Difference between revisions of "Part:BBa K1321334:Experience"

(→‎Applications of BBa_K1321334)
(→‎Applications of BBa_K1321334)
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===Applications of BBa_K1321334===
 
===Applications of BBa_K1321334===
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This part was cloned into part  BBa_K1321333 by Biobrick cloning, to yield BBa_K1321336. The destination vector, containing the AraC-pBAD regulatory elements, was linearized using SpeI and PstI, and AcsAB (previously digested with XbaI and PstI) was ligated at a 1:1 ratio using the T4 ligase. The ligation mix was transformed into chemically competent DH10B Escherichia coli and plated on LB Agar+Chloramphenicol plates, then incubated overnight at 37 degrees. 50 mL Falcon tubes containing 5 ml LB supplied with 50 ug/ml Chloramphenicol were inoculated with a selection of freshly grown colonies for further restriction analysis and gene sequencing verification.   
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BBa_K1321334 was cloned into part  BBa_K1321333 by Biobrick cloning, to yield BBa_K1321336. The destination vector, containing the AraC-pBAD regulatory elements, was linearized using SpeI and PstI, and AcsAB (previously digested with XbaI and PstI) was ligated at a 1:1 ratio using the T4 ligase. The ligation mix was transformed into chemically competent DH10B Escherichia coli and plated on LB Agar+Chloramphenicol plates, then incubated overnight at 37 degrees. 50 mL Falcon tubes containing 5 ml LB supplied with 50 ug/ml Chloramphenicol were inoculated with a selection of freshly grown colonies for further restriction analysis and gene sequencing verification.   
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[[File:LBfraction.png|700px|thumb|left|Figure 1 - Assaying Congo Red (CR) binding by measuring the changes in absorbance at 490nm]]
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WThe functionality of part BBa_K1321336 was assayed by inducing the system with 0.1% Arabinose in 5mL LB supplied with 1% Glucose and Chloramphenicol. Overnight incubations were set up at 30 °C and 37 °C, and both empty vector controls and un-induced controls were also assayed for cellulose production. During sonication, LB, soluble and non-soluble fractions were produced and kept for further analysis. Congo Red (CR) at a concentration of 20uM was added to all samples, which were then incubated for 2 hours at room temperature and static conditions, prior to absorbance measurements being taken at 490nm. By subtracting the absorbance values of those samples containing BBa_K1321336 from the absorbance value of a PBS+CR control, it is possible to qualitatively assay the shift in spectral properties of the diazo dye, driven by CR binding to the cellulose fibres.
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BBa_K1321336 was characterised in conjunction to an additional expression system containing AcsC and AcsD (optimised coding sequences submitted as Part BBa_K1321335) cloned into a medium-to-low copy number plasmid, pSB3K3. The functions of AcsC and AcsD are yet not very well known but are believed to play a crucial role in cellulose crystallisation and secretion into the extracellular space.  
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[[File:Membranefraction.png|700px|thumb|right|Figure 1 - Assaying Congo Red (CR) binding by measuring the changes in absorbance at 490nm]]
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In addition to the latter study, BBa_K1321335 was also characterised in conjunction to an additional expression system containing the AcsC and AcsD elements of the cellulose synthesis operon. Part BBa_K1321335 contains the coding sequences of the latter. The functions of AcsC and AcsD are yet not very well known but are believed to play a crucial role in cellulose crystallisation and secretion into the extracellular space. Because these elements were absent, it was expected that the LB and soluble fractions derived from sonication would contain no cellulose; the main reason being due to the inability of the cells to extrude the fibers, in addition to cellulose being highly hydrophobic hence should precipitate together with the remaining immiscible cellular elements released during sonication. As expected, no spectral changes were reported in the LB and soluble fractions, however these were observed on non-soluble samples derived from cultures grown at 30 degrees and static conditions. These results, supported with two biological repeats and technical triplicates, suggested that the AcsAB condign sequence contained in BBa_K1321334 and BBa_K1321336 is functional and optimal at 30 degrees.  
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part BBa_K1321335 was digested with XbaI and PstI and the resulting fragment, containing AcsC and AcsD, was cloned back into a low copy number plasmid (pSB3K3) containing the inducible pLAC promoter. The resulting construct, verified by GreenTaq Colony PCR, was subsequently sub-cloned into BBa_K1321336-containing electrocompetent cells. Cellulose production was assayed by plating transformed plates on Congo Red assay plates containing 20uM CR, 0.5mM IPTG, 0.1% Arabinose, 1% Glucose, 25ug/ml Chloramphenicol and 25ug/ml Kanamycin. Cellulose-producing E.coli colonies turned red in the presence of CR.
 
