a MIC-test, which is made by following the SOP0027 step. 7.2→ 7.9.

The MIC assay gave the following MIC values:

What we had done with the BioBrick K2018010 can be read in the protocols: Cloning composite part K2018010 into pSB1C3 and IMPACT Purification of K2018010

The effect of the bacteriocins is validated by a MIC-test, which is made by following the SOP0027 step. 7.2→ 7.9.

The MIC assay gave the following MIC values:

What we had done with the BioBrick K2018011 can be read in the protocols: Cloning composite part K2018011 into pSB1C3, Cloning ThuricinS with DA silk-overhangs into pSB1C3, Cloning ThuricinS with DE silk-overhangs into pSB1C3, Cloning ThuricinS with EA silk-overhangs into pSB1C3, Cloning ThuricinS with ED silk-overhangs into pSB1C3 and IMPACT Purification of K2018011

The effect of the bacteriocins is validated by a MIC-test, which is made by following the SOP0027 step. 7.2→ 7.9.

The MIC assay gave the following MIC values:

What we had done with the BioBrick K2018012 can be read in the protocols: Cloning composite part K2018012 into pSB1C3 and IMPACT Purification of K2018012

The effect of the bacteriocins is validated by a MIC-test, which is made by following the SOP0027 step. 7.2→ 7.9.

The MIC assay gave the following MIC values:

What we had done with the BioBrick K2018014 can be read in the protocols: Cloning composite part K2018014 into pSB1C3 and IMPACT Purification of K2018014

The effect of the bacteriocins is validated by a MIC-test, which is made by following the SOP0027 step. 7.2→ 7.9.

The MIC assay gave the following MIC values:

What we had done with the BioBrick K2018015 can be read in the protocols: <Cloning composite part K2018015 into pSB1C3 and IMPACT Purification of K2018015