Latest revision as of 23:29, 21 October 2019

Project

Results

qRT-PCR for the relative quantification of specific tRNA-species

Alongside with the generation of a climate-friendly medium, the goal of our project PhyCoVi was to optimize the strain Vibrio natriegens for a potential use in the biotech industry. The optimization is performed on the genomic level to increase the intracellular availability of tRNA species. As a result, the strain’s performance to express heterologous proteins is enhanced.

A method needs to be developed to quantify individual tRNA species specifically to prove the increased expression not only on the protein level. Multiple methods can be found to quantify non-coding RNA ^{1, 2} or total tRNA concentration^{3, 4}. Whereas finding a well-established method to quantify single tRNA species specifically is in vain. The only method paper was published in the journal “RNA biology” in 2015 by Honda et al.: “Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA” ⁵. The authors of this paper removed the amino acid at the 3’ end followed by hybridization and ligation with a DNA/RNA hybrid stem loop creating a “four-leaf clover” shaped appearance of the tRNA ligation product. The stem loop adaptor contained a TaqMan probe binding site. During the qPCR the TaqMan probe was cut by exonuclease function of the used polymerase resulting in emission of fluorescence.

Building on the work of Honda et al. we developed a new and simplified method for relative quantification of specific tRNA species without the necessity of TaqMan probes. Instead using a DNA/RNA hybrid stem loop we used a linear DNA/RNA construct as adaptor.

The first step is to isolate RNA with a length of < 200 nt from cultured V. natriegens cells. Then, the amino acid bound to the 3’ end needs to be removed by a deacylation reaction. This results in a sticky end, where a linear RNA/DNA hybrid adaptor can be ligated, which is complementary to the 3’ end overhang. Although different tRNAs show differences in length and sequence, the last three nucleotides at the 3’ end are the same for all tRNA species. The ligated adaptor contains a binding site for the forward-primer, which is identical for all tRNAs (unspecific primer). We used T4-RNA-ligase 2 that requires ATP. For this reason, a polynucleotide kinase was necessary to carry out a phosphorylation reaction at the 5’ end.

To amplify single tRNA species specifically, we distinguished between two options. First option was using the specific tRNA primer in a reverse transcription to convert the whole tRNA pool to cDNA. Following RNase H digestion results in pure cDNA of the desired tRNA species.

Later the desired tRNA species is amplified during a qPCR by using the specific reverse primer and the unspecific adaptor primer.

During qPCR a DNA-intercalating fluorescence dye (Green DNA dye) allows for relative quantification: Green DNA dye binds to double stranded DNA and absorbs blue light and emits green light. The more double stranded DNA is generated, the higher the resulting fluorescence. And the higher the concentration of the template in the sample the faster the fluorescence exceeds the threshold. The number of cycles at which this happens is called the threshold cycle (C_t). (e.g. if sample A showed a C_t of 8 and sample B showed a C_t of 11, sample A contained 2³ = 8 times more template.)

After running a DNA gel, we noticed that the obtained amplification products did not show the expected length. This may have been a result of distinct secondary structures of the tRNA species: the reverse transcription reaction was performed at 42 °C which is the enzyme’s optimum working temperature. However, this temperature is not high enough to prevent secondary structures or to break them up. Therefore, areas with secondary structures may have been inaccessible for the reverse transcriptase resulting in shorter cDNA fragments.

For this reason, we tested a second option to amplify single tRNA species specifically. A modified polymerase together with the specific reverse primer can be used to amplify the desired tRNA species using RNA as a template. This modified polymerase works at temperatures around 65 °C and can use both RNA and DNA as a template. The reverse transcription reaction is thus not needed as a consecutive step anymore. Moreover, the modified enzyme creates the specific cDNA from RNA directly and the high temperature prevents secondary structures. The relative quantification based on C_tvalues is the same as in the option described before.

References

I. A. Babarinde, Y. Li, A. P. Hutchins (2019) Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts, Computational and Structural Biotechnology Journal, Vol. 17, pp 628-637

D. Jacob, K. Thüring, A. Galliot, V. Marchand, A. Galvanin, A. Ciftci, K. Scharmann, M. Stock, J.‐Y. Roignant, S.A. Leidel, Y. Motorin, R. Schaffrath, R. Klassen, M. Helm (2019) Absolute Quantification of Noncoding RNA by Microscale Thermophoresis, Angewandte Chemie International Edition, Vol. 58, pp 9565 – 9569

T. S. Stenum, M. A. Sørensen, S. L. Svenningsen (2017) Quantification of the Abundance and Charging Levels of Transfer RNAs in Escherichia coli. Journal of Visual Experiments, Issue 126, e56212

Y. Guo, A. Bosompem, S.Mohan, B. Erdogan, F.Ye, K. C. Vickers, Q. Sheng, S. Zhao, C. Li, P.-F. Su, M. Jagasia, S. A. Strickland, E. A. Griffiths, A. S. Kim (2015) Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes, BMC Genomics, 16:727

S. Honda, M. Shigematsu, K. Morichika, A. G. Telonis, Y. Kirino (2015) Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA, RNA Biology, Vol. 12, pp 501 – 508

tRNA quantification of rare codons in V. natriegens with reverse transcription and the use of ‘GreenMasterMix without ROX’

tRNA quantification of rare codons in V. natriegens with reverse transcriptase

At the beginning different parameters such as the temperatures during the qPCR or primer and RNA concentrations in the sample preparation were tested. Samples were taken in mid exponential phase of V. natriegens. After several experiments, the results of the optimized protocol are shown in figure 1. Experiments were conducted using the following protocols: Purification_of_RNA_smaller_than_200_nucleotides.pdf, Deacetylation_and_precipitation_of_tRNA.pdf, Reverse_transcription_of_the_specific_tRNA_species.pdf, Hybridization_and_ligation_of_tRNAs.pdf, RT_qPCR.pdf.

Figure 1: tRNA quantification of V. natriegens with ‘GreenMasterMix without ROX’: fluorescent intensity over cycle number is shown. AGA is represented by the pink curve, AGG by the dark blue one, CGG is coloured in light blue, GAA in green. The orange curve shows TCC and red TGC. The black curve shows the negative control. The experiment was carried out in triplicates, the standard deviation is represented by the error bars.

The first curve that appears at a C_t value of 12.59 was AGA. AGG showed a C_t value of 21.04. It is followed by GAA with 26.26 and TGC with 27.5. The C_t value of 30.17 belongs to TCC. The highest C_t value showed CGG with 30.74 cycles.

Figure 2 – 7 show the melting curves of the qPCR products. A single peak indicates that there is only one amplified product for each codon.

Figure 2: The melting curve of the amplification product of the AGA tRNA in V. natriegens is shown. The generated product has a melting temperature of about 77.5 ° C.

Figure 3: The melting curve of the amplification product of the AGG tRNA in V. natriegens is shown. The amplification product has a melting temperature of about 77.5 ° C.

Figure 4: The melting curve of the amplification product of the CGG tRNA in V. natriegens is shown. The melting temperature of the amplification product was about 77.5 ° C.

Figure 5: The melting curve of the amplification product of the GAA tRNA in V. natriegens is shown. The generated product has a melting temperature of about 77.5 ° C.

Figure 6: The melting curve of the amplification product of the TCC tRNA in V. natriegens is shown. The amplified product has a melting temperature of about 77.5 ° C.

Figure 7: The melting curve of the amplification product of the TGC tRNA in V. natriegens is shown. . The melting temperature of the amplification product was about 77.5 ° C.

After the protocol was established, we wanted to find out if we were able to detect any differences in tRNA concentration between the exponential growth phase and the stationary phase. Therefore, we cultivated V. natriegens and harvested cells after 1.5 h and 3 h for RNA isolation. Samples were treated as usual but C_t values for each tRNA species between the sampling times showed no differences (data not shown).

To verify the RNA purification and the other steps of the protocol, purified and lyophilized E. coli tRNA (Roche, Basel, Switzerland) was treated like the purified V. natriegens RNA. Results of qPCR showed similar curve characteristics and C_t values referring to the results based on V. natriegens (data not shown).

tRNA quantification of rare codons in V. natriegens with HotScriptase

“HotScriptase RT”, a modified polymerase, is able to perform the reverse transcription of RNA and the amplification of cDNA in one step. Due to the higher temperatures, tRNA secondary structure should be reduced, which should lead to a more efficient reverse transcription. (RT_qPCR_without_prior_execution_of_a_reverse_transcription.pdf). Steps before the reverse transcription and qPCR, were the same as usual (Purification_of_RNA_smaller_than_200_nucleotides.pdf, Deacetylation_and_precipitation_of_tRNA.pdf, Hybridization_and_ligation_of_tRNAs.pdf).

Figure 8: tRNA quantification of rare codons of V. natriegens with “HotScriptase RT”. Fluorescence over cycle number is shown AGA is represented by the pink curve, AGG by the dark blue one, CGG is colored in light blue, GAA in green. The orange curve shows TCC and red TGC. The black curve shows the negative control. The experiment was carried out in duplicates.

As in the experiment before, codon AGA showed the highest intensity and the lowest C_t value (17.08). GAA, which normally should be the tRNA with the highest concentration, showed a C_t value of 25.63 followed by TGC with 25.79 and AGG with 25.92. The C_t value of TCC was 28.2. CGG showed the highest C_t value of 28.98.

Figure 9: The melting curve of the amplification product of the AGA tRNA in V. natriegens is shown. The mainly generated product has a melting temperature of about 79 ° C. A second amplification product was detected with a melting temperature of about 88 °C.

Figure 10: The melting curve of the amplification product of the AGG tRNA in V. natriegens is shown. The mainly generated product has a melting temperature of about 88 ° C.

Figure 11: The melting curve of the amplification product of the CGG tRNA in V. natriegens is shown. The amplification product has a melting temperature of about 88 ° C.

Figure 12: The melting curve of the amplification product of the GAA tRNA in V. natriegens is shown. The amplification product has a melting temperature of about 87 ° C.

Figure 13: The melting curve of the amplification product of the TCC tRNA in V. natriegens is shown. The amplification product has a melting temperature of about 87 ° C.

Figure 14: The melting curve of the amplification product of the TGC tRNA in V. natriegens is shown. The amplification product has a melting temperature of about 87 ° C.

Figure 9 – 14 show the melting curves of the qPCR products generated using “HotScriptase RT”. A single peak that there is only one amplified product for each codon. Figure 10 to 14 indicate, that unspecific by-products may have been amplified.

tRNA quantification of rare codons in V. natriegens with diluted tRNA

Because the previous experiments did not reveal the expected result, we tried to proof that the method in itself is able to detect different tRNA concentrations. Therefore the purified RNA (Purification_of_RNA_smaller_than_200_nucleotides.pdf) was diluted 1:1, 1:10 and 1:100 and prepared as usual (Deacetylation_and_precipitation_of_tRNA.pdf, Hybridization_and_ligation_of_tRNAs.pdf, Reverse_transcription_of_the_specific_tRNA_species.pdf, RT_qPCR.pdf). If sample A showed a C_t of 8 and sample B showed a C_t of 11, sample A contained 2³ = 8 times more template. Therefore, for a 10-fold dilution a difference in C_t values of around √10 was expected.

Figure 15: Quantification of diluted tRNAs of the two codons AGA und AGG in V. natriegens with RT-qPCR: Fluorescence over cycle number is shown. AGA 1:1 diluted is represented by pink color. AGA 1:10 diluted by dark blue and 1:100 diluted by light blue. GAA 1:1 is represented by the orange curve, GAA 1:10 by red and GAA 1:100 by dark grey. Also, negative controls are shown: AGA in green and GAA in black. The experiment was carried out in triplicates. Average and standard deviation are shown.

Figure 15 shows, that our assumption was fulfilled. The C_t values for AGA increased from 10.94 of the undiluted concentration over 13.17 (1:10) to the 1:100 dilution with a C_t value of 16.56. The results for GAA are quite similar: lowest C_t value was 24.15 (1:1) and increased to 27.35 (1:10) and 31.29 (1:100).

After we were able to distinguish tRNA concentrations with a dilution factor of 1:10 significantly, we tried to distinguish dilutions with factor 1:2, 1:4, 1:8 an 1:16. Because it was crucial for the results that each component of the qPCR was pipetted in the right amount, all ingredients were pipetted by a dispensing robot (iDOT, Dispendix GmbH, Stuttgart, Germany).

Figure 16: Quantification of diluted tRNAs of the AGA in V. natriegens with RT-qPCR: Fluorescence over cycle number is shown. AGA 1:1 dilution: pink, AGA 1:2 dilution: dark blue, AGA 1:4 dilution: light blue, AGA 1:8 dilution: green, AGA 1:16 dilution: orange, AGA negative control: red. Average of three technical triplicates and standard deviation are shown.

Figure 17: quantification of diluted tRNAs of the AGG in V. natriegens with RT-qPCR: Fluorescence over cycle number is shown. AGG 1:1 dilution: pink, AGG 1:2 dilution: dark blue, AGG 1:4 dilution: light blue, AGG 1:8 dilution: green, AGG 1:16 dilution: orange, AGG negative control: red. Average of three technical triplicates and standard deviation are shown.

Figure 18: quantification of diluted tRNAs of the CGG in V. natriegens with RT-qPCR: Fluorescence over cycle number is shown. CGG 1:1 dilution: pink, CGG 1:2 dilution: dark blue, CGG 1:4 dilution: light blue, CGG 1:8 dilution: green, CGG 1:16 dilution: orange, CGG negative control: red. Average of three technical triplicates and standard deviation are shown.

Figure 19: quantification of diluted tRNAs of the GAA in V. natriegens with RT-qPCR: Fluorescence over cycle number is shown. GAA 1:1 dilution: pink, GAA 1:2 dilution: dark blue, GAA 1:4 dilution: light blue, GAA 1:8 dilution: green, GAA 1:16 dilution: orange, GAA negative control: red. Average of three technical triplicates and standard deviation are shown.

Figure 20: quantification of diluted tRNAs of the TCC in V. natriegens with RT-qPCR: Fluorescence over cycle number is shown. TCC 1:1 dilution: pink, TCC 1:2 dilution: dark blue, TCC 1:4 dilution: light blue, TCC 1:8 dilution: green, TCC 1:16 dilution: orange, TCC negative control: red. Average of three technical triplicates and standard deviation are shown.

Figure 21: quantification of diluted tRNAs of the TGC in V. natriegens with RT-qPCR: Fluorescence over cycle number is shown. TGC 1:1 dilution: pink, TGC 1:2 dilution: dark blue, TGC 1:4 dilution: light blue, TGC 1:8 dilution: green, TGC 1:16 dilution: orange, TGC negative control: red. Average of three technical triplicates and standard deviation are shown.

Figures 16 – 21 show the results of the second dilution experiment. Comparing C_t values of each tRNA species show significant differences between the original samples and the 1:2 dilution for the rare codons CGG (fig. 18), GAA (fig. 19) and TGC (fig. 21). For the rare codons TCC (fig. 20) and AGG (fig. 17) significant differences in the C_t values between the original sample and the 1:4 dilution could be shown. A significant difference for the rare codon AGA (fig. 16) could be determined between the original sample and 1:8 dilution.

Significance was calculated by one way ANOVA followed by a posthoc analysis.

Comparison of tRNA concentration of rare codons in different E. coli strains

Actually, the goal was to compare the tRNA concentration of V. natriegens wildtype with the tRNA concentration of our codon-optimized strain. The optimized strain was supposed to produce higher amounts of rare tRNA species. Because the cloning turned out quite difficult, we decided to apply the qPCR method to other strains. Therefore, E. coli BL21DE3, E. coli Bl21DE3 pRARE 2 and E. coli Rosetta were cultivated (Protocol_Cultivation_Escherichia_coli_for_RNA_purification.pdf). The strain carrying the pRARE 2 plasmid, should produce higher amounts of rare tRNA species. In case of the Rosetta strain, the pRARE cassette was integrated into the genome. RNA was purified (Purification_of_RNA_smaller_than_200_nucleotides.pdf) and treated as in the experiments with V. natriegens (Deacetylation_and_precipitation_of_tRNA.pdf, Hybridization_and_ligation_of_tRNAs.pdf, RT_qPCR_without_prior_execution_of_a_reverse_transcription.pdf). In this experiment, tRNAs of the following rare codons were tested: AGA, AGG, CCC and CUA.

The results are shown in figures 21 – 28 C_tvalues from E. coli pRARE 2 and Rosetta are quite similar, but the values of the wildtype are always lower, which means that the concentration is higher. This result does not comply with the assumption, that E. coli pRARE 2 and Rosetta contain higher amounts of these tRNA species.

Figure 21: Comparison of AGA tRNA amplification behavior of E. coli BL21DE3 (pink), E. coli Bl21DE3 pRARE 2 (dark blue) and E. coli Rosetta (light blue). The negative control is shown in black. Measurements were carried out in technical triplicates. Averages and standard deviations are shown.

Figure 22: Melting curve of AGA tRNA amplification mix quantity of E. coli BL21DE3 (green), E. coli Bl21DE3 pRARE 2 (pink) and E. coli Rosetta (dark blue). The amplification product has a melting temperature of about 86 °C. Averages and standard deviations of three technical triplicates are shown.

Figure 23: Comparison of AGG tRNA amplification behavior of E. coli BL21DE3 (pink), E. coli Bl21DE3 pRARE 2 (dark blue) and E. coli Rosetta (light blue). The negative control is shown in black. Measurements were carried out in technical triplicates. Averages and standard deviations are shown.

Figure 24: Melting curve of AGG tRNA amplification mix quantity of E. coli BL21DE3 (green), E. coli Bl21DE3 pRARE 2 (pink) and E. coli Rosetta (dark blue). The amplification product has a melting temperature of about 84,5 °C. Averages and standard deviations of three technical triplicates are shown.

Figure 25: Comparison of CCC tRNA amplification behavior of E. coli BL21DE3 (pink), E. coli Bl21DE3 pRARE 2 (dark blue) and E. coli Rosetta (light blue). The negative control is shown in black. Measurements were carried out in technical triplicates. Averages and standard deviations are shown.

Figure 26: Melting curve of CCC tRNA amplification mix quantity of E. coli BL21DE3 (green), E. coli Bl21DE3 pRARE 2 (pink) and E. coli Rosetta (dark blue). The amplification product has a melting temperature of about 86 °C. Averages and standard deviations of three technical triplicates are shown.

Figure 27: Comparison of CUA tRNA amplification behavior of E. coli BL21DE3 (pink), E. coli Bl21DE3 pRARE 2 (dark blue) and E. coli Rosetta (light blue). The negative control is shown in black. Measurements were carried out in technical triplicates. Averages and standard deviations are shown.

Figure 28: Melting curve of CCC tRNA amplification mix quantity of E. coli BL21DE3 (green), E. coli Bl21DE3 pRARE 2 (pink) and E. coli Rosetta (dark blue). The amplification product has a melting temperature of about 86 °C. Averages and standard deviations of three technical triplicates are shown.

Outlook

The method shows promising results regarding detection of different tRNA concentration up to the range of very small concentration differences in diluted samples (fig. 15 – 21), nevertheless the method still needs to be further optimized. To make sure, the right amplification product for each codon is generated, it would be necessary to apply next generation sequencing. The difficulty that one faces here is the short length of the amplificate. Also, a reference method would be needed to confirm our results. As there is no method for specific tRNA quantification, another option would be, to measure artificially synthesized tRNA mixtures of known concentrations. Alternatively, deep sequencing could be used to bioinformatically examine the entire RNA for tRNAs contained in this RNA.

Growth curves Vibrio natriegens

Results

Vibrio natriegens was cultivated and samples were taken as described (Protocol_Growth_Curve_Vibrio_natriegens.pdf). The results are shown in figure 1. V. natriegens grew with a maximum growth rate of µ_max= 2,45 h^-1and reached a doubling time of t_d = 16,99 minutes.

Figure 1 : Growth curve V. Natriegens. The growth curve for the first biological replicate is in pink, the second biological replicate is shown with the dark blue curves and the thrid one in a light blue colour. Experiment was carried out in biological triplicates, the error bars represent the standard deviation.

Cloning of tRNA fragments into pSB1C3

The tRNA fragments were synthesized by IDT and amplified by PCR according to the PCR protocol (Protocol_PCR.pdf). The amplified tRNA fragments were validated via agarose gel electrophoresis (Stuttgart--Protocol_Agarose_Gel.pdf). Looking at Figure 1 all tRNA fragments showed a clear band at the desired height.

Figure 1: Amplified tRNA fragments. The tRNA fragments AGA, CGC, TGC, TCC and AGG were amplified via PCR. The PCR products were separated by agarose gel electrophoresis. A 2% agarose gel was prepared and 10 µL were loaded for each probe ((1): AGA, (2): CGC, (3): TGC, (4): TCC, (5): AGG). 3 µL of Hyberladder 1 kb Bioline were loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using MidoriGreen.

In a first step, the tRNA fragments were cloned into the pSB1C3 vector. The pSB1C3 and the tRNA fragments AGA, AGG, CGG, TGC, TCC and a combined tRNA fragment containing all 5 tRNAs were digested using the restriction enzymes XbaI and SpeI.
After purification, ( Protocol_Clean_and_Concentrate.pdf) the digested fragments were ligated using the T4 DNA ligase (see Protocol_BioBrick_Cloning.pdf). The ligated DNA fragments were transformed into DH5α ( Protocol_Transformation.pdf). The plasmid obtained from the colonies ( Protocol_Plasmid_Preparation.pdf) was digested with XbaI to gain linear Plasmid and separated by agarose gel electrophoresis ( Protocol_Agarose_Gel.pdf). Looking at Figure 2 the obtained plasmids showed no insert, only pSB1C3. Also visible is, that despite the digestion, circular, supercoiled and open circular structures of the plasmid are still present. This indicates inefficient digestion by the restriction enzymes.

Figure 2: Cloning of tRNA fragments into pSB1C3. The pSB1C3 and the tRNA fragments were digested using the restriction enzymes XbaI and SpeI. After purification, the digested fragments were ligated using the T4 DNA ligase. The ligated DNA fragments were transformed into DH5α and subsequently prepared. The obtained plasmids were digested with XbaI before the agarose gel electrophoresis. A 1% agarose gel was prepared and 10 µL were loaded for each probe ((1): AGA, (2): AGG, (3): CGG, (4): TGC, (5): TCC, (6): Combined tRNA fragment). As a control (C) the linear pSB1C3 was loaded. 3 µL of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

Since the cloning showed inefficient digestion by the enzymes XbaI and SpeI, it was performed again with the enzymes EcoRI-HF and PstI. The pSB1C3 and the tRNA fragments AGA, AGG, CGG, TGC, TCC and a combined tRNA fragment were digested using the restriction enzymes EcoRI-HF and PstI.
After purification, ( Protocol_Clean_and_Concentrate.pdf) the digested fragments were ligated using the T4 DNA ligase (see Protocol_BioBrick_Cloning.pdf). The ligated DNA fragments were transformed into DH5α cells ( Protocol_Transformation.pdf). The plasmid obtained from the colonies ( Protocol_Plasmid_Preparation.pdf) was digested with EcoRI-HF to gain linear Plasmid and separated by agarose gel electrophoresis (Protocol_Agarose_Gel.pdf). The agarose gel revealed no successful cloning as all obtained plasmids showed no insert, only pSB1C3 (data not shown).