part BBa_K1321335 was digested with XbaI and PstI and the resulting fragment, containing AcsC and AcsD, was cloned back into a low copy number plasmid (pSB3K3) containing the inducible pLAC promoter. The resulting construct, verified by GreenTaq Colony PCR, was subsequently sub-cloned into BBa_K1321336-containing electrocompetent cells. Cellulose production was assayed by plating transformed plates on Congo Red assay plates containing 20uM CR, 0.5mM IPTG, 0.1% Arabinose, 1% Glucose, 25ug/ml Chloramphenicol and 25ug/ml Kanamycin. Cellulose-producing E.coli colonies turned red in the presence of CR.
  
 
[[File:YEAH3.jpg|200px|thumb|left|Congo Red assay, positive colonies]] [[File:YEAH2.jpg|200px|thumb|left|Congo Red assay, negative control]]
 
[[File:YEAH3.jpg|200px|thumb|left|Congo Red assay, positive colonies]] [[File:YEAH2.jpg|200px|thumb|left|Congo Red assay, negative control]]
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Whilst the AcsC and AcsD elements of the cellulose synthesis operon (coded in part BBa_K1321335) are needed for cellulose secretion into the extracellular space, we were interested in exploring whether AcsAB would be enough to produce the polymer in E.coli. The functionality of part BBa_K1321336 was assayed by inducing the system with 0.1% Arabinose in 5mL LB supplied with 1% Glucose and Chloramphenicol. Overnight incubations were set up at 30 °C and 37 °C, and both empty vector controls and un-induced controls were also assayed for cellulose production. During sonication, LB, soluble and non-soluble fractions were produced and kept for further analysis. Congo Red (CR) at a concentration of 20uM was added to all samples, which were then incubated for 2 hours at room temperature and static conditions, prior to absorbance measurements being taken at 490nm. By subtracting the absorbance values of those samples containing BBa_K1321336 from the absorbance value of a PBS+CR control, it is possible to qualitatively assay the shift in spectral properties of the diazo dye, driven by CR binding to the cellulose fibres.
 +
[[File:LBfraction.png|700px|thumb|left|Figure 1 - Assaying Congo Red (CR) binding by measuring the changes in absorbance at 490nm]]
 +
[[File:Membranefraction.png|700px|thumb|right|Figure 2 - Assaying Congo Red (CR) binding by measuring the changes in absorbance at 490nm]]
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 +
Because AcsC and AcsD were absent, the LB and soluble fractions derived from sanitation were expected to contain no cellulose; the main reason being due to the inability of the cells to extrude the fibers, in addition to cellulose being highly hydrophobic hence should precipitate together with the remaining immiscible cellular elements released during sonication. As predicted, no spectral changes were reported in the LB (figure 1) and soluble fractions (data not shown), however these were observed on non-soluble samples derived from cultures grown at 30 degrees and static conditions (figure 2). These results, supported with two biological repeats and technical triplicates, suggested that the AcsAB condign sequence contained in BBa_K1321334 and BBa_K1321336 is functional and optimal at 30 degrees.
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In addition to the latter study,
  