Cloning of tRNA fragments into ptRNA_backbone via BioBrick Cloning

In a first step, the self-designed linear ptRNA_backbone from IDT was ligated according to the NEB Ligation Protocol with T4 DNA Ligase (see T--Stuttgart--Blunt_End_Ligation.pdf). Afterward, the ligated ptRNA-backbone was transformed in E. coli DH5a cells (see Protocol_Transformation.pdf). Successfully transformed DH5α cells were selected on LB agar plates containing tetracycline. The next day the circular ptRNA_backbone was prepared from the colonies according to the Plasmid Preparation protocol ( Protocol_Plasmid_Preparation.pdf). The plasmid obtained from the colonies was digested with EcoRI-HF to gain linear Plasmid and separated by agarose gel electrophoresis ( Protocol_Agarose_Gel.pdf). Looking at Figure 3 all plasmids run at the desired length which corresponds to the length of the ptRNA_backbone 2159 bp.

Figure 3: Cloning of ptRNA_backbone. The linear ptRNA_backbone fragment from IDT was ligated using the T4 DNA Ligase. The ligated ptRNA-backbone was transformed into DH5α and subsequently prepared. The obtained plasmids were digested with EcoRI-HF before the agarose gel electrophoresis. A 1% agarose gel was prepared and 10 µL were loaded for each probe ((1): ptRNA_backbone gBlock from IDT, (2): colony 2, (3): colony 3, (4): colony 4, (5): colony 5, (6): colony 6). 3 µL of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

The ptRNA_backbone and the previously amplified tRNA fragments AGA, AGG, CGG, TGC, TCC and a combined tRNA fragment were digested using the restriction enzymes EcoRI-HF and PstI. After purification, ( Protocol_Clean_and_Concentrate.pdf) the digested fragments were ligated using the T4 DNA ligase (see Protocol_BioBrick_Cloning.pdf). The ligated DNA fragments were transformed into DH5α ( Protocol_Transformation.pdf). The plasmid obtained from the colonies ( Protocol_Plasmid_Preparation.pdf) was digested with EcoRI-HF to gain linear Plasmid and separated by agarose gel electrophoresis ( Protocol_Agarose_Gel.pdf). Figure 4 reveals no successful cloning as all obtained Plasmids show no insert, only ptRNA_backbone.

Figure 4: Cloning of tRNA fragments into ptRNA_backbone. The ptRNA_backbone and the tRNA fragments were digested using the restriction enzymes EcoRI-HF and PstI. After purification, the digested fragments were ligated using the T4 DNA ligase. The ligated DNA fragments were transformed into DH5α and subsequently prepared. The obtained plasmids were digested with EcoRI-HF before the agarose gel electrophoresis. A 1% agarose gel was prepared and 10 µL were loaded for each probe ((1): AGA, (2): AGG, (3): CGG, (4): TGC, (5): TCC, (6): Combined tRNA fragment). As a control (C) the linear ptRNA_backbone was loaded. 3 µL of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

This BioBrick cloning was repeated several times using different EcoRI-HF and PstI stocks. Following transformation in DH5α revealed no successful cloning. The colonies obtained showed no insert in an agarose gel and only ptRNA_backbone. Following transformation in competent Vibrio natriegens cells also revealed no successful cloning (data not shown).

Cloning of tRNA fragments into ptRNA_backbone via Gibson Assembly

Cloning of tRNA fragments into ptRNA_backbone was also performed using Gibson Assembly. Gibson Assembly was conducted according to the protocol Gibson Assembly ( Protocol_Gibson_Assembly.pdf). The Gibson reaction was transformed into competent DH5α cells ( Protocol_Transformation.pdf). The plasmid obtained from the colonies ( Protocol_Plasmid_Preparation.pdf) was digested with EcoRI-HF to gain linear Plasmid and separated by agarose gel electrophoresis ( Protocol_Agarose_Gel.pdf). Figure 5 reveals no successful cloning as all obtained Plasmids show no insert, only ptRNA_backbone.

Figure 5: Gibson Assembly of tRNA fragments into ptRNA_backbone. Gibson Assembly was performed according to the Gibson Assembly Protocol. The Gibson Assembly reaction was transformed into DH5α and subsequently prepared. The obtained plasmids were digested with EcoRI-HF before the agarose gel electrophoresis. A 1 % agarose gel was prepared and 10 µL were loaded for each probe ((1): AGA, (2): AGG, (3): CGG, (4): TGC, (5): TCC). As a control (C) the linear ptRNA_backbone was loaded. 3 µL of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

Cloning of tRNA fragments into ptRNA_backbone via Gibson Assembly was repeated with another Gibson Assembly Master Mix and revealed no successful cloning. The colonies obtained showed no insert in an agarose gel and only ptRNA_backbone (data not shown).

Isolation of Vibrio natriegens DSM 759 genome chr.1 and amplification of tRNAs

As an alternative to cloning of tRNA fragments provided by IDT, the tRNAs AGA, AGG, CGG, TGC and TCC were amplified from the Vibrio natriegens DSM 759 genome. Therefore, the Vibrio natriegens DSM 759 genome chr.1 was isolated according to the gDNA Extraction protocol ( gDNA_extraction.pdf). The tRNA fragments AGA, AGG, CGG, TGC, TCC were amplified from the Vibrio natriegens DSM 759 genome via PCR with appropriate primers (see Protocol_PCR.pdf). Looking at Figure 6 all tRNA fragments showed a clear band at the desired height. The tRNA fragments were extracted from the agarose gel according to the gel extraction protocol ( Protocol_Gel_Extraction.pdf).

Figure 6: Amplification of tRNAs from the Vibrio natriegens DSM 759 genome. The Vibrio natriegens DSM 759 genome chr.1 was isolated according to the Protocol gDNA Extraction. The tRNA fragments AGA, AGG, CGG, TGC, TCC were amplified from the Vibrio natriegens DSM 759 genome via PCR with appropriate primers. A 1.5 % agarose gel was prepared and 10 µL were loaded for each probe ((1): AGA, (2): AGG, (3): CGG, (4): TGC, (5): TCC). 3 µL of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

Cloning of tRNA fragments (amplified from Vibrio natriegens DSM 759 genome) into ptRNA_backbone via BioBrick Cloning

The ptRNA_backbone and the previously amplified tRNA fragments AGA, AGG, CGG, TGC, TCC from the Vibrio natriegens DSM 759 genome were digested using the restriction enzymes EcoRI-HF and PstI. After purification, ( Protocol_Clean_and_Concentrate.pdf) the digested fragments were ligated using the T4 DNA ligase (see Protocol_BioBrick_Cloning.pdf). The ligated DNA fragments were transformed into competent DH5α cells ( Protocol_Transformation.pdf). The plasmid obtained from the colonies ( Protocol_Plasmid_Preparation.pdf) was digested with EcoRI-HF and PstI to release inserted tRNA fragments from the ptRNA_backbone and gain linear plasmid. The DNA fragments were separated by agarose gel electrophoresis ( Protocol_Agarose_Gel.pdf). Looking at Figure 7 no insert band was visible for the obtained plasmids, only ptRNA_backbone, suggesting no successful cloning.

Figure 7: BioBrick cloning of tRNA fragments into ptRNA_backbone. The tRNA fragments were previously amplified from the Vibrio natriegens DSM 759 genome. The ptRNA_backbone and the tRNA fragments were digested using the restriction enzymes EcoRI-HF and PstI. After purification, the digested fragments were ligated using the T4 DNA ligase. The ligated DNA fragments were transformed into DH5α and subsequently prepared. The obtained plasmids were digested with EcoRI-HF and PstI before the agarose gel electrophoresis. A 1% agarose gel was prepared and 10 µL were loaded for each probe ((1): AGA, (2): AGG, (3): CGG, (4): TGC, (5): ACC). As a control (C) the linear ptRNA_backbone was loaded. 3 µL of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

Following transformation in competent Vibrio natriegens cells also revealed no successful cloning (data not shown).

Cloning of tRNA fragments (amplified from Vibrio natriegens DSM 759 genome) into ptRNA_backbone via NEBuilder HiFi DNA Assembly

The tRNA fragments were previously amplified from Vibrio natriegens DSM 759 genome. The NEBuilder HiFi DNA Assembly was performed according to the Protocol NEBuilder HiFi DNA Assembly (https://2019.igem.org/wiki/images/2/25/T--Stuttgart--Protocols_NEBuilder_HiFi_DNA_Assembly.pdf). Following transformation into competent DH5α cells revealed no successful cloning as no colonies were obtained. Following transformation in competent Vibrio natriegens cells also revealed no successful cloning (data not shown).

Cloning of tRNA fragments (amplified from Vibrio natriegens DSM 759 genome) into ptRNA_backbone via Gibson Assembly

Gibson Assembly was performed according to the protocol Gibson Assembly ( https://2019.igem.org/wiki/images/6/6c/T--Stuttgart--Protocol_Gibson_Assembly.pdf). Due to the orientation in the Vibrio natriegens DSM 759 genome only the tRNA fragments AGG and TGC could be used for Gibson Assembly. The Gibson reaction was transformed into competent DH5α cells ( Protocol_Transformation.pdf). The plasmid obtained from the colonies ( Protocol_Plasmid_Preparation.pdf) was digested with EcoRI-HF and PstI to release inserted tRNA fragments from the ptRNA_backbone and gain linear plasmid. The DNA fragments were separated by agarose gel electrophoresis ( Protocol_Agarose_Gel.pdf). Looking at Figure 8 no insert band was visible for the obtained plasmids, only ptRNA_backbone, suggesting no successful cloning.

Figure 8: Gibson Assembly of tRNA fragments into ptRNA_backbone. Gibson Assembly was performed according to the Gibson Assembly Protocol. The tRNA fragments were previously amplified from the Vibrio natriegens DSM 759 genome. The Gibson Assembly reaction was transformed into DH5α and subsequently prepared. The obtained plasmids were digested with EcoRI-HF and PstI before the agarose gel electrophoresis. A 1% agarose gel was prepared and 10 µL were loaded for each probe ((1): AGG colony 1, (2): AGG colony 2, (3): TGC colony 1, (4): TGC colony 2). 3 µL of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

Cloning of tRNA fragments into ptRNA_backbone via Gibson Assembly was repeated with another Gibson Assembly Master Mix and revealed no successful cloning. The colonies obtained showed no insert in an agarose gel and only ptRNA_backbone. Following transformation of the Gibson reaction in competent Vibrio natriegens cells also revealed no successful cloning (data not shown).

Outlook

Regarding all experiments, several different cloning methods did not result in successful insertion of tRNA fragments in ptRNA_backbone or pSB1C3. Therefore, we commissioned Synbio-Technologies to perform the cloning. After three weeks the company was also unable to perform the cloning successfully. Since the company has newly synthesized the tRNA inserts and the ptRNA_backbone there should be no error in the DNA sequences and cloning. One explanation for unsuccessful cloning could be the toxicity of the tRNA constructs. Only cells that have taken up the ptRNA_backbone without insert survive and result in colonies due to spurious transcription. Impaired cell function can be due to de-repression of spurious transcription in bacteria. ¹ Constitutive transcription initiation can lead to titration of RNA polymerase and global downregulation in host gene expression. ²

For future experiments one conceivable approach would be the genomic integration of tRNA genes in order to increase the tRNA concentration without a plasmid system.

References

Wade JT, Grainger DC. Spurious transcription and its impact on cell function. Transcription. 2018. doi:10.1080/21541264.2017.1381794
Lamberte LE, Baniulyte G, Singh SS, et al. Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol. 2017. doi:10.1038/nmicrobiol.2016.249

Transformation of pRARE into Vibrio natriegens

As an alternative to cloning our self-designed ptRNA_backbone containing tRNAs of rare codons into Vibrio natriegens we used the pRARE plasmid. It carries genes for several rare tRNAs in Escherichia coli, which allows their concentration to be increased. The pRARE plasmid was prepared from E. coli Rosetta and transformed into Vibrio natriegens (Protocol_Transformation.pdf). Growth curves of the wild type Vibrio natriegens and Vibrio natriegens containing pRARE were performed (Protocol_Growth_Curve_Vibrio_natriegens.pdf). The growth curves represented in Figure 1 show no differences in the growth velocity between both Vibrio natriegens strain variants. Thus, the enhanced expression of tRNAs has no obvious negative effect on the metabolic activity of Vibrio natriegens cells.

Figure 1: Growth curve of Vibrio natriegens containing pRARE. The pRARE plasmid was prepared from E. coli Rosetta and transformed into Vibrio natriegens. Two colonies were selected for each Vibrio natriegens strain variants and a 5 mL starter culture of BHIN was inoculated. The culture was grown at 37 °C and 150 rpm overnight. 150 mL BHIN (500 mL shaking flask) were inoculated with preculture to an initial OD_{600 nm} of 0.05. Vibrio natriegens was cultivated at 37 °C and 150 rpm. OD_600nm was measured every 30 minutes in duplicates.

In order to investigate the possible positive effects of increased tRNA expression on protein expression, special sfGFP variants were supposed to be developed as explained in section Mutagenesis of sfGFP.

Mutagenesis of sfGFP

The vector pYTK047 containing sfGFP-Sequence was kindly provided by iGEM Team Marburg. To evaluate the expression of proteins containing rare codons (AGA, AGG, CGG, TGC, TCC) the tags of rare codons were introduced into the pYTK047. During the expression, the tags are fused to the N-terminus of the protein sfGFP. Thereby they determine the initial translation velocity of the expression of the fusion protein.

To insert the tags of rare codons into the pYTK047 genome, PCR with specialized primers was performed (for more detailed information see Q5_Site-directed_mutagenesis.pdf). To remove the unamplified template vector the PCR reaction was digested with Dpn1 and separated by agarose gel electrophoresis (Protocol_Agarose_Gel.pdf). Looking at Figure 1 only the constructs containing the tags AGA (1), AGG (2) and TGC (4) could be amplified by PCR.

Figure 1: Amplified pYTK047 with tags of rare codons. pYTK047 with tags of rare codons (AGA, AGG, CGC, TGC and TCC) were amplified via PCR. The PCR products were separated by agarose gel electrophoresis. A 1 % agarose gel was prepared and 50 µL were loaded for each probe ((1): pYTK047-AGA, (2): pYTK047-AGG, (3): pYTK047-CGG, (4): pYTK047-TGC, (5): pYTK047-TCC). 3 µL of Quick-Load® Purple 1 kb Plus DNA Ladder (NEB) were loaded as a Marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.

The bands of the desired size were cut out of the agarose gel and the DNA was extracted (Protocol_Gel_Extraction.pdf). A KLD ligation was performed according to the NEB KLD Enzyme Mix Reaction Protocol to circularize the extracted linear DNA. After ligation, the pYTK047 with the tags of rare codons was transformed in E. coli DH5α following the transformation protocol for chemical transformation (Protocol_Transformation.pdf). No colonies were obtained after transformation. The transformation was repeated, but the plasmid was not transformed successfully. The plasmid was supposed to be isolated from an overnight culture (Protocol_Plasmid_Preparation.pdf) and successful introduction of rare codons into plasmid pYTK047 should have been validated through sequencing. Transformation into Vibrio natriegens (Protocol_Transformation.pdf) and following growth curves or expression analysis should reveal if protein expression is impaired when rare codons are present.

In the last step, we wanted to investigate if the expression of proteins with rare codons can be rescued or even increased when a higher concentration of tRNAs for those rare codons are present. Therefore, pRARE from E. coli Rosetta was supposed to be transformed into V. natriegens together with pYTK047 containing sfGFP with rare codons. The plasmid pRARE codes for the tRNA of proL, leuW, metT, argW, thrT, glyT tyrU, thrU, argU and ileX and therefore increases their concentrations.

Media based on algae: first tests determining important substrates

Medium based on LB

To first determine whether the extract of chlorella vulgaris was a substitute for yeast extract, LB medium and medium containing chlorella vulgaris extract instead of yeast extract were produced.

Media were produced (Protocol_media_first_experiments.pdf).
Media were inoculated with escherichia coli or vibrio natriegens.
After the over night culture, the turbidity of the tubes was observed.

Result: Growth of both bacteria was observed in both media.

Medium without tryptone

To determine whether Chlorella vulgaris extract was able to substitute tryptone as a medium component, additionally, media containing different concentrations of NaCl Chlorella vulgaris extract and yeast extract were prepared.

Media were produced (Protocol_media_first_experiments.pdf).
Media were inoculated with vibrio natriegens.
After the overnight culture, the turbidity of the tubes was observed.

Result: No growth was detected in media without tryptone.

Autolysis in combination with bead-milling results

Free amino acid estimation with rFAN assay

Samples from Experiment Cell_extraction_with_autolysis_combined_with_bead-milling.pdf were used for the analysis.

Yeast extract is mostly obtained by autolysis ¹. In autolysis cells digest their own cell compounds with their own enzymes ². The idea was to transfer this commonly used principal on algae. Therefore, C. vulgaris and C. sorokiniana were heated to 50 °C in alkaline or acidic environment for 41 h. To further crack the cell wall, both algae were treated with bead-milling afterwards. To quantify the success of cell wall disruption free amino acids were measured with rFAN-assay.

The yield of free amino acids was set into relation with the amount of biomass used in the experiment (figure 1).

Figure 1: Autolysis and subsequent bead-milling of algae C. vulgaris and C. sorokiniana. The percentage of free amino acids [%] relates to the biomass used in the experiment.

The highest amounts of free amino acids (4.85 %) were reached with yeast at pH 12. Both algae showed very low yield in free amino acids. The best results showed C. sorokiniana at pH 12. It is possible, that the amount of glass beads and the size of the glass beads were too little, which led to less cell wall disruption. Therefore, amino acids would have been retained within the cells. This would explain the little amounts of free amino acids achieved with this method. Also, C. vulgaris and C. sorokinia have a cell wall, in contrast to yeast ³. Cell walls are harder to break, than a plasma membrane. This could explain the difference between the yeast samples and the algae samples. Due to the low yield in free amino acids, it was decided to investigate other methods for cell disruption of algae.

Anthrone assay to Determine Soluble Carbohydrate Concentration

Similar to the rFAN assay the anthrone assay is a method to detect free monosaccharides in a liquid. Therefor samples from the experiment

Experiments_AnthroneAssay.pdf were analyzed. Hereby a calibration curve with known amounts of glucose is created (Figure 2, left side). This calibration curve creates the possibility to calculate the sugar concentration of the samples (Figure 2, right side).

Figure 2: Pictures of the anthrone calibration curve as well as the anthrone assay of samples. For the calibration curve known amounts of glucose is dissolved in water and the optical density at 620 nm is measured (left side). This can be used to determine the monosaccharide concentration of anthone treated samples which previously underwent autolysis (pH3 or pH6) with or without subsequent bead-mill treatment (RKM) (right side).

One can tell from the coloring of the samples in figure 2, that the carbohydrate concentration should differ very slightly between the samples pH3, pH6, bead mill extraction +pH3 and bead mill extraction +pH6. Due to the cloudiness of the control sample, a background corrected optical density could not be determined. Therefore, the coloring scheme served as evaluation for successful carbohydrate determination.

Hereby, bead-mill (RKM) with subsequent autolysis at pH3 was determined to be the method of choice.

References

Kim et al., “Preparation of flavor-enhancing yeast extract using a Saccharomyces cerevisiae strain with high RNA content”, Korean J Food Sci Technol, 31 (2) (1999), pp. 475-481.
T.L. Babayan, M.G. Bezrukov, “Autolysis in yeasts”, Acta Biotechnol, 5 (2) (1985), pp. 129-136.
van der Rest, M E et al. “The plasma membrane of Saccharomyces cerevisiae: structure, function, and biogenesis.” Microbiological reviews vol. 59,2 (1995): 304-22.
Takeda, “Classification of Chlorella strains by cell wall sugar composition” Phytochemistry, vol. 27, 12, (1988), pp. 3823-3826.
[4} Takeda, “Classification of Chlorella strains by cell wall sugar composition” Phytochemistry, vol. 27, 12, (1988), pp. 3823-3826.

Results: Cell wall disruption of C. vulgaris and C. sorokiniana

For cell wall disruption of C. vulgaris and C. sorokiniana physical and chemical approaches were tested. One physical approach was bead milling with different amounts and sizes of glass beads. Also, one experiment was performed with beads with sharp edges. As an chemical approach for cell wall disruption, algae were boiled in acid or base at 100 °C for one hour (https://2019.igem.org/wiki/images/e/ec/T--Stuttgart--Protocol_Cell_extraction_with_autolysis_combined_with_bead-milling.pdf).

To quantify the amount of protein, received from the respective cell wall disruption method, Bradford-Assay (https://2019.igem.org/File:T--Stuttgart--Experiments_BradfordAssay.pdf) was performed. The amount of protein was related with the amount of used biomass. First we decided to test physical cell wall disruption (Fig. 1).

Figure 1: Percentage of protein [%] related to the used biomass of C. sorokiniana. The cell wall was disrupted by bead milling with glass beads in size 45-75 µm and 200-300 µm. 50 % and 80 % of glass beads were tested. The amount of protein was quantified with Bradford-Assay.

The highest amount of protein (15.6 %) was achieved with 80 % of glass beads with a size between 200-300 µm. The smaller glass beads reached up to 14.04 % of protein and were less efficient. A drastic difference can be seen between 50 % glass beads and 80 % glass beads. With the smaller beads the amount of glass beads used led to a difference of 11.93 %, similar to the bigger beads with a difference of 11.77 %. Therefore, 80% of glass beads was used for future cell wall disruption to create our PhyCoVi medium. Also, the bigger beads led to a higher yield of protein and were therefore chosen to be the future method for cell wall disruption.

An additional approach of physical cell wall disruption was to use special beads with sharp edges at different speeds (Fig. 2). The beads had a size of 2 mm.

Figure 2: Cell wall disruption with beads with sharp edges. Percentage of protein [%] is related to the used biomass of C. sorokiniana and C. vulgaris, respectively. For quantification of Protein, Bradford-Assay was used.

The highest yield of protein was gained with C. vulgaris at speed 8. Speed 4 always led to a lower yield of protein. C. sorokiniana reached a lower yield of protein with 1.19 %. The sharp-edged beads reached a lower yield of protein compared to the glass beads with a size of 200-300 µm. Hence, this method was not considered for further use.

To further optimate the cell wall disruption methods and increase the amount of usable sample, cell wall disruption with acid and base was tested. As bases we used 1 M KOH, 5 M KOH and 1 M NaOH, as acid 1 M HCl was used (Fig. 3).

Figure 3: Cell wall disruption with 1 M HCl, 1 M NaOH, 1 M KOH and 5 M KOH. The percentage of protein was related to the used biomass of C. sorokiniana. Samples were boiled for 1 h at 100 °C and later quantified with Bardford-Assay.

The highest yield of protein was reached with 5 M KOH with 9.03%. Lower amounts of protein were gained with 1M HCl and 1M KOH. NaOH led to the least yield of protein with 3.59 %.

After boiling the solutions had to be neutralized. Therefore, we used 1 M NaOH and 1 M HCl. Neutralizing HCl with NaOH leads to the formation of NaCl, which is a compound of the common cultivation medium for V. natriegens. Our PhyCoVi medium was primary created to be a medium for v. natriegens. Therefore, we chose cell disruption with 1 M HCl to be the future method.

All samples were also analyzed by the Anthrone Method (https://2019.igem.org/wiki/images/f/f3/T--Stuttgart--Experiments_AnthroneAssay.pdf), to quantify the amount of free sugars and starch. The anthrone reagent coagulates with sugars and starch. The more carbohydrates are available, the greener the samples appears and the higher the absorbance at 620 nm. Concerning different sizes of the glass beads, the small beads with 100 to 200 µm showed the best results. But also the high speed disruption with sharp edged glass beads around 2.0 mm showed good results (Fig. 4). Since this option is only available at the Max-Planck-Institute in Tübingen, we chose the options we had available in Stuttgart.

Figure 4: Amount of Carbohydrates [AU] in disrupted C. vulgaris and C. sorokiniana cells. The cell wall was disrupted by bead milling with glass beads in size 2.0 mm at high speed, 0.75 to 1.0 mm, 2.0 mm and 2.1 mm. The amount of Carbohydrates were quantified with anthrone assay

For the two volume ratios of glass beads to sample, the 80 % of 200 µm glass beads showed the best result. Generally more and bigger glass beads show better cell disruption.

Figure 5: Amount of Carbohydrates [AU] in disrupted C. sorokiniana cells. The cell wall was disrupted by bead milling with glass beads in size 45-75 µm and 200-300 µm. 50 % and 80 % of glass beads were tested. The amount of Carbohydrates were quantified with anthrone assay.

At last the acid and base disruption was examined. As seen in Fig. 6, all bases show low values, with 5 M KOH being unusable. With HCl reaching a similar level like glass beads, we chose this acid as our method for cell disruption. In combination with glass bead disruption, we hoped to have an efficient method for cell disruption of micro algaes.

Figure 6: Cell wall disruption with 1 M HCl, 1 M NaOH, 1 M KOH and 5 M KOH. Samples were boiled for 1 h at 100 °C. The amount of Carbohydrates were quantified with anthrone assay.

CDW correlation of algae Chlorella vulgaris Results

By plotting the measured optical densities against the means of the calculated cellular dry weights, a correlation was obtained. It is shown in the following figure.

Figure 1: OD-CDW correlation of the algae Chlorella vulgaris. Mean of cellular dry weight in g/L (n=2) was plotted against the measured optical density at 750 nm. Trend line was shown in red.

The trend line in figure 1 is poorly matching the trend of the measurement points. For this reason, the correlation curve was rejected. For improvement of this experiment, measurements should be performed only by one experimenter to reduce pipetting errors or other handling mistakes. Also the measurements should be taken over a longer time period to gain more trust worthy results.

CDW-OD correlation by dilution Results

In the following table you can see the calculated cell dry weights with the corresponding optical density of the tubes. Some tubes broke during the experiment so corresponding measurements could not occur.

Table 2: Calculated values of the cellular dry weight in g/l with the corresponding optical density measured at 750 nm.

OD	CDW[g/l]
4.87	0.98
4.41	0.88
4.44	0.91
4.02	0.8
3.92	0.82
3.52	0.68
3.57	0.71
3.03	0.57
2.65	0.49
2.8	0.5
2.43	0.48
2.56	0.46
2.29	0.4
2.28	0.4

The cellular dry weight in g/l was then plotted against the optical density measured at 750 nm. The plot with the corresponding trend line is shown in the following figure. Figure 1: Cellular dry weight in g/l is plotted against the optical density measured at 750 nm. The linear fit is shown in blue together with its formula.

The slope of the formula further been used for fast estimation of the CDW by measuring the optical density at 750 nm.

Results preliminary Chlorella vulgaris extraction methods (FACS analysis)

The obtained samples were measured at a flow-cytometer for green fluorescence (intact chlorophyll) as well as cell size (SSC and FSC). A distinct amount of liquid (50 µL) was measured. Based on the cell size (intact cells show a clear population) and green fluorescence, viable cells were able to be gated into a distinct population. With obtaining a distinct number of viable cells within a constant volume we were able to determine the number of viable cells per µL. The number of cells/µL of the control sample was set to 100% with the extraction methods (high-pressure-homogenizer passages 1 - 4, mortar, bead-mill, autoclave and sonification) set in relation of the control. We hereby obtained the percentage of viable cells for each cell disruption method (Figure 1).

Figure 1: Measured cell viability of Chlorella vulgaris after cell disruption methods. A distinct amount of cells was used to test each disruption method: high-pressure-homogenizer passage 1 - 4, mortar, bead-mill, autoclave and sonification. Afterwards 50 µL of the obtained samples were analyzed at the flow cytometry based on positive green fluorescence signal as well as intact cell signal (FSC, SSC). The cell count was measured, and the control was set to 100% cell viability with the cell count of the disruption methods set in relation to the control.

Conclusion:

In terms of feasibility and up-scaling problems the method we further wanted to analyze was the bead-mill. With a 50% cell viability it proved to be a rather solid method for cell disruption. We concluded that further research for the optimal bead size should be conducted as well as a combination with an autolytic process. The idea was that acid induced autolysis prior to the bead-mill treatment should weaken the strong microalgae cell wall and therefore decrease cell viability.

Growth Curves of various bacteria in PhyCoVi Medium

The PhyCoVi medium was tested with various microorganism including Vibrio natriegens, Escherichia coli, Bacillus subtillis and Corynebacterium glutamicum. Therefore, optical density was measured at 600 nm with a photometer . Different medium variations were tested to find the best medium composition. For control also normal LB medium, Brain-Heart-Infusion (BHIN) medium and medium containing only soy peptone was tested. Medium composition is shown in table 1.

Table 1: Specification for all media used during the algae based PhyCoVi medium (PCV) validation.

Ingredients	PCV [g/L]	PCV + Soy Peptone [g/L]	LB medium [g/L]	BHIN [g/L]	Soy Peptone Control [g/L]
NaCl	10 or 20
Algae extract	30	30	--	--	--
Soy Peptone	10	10	10	--	10
Yeast extract	--	--	5	--	--
BHI	--	--	--	37	--

To estimate the optimal medium composition for V. natriegens different NaCl concentrations were tested as well as the addition of soy peptone (Figure 1).

Figure 1: Growth curve of V. natriegens on PhyCoVi Medium (PCV) and PCV + Soy peptone. LB-Medium, Brain-Heart infusion Medium (BHIN) and soy peptone served as control. The medium contained different amounts of NaCl (10 or 20 g/L). Sampling for measuring optical density was performed every 45 minutes over a time course of 315 minutes.

The PCV medium containing additional soy peptone revealed the highest growth of V. natriegens. It even outcompeted the commonly used BHIN medium. V. natriegens cultivated in PCV medium without additional soy peptone showed remarkably less growth. LB and Soy peptone alone showed the least bacterial growth.

Next, bacterial growth of Escherichia coli MG1655 on PhyCoVi medium was tested (Figure 2).

Figure 2: Growth curve of E. coli in PhyCoVi Medium (PCV) and PCV + Soy peptone. LB-Medium, Brain-Heart infusion Medium (BHIN) and soy peptone served as control. The medium contained different amounts of NaCl (10 or 20 g/L). Sampling for measuring optical density was performed every 45 minutes over a time course of 315 minutes.

Highest bacterial growth was reached with PCV medium containing soy peptone and 10 g/L NaCl followed by the 20 g/L NaCl variant. The differences in E. coli growth on various media is not as clear as it was with V. natriegens (Figure 1). Also, the adapation phase is longer. Nevertheless, PhyCoVi medium with soy peptone is applicable for cultivation of E. coli.

Further, growth of Bacillus subtilis (Figure 3) and Corynebacterium glutamicum (Figure 4) were tested. Only medium containing 10 g/L NaCl was used.

Figure 3: Growth curve of Bacillus subtillis on PhyCoVi Medium (PCV) and PCV + soy peptone. LB-Medium, Brain-Heart infusion Medium (BHIN) and soy peptone served as control. The medium contained 10 g/L NaCl. Sampling for measurements of the optical density was performed every 45 minutes over a time course of 360 minutes.

Bacillus subitilis grew best on BHIN followed by LB medium. PCV medium with soy peptone was still better than PCV without it. Nevertheless, there was no remarkable increase in absorbance and thus only little growth of bacteria after 6 h.

Figure 4: Growth curve of Corynebacterium glutamicum on PhyCoVi Medium (PCV) and PCV + soy peptone. LB-Medium, Brain-Heart infusion Medium (BHIN) and soy pepton served as control. The medium contained 10 g/L NaCl. Sampling for measurements of the optical density was performed every 45 minutes over a time course of 360 minutes.

Corynebacterium glutamicum grew better on BHIN and LB than on PCV with or without soy peptone. PCV with additional soy peptone showed higher growth than medium without soy peptone. Comparing Bacillus subtilis with Corynebacterium glutamicum, C. glutamicum shows better growth on PCV containing soy peptone. Although both bacteria prefer BHIN and LB medium.

Sugar HPLC Results

The measurement was performed in six technical replicates of the algae extract batch PCV#2 from Chlorella vulgaris. The molar concentration of glucose, fructose, sucrose and raffinose were determined. The results of the carbohydrate HPLC measurement are shown in Table 1.

Table 1: Molar concentration [µM] of glucose, fructose, sucrose and raffinose in 30 g/l Chlorella vulgaris extract diluted in dH₂O measured in 6 technical replicates.

Carbohydrate	PCV#2.1 [µM]	PCV#2.2 [µM]	PCV#2.3 [µM]	PCV#2.4 [µM]	PCV#2.5 [µM]	PCV#2.6 [µM]
Glucose	2075.56	2040	1987.23	2199.63	2208.8	2119.68
Fructose	707.92	681.28	654.26	639.44	625.7	593.94
Sucrose	2.87	0	0	0	0	0
Raffinose	0	0	0	0	0	0

We were able to measure glucose and fructose in our samples. Raffinose was not detected at all. Sucrose was measured only in one sample, so we decided to reject its concentration.

By calculating the averages of the 6 replicates we were able to determine the amount of certain carbohydrate in gram per 100-gram Chlorella vulgaris extract. In 100 g C. vulgaris extract we obtained 1.264 g glucose and 0.391 g fructose.

Amino acid HPLC Results

For this experiment we measured three technical replicates of two batches of our self-made algae extract from Chlorella vulgaris with two concentrations 30 g/L and 60 g/L. The two measurements were performed to have a detectable amount of amino acids. Histidine in batch PCV#3 was only measured in the 60 g/L sample, he corresponding values were divided by 2 and added to the 30 g/L values. We calculated averages and standard deviations of the molar concentrations from the HPLC data for all 20 proteinogenic amino acids. To be able to compare the two batches PCV#2 and PCV#3, we plotted the average concentrations in a bar diagram. We were not able to distinguish between the peaks of alanine and arginine. For that reason, they were analyzed as one peak.

Figure 1: Bar diagram of average molar concentration of 20 proteinogenic amino acids from two batches of self-made algae extract from Chlorella vulgaris diluted in water (30g/l). In blue the prior extract with the ID: PCV#2. In green the final batch with ID: PCV#3.

It is noteworthy, that the batch PCV#3 shows a brighter spectrum of amino acids, than the prior batch PCV#2. When harvesting the algae for the batch PCV#3, we tried to optimize the protocol for extraction. The prior extraction protocol had some issues with product purity. The powder contained some disintegrated algae contaminants. However, we could achieve an improvement when it comes to amino acid content.

To create a content list for our algae C.vulgaris extract, we calculated the mass of amino acids per 100 gram extract for both batches PCV#2 and PCV#3. The corresponding list is shown in the following table.

Table 1: List of amino acid content in gram per 100 g Chlorella vulgaris extract.

Amino acid	g per 100 g PCV#2	g per 100 g PCV#3
Asp	0.070086304	0.057490545
Glu	0.040912751	0.049566772
Ser	0.010175455	0.017357337
His	0	0.000597254
Gly	0.010794219	0.022097401
Thr	0.044205579	0.007266782
Tyr	0	0.006698225
Cys	0	0.024702034
Val	0	0.01251605
Met	0.003853789	0.052499327
Trp	0	0.00494474
Phe	0	0.011192791
Ile	0	0.004606983
Leu	0.00132329	0.011335256
Lys	0	0.038419982
Pro	0.025929325	0.018145512

The total amount of proteinogenic amino acids in PCV#2 is 0.207 g per 100 g extract. In PCV#3 we have a total amount of 0.339 g per 100 g extract. With the optimized protocol we were able to achieve 0.6 times more proteinogenic amino acids per gram extract than before.