 
===User Reviews===
 
===User Reviews===

Revision as of 15:46, 22 October 2014

This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K1321334

BBa_K1321334 was cloned into part BBa_K1321333 by Biobrick cloning, to yield BBa_K1321336. The destination vector, containing the AraC-pBAD regulatory elements, was linearized using SpeI and PstI, and AcsAB (previously digested with XbaI and PstI) was ligated at a 1:1 ratio using the T4 ligase. The ligation mix was transformed into chemically competent DH10B Escherichia coli and plated on LB Agar+Chloramphenicol plates, then incubated overnight at 37 degrees. 50 mL Falcon tubes containing 5 ml LB supplied with 50 ug/ml Chloramphenicol were inoculated with a selection of freshly grown colonies for further restriction analysis and gene sequencing verification.

BBa_K1321336 was characterised in conjunction to an additional expression system containing AcsC and AcsD (optimised coding sequences submitted as Part BBa_K1321335) cloned into a medium-to-low copy number plasmid, pSB3K3. The functions of AcsC and AcsD are yet not very well known but are believed to play a crucial role in cellulose crystallisation and secretion into the extracellular space.

part BBa_K1321335 was digested with XbaI and PstI and the resulting fragment, containing AcsC and AcsD, was cloned back into a low copy number plasmid (pSB3K3) containing the inducible pLAC promoter. The resulting construct, verified by GreenTaq Colony PCR, was subsequently sub-cloned into BBa_K1321336-containing electrocompetent cells. Cellulose production was assayed by plating transformed plates on Congo Red assay plates containing 20uM CR, 0.5mM IPTG, 0.1% Arabinose, 1% Glucose, 25ug/ml Chloramphenicol and 25ug/ml Kanamycin. Cellulose-producing E.coli colonies turned red in the presence of CR.

Congo Red assay, positive colonies
Congo Red assay, negative control

Whilst the AcsC and AcsD elements of the cellulose synthesis operon (coded in part BBa_K1321335) are needed for cellulose secretion into the extracellular space, we were interested in exploring whether AcsAB would be enough to produce the polymer in E.coli. The functionality of part BBa_K1321336 was assayed by inducing the system with 0.1% Arabinose in 5mL LB supplied with 1% Glucose and Chloramphenicol. Overnight incubations were set up at 30 °C and 37 °C, and both empty vector controls and un-induced controls were also assayed for cellulose production. During sonication, LB, soluble and non-soluble fractions were produced and kept for further analysis. Congo Red (CR) at a concentration of 20uM was added to all samples, which were then incubated for 2 hours at room temperature and static conditions, prior to absorbance measurements being taken at 490nm. By subtracting the absorbance values of those samples containing BBa_K1321336 from the absorbance value of a PBS+CR control, it is possible to qualitatively assay the shift in spectral properties of the diazo dye, driven by CR binding to the cellulose fibres.

Figure 1 - Assaying Congo Red (CR) binding by measuring the changes in absorbance at 490nm
Figure 2 - Assaying Congo Red (CR) binding by measuring the changes in absorbance at 490nm

Because AcsC and AcsD were absent, the LB and soluble fractions derived from sanitation were expected to contain no cellulose; the main reason being due to the inability of the cells to extrude the fibers, in addition to cellulose being highly hydrophobic hence should precipitate together with the remaining immiscible cellular elements released during sonication. As predicted, no spectral changes were reported in the LB (figure 1) and soluble fractions (data not shown), however these were observed on non-soluble samples derived from cultures grown at 30 degrees and static conditions (figure 2). These results, supported with two biological repeats and technical triplicates, suggested that the AcsAB condign sequence contained in BBa_K1321334 and BBa_K1321336 is functional and optimal at 30 degrees.

In addition to the latter study,

User Reviews

UNIQ669b6774adb6fbaf-partinfo-00000000-QINU UNIQ669b6774adb6fbaf-partinfo-00000001-QINU