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+  small {
-        position: sticky;
+     text-align: justify;
-        top: 10rem;
+  }
-     }
-    .section-container {
-        padding: 3rem;
-    }
-</style>
+  .sticky {
+    position: sticky;
+    top: 10rem;
+  }
+  .section-container {
+    padding: 7rem 0 0 0;
+  }
+  .menu.sticky {
+    font-size: 12px;
+  }
+</style>
 <section class="hero is-primary">
-    <div class="hero-body">
+  <div class="hero-body">
-        <div class="container has-text-centered">
+    <div class="container has-text-centered">
-            <h2 class="subtitle">
+      <h2 class="subtitle">
-                Project
+        Project
-            </h2>
+      </h2>
-            <h1 class="title">
+      <h1 class="title">
-                Results
+        Results
-            </h1>
+      </h1>
-        </div>
      </div>
+  </div>
 </section>
 <div style="padding: 4rem 0;" class="container">
-    <div class="columns">
+  <div class="columns">
-        <div class="column is-one-fifth">
+    <div class="column is-one-fifth">
-            <aside class="menu sticky">
+      <aside class="menu sticky">
-                <p class="menu-label">
+        <p class="menu-label">
-                    Vibrio
+          Vibrio
-                </p>
+        </p>
-                <ul class="menu-list">
+        <ul class="menu-list">
-                    <li><a href="#qPCR">qPCR</a></li>
+          <li><a href="#qPCR">qPCR</a></li>
-                    <li><a href="#autolysis">Autolysis in combination <br/> with bead-milling Results</a></li>
+          <li>
-                    <li><a href="#cdwcorrelation">CDW correlation</a></li>
+            <a href="#growthVibrio">Growth curves <i>Vibrio natriegens</i></a>
-                    <li><a href="#cdwodcorrelation">CDW-OD correlation by dilution
+          </li>
-                        Results</a></li>
+          <li><a href="#cloningtRNA">Cloning of tRNA fragments</a></li>
-                </ul>
+          <li><a href="#transformationpRARE">Tansformation of pRARE into Vibrio natriegens</a></li>
-                <p class="menu-label">
+          <li><a href="#mutagenesis">Mutagenesis of sfGFP</a></li>
-                    Algae
+        </ul>
-                </p>
+        <p class="menu-label">
-             </aside>
+          Algae
+        </p>
+        <ul id="menu" class="menu-list">
+          <li><a href="#algae-media-based">Media based on algae</a></li>
+          <li>
+            <a href="#autolysis"
+            >Autolysis in combination <br />
+              with bead-milling Results</a
+            >
+          </li>
+          <li>
+            <a href="#celldisruption">Cell wall disruption of <i>C. vulgaris</i> and <i>C. sorokiniana</i> </a>
+          </li>
+          <li><a href="#cdwcorrelation">CDW correlation</a></li>
+          <li>
+            <a href="#cdwodcorrelation">CDW-OD correlation by dilution</a>
+          </li>
+          <li>
+            <a href="#preliminarycelldisruption">Preliminary Cell Disruption</a>
+          </li>
+          <li>
+            <a href="#growthCurvesOnBacteria">Growth Curves of various bacteria on PhyCoVi Medium </a>
+          </li>
+          <li>
+            <a href="#sugarHPLCResults">Sugar HPLC Results</a>
+          </li>
+        </ul>
+      </aside>
+    </div>
+    <div class="column">
+      <div id="qPCR" class="section-container">
+        <h2 class="title is-3">
+          qRT-PCR for the relative quantification of specific tRNA-species
+        </h2>
+        <p>
+          Alongside with the generation of a climate-friendly medium, the goal of our project PhyCoVi was to optimize
+          the strain
+          <em>Vibrio natriegens</em> for a potential use in the biotech industry. The optimization is performed on the
+          genomic level to increase the intracellular availability of tRNA species. As a result, the strain&rsquo;s
+          performance to express heterologous proteins is enhanced.
+        </p>
+        <br />
+        <p>
+          A method needs to be developed to quantify individual tRNA species specifically to prove the increased
+          expression not only on the protein level. &nbsp;Multiple methods can be found to quantify non-coding RNA
+          <sup>1, 2</sup> or total tRNA concentration<sup> 3, 4</sup>. Whereas finding a well-established method to
+          quantify single tRNA species specifically is in vain. The only method paper was published in the journal
+          &ldquo;RNA biology&rdquo; in 2015 by Honda <em>et al.</em>: &ldquo;Four-leaf clover qRT-PCR: A convenient
+          method for selective quantification of mature tRNA&rdquo; <sup>5</sup>. The authors of this paper removed
+          the amino acid at the 3&rsquo; end followed by hybridization and ligation with a DNA/RNA hybrid stem loop
+          creating a &ldquo;four-leaf clover&rdquo; shaped appearance of the tRNA ligation product. The stem loop
+          adaptor contained a TaqMan probe binding site. During the qPCR the TaqMan probe was cut by exonuclease
+          function of the used polymerase resulting in emission of fluorescence.
+        </p>
+        <br />
+        <p>
+          Building on the work of Honda <em>et al.</em> we developed a new and simplified method for relative
+          quantification of specific tRNA species without the necessity of TaqMan probes. Instead using a DNA/RNA
+          hybrid stem loop we used a linear DNA/RNA construct as adaptor.
+        </p>
+        <br />
+        <p>
+          The first step is to isolate RNA with a length of &lt; 200 nt from cultured <em>V. natriegens</em> cells.
+          Then, the amino acid bound to the 3&rsquo; end needs to be removed by a deacylation reaction. This results
+          in a sticky end, where a linear RNA/DNA hybrid adaptor can be ligated, which is complementary to the
+&rsquo; end overhang. Although different tRNAs show differences in length and sequence, the last three
+          nucleotides at the 3&rsquo; end are the same for all tRNA species. The ligated adaptor contains a binding
+          site for the forward-primer, which is identical for all tRNAs (unspecific primer). We used T4-RNA-ligase 2
+          that requires ATP. For this reason, a polynucleotide kinase was necessary to carry out a phosphorylation
+          reaction at the 5&rsquo; end.
+        </p>
+        <br />
+        <p>
+          To amplify single tRNA species specifically, we distinguished between two options. First option was using
+          the specific tRNA primer in a reverse transcription to convert the whole tRNA pool to cDNA. Following RNase
+          H digestion results in pure cDNA of the desired tRNA species.
+        </p>
+        <p>
+          Later the desired tRNA species is amplified during a qPCR by using the specific reverse primer and the
+          unspecific adaptor primer.
+        </p>
+        <p>
+          During qPCR a DNA-intercalating fluorescence dye (Green DNA dye) allows for relative quantification: Green
+          DNA dye binds to double stranded DNA and absorbs blue light and emits green light. The more double stranded
+          DNA is generated, the higher the resulting fluorescence. And the higher the concentration of the template in
+          the sample the faster the fluorescence exceeds the threshold. The number of cycles at which this happens is
+          called the threshold cycle (C<sub>t</sub>). (e.g. if sample A showed a C<sub>t</sub> of 8 and sample B
+          showed a C<sub>t</sub> of 11, sample A contained 2<sup>3</sup>&nbsp;= 8 times more template.)
+        </p>
+        <br />
+        <p>
+          After running a DNA gel, we noticed that the obtained amplification products did not show the expected
+          length. This may have been a result of distinct secondary structures of the tRNA species: the reverse
+          transcription reaction was performed at 42 &deg;C which is the enzyme&rsquo;s optimum working temperature.
+          However, this temperature is not high enough to prevent secondary structures or to break them up. Therefore,
+          areas with secondary structures may have been inaccessible for the reverse transcriptase resulting in
+          shorter cDNA fragments.
+        </p>
+        <br />
+        <p>
+          For this reason, we tested a second option to amplify single tRNA species specifically. A modified
+          polymerase together with the specific reverse primer can be used to amplify the desired tRNA species using
+          RNA as a template. This modified polymerase works at temperatures around 65 &deg;C and can use both RNA and
+          DNA as a template. The reverse transcription reaction is thus not needed as a consecutive step anymore.
+          Moreover, the modified enzyme creates the specific cDNA from RNA directly and the high temperature prevents
+          secondary structures. The relative quantification based on C<sub>t </sub>values is the same as in the option
+          described before.
+        </p>
+        <br /><br />
+        <div class="notification">
+          <h3 class="title is-5">References</h3>
+          <ol>
+            <li>
+              I. A. Babarinde, Y. Li, A. P. Hutchins (2019) Computational Methods for Mapping, Assembly and
+              Quantification for Coding and Non-coding Transcripts, Computational and Structural Biotechnology
+              Journal, Vol. 17, pp 628-637
+             </li>
+          </ol>
+          <br />
+          <ol start="2">
+            <li>
+              D. Jacob, K. Th&uuml;ring, A. Galliot, V. Marchand, A. Galvanin, A. Ciftci, K. Scharmann, M. Stock,
+              J.‐Y. Roignant, S.A. Leidel, Y. Motorin, R. Schaffrath, R. Klassen, M. Helm (2019) Absolute
+              Quantification of Noncoding RNA by Microscale Thermophoresis, Angewandte Chemie International Edition,
+              Vol. 58, pp 9565 &ndash; 9569
+            </li>
+          </ol>
+          <br />
+          <ol start="3">
+            <li>
+              T. S. Stenum, M. A. S&oslash;rensen, S. L. Svenningsen (2017) Quantification of the Abundance and
+              Charging Levels of Transfer RNAs in&nbsp;<em>Escherichia coli</em>.&nbsp;Journal of Visual Experiments,
+              Issue 126, e56212
+            </li>
+          </ol>
+          <br />
+          <ol start="4">
+            <li>
+              Y. Guo, A. Bosompem, S.Mohan, B. Erdogan, F.Ye, K. C. Vickers, Q. Sheng, S. Zhao, C. Li, P.-F. Su, M.
+              Jagasia, S. A. Strickland, E. A. Griffiths, A. S. Kim (2015) Transfer RNA detection by small RNA deep
+              sequencing and disease association with myelodysplastic syndromes, BMC Genomics, 16:727
+            </li>
+          </ol>
+          <br />
+          <ol start="5">
+            <li>
+              S. Honda, M. Shigematsu, K. Morichika, A. G. Telonis, Y. Kirino (2015) Four-leaf clover qRT-PCR: A
+              convenient method for selective quantification of mature tRNA, RNA Biology, Vol. 12, pp 501 &ndash; 508
+            </li>
+          </ol>
          </div>
-        <div class="column">
-            <div id="qPCR" class="section-container">
-                <h2 class="title is-3">qRT-PCR for the relative quantification of specific tRNA-species</h2>
-                <p>Alongside with the generation of a climate-friendly medium, the goal of our project PhyCoVi was to
-                    optimize the strain <em>Vibrio natriegens</em> for a potential use in the biotech industry. The
-                    optimization is performed on the genomic level to increase the intracellular availability of tRNA
-                    species. As a result, the strain&rsquo;s performance to express heterologous proteins is enhanced.
-                </p>
-                <br/>
-                <p>A method needs to be developed to quantify individual tRNA species specifically to prove the
-                    increased expression not only on the protein level. &nbsp;Multiple methods can be found to quantify
-                    non-coding RNA <sup>1, 2</sup> or total tRNA concentration<sup> 3, 4</sup>. Whereas finding a
-                    well-established method to quantify single tRNA species specifically is in vain. The only method
-                    paper was published in the journal &ldquo;RNA biology&rdquo; in 2015 by Honda <em>et al.</em>:
-                    &ldquo;Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA&rdquo;
-                    <sup>5</sup>. The authors of this paper removed the amino acid at the 3&rsquo; end followed by
-                    hybridization and ligation with a DNA/RNA hybrid stem loop creating a &ldquo;four-leaf clover&rdquo;
-                    shaped appearance of the tRNA ligation product. The stem loop adaptor contained a TaqMan probe
-                    binding site. During the qPCR the TaqMan probe was cut by exonuclease function of the used
-                    polymerase resulting in emission of fluorescence.</p>
-                <br/>
-                <p>Building on the work of Honda <em>et al.</em> we developed a new and simplified method for relative
-                    quantification of specific tRNA species without the necessity of TaqMan probes. Instead using a
-                    DNA/RNA hybrid stem loop we used a linear DNA/RNA construct as adaptor.</p>
-                <br/>
-                <p>The first step is to isolate RNA with a length of &lt; 200 nt from cultured <em>V. natriegens</em>
-                    cells. Then, the amino acid bound to the 3&rsquo; end needs to be removed by a deacylation reaction.
-                    This results in a sticky end, where a linear RNA/DNA hybrid adaptor can be ligated, which is
-                    complementary to the 3&rsquo; end overhang. Although different tRNAs show differences in length and
-                    sequence, the last three nucleotides at the 3&rsquo; end are the same for all tRNA species. The
-                    ligated adaptor contains a binding site for the forward-primer, which is identical for all tRNAs
-                    (unspecific primer). We used T4-RNA-ligase 2 that requires ATP. For this reason, a polynucleotide
-                    kinase was necessary to carry out a phosphorylation reaction at the 5&rsquo; end.</p>
-                <br/>
-                <p>To amplify single tRNA species specifically, we distinguished between two options. First option was
-                    using the specific tRNA primer in a reverse transcription to convert the whole tRNA pool to cDNA.
-                    Following RNase H digestion results in pure cDNA of the desired tRNA species.</p>
-                <p>Later the desired tRNA species is amplified during a qPCR by using the specific reverse primer and
-                    the unspecific adaptor primer.</p>
-                <p>During qPCR a DNA-intercalating fluorescence dye (Green DNA dye) allows for relative quantification:
-                    Green DNA dye binds to double stranded DNA and absorbs blue light and emits green light. The more
-                    double stranded DNA is generated, the higher the resulting fluorescence. And the higher the
-                    concentration of the template in the sample the faster the fluorescence exceeds the threshold. The
-                    number of cycles at which this happens is called the threshold cycle (C<sub>t</sub>). (e.g. if
-                    sample A showed a C<sub>t</sub> of 8 and sample B showed a C<sub>t</sub> of 11, sample A contained 2<sup>3</sup>&nbsp;=
-times more template.)</p>
-                <br/>
-                <p>After running a DNA gel, we noticed that the obtained amplification products did not show the
-                    expected length. This may have been a result of distinct secondary structures of the tRNA species:
-                    the reverse transcription reaction was performed at 42 &deg;C which is the enzyme&rsquo;s optimum
-                    working temperature. However, this temperature is not high enough to prevent secondary structures or
-                    to break them up. Therefore, areas with secondary structures may have been inaccessible for the
-                    reverse transcriptase resulting in shorter cDNA fragments.</p>
-                <br/>
-                <p>For this reason, we tested a second option to amplify single tRNA species specifically. A modified
-                    polymerase together with the specific reverse primer can be used to amplify the desired tRNA species
-                    using RNA as a template. This modified polymerase works at temperatures around 65 &deg;C and can use
-                    both RNA and DNA as a template. The reverse transcription reaction is thus not needed as a
-                    consecutive step anymore. Moreover, the modified enzyme creates the specific cDNA from RNA directly
-                    and the high temperature prevents secondary structures. The relative quantification based on
-                    C<sub>t </sub>values is the same as in the option described before.</p>
-                <br><br>
-                <div class="notification">
-                    <h3 class="title is-5">References</h3>
-                    <ol>
-                        <li>I. A. Babarinde, Y. Li, A. P. Hutchins (2019) Computational Methods for Mapping, Assembly
-                            and Quantification for Coding and Non-coding Transcripts, Computational and Structural
-                            Biotechnology Journal, Vol. 17, pp 628-637
-                        </li>
-                    </ol>
-                    <p>&nbsp;</p>
-                    <ol start="2">
-                        <li>D. Jacob, K. Th&uuml;ring, A. Galliot, V. Marchand, A. Galvanin, A. Ciftci, K. Scharmann, M.
-                            Stock, J.‐Y. Roignant, S.A. Leidel, Y. Motorin, R. Schaffrath, R. Klassen, M. Helm (2019)
-                            Absolute Quantification of Noncoding RNA by Microscale Thermophoresis, Angewandte Chemie
-                            International Edition, Vol. 58, pp 9565 &ndash; 9569
-                        </li>
-                    </ol>
-                    <p>&nbsp;</p>
-                    <ol start="3">
-                        <li>T. S. Stenum, M. A. S&oslash;rensen, S. L. Svenningsen (2017) Quantification of the
-                            Abundance and Charging Levels of Transfer RNAs in&nbsp;<em>Escherichia coli</em>.&nbsp;Journal
-                            of Visual Experiments, Issue 126, e56212
-                        </li>
-                    </ol>
-                    <p>&nbsp;</p>
-                    <ol start="4">
-                        <li>Y. Guo, A. Bosompem, S.Mohan, B. Erdogan, F.Ye, K. C. Vickers, Q. Sheng, S. Zhao, C. Li,
-                            P.-F. Su, M. Jagasia, S. A. Strickland, E. A. Griffiths, A. S. Kim (2015) Transfer RNA
-                            detection by small RNA deep sequencing and disease association with myelodysplastic
-                            syndromes, BMC Genomics, 16:727
-                        </li>
-                    </ol>
-                    <p>&nbsp;</p>
-                    <ol start="5">
-                        <li>S. Honda, M. Shigematsu, K. Morichika, A. G. Telonis, Y. Kirino (2015) Four-leaf clover
-                            qRT-PCR: A convenient method for selective quantification of mature tRNA, RNA Biology, Vol.
-, pp 501 &ndash; 508
-                        </li>
-                    </ol>
-                </div>
-            </div>
-            <br/><br/>
-            <div id="autolysis" class="section-container">
-                <h2 class="title is-3">Autolysis in combination with bead-milling Results</h2>
-                <h3 class="title is-4">Free amino acid estimation with rFAN assay</h3>
-                <p>
-                    Samples from Experiment <a target="_blank"
-                                               href="https://2019.igem.org/wiki/images/e/ec/T--Stuttgart--Protocol_Cell_extraction_with_autolysis_combined_with_bead-milling.pdf">Cell_extraction_with_autolysis_combined_with_bead-milling.pdf</a>
-                    were used for the analysis.
-                </p>
-                <br/>
-                <p>Yeast extract is mostly obtained by autolysis <sup>1</sup>. In autolysis cells digest their own cell
-                    compounds
-                    with their own enzymes <sup>2</sup>. The idea was to transfer this commonly used principal on algae.
-                    Therefore,
-                    <em>C. vulgaris </em>and <em>C. sorokiniana </em>were heated to 50&nbsp;&deg;C in alkaline or acidic
-                    environment for 41&nbsp;h. To further crack the cell wall, both algae were treated with bead-milling
-                    afterwards. To quantify the success of cell wall disruption free amino acids were measured with
-                    rFAN-assay.</p>
-                <br/>
-                <p>The yield of free amino acids was set into relation with the amount of biomass used in the experiment
-                    (figure 1).</p>
-                <div class="has-text-centered" style="width: 75%; margin:0 auto;">
+        <h2 class="title is-4">
-                    <canvas id="autolysis-figure-1"></canvas>
+          tRNA quantification of rare codons in <em>V. natriegens </em>with reverse transcription and the use of
-                 </div>
+          &lsquo;GreenMasterMix without ROX&rsquo;
+        </h2>
+        <p>
+          <strong>tRNA quantification of rare codons in <em>V. natriegens </em>with reverse transcriptase</strong>
+        </p>
+        <br />
+        <p>
+          At the beginning different parameters such as the temperatures during the qPCR or primer and RNA
+          concentrations in the sample preparation were tested. Samples were taken in mid exponential phase of
+          <em>V. natriegens</em>. After several experiments, the results of the optimized protocol are shown in figure
+. Experiments were conducted using the following protocols: <a
+                href="https://2019.igem.org/wiki/images/3/3d/T--Stuttgart--Purification_of_RNA_smaller_than_200_nucleotides.pdf"
+        >Purification_of_RNA_smaller_than_200_nucleotides.pdf</a
+        >,
+          <a href="https://2019.igem.org/wiki/images/f/f3/T--Stuttgart--Deacetylation_and_precipitation_of_tRNA.pdf"
+          >Deacetylation_and_precipitation_of_tRNA.pdf</a
+          >,
+          <a
+                  href="https://2019.igem.org/wiki/images/9/9f/T--Stuttgart--Reverse_transcription_of_the_specific_tRNA_species.pdf"
+          >Reverse_transcription_of_the_specific_tRNA_species.pdf</a
+          >,
+          <a href="https://2019.igem.org/wiki/images/a/a8/T--Stuttgart--Hybridization_and_ligation_of_tRNAs.pdf"
+          >Hybridization_and_ligation_of_tRNAs.pdf</a
+          >, <a href="https://2019.igem.org/wiki/images/7/73/T--Stuttgart--RT_qPCR.pdf">RT_qPCR.pdf</a>.
+        </p>
+        <br />
+        <div style=" ">
+          <canvas id="ReverseTranskriptaseAmplifikation"></canvas>
+        </div>
+        <br />
+        <small>
+          Figure 1: tRNA quantification of V. natriegens with &lsquo;GreenMasterMix without ROX&rsquo;: fluorescent
+          intensity over cycle number is shown. AGA is represented by the pink curve, AGG by the dark blue one, CGG is
+          coloured in light blue, GAA in green. The orange curve shows TCC and red TGC. The black curve shows the
+          negative control. The experiment was carried out in triplicates, the standard deviation is represented by
+          the error bars.
+        </small>
+        <br />
+        <br />
+        <p>
+          The first curve that appears at a C<sub>t</sub> value of 12.59 was AGA. AGG showed a C<sub>t</sub> value of
+.04. It is followed by GAA with 26.26 and TGC with 27.5. The C<sub>t</sub> value of 30.17 belongs to TCC.
+          The highest C<sub>t</sub> value showed CGG with 30.74 cycles.
+        </p>
+        Figure 2 &ndash; 7 show the melting curves of the qPCR products. A single peak indicates that there is only
+        one amplified product for each codon.
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="DispendixAGASchmelzkurve"></canvas>
+        </div>
+        <br />
+        <small>
+          Figure 2: The melting curve of the amplification product of the AGA tRNA in V. natriegens is shown. The
+          generated product has a melting temperature of about 77.5 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixAGGSchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 3: The melting curve of the amplification product of the AGG tRNA in V. natriegens is shown. The
+          amplification product has a melting temperature of about 77.5 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixCGGshmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 4: The melting curve of the amplification product of the CGG tRNA in V. natriegens is shown. The
+          melting temperature of the amplification product was about 77.5 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixGAASchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 5: The melting curve of the amplification product of the GAA tRNA in V. natriegens is shown. The
+          generated product has a melting temperature of about 77.5 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixTCCSchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 6: The melting curve of the amplification product of the TCC tRNA in V. natriegens is shown. The
+          amplified product has a melting temperature of about 77.5 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixTGCchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 7: The melting curve of the amplification product of the TGC tRNA in V. natriegens is shown. . The
+          melting temperature of the amplification product was about 77.5&nbsp;&deg;&nbsp;C.
+        </small>
+        <br />
+        <br />
+        <p>
+          After the protocol was established, we wanted to find out if we were able to detect any differences in tRNA
+          concentration between the exponential growth phase and the stationary phase. Therefore, we cultivated
+          <em>V. natriegens</em> and harvested cells after 1.5 h and 3 h for RNA isolation. Samples were treated as
+          usual but C<sub>t</sub> values for each tRNA species between the sampling times showed no differences (data
+          not shown).
+        </p>
+        <p>
+          To verify the RNA purification and the other steps of the protocol, purified and lyophilized
+          <em>E. coli</em> tRNA (Roche, Basel, Switzerland) was treated like the purified <em>V. natriegens</em> RNA.
+          Results of qPCR showed similar curve characteristics and C<sub>t</sub> values referring to the results based
+          on <em>V. natriegens </em>(data not shown).
+        </p>
+        <br />
+        <p>
+          <strong>tRNA quantification of rare codons in <em>V. natriegens </em>with HotScriptase</strong>
+        </p>
+        <br />
+        <p>
+          &ldquo;HotScriptase RT&rdquo;, a modified polymerase, is able to perform the reverse transcription of RNA
+          and the amplification of cDNA in one step. Due to the higher temperatures, tRNA secondary structure should
+          be reduced, which should lead to a more efficient reverse transcription. (<a
+                href="https://2019.igem.org/wiki/images/8/85/T--Stuttgart--RT_qPCR_without_prior_execution_of_a_reverse_transcription.pdf"
+        >RT_qPCR_without_prior_execution_of_a_reverse_transcription.pdf</a
+        >). Steps before the reverse transcription and qPCR, were the same as usual (<a
+                 href="Purification_of_RNA_smaller_than_200_nucleotides.pdf"
+        >Purification_of_RNA_smaller_than_200_nucleotides.pdf</a
+        >, <a href="Deacetylation_and_precipitation_of_tRNA.pdf">Deacetylation_and_precipitation_of_tRNA.pdf</a>,
+          <a href="https://2019.igem.org/wiki/images/a/a8/T--Stuttgart--Hybridization_and_ligation_of_tRNAs.pdf"
+          >Hybridization_and_ligation_of_tRNAs.pdf</a
+          >).
+        </p>
+        <br />
+        <div style=" ">
+          <canvas id="HotScriptaseAmplifikation"></canvas>
+        </div>
+        <small>
+          Figure 8: tRNA quantification of rare codons of V. natriegens with &ldquo;HotScriptase RT&rdquo;.
+          Fluorescence over cycle number is shown AGA is represented by the pink curve, AGG by the dark blue one, CGG
+          is colored in light blue, GAA in green. The orange curve shows TCC and red TGC. The black curve shows the
+          negative control. The experiment was carried out in duplicates.&nbsp;
+        </small>
+        <p>
+          <br />
+          As in the experiment before, codon AGA showed the highest intensity and the lowest C<sub>t</sub> value
+          (17.08). GAA, which normally should be the tRNA with the highest concentration, showed a C<sub>t</sub> value
+          of 25.63 followed by TGC with 25.79 and AGG with 25.92. The C<sub>t</sub> value of TCC was 28.2. CGG showed
+          the highest C<sub>t</sub> value of 28.98.
+        </p>
+        <div style=" ">
+          <canvas id="HotScriptaseSchmelzkurveAGA"></canvas>
+        </div>
+        <small>
+          Figure 9: The melting curve of the amplification product of the AGA tRNA in V. natriegens is shown. The
+          mainly generated product has a melting temperature of about 79 &deg; C. A second amplification product was
+          detected with a melting temperature of about 88 &deg;C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="HotScriptaseSchmelzkurveAGG"></canvas>
+        </div>
+        <small>
+          Figure 10: The melting curve of the amplification product of the AGG tRNA in V. natriegens is shown. The
+          mainly generated product has a melting temperature of about 88&nbsp;&deg;&nbsp;C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="HotScriptaseSchmelzkurveCGG"></canvas>
+        </div>
+        <small>
+          Figure 11: The melting curve of the amplification product of the CGG tRNA in V. natriegens is shown. The
+          amplification product has a melting temperature of about 88 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="HotScriptaseSchmelzkurveGAA"></canvas>
+        </div>
+        <small>
+          Figure 12: The melting curve of the amplification product of the GAA tRNA in V. natriegens is shown. The
+          amplification product has a melting temperature of about 87 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="HotScriptaseSchmelzkurveTCC"></canvas>
+        </div>
+        <small>
+          Figure 13: The melting curve of the amplification product of the TCC tRNA in V. natriegens is shown. The
+          amplification product has a melting temperature of about 87 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="HotScriptaseSchmelzkurveTGC"></canvas>
+        </div>
+        <small>
+          Figure 14: The melting curve of the amplification product of the TGC tRNA in V. natriegens is shown. The
+          amplification product has a melting temperature of about 87 &deg; C.
+        </small>
+        <br />
+        <br />
+        <br />
+        <br />
+        Figure 9 &ndash; 14 show the melting curves of the qPCR products generated using &ldquo;HotScriptase
+        RT&rdquo;. A single peak that there is only one amplified product for each codon. Figure 10 to 14 indicate,
+        that unspecific by-products may have been amplified.
+        <br />
+        <br />
+        <p>
+          <strong>tRNA quantification of rare codons in <em>V. natriegens </em>with diluted tRNA</strong>
+        </p>
+        <br />
+        <p>
+          Because the previous experiments did not reveal the expected result, we tried to proof that the method in
+          itself is able to detect different tRNA concentrations. Therefore the purified RNA (<a
+                href="https://2019.igem.org/wiki/images/3/3d/T--Stuttgart--Purification_of_RNA_smaller_than_200_nucleotides.pdf"
+        >Purification_of_RNA_smaller_than_200_nucleotides.pdf</a
+        >) was diluted 1:1, 1:10 and 1:100 and prepared as usual (<a
+                href="Deacetylation_and_precipitation_of_tRNA.pdf"
+        >Deacetylation_and_precipitation_of_tRNA.pdf</a
+        >, <a href="Hybridization_and_ligation_of_tRNAs.pdf">Hybridization_and_ligation_of_tRNAs.pdf</a>,
+          <a
+                  href="https://2019.igem.org/wiki/images/9/9f/T--Stuttgart--Reverse_transcription_of_the_specific_tRNA_species.pdf"
+          >Reverse_transcription_of_the_specific_tRNA_species.pdf</a
+          >, <a href="https://2019.igem.org/wiki/images/7/73/T--Stuttgart--RT_qPCR.pdf">RT_qPCR.pdf</a>). If sample A
+          showed a C<sub>t</sub> of 8 and sample B showed a C<sub>t</sub> of 11, sample A contained 2<sup>3</sup> = 8
+          times more template. Therefore, for a 10-fold dilution a difference in C<sub>t</sub> values of around &#8730;10
+          was expected.
+        </p>
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="VerduennungsversuchAmplifikation"></canvas>
+        </div>
+        <small>
+          Figure 15: Quantification of diluted tRNAs of the two codons AGA und AGG in <em>V. natriegens </em>with
+          RT-qPCR: Fluorescence over cycle number is shown. AGA 1:1 diluted is represented by pink color. AGA 1:10
+          diluted by dark blue and 1:100 diluted by light blue. GAA 1:1 is represented by the orange curve, GAA 1:10
+          by red and GAA 1:100 by dark grey. Also, negative controls are shown: AGA in green and GAA in black.&nbsp;
+          The experiment was carried out in triplicates. Average and standard deviation are shown.
+        </small>
+        <br />
+        <br />
+        <p>
+          Figure 15 shows, that our assumption was fulfilled. The C<sub>t</sub> values for AGA increased from 10.94 of
+          the undiluted concentration over 13.17 (1:10) to the 1:100 dilution with a C<sub>t</sub> value of 16.56. The
+          results for GAA are quite similar: lowest C<sub>t</sub> value was 24.15 (1:1) and increased to 27.35 (1:10)
+          and 31.29 (1:100).
+        </p>
+        <br />
+        <br />
+        <p>
+          After we were able to distinguish tRNA concentrations with a dilution factor of 1:10 significantly, we tried
+          to distinguish dilutions with factor 1:2, 1:4, 1:8 an 1:16.&nbsp; Because it was crucial for the results
+          that each component of the qPCR was pipetted in the right amount, all ingredients were pipetted by a
+          dispensing robot (iDOT, Dispendix GmbH, Stuttgart, Germany).
+        </p>
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixAGAamplifikation"></canvas>
+        </div>
+        <small>
+          Figure 16: Quantification of diluted tRNAs of the AGA in <em>V. natriegens </em>with RT-qPCR: Fluorescence
+          over cycle number is shown. AGA 1:1 dilution: pink, AGA 1:2 dilution: dark blue, AGA 1:4 dilution: light
+          blue, AGA 1:8 dilution: green, AGA 1:16 dilution: orange, AGA negative control: red. Average of three
+          technical triplicates and standard deviation are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixAGGamplifikation"></canvas>
+        </div>
+        <small>
+          Figure 17: quantification of diluted tRNAs of the AGG in <em>V. natriegens </em>with RT-qPCR: Fluorescence
+          over cycle number is shown. AGG 1:1 dilution: pink, AGG 1:2 dilution: dark blue, AGG 1:4 dilution: light
+          blue, AGG 1:8 dilution: green, AGG 1:16 dilution: orange, AGG negative control: red. Average of three
+          technical triplicates and standard deviation are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixCGGamplifikation"></canvas>
+        </div>
+        <small>
+          Figure 18: quantification of diluted tRNAs of the CGG&nbsp; in <em>V. natriegens </em>with RT-qPCR:
+          Fluorescence over cycle number is shown. CGG 1:1 dilution: pink, CGG 1:2 dilution: dark blue, CGG 1:4
+          dilution: light blue, CGG 1:8 dilution: green, CGG 1:16 dilution: orange, CGG negative control: red. Average
+          of three technical triplicates and standard deviation are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixGAAamplifikation"></canvas>
+        </div>
+        <small>
+          Figure 19: quantification of diluted tRNAs of the GAA in <em>V. natriegens </em>with RT-qPCR: Fluorescence
+          over cycle number is shown. GAA 1:1 dilution: pink, GAA 1:2 dilution: dark blue, GAA 1:4 dilution: light
+          blue, GAA 1:8 dilution: green, GAA 1:16 dilution: orange, GAA negative control: red. Average of three
+          technical triplicates and standard deviation are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixTCCamplifikation"></canvas>
+        </div>
+        <small>
+          Figure 20: quantification of diluted tRNAs of the TCC&nbsp; in <em>V. natriegens </em>with RT-qPCR:
+          Fluorescence over cycle number is shown. TCC 1:1 dilution: pink, TCC 1:2 dilution: dark blue, TCC 1:4
+          dilution: light blue, TCC 1:8 dilution: green, TCC 1:16 dilution: orange, TCC negative control: red. Average
+          of three technical triplicates and standard deviation are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="dispendixTGCamplifikation"></canvas>
+        </div>
+        <small>
+          Figure 21: quantification of diluted tRNAs of the TGC&nbsp; in <em>V. natriegens </em>with RT-qPCR:
+          Fluorescence over cycle number is shown. TGC 1:1 dilution: pink, TGC 1:2 dilution: dark blue, TGC 1:4
+          dilution: light blue, TGC 1:8 dilution: green, TGC 1:16 dilution: orange, TGC negative control: red. Average
+          of three technical triplicates and standard deviation are shown.
+        </small>
+        <br />
+        <br />
+        <p>
+          Figures 16 &ndash; 21 show the results of the second dilution experiment. Comparing C<sub>t</sub> values of
+          each tRNA species show significant differences between the original samples and the 1:2 dilution for the
+          rare codons CGG (fig. 18), GAA (fig. 19) and TGC (fig. 21). For the rare codons TCC (fig. 20) and AGG (fig.
+) significant differences in the C<sub>t</sub> values between the original sample and the 1:4 dilution
+          could be shown. A significant difference for the rare codon AGA (fig. 16) could be determined between the
+          original sample and 1:8 dilution.
+        </p>
+        <p>Significance was calculated by one way ANOVA followed by a posthoc analysis.</p>
+        <p>
+          <strong
+          ><em><br /> </em
+          ></strong>
+        </p>
+        <p><strong>&nbsp;</strong></p>
+        <p>
+          <strong>Comparison of tRNA concentration of rare codons in different <em>E. coli</em> strains</strong>
+        </p>
+        <br />
+        <p>
+          Actually, the goal was to compare the tRNA concentration of <em>V. natriegens</em> wildtype with the tRNA
+          concentration of our codon-optimized strain. The optimized strain was supposed to produce higher amounts of
+          rare tRNA species. Because the cloning turned out quite difficult, we decided to apply the qPCR method to
+          other strains. Therefore, <em>E. coli</em> BL21DE3, <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 and
+          <em>E. coli</em> Rosetta were cultivated (<a
+                href="https://2019.igem.org/wiki/images/6/64/T--Stuttgart--Protocol_Cultivation_Escherichia_coli_for_RNA_purification.pdf"
+        >Protocol_Cultivation_Escherichia_coli_for_RNA_purification.pdf</a
+        >). The strain carrying the pRARE 2 plasmid, should produce higher amounts of rare tRNA species. In case of
+          the Rosetta strain, the pRARE cassette was integrated into the genome. RNA was purified (<a
+                href="https://2019.igem.org/wiki/images/3/3d/T--Stuttgart--Purification_of_RNA_smaller_than_200_nucleotides.pdf"
+        >Purification_of_RNA_smaller_than_200_nucleotides.pdf</a
+        >) and treated as in the experiments with <em>V.&nbsp;natriegens</em> (<a
+                href="Deacetylation_and_precipitation_of_tRNA.pdf"
+        >Deacetylation_and_precipitation_of_tRNA.pdf</a
+        >, <a href="Hybridization_and_ligation_of_tRNAs.pdf">Hybridization_and_ligation_of_tRNAs.pdf</a>,
+          <a
+                  href="https://2019.igem.org/wiki/images/8/85/T--Stuttgart--RT_qPCR_without_prior_execution_of_a_reverse_transcription.pdf"
+          >RT_qPCR_without_prior_execution_of_a_reverse_transcription.pdf</a
+          >). In this experiment, tRNAs of the following rare codons were tested: AGA, AGG, CCC and CUA.
+        </p>
+        <p>
+          The results are shown in figures 21 &ndash; 28 C<sub>t </sub>values from <em>E. coli</em> pRARE 2 and
+          Rosetta are quite similar, but the values of the wildtype are always lower, which means that the
+          concentration is higher. This result does not comply with the assumption, that <em>E. coli</em> pRARE 2 and
+          Rosetta contain higher amounts of these tRNA species.
+        </p>
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichAGAAmplifikation"></canvas>
+        </div>
+        <small>
+          Figure 21: Comparison of AGA tRNA amplification behavior of <em>E. coli</em> BL21DE3 (pink),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (dark blue) and <em>E. coli</em> Rosetta (light blue). The negative
+          control is shown in black. Measurements were carried out in technical triplicates. Averages and standard
+          deviations are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichAGASchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 22: Melting curve of AGA tRNA amplification mix quantity of <em>E. coli</em> BL21DE3 (green),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (pink) and <em>E. coli</em> Rosetta (dark blue). The amplification
+          product has a melting temperature of about 86 &deg;C. Averages and standard deviations of three technical
+          triplicates are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichAGGAmplifikation"></canvas>
+        </div>
+        <small>
+          Figure 23: Comparison of AGG tRNA amplification behavior of <em>E. coli</em> BL21DE3 (pink),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (dark blue) and <em>E. coli</em> Rosetta (light blue). The negative
+          control is shown in black. Measurements were carried out in technical triplicates. Averages and standard
+          deviations are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichAGGSchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 24: Melting curve of AGG tRNA amplification mix quantity of <em>E. coli</em> BL21DE3 (green),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (pink) and <em>E. coli</em> Rosetta (dark blue). The amplification
+          product has a melting temperature of about 84,5 &deg;C. Averages and standard deviations of three technical
+          triplicates are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichCCCAmplifikation"></canvas>
+        </div>
+        <small>
+          Figure 25: Comparison of CCC tRNA amplification behavior of <em>E. coli</em> BL21DE3 (pink),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (dark blue) and <em>E. coli</em> Rosetta (light blue). The negative
+          control is shown in black. Measurements were carried out in technical triplicates. Averages and standard
+          deviations are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichCCCSchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 26: Melting curve of CCC tRNA amplification mix quantity of <em>E. coli</em> BL21DE3 (green),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (pink) and <em>E. coli</em> Rosetta (dark blue). The amplification
+          product has a melting temperature of about 86 &deg;C. Averages and standard deviations of three technical
+          triplicates are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichCUAAmplifikation"></canvas>
+        </div>
+        <small>
+          Figure 27: Comparison of CUA tRNA amplification behavior of <em>E. coli</em> BL21DE3 (pink),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (dark blue) and <em>E. coli</em> Rosetta (light blue). The negative
+          control is shown in black. Measurements were carried out in technical triplicates. Averages and standard
+          deviations are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <div style=" ">
+          <canvas id="EcoliVergleichCUASchmelzkurve"></canvas>
+        </div>
+        <small>
+          Figure 28: Melting curve of CCC tRNA amplification mix quantity of <em>E. coli</em> BL21DE3 (green),
+          <em>E.&nbsp;coli</em> Bl21DE3 pRARE 2 (pink) and <em>E. coli</em> Rosetta (dark blue). The amplification
+          product has a melting temperature of about 86 &deg;C. Averages and standard deviations of three technical
+          triplicates are shown.
+        </small>
+        <br />
+        <br />
+        <br />
+        <br />
-                <script>
+        <h2 class="title is-4">
-                    window.onload = function () {
+          Outlook
-                        var autolysisfigure1 = document.getElementById('autolysis-figure-1').getContext('2d');
+        </h2>
-                        window.myBar = new Chart(autolysisfigure1, {
+        <p>
-                            type: 'bar',
+          The method shows promising results regarding detection of different tRNA concentration up to the range of
-                            data: {
+          very small concentration differences in diluted samples (fig. 15 &ndash; 21), nevertheless the method still
-                                labels: ["yeast pH3",
+          needs to be further optimized. To make sure, the right amplification product for each codon is generated, it
-                                    "yeast pH12",
+          would be necessary to apply next generation sequencing. The difficulty that one faces here is the short
-                                    "C.vulgaris pH3",
+          length of the amplificate. Also, a reference method would be needed to confirm our results. As there is no
-                                    "C.vulgaris pH12",
+          method for specific tRNA quantification, another option would be, to measure artificially synthesized tRNA
-                                    "C.sorokeniana pH3",
+          mixtures of known concentrations. Alternatively, deep sequencing could be used to bioinformatically examine
-                                    "C.sorokeniana pH12",
+          the entire RNA for tRNAs contained in this RNA.
-                                ],
+        </p>
-                                datasets: [
+      </div>
-                                    {
+      <br />
-                                        backgroundColor: ["#3e95cd", "#3e95cd", "#3e95cd", "#3e95cd", "#3e95cd", "#3e95cd"],
+      <br />
-                                        label: "Population (millions)",
+      <div id="growthVibrio" class="section-container">
-                                        data: [3.132222386,
+        <h2 class="title is-3">Growth curves <em>Vibrio natriegens</em></h2>
-.852523798,
+        <br />
-.021842627,
+        <h2 class="title is-4">Results</h2>
-.037566219,
+        <p>
-.043678259,
+          Vibrio natriegens was cultivated and samples were taken as described (<a
-.087077261,
+                href="https://2019.igem.org/wiki/images/f/f0/T--Stuttgart--Protocol_Growth_Curve_Vibrio_natriegens.pdf"
-                                        ]
+        >Protocol_Growth_Curve_Vibrio_natriegens.pdf</a
-                                    }]
+        >). The results are shown in figure 1. <em>V. natriegens</em> grew with a maximum growth rate of
+          &micro;<sub>max</sub>= 2,45 h<sup>-1&nbsp; </sup>and reached a doubling time of
+          t<sub>d</sub>&nbsp;=&nbsp;16,99&nbsp;minutes.
+        </p>
+        <br />
-                            },
+        <div class="container">
-                            options: {
+          <div class="has-text-centered" style="width: 75%; margin:0 auto;">
-                                responsive: true,
+            <canvas id="growthVibrioFigure"></canvas>
-                                legend: {
+          </div>
-                                    position: 'top',
+        </div>
-                                }, scales: {
-                                    yAxes: [
-                                        {
-                                            scaleLabel: {
-                                                display: true,
-                                                labelString: "percentage of free amio acids [%]"
-                                            }
-                                        }
-                                    ]
-                                },
-                            }
-                        });
-                     };
+        <small>
-                 </script>
+          Figure 1
+          : Growth curve <em>V. Natriegens</em>. The growth curve for the first biological replicate is in pink,
+          the second biological replicate is shown with the dark blue curves and the thrid one in a light blue
+          colour.
+          Experiment was carried out in biological triplicates, the error bars represent the standard deviation.
+        </small>
+      </div>
+      <br />
+      <br />
+      <div id="cloningtRNA" class="section-container">
+        <h2 class="title is-3">Cloning of tRNA fragments into pSB1C3</h2>
+        <div class="columns">
+          <div class="column">
+            <p>
+              The tRNA fragments were synthesized by IDT and amplified by PCR according to the PCR protocol (<a
+                     href="https://2019.igem.org/wiki/images/f/f4/T--Stuttgart--Protocol_PCR.pdf"
+            >Protocol_PCR.pdf</a
+            >). The amplified tRNA fragments were validated via agarose gel electrophoresis (<a
+                    href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
+            >Stuttgart--Protocol_Agarose_Gel.pdf</a
+            >). Looking at Figure 1 all tRNA fragments showed a clear band at the desired height.
+            </p>
+            <img
+                    style="display: block; max-width: 500px; margin: 0 auto;"
+                    src="https://2019.igem.org/wiki/images/thumb/8/86/T--Stuttgart--Amplified_tRNA_fragments.png/592px-T--Stuttgart--Amplified_tRNA_fragments.png"
+            />
+            <small>
+              Figure 1: Amplified tRNA fragments. The tRNA fragments AGA, CGC, TGC, TCC and AGG were amplified via
+              PCR. The PCR products were separated by agarose gel electrophoresis. A 2% agarose gel was prepared and
+&micro;L were loaded for each probe ((1): AGA, (2): CGC, (3): TGC, (4): TCC, (5): AGG). 3 &micro;L of
+              Hyberladder 1 kb Bioline were loaded as a marker (M). The gel was run at 90 V for 1 hour and stained
+              using MidoriGreen.
+            </small>
+            <br />
+            <br />
+            <p>
+              In a first step, the tRNA fragments were cloned into the pSB1C3 vector. The pSB1C3 and the tRNA
+              fragments AGA, AGG, CGG, TGC, TCC and a combined tRNA fragment containing all 5 tRNAs were digested
+              using the restriction enzymes XbaI and SpeI. <br />
+              After purification, (<a
+                    href="https://2019.igem.org/wiki/images/3/3f/T--Stuttgart--Protocol_Clean_and_Concentrate.pdf"
+            >
+              Protocol_Clean_and_Concentrate.pdf</a
+            >) the digested fragments were ligated using the T4 DNA ligase (see
+              <a href="https://2019.igem.org/wiki/images/0/03/T--Stuttgart--Protocol_BioBrick_Cloning.pdf">
+                 Protocol_BioBrick_Cloning.pdf</a
+              >). The ligated DNA fragments were transformed into DH5&alpha; (<a
+                    href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
+            >
+              Protocol_Transformation.pdf</a
+            >). The plasmid obtained from the colonies (<a
+                    href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
+            >
+              Protocol_Plasmid_Preparation.pdf</a
+            >) was digested with XbaI to gain linear Plasmid and separated by agarose gel electrophoresis (<a
+                    href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
+            >
+              Protocol_Agarose_Gel.pdf</a
+            >). Looking at Figure 2 the obtained plasmids showed no insert, only pSB1C3. Also visible is, that
+              despite the digestion, circular, supercoiled and open circular structures of the plasmid are still
+              present. This indicates inefficient digestion by the restriction enzymes.
+            </p>
+            <br />
+            <img
+                    style="display: block; max-width: 500px; margin: 0 auto;"
+                    src="https://2019.igem.org/wiki/images/thumb/8/8f/T--Stuttgart--Cloning_of_tRNA_fragments_into_pSB1C3.png/722px-T--Stuttgart--Cloning_of_tRNA_fragments_into_pSB1C3.png"
+            />
+            <small>
+              Figure 2: Cloning of tRNA fragments into pSB1C3. The pSB1C3 and the tRNA fragments were digested using
+              the restriction enzymes XbaI and SpeI. After purification, the digested fragments were ligated using the
+              T4 DNA ligase. The ligated DNA fragments were transformed into DH5&alpha; and subsequently prepared. The
+              obtained plasmids were digested with XbaI before the agarose gel electrophoresis. A 1% agarose gel was
+              prepared and 10 &micro;L were loaded for each probe ((1): AGA, (2): AGG, (3): CGG, (4): TGC, (5): TCC,
+              (6): Combined tRNA fragment). As a control (C) the linear pSB1C3 was loaded. 3 &micro;L of GeneRuler,
+kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using
+              GelRed.
+            </small>
+            <br />
+            <br />
-                <small>Figure 1 -Autolysis and subsequent bead-milling of algae C. vulgaris and C. sorokiniana. The
+            <p>
-                    percentage of free amino acids [%] relates to the biomass used in the experiment.</small>
+              Since the cloning showed inefficient digestion by the enzymes XbaI and SpeI, it was performed again with
-                <br>
+              the enzymes EcoRI-HF and PstI. The pSB1C3 and the tRNA fragments AGA, AGG, CGG, TGC, TCC and a combined
-                <p>The highest amounts of free amino acids were reached with yeast at pH 12 with 4.85&nbsp;%. Both algae
+              tRNA fragment were digested using the restriction enzymes EcoRI-HF and PstI.<br />
-                    showed very low yield in free amino acids. The best results showed <em>C. sorokiniana</em> at pH&nbsp;12.
+              After purification, (<a
-                    It is possible, that the amount of glass beads and the size of the glass beads were to little, which
+                    href="https://2019.igem.org/wiki/images/3/3f/T--Stuttgart--Protocol_Clean_and_Concentrate.pdf"
-                    led
+            >
-                    to less cell wall disruption. Therefore, amino acids would have been retained within the cells. This
+              Protocol_Clean_and_Concentrate.pdf</a
-                    would explain the little amounts of free amino acids achieved with this method. Also, <em>C.
+            >) the digested fragments were ligated using the T4 DNA ligase (see
-                        vulgaris </em>and <em>C. sorokinia </em>have a cell wall, in contrast to yeast <sup>3</sup>>.
+              <a href="https://2019.igem.org/wiki/images/0/03/T--Stuttgart--Protocol_BioBrick_Cloning.pdf">
-                    Cell walls
+                Protocol_BioBrick_Cloning.pdf</a
-                    are
+              >). The ligated DNA fragments were transformed into DH5&alpha; cells (<a
-                    harder to break, than a plasma membrane. This could explain the difference between the yeast samples
+                     href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
-                    and
+            >
-                     the algae samples. Due to the low yield in free amino acids, it was decided to investigate other
+              Protocol_Transformation.pdf</a
-                    methods
+            >). The plasmid obtained from the colonies (<a
-                    for cell extraction of algae.</p>
+                    href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
-                <br>
+            >
-                <br>
+              Protocol_Plasmid_Preparation.pdf</a
-                <h3 class="title is-4">Anthrone assay to Determine Soluble Carbohydrate Concentration</h3>
+            >) was digested with EcoRI-HF to gain linear Plasmid and separated by agarose gel electrophoresis (<a
-                <p>Similar to the rFAN assay the anthrone assay is a method to detect free monosaccharides in a liquid.
+                    href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
-                    Therefor samples from the experiment <a
+            >Protocol_Agarose_Gel.pdf</a
-                            href="https://2019.igem.org/wiki/images/f/f3/T--Stuttgart--Experiments_AnthroneAssay.pdf">Experiments_AnthroneAssay.pdf</a>
+            >). The agarose gel revealed no successful cloning as all obtained plasmids showed no insert, only
-                    were analyzed. Hereby a calibration curve with known amounts of glucose is created (Figure 2, left
+              pSB1C3 (data not shown).
-                    side). This calibration curve creates the possibility to calculate the sugar concentration of the
+            </p>
-                    samples (Figure 2, right side).</p>
+            <br />
-                <img style="display: block; margin:0 auto;"
+            <h2 class="title is-5">
-                     src="https://2019.igem.org/wiki/images/thumb/2/2f/T--Stuttgart--FigureAutolysis_in_combination_with_bead-milling_Results2.png/800px-T--Stuttgart--FigureAutolysis_in_combination_with_bead-milling_Results2.png">
+              Cloning of tRNA fragments into ptRNA_backbone via BioBrick Cloning
-                <small>Figure 2: Pictures of the anthrone calibration curve as well as the anthrone assay of samples.
+            </h2>
-                    For the calibration curve known amounts of glucose is dissolved in water and the optical density at
-nm is measured (left side). This can be used to determine the monosaccharide concentration of
-                    anthone treated samples which previously underwent autolysis (pH3 or pH6) with or without subsequent
-                    bead-mill treatment (RKM) (right side).</small>
-                <br>
+            <p>
-                <br>
+              In a first step, the self-designed linear ptRNA_backbone from IDT was ligated according to the NEB
-                <p>One can tell from the coloring of the samples in figure 2, that the carbohydrate concentration should
+              Ligation Protocol with T4 DNA Ligase (see
-                    differ very slightly between the samples pH3, pH6, bead mill extraction +pH3 and bead mill
+              <a href="https://2019.igem.org/wiki/images/2/2e/T--Stuttgart--Blunt_End_Ligation.pdf">
-                    extraction +pH6. Due to the cloudiness of the control sample, a background corrected optical density
+                T--Stuttgart--Blunt_End_Ligation.pdf</a
-                    could not be determined. Therefore, the coloring scheme served as evaluation for successful
+              >). Afterward, the ligated ptRNA-backbone was transformed in <em>E. coli</em> DH5a cells (see
-                    carbohydrate determination.</p>
+              <a href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf">
-                <p>Hereby, bead-mill (RKM) with subsequent autolysis at pH3 was determined to be the method of
+                Protocol_Transformation.pdf</a
-                    choice.</p>
+              >). Successfully transformed DH5&alpha; cells were selected on LB agar plates containing tetracycline.
-                <br><br>
+              The next day the circular ptRNA_backbone was prepared from the colonies according to the Plasmid
-                <div class="notification">
+              Preparation protocol (<a
-                    <h3 class="title is-5">References</h3>
+                    href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
-                    <ol>
+            >
-                        <li>Kim et al., &ldquo;Preparation of flavor-enhancing yeast extract using a Saccharomyces
+              Protocol_Plasmid_Preparation.pdf</a
-                            cerevisiae strain with high RNA content&rdquo;, Korean J Food Sci Technol, 31 (2) (1999),
+            >). The plasmid obtained from the colonies was digested with EcoRI-HF to gain linear Plasmid and
-                            pp.
+              separated by agarose gel electrophoresis (<a
--481.
+                     href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
-                        </li>
+             >
-                        <li>T.L. Babayan, M.G. Bezrukov, &ldquo;Autolysis in yeasts&rdquo;, Acta Biotechnol, 5 (2)
+              Protocol_Agarose_Gel.pdf</a
-                            (1985), pp. 129-136.
+            >). Looking at Figure 3 all plasmids run at the desired length which corresponds to the length of the
-                        </li>
+              ptRNA_backbone 2159 bp.
-                        <li>van der Rest, M E et al. &ldquo;The plasma membrane of Saccharomyces cerevisiae: structure,
+            </p>
-                            function, and biogenesis.&rdquo; Microbiological reviews vol. 59,2 (1995): 304-22.
+            <br />
-                        </li>
+            <br />
-                        <li>Takeda, &ldquo;Classification of Chlorella strains by cell wall sugar composition&rdquo;
+            <img
-                            Phytochemistry, vol. 27, 12, (1988), pp. 3823-3826.
+                    style="display: block; max-width: 500px; margin: 0 auto;"
-                        </li>
+                    src="https://2019.igem.org/wiki/images/thumb/9/9f/T--Stuttgart--Cloning_of_ptRNA_backbone.png/510px-T--Stuttgart--Cloning_of_ptRNA_backbone.png"
-                        <li>[4} Takeda, &ldquo;Classification of Chlorella strains by cell wall sugar composition&rdquo;
+            />
-                            Phytochemistry, vol. 27, 12, (1988), pp. 3823-3826.
+            <small style="text-align: justify">
-                        </li>
+              Figure 3: Cloning of ptRNA_backbone. The linear ptRNA_backbone fragment from IDT was ligated using the
-                     </ol>
+              T4 DNA Ligase. The ligated ptRNA-backbone was transformed into DH5&alpha; and subsequently prepared. The
-                </div>
+              obtained plasmids were digested with EcoRI-HF before the agarose gel electrophoresis. A 1% agarose gel
-            </div>
+              was prepared and 10 &micro;L were loaded for each probe ((1): ptRNA_backbone gBlock from IDT, (2):
-            <br/><br/>
+              colony 2, (3): colony 3, (4): colony 4, (5): colony 5, (6): colony 6). 3 &micro;L of GeneRuler, 1kb Plus
-             <div id="cdwcorrelation" class="section-container">
+              DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.
-                <h2 class="title is-3">CDW correlation of algae <em>Chlorella vulgaris</em> Results</h2>
+            </small>
-                <p>
+            <br />
-                    By plotting the measured optical densities against the means of the calculated cellular dry weights,
+            <br />
-                    a correlation was obtained. It is shown in the following figure.
+            <p>
-                </p>
+              The ptRNA_backbone and the previously amplified tRNA fragments AGA, AGG, CGG, TGC, TCC and a combined
-                <br/>
+              tRNA fragment were digested using the restriction enzymes EcoRI-HF and PstI. After purification, (<a
-                <img style="display: block; max-width: 500px; margin: 0 auto;"
+                     href="https://2019.igem.org/wiki/images/3/3f/T--Stuttgart--Protocol_Clean_and_Concentrate.pdf"
-                     src="https://2019.igem.org/wiki/images/a/ad/T--Stuttgart--FigureOD-CDW_correlation_of_algae_Chlorella_vulgaris_Results1.png"/>
+            >
-                <small>Figure 1 - OD-CDW correlation of the algae <em>Chlorella vulgaris</em>. Mean of cellular dry
+              Protocol_Clean_and_Concentrate.pdf</a
-                    weight in g/L (n=2) was plotted against the measured optical density at 750 nm. Trend line was shown
+             >) the digested fragments were ligated using the T4 DNA ligase (see
-                    in red. </small>
+              <a href="https://2019.igem.org/wiki/images/0/03/T--Stuttgart--Protocol_BioBrick_Cloning.pdf">
-                <br>
+                 Protocol_BioBrick_Cloning.pdf</a
-                <br>
+              >). The ligated DNA fragments were transformed into DH5&alpha; (<a
-                <br>
+                    href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
-                <p>The trend line in figure 1 is poorly matching the trend of the measurement points. For this reason,
+            >
-                    the correlation curve was rejected. For improvement of this experiment, measurements should be
+              Protocol_Transformation.pdf</a
-                     performed only by one experimenter to reduce pipetting errors or other handling mistakes. Also the
+            >). The plasmid obtained from the colonies (<a
-                    measurements should be taken over a longer time period to gain more trust worthy results.</p>
+                     href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
-                <br>
+            >
-            </div>
+              Protocol_Plasmid_Preparation.pdf</a
-             <br/><br/>
+            >) was digested with EcoRI-HF to gain linear Plasmid and separated by agarose gel electrophoresis (<a
-            <div id="cdwodcorrelation" class="section-container">
+                     href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
-                 <h2 class="title is-3">CDW-OD correlation by dilution Results</h2>
+            >
-                <p>
+              Protocol_Agarose_Gel.pdf</a
-                    In the following table you can see the calculated cell dry weights with the corresponding optical
+            >). Figure 4 reveals no successful cloning as all obtained Plasmids show no insert, only ptRNA_backbone.
-                    density of the tubes. Some tubes broke during the experiment so corresponding measurements could not
+            </p>
-                     occur.
+            <br />
-                    <br/>
+            <br />
-                    <br/>
+            <br />
-                     <div class="columns">
-                        <div class="column">
-                            <small>Table 2 -Calculated values of the cellular dry weight in g/l with the corresponding
-                                optical
-                                density measured at 750 nm. </small>
-                            <table class="table is-fullwidth">
+            <img
-                                <thead>
+                    style="display: block; max-width: 500px; margin: 0 auto;"
-                                <tr>
+                    src="https://2019.igem.org/wiki/images/thumb/6/6a/T--Stuttgart--Cloning_of_tRNA_fragments_into_ptRNA_backbone.png/576px-T--Stuttgart--Cloning_of_tRNA_fragments_into_ptRNA_backbone.png"
-                                    <th>OD</th>
+            />
-                                    <th>CDW[g/l]</th>
+            <small>
-                                </tr>
+              Figure 4: Cloning of tRNA fragments into ptRNA_backbone. The ptRNA_backbone and the tRNA fragments were
-                                </thead>
+              digested using the restriction enzymes EcoRI-HF and PstI. After purification, the digested fragments
-                                <tbody>
+              were ligated using the T4 DNA ligase. The ligated DNA fragments were transformed into DH5&alpha; and
-                                <tr>
+              subsequently prepared. The obtained plasmids were digested with EcoRI-HF before the agarose gel
-                                    <td>4.87</td>
+              electrophoresis. A 1% agarose gel was prepared and 10 &micro;L were loaded for each probe ((1): AGA,
-                                    <td>0.98</td>
+              (2): AGG, (3): CGG, (4): TGC, (5): TCC, (6): Combined tRNA fragment). As a control (C) the linear
-                                </tr>
+              ptRNA_backbone was loaded. 3 &micro;L of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The
-                                <tr>
+              gel was run at 90 V for 1 hour and stained using GelRed.
-                                    <td>4.41</td>
+            </small>
-                                    <td>0.88</td>
+            <br />
-                                </tr>
+            <br />
-                                <tr>
+            <br />
-                                    <td>4.44</td>
+            <p>
-                                    <td>0.91</td>
+              This BioBrick cloning was repeated several times using different EcoRI-HF and PstI stocks. Following
-                                </tr>
+              transformation in DH5&alpha; revealed no successful cloning. The colonies obtained showed no insert in
-                                <tr>
+              an agarose gel and only ptRNA_backbone. Following transformation in competent Vibrio natriegens cells
-                                    <td>4.02</td>
+              also revealed no successful cloning (data not shown).
-                                    <td>0.8</td>
+            </p>
-                                </tr>
+            <br />
-                                <tr>
+            <br />
-                                    <td>3.92</td>
+            <h2 class="title is-5">
-                                    <td>0.82</td>
+              Cloning of tRNA fragments into ptRNA_backbone via Gibson Assembly
-                                </tr>
+            </h2>
-                                <tr>
-                                    <td>3.52</td>
-                                    <td>0.68</td>
-                                </tr>
-                                <tr>
-                                    <td>3.57</td>
-                                    <td>0.71</td>
-                                </tr>
-                                <tr>
-                                    <td>3.03</td>
-                                    <td>0.57</td>
-                                </tr>
-                                <tr>
-                                    <td>2.65</td>
-                                    <td>0.49</td>
-                                </tr>
-                                <tr>
-                                    <td>2.8</td>
-                                    <td>0.5</td>
-                                </tr>
-                                <tr>
-                                    <td>2.43</td>
-                                    <td>0.48</td>
-                                </tr>
-                                <tr>
-                                    <td>2.56</td>
-                                    <td>0.46</td>
-                                </tr>
-                                <tr>
-                                    <td>2.29</td>
-                                    <td>0.4</td>
-                                </tr>
-                                <tr>
-                                    <td>2.28</td>
-                                    <td>0.4</td>
-                                </tr>
-                                </tbody>
-                            </table>
-                        </div>
-                        <div class="column">
-                <p>
-                    The cellular dry weight in g/l was then plotted against the optical density measured at 750 nm. The
-                    plot with the corresponding trend line is shown in the following figure.
-                </p>
-                <img style="display: block; max-width: 500px; margin: 0 auto;"
+            <p>
-                     src="https://2019.igem.org/wiki/images/d/df/T--Stuttgart--FigureOD-CDW_correlation_of_Chlorella_vulgaris_by_dilution_Results1.png"/>
+              Cloning of tRNA fragments into ptRNA_backbone was also performed using Gibson Assembly. Gibson Assembly
-                <small>Figure 1 - Cellular dry weight in g/l is plotted against the optical density measured at 750 nm.
+              was conducted according to the protocol Gibson Assembly (<a
-                     The linear fit is shown in blue together with its formula.</small>
+                    href="https://2019.igem.org/wiki/images/6/6c/T--Stuttgart--Protocol_Gibson_Assembly.pdf"
-                <br>
+            >
-                <br>
+              Protocol_Gibson_Assembly.pdf</a
-                 <p>The slope of the formula further been used for fast estimation of the CDW by measuring the optical
+            >). The Gibson reaction was transformed into competent DH5&alpha; cells (<a
-                     density at 750 nm. </p>
+                    href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
+            >
+              Protocol_Transformation.pdf</a
+            >). The plasmid obtained from the colonies (<a
+                    href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
+            >
+              Protocol_Plasmid_Preparation.pdf</a
+            >) was digested with EcoRI-HF to gain linear Plasmid and separated by agarose gel electrophoresis (<a
+                    href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
+            >
+              Protocol_Agarose_Gel.pdf</a
+            >). Figure 5 reveals no successful cloning as all obtained Plasmids show no insert, only ptRNA_backbone.
+            </p>
+            <br />
+            <br />
+            <br />
+            <img
+                    style="display: block; max-width: 500px; margin: 0 auto;"
+                    src="https://2019.igem.org/wiki/images/thumb/8/82/T--Stuttgart--Gibson_Assembly_of_tRNA_fragments_into_ptRNA_backbone.png/527px-T--Stuttgart--Gibson_Assembly_of_tRNA_fragments_into_ptRNA_backbone.png"
+            />
+            <small
+            >Figure 5: Gibson Assembly of tRNA fragments into ptRNA_backbone. Gibson Assembly was performed
+              according to the Gibson Assembly Protocol. The Gibson Assembly reaction was transformed into DH5&alpha;
+              and subsequently prepared. The obtained plasmids were digested with EcoRI-HF before the agarose gel
+              electrophoresis. A 1 % agarose gel was prepared and 10 &micro;L were loaded for each probe ((1): AGA,
+              (2): AGG, (3): CGG, (4): TGC, (5): TCC). As a control (C) the linear ptRNA_backbone was loaded. 3
+              &micro;L of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1
+              hour and stained using GelRed.</small
+            >
+            <br />
+            <br />
+            <p>
+              Cloning of tRNA fragments into ptRNA_backbone via Gibson Assembly was repeated with another Gibson
+              Assembly Master Mix and revealed no successful cloning. The colonies obtained showed no insert in an
+              agarose gel and only ptRNA_backbone (data not shown).
+            </p>
+            <br />
+            <br />
+            <h2 class="title is-5">
+              Isolation of <em>Vibrio natriegens</em> DSM 759 genome chr.1 and amplification of tRNAs
+            </h2>
+            <p>
+              As an alternative to cloning of tRNA fragments provided by IDT, the tRNAs AGA, AGG, CGG, TGC and TCC
+              were amplified from the
+              <em>Vibrio natriegens</em> DSM 759 genome. Therefore, the <em>Vibrio natriegens</em> DSM 759 genome
+              chr.1 was isolated according to the gDNA Extraction protocol (<a
+                    href="https://2019.igem.org/wiki/images/c/c0/T--Stuttgart--gDNA_extraction.pdf"
+            >
+              gDNA_extraction.pdf</a
+            >). The tRNA fragments AGA, AGG, CGG, TGC, TCC were amplified from the <em>Vibrio natriegens</em> DSM
+genome via PCR with appropriate primers (see
+              <a href="https://2019.igem.org/wiki/images/f/f4/T--Stuttgart--Protocol_PCR.pdf"> Protocol_PCR.pdf</a>).
+              Looking at Figure 6 all tRNA fragments showed a clear band at the desired height. The tRNA fragments
+              were extracted from the agarose gel according to the gel extraction protocol (<a
+                     href="https://2019.igem.org/wiki/images/3/32/T--Stuttgart--Protocol_Gel_Extraction.pdf"
+            >
+              Protocol_Gel_Extraction.pdf</a
+            >).
+            </p>
+            <br />
+            <br />
+            <img
+                    style="display: block; max-width: 500px; margin: 0 auto;"
+                    src="https://2019.igem.org/wiki/images/thumb/3/31/T--Stuttgart--Amplification_of_tRNAs_from_Vibrio_natriegens_genome.png/800px-T--Stuttgart--Amplification_of_tRNAs_from_Vibrio_natriegens_genome.png"
+            />
+            <small
+            >Figure 6: Amplification of tRNAs from the Vibrio natriegens DSM 759 genome. The Vibrio natriegens DSM
+genome chr.1 was isolated according to the Protocol gDNA Extraction. The tRNA fragments AGA, AGG,
+              CGG, TGC, TCC were amplified from the Vibrio natriegens DSM 759 genome via PCR with appropriate primers.
+              A 1.5 % agarose gel was prepared and 10 &micro;L were loaded for each probe ((1): AGA, (2): AGG, (3):
+              CGG, (4): TGC, (5): TCC). 3 &micro;L of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The
+              gel was run at 90 V for 1 hour and stained using GelRed.
+            </small>
+            <br />
+            <br />
+            <br />
+            <br />
+            <h2 class="title is-5">
+              Cloning of tRNA fragments (amplified from <em>Vibrio natriegens</em> DSM 759 genome) into ptRNA_backbone
+              via BioBrick Cloning
+            </h2>
+            <p>
+              The ptRNA_backbone and the previously amplified tRNA fragments AGA, AGG, CGG, TGC, TCC from the
+              <em>Vibrio natriegens</em> DSM 759 genome were digested using the restriction enzymes EcoRI-HF and PstI.
+              After purification, (<a
+                    href="https://2019.igem.org/wiki/images/3/3f/T--Stuttgart--Protocol_Clean_and_Concentrate.pdf"
+            >
+              Protocol_Clean_and_Concentrate.pdf</a
+            >) the digested fragments were ligated using the T4 DNA ligase (see
+              <a href="https://2019.igem.org/wiki/images/0/03/T--Stuttgart--Protocol_BioBrick_Cloning.pdf">
+                 Protocol_BioBrick_Cloning.pdf</a
+              >). The ligated DNA fragments were transformed into competent DH5&alpha; cells (<a
+                    href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
+            >
+              Protocol_Transformation.pdf</a
+            >). The plasmid obtained from the colonies (<a
+                    href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
+            >
+              Protocol_Plasmid_Preparation.pdf</a
+            >) was digested with EcoRI-HF and PstI to release inserted tRNA fragments from the ptRNA_backbone and
+              gain linear plasmid. The DNA fragments were separated by agarose gel electrophoresis (<a
+                    href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
+            >
+              Protocol_Agarose_Gel.pdf</a
+            >). Looking at Figure 7 no insert band was visible for the obtained plasmids, only ptRNA_backbone,
+              suggesting no successful cloning.
+            </p>
+            <br />
+            <br />
+            <br />
+            <img
+                    style="display: block; max-width: 500px; margin: 0 auto;"
+                    src="https://2019.igem.org/wiki/images/thumb/5/5e/T--Stuttgart--Biobrick_cloning_of_tRNA_fragments_into_ptRNA_backbone.png/521px-T--Stuttgart--Biobrick_cloning_of_tRNA_fragments_into_ptRNA_backbone.png"
+            />
+            <small>
+              Figure 7: BioBrick cloning of tRNA fragments into ptRNA_backbone. The tRNA fragments were previously
+              amplified from the Vibrio natriegens DSM 759 genome. The ptRNA_backbone and the tRNA fragments were
+              digested using the restriction enzymes EcoRI-HF and PstI. After purification, the digested fragments
+              were ligated using the T4 DNA ligase. The ligated DNA fragments were transformed into DH5&alpha; and
+              subsequently prepared. The obtained plasmids were digested with EcoRI-HF and PstI before the agarose gel
+              electrophoresis. A 1% agarose gel was prepared and 10 &micro;L were loaded for each probe ((1): AGA,
+              (2): AGG, (3): CGG, (4): TGC, (5): ACC). As a control (C) the linear ptRNA_backbone was loaded. 3
+              &micro;L of GeneRuler, 1kb Plus DNA Ladder was loaded as a marker (M). The gel was run at 90 V for 1
+              hour and stained using GelRed.
+            </small>
+            <p>
+              Following transformation in competent Vibrio natriegens cells also revealed no successful cloning (data
+              not shown).
+            </p>
+            <br />
+            <br />
+            <h3 class="title is-5">
+              Cloning of tRNA fragments (amplified from
+              <em>Vibrio natriegens</em> DSM 759 genome) into ptRNA_backbone via NEBuilder HiFi DNA Assembly
+            </h3>
+            <p>
+              The tRNA fragments were previously amplified from
+              <em>Vibrio natriegens</em> DSM 759 genome. The NEBuilder HiFi DNA Assembly was performed according to
+              the Protocol NEBuilder HiFi DNA Assembly (<a
+                    href="https://2019.igem.org/wiki/images/2/25/T--Stuttgart--Protocols_NEBuilder_HiFi_DNA_Assembly.pdf"
+            >https://2019.igem.org/wiki/images/2/25/T--Stuttgart--Protocols_NEBuilder_HiFi_DNA_Assembly.pdf</a
+            >). Following transformation into competent DH5&alpha; cells revealed no successful cloning as no
+              colonies were obtained. Following transformation in competent <em>Vibrio natriegens</em> cells also
+              revealed no successful cloning (data not shown).
+            </p>
+            <br />
+            <br />
+            <h3 class="title is-5">
+              Cloning of tRNA fragments (amplified from
+              <em>Vibrio natriegens</em> DSM 759 genome) into ptRNA_backbone via Gibson Assembly
+            </h3>
+            <p>
+              Gibson Assembly was performed according to the protocol Gibson Assembly (<a
+                    href="https://2019.igem.org/wiki/images/6/6c/T--Stuttgart--Protocol_Gibson_Assembly.pdf"
+            >
+              https://2019.igem.org/wiki/images/6/6c/T--Stuttgart--Protocol_Gibson_Assembly.pdf</a
+            >). Due to the orientation in the <em>Vibrio natriegens</em> DSM 759 genome only the tRNA fragments AGG
+              and TGC could be used for Gibson Assembly. The Gibson reaction was transformed into competent DH5&alpha;
+              cells (<a href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf">
+              Protocol_Transformation.pdf</a
+            >). The plasmid obtained from the colonies (<a
+                    href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
+            >
+              Protocol_Plasmid_Preparation.pdf</a
+            >) was digested with EcoRI-HF and PstI to release inserted tRNA fragments from the ptRNA_backbone and
+              gain linear plasmid. The DNA fragments were separated by agarose gel electrophoresis (<a
+                    href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
+            >
+              Protocol_Agarose_Gel.pdf</a
+            >). Looking at Figure 8 no insert band was visible for the obtained plasmids, only ptRNA_backbone,
+              suggesting no successful cloning.
+            </p>
+            <br />
+            <br />
+            <br />
+            <img
+                     style="display: block; max-width: 500px; margin: 0 auto;"
+                    src="https://2019.igem.org/wiki/images/thumb/9/99/T--Stuttgart--Gibson_Assembly_of_tRNA_fragments_-2.png/512px-T--Stuttgart--Gibson_Assembly_of_tRNA_fragments_-2.png"
+            />
+            <small>
+              Figure 8: Gibson Assembly of tRNA fragments into ptRNA_backbone. Gibson Assembly was performed according
+              to the Gibson Assembly Protocol. The tRNA fragments were previously amplified from the Vibrio natriegens
+              DSM 759 genome. The Gibson Assembly reaction was transformed into DH5&alpha; and subsequently prepared.
+              The obtained plasmids were digested with EcoRI-HF and PstI before the agarose gel electrophoresis. A 1%
+              agarose gel was prepared and 10 &micro;L were loaded for each probe ((1): AGG colony 1, (2): AGG colony
+, (3): TGC colony 1, (4): TGC colony 2). 3 &micro;L of GeneRuler, 1kb Plus DNA Ladder was loaded as a
+              marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.
+            </small>
+            <br />
+            <br />
+            <br />
+            <p>
+              Cloning of tRNA fragments into ptRNA_backbone via Gibson Assembly was repeated with another Gibson
+              Assembly Master Mix and revealed no successful cloning. The colonies obtained showed no insert in an
+              agarose gel and only ptRNA_backbone. Following transformation of the Gibson reaction in competent
+              <em>Vibrio natriegens</em> cells also revealed no successful cloning (data not shown).
+            </p>
+            <br />
+            <br />
+            <br />
+            <h3 class="title is-4">Outlook</h3>
+            <p>
+              Regarding all experiments, several different cloning methods did not result in successful insertion of
+              tRNA fragments in ptRNA_backbone or pSB1C3. Therefore, we commissioned Synbio-Technologies to perform
+              the cloning. After three weeks the company was also unable to perform the cloning successfully. Since
+              the company has newly synthesized the tRNA inserts and the ptRNA_backbone there should be no error in
+              the DNA sequences and cloning. One explanation for unsuccessful cloning could be the toxicity of the
+              tRNA constructs. Only cells that have taken up the ptRNA_backbone without insert survive and result in
+              colonies due to spurious transcription. Impaired cell function can be due to de-repression of spurious
+              transcription in bacteria. <sup>1</sup> Constitutive transcription initiation can lead to titration of
+              RNA polymerase and global downregulation in host gene expression. <sup>2</sup>
+            </p>
+            <br />
+            <p>
+              For future experiments one conceivable approach would be the genomic integration of tRNA genes in order
+              to increase the tRNA concentration without a plasmid system.
+            </p>
+            <br />
+            <br />
+            <br />
+            <div class="notification">
+              <h3 class="title is-5">References</h3>
+              <ol>
+                <li>
+                  Wade JT, Grainger DC. Spurious transcription and its impact on cell function.
+                  <em>Transcription</em>. 2018. doi:10.1080/21541264.2017.1381794
+                </li>
+                <li>
+                  Lamberte LE, Baniulyte G, Singh SS, et al. Horizontally acquired AT-rich genes in Escherichia coli
+                  cause toxicity by sequestering RNA polymerase. <em>Nat Microbiol</em>. 2017.
+                  doi:10.1038/nmicrobiol.2016.249
+                </li>
+              </ol>
              </div>
+          </div>
          </div>
+      </div>
+      <br />
+      <br />
+      <div id="transformationpRARE" class="section-container">
+        <h1 class="title is-3">Transformation of pRARE into <em>Vibrio natriegens</em></h1>
+        <p>
+          As an alternative to cloning our self-designed ptRNA_backbone containing tRNAs of rare codons into
+          <em>Vibrio natriegens</em> we used the pRARE plasmid. It carries genes for several rare tRNAs in
+          <em>Escherichia coli</em>, which allows their concentration to be increased. The pRARE plasmid was prepared
+          from <em>E. coli</em> Rosetta and transformed into <em>Vibrio natriegens&nbsp;(</em
+        ><a href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
+        >Protocol_Transformation.pdf</a
+        >). Growth curves of the wild type <em>Vibrio natriegens</em> and <em>Vibrio natriegens</em> containing
+          pRARE were performed (<a
+                href="https://2019.igem.org/wiki/images/f/f0/T--Stuttgart--Protocol_Growth_Curve_Vibrio_natriegens.pdf"
+        >Protocol_Growth_Curve_Vibrio_natriegens.pdf</a
+        >). The growth curves represented in Figure 1 show no differences in the growth velocity between both
+          <em>Vibrio natriegens</em> strain variants. Thus, the enhanced expression of tRNAs has no obvious negative
+          effect on the metabolic activity of <em>Vibrio natriegens</em> cells.
+        </p>
+        <br />
+        <div class="has-text-centered" style="width: 75%; margin:0 auto;">
+          <canvas id="transformationprare1"></canvas>
+        </div>
+        <small>
+          Figure 1:&nbsp; Growth curve of Vibrio natriegens containing pRARE. The pRARE plasmid was prepared from E.
+          coli Rosetta and transformed into Vibrio natriegens. Two colonies were selected for each Vibrio natriegens
+          strain variants and a 5 mL starter culture of BHIN was inoculated. The culture was grown at 37 &deg;C and
+rpm overnight. 150 mL BHIN (500 mL shaking flask) were inoculated with preculture to an initial OD<sub
+        >600 nm</sub
+        >
+          of 0.05. Vibrio natriegens was cultivated at 37 &deg;C and 150 rpm. OD<sub>600nm</sub> was measured every 30
+          minutes in duplicates.
+        </small>
+        <br />
+        <br />
+        <p>
+          In order to investigate the possible positive effects of increased tRNA expression on protein expression,
+          special sfGFP variants were supposed to be developed as explained in section Mutagenesis of
+          sfGFP.&nbsp;&nbsp;
+        </p>
+      </div>
+      <br />
+      <br />
+      <div id="mutagenesis" class="section-container">
+        <h2 class="title is-3">
+          Mutagenesis of sfGFP
+        </h2>
+        <p>
+          The vector pYTK047 containing sfGFP-Sequence was kindly provided by iGEM Team Marburg. To evaluate the
+          expression of proteins containing rare codons (AGA, AGG, CGG, TGC, TCC) the tags of rare codons were
+          introduced into the pYTK047. During the expression, the tags are fused to the N-terminus of the protein
+          sfGFP. Thereby they determine the initial translation velocity of the expression of the fusion protein.
+        </p>
+        <p>
+          To insert the tags of rare codons into the pYTK047 genome, PCR with specialized primers was performed (for
+          more detailed information see
+          <a href="https://2019.igem.org/wiki/images/e/ed/T--Stuttgart--Q5_Site-directed_mutagenesis.pdf"
+          >Q5_Site-directed_mutagenesis.pdf</a
+          >). To remove the unamplified template vector the PCR reaction was digested with Dpn1 and separated by
+          agarose gel electrophoresis (<a
+                href="https://2019.igem.org/wiki/images/b/ba/T--Stuttgart--Protocol_Agarose_Gel.pdf"
+        >Protocol_Agarose_Gel.pdf</a
+        >). Looking at Figure 1 only the constructs containing the tags AGA (1), AGG (2) and TGC (4) could be
+          amplified by PCR.&nbsp;
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                style="display: block; margin: 0 auto;"
+                src="https://2019.igem.org/wiki/images/4/4e/T--Stuttgart--Amplified_pYTK047_with_tags_of_rare_codons.png"
+        />
+        <small>
+          Figure 1: Amplified pYTK047 with tags of rare codons. pYTK047 with tags of rare codons (AGA, AGG, CGC, TGC
+          and TCC) were amplified via PCR. The PCR products were separated by agarose gel electrophoresis. A 1 %
+          agarose gel was prepared and 50 &micro;L were loaded for each probe ((1): pYTK047-AGA, (2): pYTK047-AGG,
+          (3): pYTK047-CGG, (4): pYTK047-TGC, (5): pYTK047-TCC). 3 &micro;L of Quick-Load&reg; Purple 1 kb Plus DNA
+          Ladder (NEB) were loaded as a Marker (M). The gel was run at 90 V for 1 hour and stained using GelRed.
+        </small>
+        <br />
+        <br />
+        <p>
+          The bands of the desired size were cut out of the agarose gel and the DNA was extracted (<a
+                href="https://2019.igem.org/wiki/images/3/32/T--Stuttgart--Protocol_Gel_Extraction.pdf"
+        >Protocol_Gel_Extraction.pdf</a
+        >). A KLD ligation was performed according to the NEB KLD Enzyme Mix Reaction Protocol to circularize the
+          extracted linear DNA. After ligation, the pYTK047 with the tags of rare codons was transformed in
+          <em>E. coli</em>&nbsp; DH5&alpha; following the transformation protocol for chemical transformation (<a
+                href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
+        >Protocol_Transformation.pdf</a
+        >). No colonies were obtained after transformation. The transformation was repeated, but the plasmid was not
+          transformed successfully. The plasmid was supposed to be isolated from an overnight culture (<a
+                href="https://2019.igem.org/wiki/images/2/2c/T--Stuttgart--Protocol_Plasmid_Preparation.pdf"
+        >Protocol_Plasmid_Preparation.pdf</a
+        >) and successful introduction of rare codons into plasmid pYTK047 should have been validated through
+          sequencing. Transformation into <em>Vibrio natriegens</em> (<a
+                href="https://2019.igem.org/wiki/images/8/83/T--Stuttgart--Protocol_Transformation.pdf"
+        >Protocol_Transformation.pdf</a
+        >) and following growth curves or expression analysis should reveal if protein expression is impaired when
+          rare codons are present.
+        </p>
+        <p>
+          In the last step, we wanted to investigate if the expression of proteins with rare codons can be rescued or
+          even increased when a higher concentration of tRNAs for those rare codons are present. Therefore, pRARE from
+          <em>E. coli</em> Rosetta was supposed to be transformed into <em>V. natriegens</em> together with pYTK047
+          containing sfGFP with rare codons. The plasmid pRARE codes for the tRNA of proL, leuW, metT, argW, thrT,
+          glyT tyrU, thrU, argU and ileX and therefore increases their concentrations.
+        </p>
+      </div>
+      <br /><br />
+      <!-- ALGAE  -->
+      <div id="algae-media-based" class="section-container">
+        <h2 class="title is-3">
+          Media based on algae: first tests determining important substrates
+        </h2>
+        <h3 class="title is-4">Medium based on LB</h3>
+        <p>
+          To first determine whether the extract of
+          <em>chlorella vulgaris </em>was a substitute for yeast extract, LB medium and medium containing
+          <em>chlorella vulgaris</em> extract instead of yeast extract were produced.
+        </p>
+        <ol>
+          <li>
+            Media were produced (<a
+                  href="https://2019.igem.org/File:T--Stuttgart--Protocol_media_first_experiments.pdf"
+          >Protocol_media_first_experiments.pdf</a
+          >).
+          </li>
+          <li>
+            Media were inoculated with <em>escherichia coli</em> or
+            <em>vibrio natriegens.</em>
+          </li>
+          <li>
+            After the over night culture, the turbidity of the tubes was observed.
+          </li>
+        </ol>
+        <br />
+        <p>Result: Growth of both bacteria was observed in both media.</p>
+        <br />
+        <h3 class="title is-4">Medium without tryptone</h3>
+        <p>
+          To determine whether <em>Chlorella vulgaris</em> extract was able to substitute tryptone as a medium
+          component, additionally, media containing different concentrations of NaCl
+          <em>Chlorella vulgaris</em> extract and yeast extract were prepared.
+        </p>
+        <ol>
+          <li>
+            Media were produced (<a
+                  href="https://2019.igem.org/File:T--Stuttgart--Protocol_media_first_experiments.pdf"
+          >Protocol_media_first_experiments.pdf</a
+          >).
+          </li>
+          <li>Media were inoculated with <em>vibrio natriegens.</em></li>
+          <li>
+            After the overnight culture, the turbidity of the tubes was observed.
+          </li>
+        </ol>
+        <br />
+        <br />
+        <p>Result: No growth was detected in media without tryptone.</p>
+      </div>
+      <br /><br />
+      <div id="autolysis" class="section-container">
+        <h2 class="title is-3">
+          Autolysis in combination with bead-milling results
+        </h2>
+        <h3 class="title is-4">Free amino acid estimation with rFAN assay</h3>
+        <p>
+          Samples from Experiment
+          <a
+                  target="_blank"
+                  href="https://2019.igem.org/wiki/images/e/ec/T--Stuttgart--Protocol_Cell_extraction_with_autolysis_combined_with_bead-milling.pdf"
+          >Cell_extraction_with_autolysis_combined_with_bead-milling.pdf</a
+          >
+          were used for the analysis.
+        </p>
+        <br />
+        <p>
+          Yeast extract is mostly obtained by autolysis <sup>1</sup>. In autolysis cells digest their own cell
+          compounds with their own enzymes <sup>2</sup>. The idea was to transfer this commonly used principal on
+          algae. Therefore, <em>C. vulgaris </em>and <em>C. sorokiniana </em>were heated to 50&nbsp;&deg;C in alkaline
+          or acidic environment for 41&nbsp;h. To further crack the cell wall, both algae were treated with
+          bead-milling afterwards. To quantify the success of cell wall disruption free amino acids were measured with
+          rFAN-assay.
+        </p>
+        <br />
+        <p>
+          The yield of free amino acids was set into relation with the amount of biomass used in the experiment
+          (figure 1).
+        </p>
+        <br />
+        <br />
+        <div class="has-text-centered" style="width: 75%; margin:0 auto;">
+          <canvas id="autolysis-figure-1"></canvas>
+        </div>
+        <small
+        >Figure 1: Autolysis and subsequent bead-milling of algae C. vulgaris and C. sorokiniana. The percentage of
+          free amino acids [%] relates to the biomass used in the experiment.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          The highest amounts of free amino acids (4.85&nbsp;%) were reached with yeast at pH 12. Both algae showed
+          very low yield in free amino acids. The best results showed <em>C. sorokiniana</em> at pH&nbsp;12. It is
+          possible, that the amount of glass beads and the size of the glass beads were too little, which led to less
+          cell wall disruption. Therefore, amino acids would have been retained within the cells. This would explain
+          the little amounts of free amino acids achieved with this method. Also, <em>C. vulgaris </em>and
+          <em>C. sorokinia </em>have a cell wall, in contrast to yeast <sup>3</sup>. Cell walls are harder to break,
+          than a plasma membrane. This could explain the difference between the yeast samples and the algae samples.
+          Due to the low yield in free amino acids, it was decided to investigate other methods for cell disruption of
+          algae.
+        </p>
+        <br />
+        <br />
+        <h3 class="title is-4">
+          Anthrone assay to Determine Soluble Carbohydrate Concentration
+        </h3>
+        <p>
+          Similar to the rFAN assay the anthrone assay is a method to detect free monosaccharides in a liquid.
+          Therefor samples from the experiment
+          <br />
+          <br />
+          <br />
+          <a href="https://2019.igem.org/wiki/images/f/f3/T--Stuttgart--Experiments_AnthroneAssay.pdf"
+          >Experiments_AnthroneAssay.pdf</a
+          >
+          were analyzed. Hereby a calibration curve with known amounts of glucose is created (Figure 2, left side).
+          This calibration curve creates the possibility to calculate the sugar concentration of the samples (Figure
+, right side).
+        </p>
+        <img
+                style="display: block; margin:0 auto;"
+                src="https://2019.igem.org/wiki/images/thumb/2/2f/T--Stuttgart--FigureAutolysis_in_combination_with_bead-milling_Results2.png/800px-T--Stuttgart--FigureAutolysis_in_combination_with_bead-milling_Results2.png"
+        />
+        <small
+        >Figure 2: Pictures of the anthrone calibration curve as well as the anthrone assay of samples. For the
+          calibration curve known amounts of glucose is dissolved in water and the optical density at 620 nm is
+          measured (left side). This can be used to determine the monosaccharide concentration of anthone treated
+          samples which previously underwent autolysis (pH3 or pH6) with or without subsequent bead-mill treatment
+          (RKM) (right side).</small
+        >
+        <br />
+        <br />
+        <p>
+          One can tell from the coloring of the samples in figure 2, that the carbohydrate concentration should differ
+          very slightly between the samples pH3, pH6, bead mill extraction +pH3 and bead mill extraction +pH6. Due to
+          the cloudiness of the control sample, a background corrected optical density could not be determined.
+          Therefore, the coloring scheme served as evaluation for successful carbohydrate determination.
+        </p>
+        <p>
+          Hereby, bead-mill (RKM) with subsequent autolysis at pH3 was determined to be the method of choice.
+        </p>
+        <br /><br />
+        <div class="notification">
+          <h3 class="title is-5">References</h3>
+          <ol>
+            <li>
+              Kim et al., &ldquo;Preparation of flavor-enhancing yeast extract using a Saccharomyces cerevisiae strain
+              with high RNA content&rdquo;, Korean J Food Sci Technol, 31 (2) (1999), pp. 475-481.
+            </li>
+            <li>
+              T.L. Babayan, M.G. Bezrukov, &ldquo;Autolysis in yeasts&rdquo;, Acta Biotechnol, 5 (2) (1985), pp.
+-136.
+            </li>
+            <li>
+              van der Rest, M E et al. &ldquo;The plasma membrane of Saccharomyces cerevisiae: structure, function,
+              and biogenesis.&rdquo; Microbiological reviews vol. 59,2 (1995): 304-22.
+            </li>
+            <li>
+              Takeda, &ldquo;Classification of Chlorella strains by cell wall sugar composition&rdquo; Phytochemistry,
+              vol. 27, 12, (1988), pp. 3823-3826.
+            </li>
+            <li>
+              [4} Takeda, &ldquo;Classification of Chlorella strains by cell wall sugar composition&rdquo;
+              Phytochemistry, vol. 27, 12, (1988), pp. 3823-3826.
+            </li>
+          </ol>
+        </div>
+      </div>
+      <br /><br />
+      <div id="celldisruption" class="section-container">
+        <h1 class="title is-3">Results: Cell wall disruption of <em>C. vulgaris</em> and <em>C. sorokiniana</em></h1>
+        <p>
+          For cell wall disruption of <em>C. vulgaris </em>and <em>C. sorokiniana </em>physical and chemical
+          approaches were tested. One physical approach was bead milling with different amounts and sizes of glass
+          beads. Also, one experiment was performed with beads with sharp edges. As an chemical approach for cell wall
+          disruption, algae were boiled in acid or base at 100 &deg;C for one hour (<a
+                href="https://2019.igem.org/wiki/images/e/ec/T--Stuttgart--Protocol_Cell_extraction_with_autolysis_combined_with_bead-milling.pdf"
+        >https://2019.igem.org/wiki/images/e/ec/T--Stuttgart--Protocol_Cell_extraction_with_autolysis_combined_with_bead-milling.pdf</a
+        >).
+        </p>
+        <p>
+          To quantify the amount of protein, received from the respective cell wall disruption method, Bradford-Assay
+          (<a href="https://2019.igem.org/File:T--Stuttgart--Experiments_BradfordAssay.pdf"
+        >https://2019.igem.org/File:T--Stuttgart--Experiments_BradfordAssay.pdf</a
+        >) was performed. The amount of protein was related with the amount of used biomass. First we decided to
+          test physical cell wall disruption (Fig. 1).
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                style="margin: 0 auto; display: block; max-width: 700px"
+                src="https://2019.igem.org/wiki/images/9/94/T--Stuttgart--Fig1Results_CellWall_Bradford_Anthrone.png"
+        />
+        <small
+        >Figure 1: Percentage of protein [%] related to the used biomass of C. sorokiniana. The cell wall was
+          disrupted by bead milling with glass beads in size 45-75&nbsp;&micro;m and 200-300&nbsp;&micro;m. 50&nbsp;%
+          and 80&nbsp;% of glass beads were tested. The amount of protein was quantified with Bradford-Assay.</small
+        >
+        <br />
+        <br />
+        <p>
+          The highest amount of protein (15.6&nbsp;%) was achieved with 80&nbsp;% of glass beads with a size between
+-300&nbsp;&micro;m. The smaller glass beads reached up to 14.04 % of protein and were less efficient. A
+          drastic difference can be seen between 50&nbsp;% glass beads and 80&nbsp;% glass beads. With the smaller
+          beads the amount of glass beads used led to a difference of 11.93&nbsp;%, similar to the bigger beads with a
+          difference of 11.77&nbsp;%. Therefore, 80% of glass beads was used for future cell wall disruption to create
+          our PhyCoVi medium. Also, the bigger beads led to a higher yield of protein and were therefore chosen to be
+          the future method for cell wall disruption.
+        </p>
+        <p>
+          An additional approach of physical cell wall disruption was to use special beads with sharp edges at
+          different speeds (Fig. 2). The beads had a size of 2&nbsp;mm.
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                style="margin: 0 auto; display: block; max-width: 700px"
+                src="https://2019.igem.org/wiki/images/c/cb/T--Stuttgart--Fig2Results_CellWall_Bradford_Anthrone.png"
+        />
+        <small
+        >Figure 2: Cell wall disruption with beads with sharp edges. Percentage of protein [%] is related to the
+          used biomass of C. sorokiniana and C. vulgaris, respectively. For quantification of Protein, Bradford-Assay
+          was used.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          The highest yield of protein was gained with <em>C. vulgaris</em> at speed 8. Speed 4 always led to a lower
+          yield of protein. <em>C. sorokiniana</em> reached a lower yield of protein with 1.19&nbsp;%. The sharp-edged
+          beads reached a lower yield of protein compared to the glass beads with a size of 200-300&nbsp;&micro;m.
+          Hence, this method was not considered for further use.
+        </p>
+        <p>
+          To further optimate the cell wall disruption methods and increase the amount of usable sample, cell wall
+          disruption with acid and base was tested. As bases we used 1&nbsp;M KOH, 5&nbsp;M KOH and 1&nbsp;M NaOH, as
+          acid 1&nbsp;M HCl was used (Fig. 3).
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                style="margin: 0 auto; display: block; max-width: 700px"
+                src="https://2019.igem.org/wiki/images/9/9f/T--Stuttgart--Fig3Results_CellWall_Bradford_Anthrone.png"
+        />
+        <small
+        >Figure 3: Cell wall disruption with 1&nbsp;M HCl, 1&nbsp;M NaOH, 1&nbsp;M KOH and 5&nbsp;M KOH. The
+          percentage of protein was related to the used biomass of C. sorokiniana. Samples were boiled for 1&nbsp;h at
+&nbsp;&deg;C and later quantified with Bardford-Assay.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          The highest yield of protein was reached with 5&nbsp;M KOH with 9.03%. Lower amounts of protein were gained
+          with 1M HCl and 1M KOH. NaOH led to the least yield of protein with 3.59&nbsp;%.
+        </p>
+        <p>
+          After boiling the solutions had to be neutralized. Therefore, we used 1&nbsp;M NaOH and 1&nbsp;M HCl.
+          Neutralizing HCl with NaOH leads to the formation of NaCl, which is a compound of the common cultivation
+          medium for <em>V. natriegens</em>. Our PhyCoVi medium was primary created to be a medium for
+          <em>v. natriegens</em>. Therefore, we chose cell disruption with 1&nbsp;M HCl to be the future method.
+        </p>
+        <p>
+          All samples were also analyzed by the Anthrone Method (<a
+                href="https://2019.igem.org/wiki/images/f/f3/T--Stuttgart--Experiments_AnthroneAssay.pdf"
+        >https://2019.igem.org/wiki/images/f/f3/T--Stuttgart--Experiments_AnthroneAssay.pdf</a
+        >), to quantify the amount of free sugars and starch. The anthrone reagent coagulates with sugars and
+          starch. The more carbohydrates are available, the greener the samples appears and the higher the absorbance
+          at 620&nbsp;nm. Concerning different sizes of the glass beads, the small beads with 100 to 200&nbsp;&micro;m
+          showed the best results. But also the high speed disruption with sharp edged glass beads around 2.0&nbsp;mm
+          showed good results (Fig. 4). Since this option is only available at the Max-Planck-Institute in
+          T&uuml;bingen, we chose the options we had available in Stuttgart.
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                style="margin: 0 auto; display: block; max-width: 700px"
+                src="https://2019.igem.org/wiki/images/a/a5/T--Stuttgart--Fig4Results_CellWall_Bradford_Anthrone.png"
+        />
+        <small
+        >Figure 4: Amount of Carbohydrates [AU] in disrupted C. vulgaris and C. sorokiniana cells. The cell wall was
+          disrupted by bead milling with glass beads in size 2.0&nbsp;mm at high speed, 0.75 to 1.0 mm, 2.0&nbsp;mm
+          and 2.1&nbsp;mm.&nbsp; The amount of Carbohydrates were quantified with anthrone assay</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          For the two volume ratios of glass beads to sample, the 80&nbsp;% of 200&nbsp;&micro;m glass beads showed
+          the best result. Generally more and bigger glass beads show better cell disruption.
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                style="margin: 0 auto; display: block; max-width: 700px"
+                src="https://2019.igem.org/wiki/images/2/2a/T--Stuttgart--Fig5Results_CellWall_Bradford_Anthrone.png"
+        />
+        <small
+        >Figure 5: Amount of Carbohydrates [AU] in disrupted C. sorokiniana cells. The cell wall was disrupted by
+          bead milling with glass beads in size 45-75&nbsp;&micro;m and 200-300&nbsp;&micro;m. 50&nbsp;% and 80&nbsp;%
+          of glass beads were tested. The amount of Carbohydrates were quantified with anthrone assay.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          At last the acid and base disruption was examined. As seen in Fig. 6, all bases show low values, with
+&nbsp;M KOH being unusable. With HCl reaching a similar level like glass beads, we chose this acid as our
+          method for cell disruption. In combination with glass bead disruption, we hoped to have an efficient method
+          for cell disruption of micro algaes.
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                style="margin: 0 auto; display: block; max-width: 700px"
+                src="https://2019.igem.org/wiki/images/7/70/T--Stuttgart--Fig6Results_CellWall_Bradford_Anthrone.png"
+        />
+        <small
+        >Figure 6: Cell wall disruption with 1&nbsp;M HCl, 1&nbsp;M NaOH, 1&nbsp;M KOH and 5&nbsp;M KOH. Samples
+          were boiled for 1&nbsp;h at 100&nbsp;&deg;C. The amount of Carbohydrates were quantified with anthrone
+          assay.</small
+        >
+      </div>
+      <br /><br />
+      <div id="cdwcorrelation" class="section-container">
+        <h2 class="title is-3">CDW correlation of algae <em>Chlorella vulgaris</em> Results</h2>
+        <p>
+          By plotting the measured optical densities against the means of the calculated cellular dry weights, a
+          correlation was obtained. It is shown in the following figure.
+        </p>
+        <br />
+        <img
+                style="display: block; max-width: 500px; margin: 0 auto;"
+                src="https://2019.igem.org/wiki/images/a/ad/T--Stuttgart--FigureOD-CDW_correlation_of_algae_Chlorella_vulgaris_Results1.png"
+        />
+        <small
+        >Figure 1: OD-CDW correlation of the algae <em>Chlorella vulgaris</em>. Mean of cellular dry weight in g/L
+          (n=2) was plotted against the measured optical density at 750 nm. Trend line was shown in red.
+        </small>
+        <br />
+        <br />
+        <br />
+        <p>
+          The trend line in figure 1 is poorly matching the trend of the measurement points. For this reason, the
+          correlation curve was rejected. For improvement of this experiment, measurements should be performed only by
+          one experimenter to reduce pipetting errors or other handling mistakes. Also the measurements should be
+          taken over a longer time period to gain more trust worthy results.
+        </p>
+        <br />
+      </div>
+      <br /><br />
+      <div id="cdwodcorrelation" class="section-container">
+        <h2 class="title is-3">CDW-OD correlation by dilution Results</h2>
+        In the following table you can see the calculated cell dry weights with the corresponding optical density of
+        the tubes. Some tubes broke during the experiment so corresponding measurements could not occur.
+        <br />
+        <br />
+        <div class="columns">
+          <div class="column">
+            <small
+            >Table 2: Calculated values of the cellular dry weight in g/l with the corresponding optical density
+              measured at 750 nm.
+            </small>
+            <table class="table is-fullwidth">
+              <thead>
+              <tr>
+                <th>OD</th>
+                <th>CDW[g/l]</th>
+              </tr>
+              </thead>
+              <tbody>
+              <tr>
+                <td>4.87</td>
+                <td>0.98</td>
+              </tr>
+              <tr>
+                <td>4.41</td>
+                <td>0.88</td>
+              </tr>
+              <tr>
+                <td>4.44</td>
+                <td>0.91</td>
+              </tr>
+              <tr>
+                <td>4.02</td>
+                <td>0.8</td>
+              </tr>
+              <tr>
+                <td>3.92</td>
+                <td>0.82</td>
+              </tr>
+              <tr>
+                <td>3.52</td>
+                <td>0.68</td>
+              </tr>
+              <tr>
+                <td>3.57</td>
+                <td>0.71</td>
+              </tr>
+              <tr>
+                <td>3.03</td>
+                <td>0.57</td>
+              </tr>
+              <tr>
+                <td>2.65</td>
+                <td>0.49</td>
+              </tr>
+              <tr>
+                <td>2.8</td>
+                <td>0.5</td>
+              </tr>
+              <tr>
+                <td>2.43</td>
+                <td>0.48</td>
+              </tr>
+              <tr>
+                <td>2.56</td>
+                <td>0.46</td>
+              </tr>
+              <tr>
+                <td>2.29</td>
+                <td>0.4</td>
+              </tr>
+              <tr>
+                <td>2.28</td>
+                <td>0.4</td>
+              </tr>
+              </tbody>
+            </table>
+          </div>
+          <div class="column">
+            <p>
+              The cellular dry weight in g/l was then plotted against the optical density measured at 750 nm. The plot
+              with the corresponding trend line is shown in the following figure.
+              <img
+                      style="display: block; max-width: 500px; margin: 0 auto;"
+                      src="https://2019.igem.org/wiki/images/d/df/T--Stuttgart--FigureOD-CDW_correlation_of_Chlorella_vulgaris_by_dilution_Results1.png"
+              />
+              <small
+              >Figure 1: Cellular dry weight in g/l is plotted against the optical density measured at 750 nm. The
+                linear fit is shown in blue together with its formula.</small
+              >
+              <br />
+              <br />
+            </p>
+            <p>
+              The slope of the formula further been used for fast estimation of the CDW by measuring the optical
+              density at 750 nm.
+            </p>
+          </div>
+        </div>
+      </div>
+      <br /><br />
+      <div id="preliminarycelldisruption" class="section-container">
+        <h2 class="title is-3">Results preliminary <em>Chlorella vulgaris</em> extraction methods (FACS analysis)</h2>
+        <p>
+          The obtained samples were measured at a flow-cytometer for green fluorescence (intact chlorophyll) as well
+          as cell size (SSC and FSC). A distinct amount of liquid (50 &micro;L) was measured. Based on the cell size
+          (intact cells show a clear population) and green fluorescence, viable cells were able to be gated into a
+          distinct population. With obtaining a distinct number of viable cells within a constant volume we were able
+          to determine the number of viable cells per &micro;L. The number of cells/&micro;L of the control sample was
+          set to 100% with the extraction methods (high-pressure-homogenizer passages 1 - 4, mortar, bead-mill,
+          autoclave and sonification) set in relation of the control. We hereby obtained the percentage of viable
+          cells for each cell disruption method (Figure 1).
+        </p>
+        <br />
+        <br />
+        <img
+                style="display: block; max-width: 800px; margin: 0 auto;"
+                src="https://2019.igem.org/wiki/images/2/2b/T--Stuttgart--Bilder_Aufschluss.png"
+        />
+        <small>
+          Figure 1: Measured cell viability of <em>Chlorella vulgaris</em> after cell disruption methods. A
+          distinct amount of cells was used to test each disruption method: high-pressure-homogenizer passage 1 - 4,
+          mortar, bead-mill, autoclave and sonification. Afterwards 50 &micro;L of the obtained samples were analyzed
+          at the flow cytometry based on positive green fluorescence signal as well as intact cell signal (FSC, SSC).
+          The cell count was measured, and the control was set to 100% cell viability with the cell count of the
+          disruption methods set in relation to the control.
+        </small>
+        <br />
+        <br />
+        <br />
+        <h2 class="title is-4">Conclusion:</h2>
+        <p>
+          In terms of feasibility and up-scaling problems the method we further wanted to analyze was the bead-mill.
+          With a 50% cell viability it proved to be a rather solid method for cell disruption. We concluded that
+          further research for the optimal bead size should be conducted as well as a combination with an autolytic
+          process. The idea was that acid induced autolysis prior to the bead-mill treatment should weaken the strong
+          microalgae cell wall and therefore decrease cell viability.
+        </p>
+      </div>
+      <br /><br />
+      <div id="growthCurvesOnBacteria" class="section-container">
+        <h2 class="title is-3">Growth Curves of various bacteria in PhyCoVi Medium</h2>
+        <p>
+          The PhyCoVi medium was tested with various microorganism including
+          <em>Vibrio natriegens, Escherichia coli</em>, <em>Bacillus subtillis</em> and
+          <em>Corynebacterium glutamicum</em>. Therefore, optical density was measured at 600&nbsp;nm with a photometer .
+          Different medium variations were tested to find the best medium composition. For control
+          also normal LB medium, Brain-Heart-Infusion (BHIN) medium and medium containing only soy peptone was tested. Medium
+          composition is shown in table 1.
+        </p>
+        <br />
+        <br />
+        <small>
+          Table 1:  Specification for all media used during the algae based PhyCoVi medium (PCV) validation.
+        </small>
+        <table class="table is-fullwidth is-bordered  ">
+          <thead>
+          <tr>
+            <th>Ingredients</th>
+            <th>PCV [g/L]</th>
+            <th>PCV + Soy Peptone [g/L]</th>
+            <th>LB medium [g/L]</th>
+            <th>BHIN [g/L]</th>
+            <th>Soy Peptone Control [g/L]</th>
+          </tr>
+          </thead>
+          <tbody>
+          <tr>
+            <td>NaCl</td>
+            <td colspan="5">10 or 20</td>
+          </tr>
+          <tr>
+            <td>Algae extract</td>
+            <td>30</td>
+            <td>30</td>
+            <td>--</td>
+            <td>--</td>
+            <td>--</td>
+          </tr>
+          <tr>
+            <td>Soy Peptone</td>
+            <td>10</td>
+            <td>10</td>
+            <td>10</td>
+            <td>--</td>
+            <td>10</td>
+          </tr>
+          <tr>
+            <td>Yeast extract</td>
+            <td>--</td>
+            <td>--</td>
+            <td>5</td>
+            <td>--</td>
+            <td>--</td>
+          </tr>
+          <tr>
+            <td>BHI</td>
+            <td>--</td>
+            <td>--</td>
+            <td>--</td>
+            <td>37</td>
+            <td>--</td>
+          </tr>
+          </tbody>
+        </table>
+        <br />
+        <p>
+          To estimate the optimal medium composition for <em>V. natriegens</em> different NaCl concentrations were
+          tested as well as the addition of soy peptone (Figure 1).
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                src="https://2019.igem.org/wiki/images/f/f3/T--Stuttgart--Fig2Demonstrate.png"
+                class="image"
+                style="max-width: 700px;margin: 0 auto; display: block"
+        />
+        <small
+        >Figure 1: Growth curve of <em>V. natriegens</em> on PhyCoVi Medium (PCV) and PCV + Soy peptone. LB-Medium,
+          Brain-Heart infusion Medium (BHIN) and soy peptone served as control. The medium contained different amounts
+          of NaCl (10 or 20&nbsp;g/L). Sampling for measuring optical density was performed every 45&nbsp;minutes over a time course of
+&nbsp;minutes.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          The PCV medium containing additional soy peptone revealed the highest growth of <em>V. natriegens</em>. It
+          even outcompeted the commonly used BHIN medium. <em>V. natriegens </em>cultivated in PCV medium without
+          additional soy peptone showed remarkably less growth. LB and Soy peptone alone showed the least bacterial
+          growth.
+        </p>
+        <br />
+        <p>Next, bacterial growth of <em>Escherichia coli MG1655 </em>on PhyCoVi medium was tested (Figure 2).</p>
+        <br />
+        <br />
+        <br />
+        <img
+                src="https://2019.igem.org/wiki/images/f/f2/T--Stuttgart--Fig3Demonstrate.png"
+                class="image"
+                style="max-width: 700px;margin: 0 auto; display: block"
+        />
+        <small
+        >Figure 2: Growth curve of <em>E. coli</em> in PhyCoVi Medium (PCV) and PCV + Soy peptone. LB-Medium, Brain-Heart
+          infusion Medium (BHIN) and soy peptone served as control. The medium contained different amounts of NaCl (10
+          or 20&nbsp;g/L). Sampling for measuring optical density was performed every 45&nbsp;minutes over a time course of
+&nbsp;minutes.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          Highest bacterial growth was reached with PCV medium containing soy peptone and 10&nbsp;g/L NaCl
+          followed by the 20&nbsp;g/L NaCl variant. The differences in <em>E. coli</em> growth on various media is not as clear
+          as it was with <em>V. natriegens</em> (Figure 1). Also, the adapation phase is longer. Nevertheless, PhyCoVi
+          medium with soy peptone is applicable for cultivation of <em>E. coli</em>.
+        </p>
+        <br />
+        <p>
+          Further, growth of <em>Bacillus subtilis</em> (Figure 3) and
+          <em>Corynebacterium glutamicum</em> (Figure 4) were tested. Only medium containing 10&nbsp;g/L NaCl was
+          used.
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                src="https://2019.igem.org/wiki/images/4/48/T--Stuttgart--Fig4Demonstrate.png"
+                class="image"
+                style="max-width: 700px;margin: 0 auto; display: block"
+        />
+        <small
+        >Figure 3: Growth curve of <em>Bacillus subtillis</em> on PhyCoVi Medium (PCV) and PCV + soy peptone. LB-Medium,
+          Brain-Heart infusion Medium (BHIN) and soy peptone served as control. The medium contained 10&nbsp;g/L NaCl.
+          Sampling for measurements of the optical density was performed every 45 minutes over a time course of 360 minutes.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          <em>Bacillus subitilis</em> grew best on BHIN followed by LB medium. PCV medium with soy peptone was still
+          better than PCV without it. Nevertheless, there was no remarkable increase in absorbance and thus only
+          little growth of bacteria after 6&nbsp;h.
+        </p>
+        <br />
+        <br />
+        <br />
+        <img
+                src="https://2019.igem.org/wiki/images/8/8b/T--Stuttgart--Fig5Demonstrate.png"
+                class="image"
+                style="max-width: 700px;margin: 0 auto; display: block"
+        />
+        <small
+        >Figure 4: Growth curve of <em>Corynebacterium glutamicum</em> on PhyCoVi Medium (PCV) and PCV + soy peptone.
+          LB-Medium, Brain-Heart infusion Medium (BHIN) and soy pepton served as control. The medium contained
+&nbsp;g/L NaCl. Sampling for measurements of the optical density was performed every 45 minutes over a time course of 360 minutes.</small
+        >
+        <br />
+        <br />
+        <br />
+        <p>
+          <em>Corynebacterium glutamicum</em> grew better on BHIN and LB than on PCV with or without soy peptone. PCV
+          with additional soy peptone showed higher growth than medium without soy peptone. Comparing
+          <em>Bacillus subtilis</em> with <em>Corynebacterium glutamicum</em>, <em>C. glutamicum</em> shows better
+          growth on PCV containing soy peptone. Although both bacteria prefer BHIN and LB medium.
+        </p>
+      </div>
+      <br /><br />
+      <div id="sugarHPLCResults" class="section-container">
+        <h2 class="title is-3">Sugar HPLC Results</h2>
+        <p>
+          The measurement was performed in six technical replicates of the algae extract batch PCV#2 from
+          <i>Chlorella vulgaris</i>. The molar concentration of glucose, fructose, sucrose and raffinose were
+          determined. The results of the carbohydrate HPLC measurement are shown in Table 1. &nbsp;
+        </p>
+        <br />
+        <small>
+          Table 1: Molar concentration [&micro;M] of glucose, fructose, sucrose and raffinose in 30 g/l
+          <i>Chlorella vulgaris</i> extract diluted in dH<sub>2</sub>O measured in 6 technical replicates.
+        </small>
+        <table class="table">
+          <tbody>
+          <tr>
+            <td width="143">
+              <p><strong>Carbohydrate</strong></p>
+            </td>
+            <td width="77">
+              <p><strong>PCV#2.1 [&micro;M]</strong></p>
+            </td>
+            <td width="77">
+              <p><strong>PCV#2.2 [&micro;M]</strong></p>
+            </td>
+            <td width="77">
+              <p><strong>PCV#2.3 [&micro;M]</strong></p>
+            </td>
+            <td width="77">
+              <p><strong>PCV#2.4 [&micro;M]</strong></p>
+            </td>
+            <td width="77">
+              <p><strong>PCV#2.5 [&micro;M]</strong></p>
+            </td>
+            <td width="77">
+              <p><strong>PCV#2.6 [&micro;M]</strong></p>
+            </td>
+          </tr>
+          <tr>
+            <td width="143">
+              <p>Glucose</p>
+            </td>
+            <td width="77">
+              <p>2075.56</p>
+            </td>
+            <td width="77">
+              <p>2040</p>
+            </td>
+            <td width="77">
+              <p>1987.23</p>
+            </td>
+            <td width="77">
+              <p>2199.63</p>
+            </td>
+            <td width="77">
+              <p>2208.8</p>
+            </td>
+            <td width="77">
+              <p>2119.68</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="143">
+              <p>Fructose</p>
+            </td>
+            <td width="77">
+              <p>707.92</p>
+            </td>
+            <td width="77">
+              <p>681.28</p>
+            </td>
+            <td width="77">
+              <p>654.26</p>
+            </td>
+            <td width="77">
+              <p>639.44</p>
+            </td>
+            <td width="77">
+              <p>625.7</p>
+            </td>
+            <td width="77">
+              <p>593.94</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="143">
+              <p>Sucrose</p>
+            </td>
+            <td width="77">
+              <p>2.87</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="143">
+              <p>Raffinose</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+            <td width="77">
+              <p>0</p>
+            </td>
+          </tr>
+          </tbody>
+        </table>
+        <br />
+        <p>
+          We were able to measure glucose and fructose in our samples. Raffinose was not detected at all. Sucrose was
+          measured only in one sample, so we decided to reject its concentration.
+        </p>
+        <br />
+        <p>
+          By calculating the averages of the 6 replicates we were able to determine the amount of certain carbohydrate
+          in gram per 100-gram <em>Chlorella vulgaris</em> extract. In 100 g <em>C. vulgaris</em> extract we obtained
+.264 g glucose and 0.391 g fructose.
+        </p>
+        <br />
+        <h2 class="title is-4">Amino acid HPLC Results</h2>
+        <p>
+          For this experiment we measured three technical replicates of two batches of our self-made algae extract
+          from <em>Chlorella vulgaris</em> with two concentrations 30 g/L and 60 g/L. The two measurements were
+          performed to have a detectable amount of amino acids. Histidine in batch PCV#3 was only measured in the 60
+          g/L sample, he corresponding values were divided by 2 and added to the 30 g/L values. We calculated averages
+          and standard deviations of the molar concentrations from the HPLC data for all 20 proteinogenic amino acids.
+          To be able to compare the two batches PCV#2 and PCV#3, we plotted the average concentrations in a bar
+          diagram. We were not able to distinguish between the peaks of alanine and arginine. For that reason, they
+          were analyzed as one peak.&nbsp;
+        </p>
+        <br />
+        <br />
+        <img
+                class="image"
+                style="margin: 0 auto; display: block; max-width: 700px"
+                src="https://2019.igem.org/wiki/images/4/4b/T--Stuttgart--FigureHPLC2.png"
+        />
+        <small>
+          Figure 1: Bar diagram of average molar concentration of 20 proteinogenic amino acids from two batches of
+          self-made algae extract from <em>Chlorella vulgaris</em> diluted in water (30g/l). In blue the prior extract with the
+          ID: PCV#2. In green the final batch with ID: PCV#3.&nbsp;&nbsp;
+        </small>
+        <br />
+        <br />
+        <p>
+          It is noteworthy, that the batch PCV#3 shows a brighter spectrum of amino acids, than the prior batch PCV#2.
+          When harvesting the algae for the batch PCV#3, we tried to optimize the protocol for extraction. The prior
+          extraction protocol had some issues with product purity. The powder contained some disintegrated algae
+          contaminants. However, we could achieve an improvement when it comes to amino acid content.
+        </p>
+        <br />
+        <p>
+          To create a content list for our algae <em>C.vulgaris</em> extract, we calculated the mass of amino acids
+          per 100 gram extract for both batches PCV#2 and PCV#3. The corresponding list is shown in the following
+          table.
+        </p>
+        <br />
+        <br />
+        <small>Table 1: List of amino acid content in gram per 100 g <i>Chlorella vulgaris</i> extract.</small>
+        <table class="table">
+          <tbody>
+          <tr>
+            <td width="123">
+              <p><strong>Amino acid</strong></p>
+            </td>
+            <td width="208">
+              <p><strong>g per 100 g PCV#2</strong></p>
+            </td>
+            <td width="217">
+              <p><strong>g per 100 g PCV#3</strong></p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Asp</p>
+            </td>
+            <td width="208">
+              <p>0.070086304</p>
+            </td>
+            <td width="217">
+              <p>0.057490545</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Glu</p>
+            </td>
+            <td width="208">
+              <p>0.040912751</p>
+            </td>
+            <td width="217">
+              <p>0.049566772</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Ser</p>
+            </td>
+            <td width="208">
+              <p>0.010175455</p>
+            </td>
+            <td width="217">
+              <p>0.017357337</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>His</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.000597254</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Gly</p>
+            </td>
+            <td width="208">
+              <p>0.010794219</p>
+            </td>
+            <td width="217">
+              <p>0.022097401</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Thr</p>
+            </td>
+            <td width="208">
+              <p>0.044205579</p>
+            </td>
+            <td width="217">
+              <p>0.007266782</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Tyr</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.006698225</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Cys</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.024702034</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Val</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.01251605</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Met</p>
+            </td>
+            <td width="208">
+              <p>0.003853789</p>
+            </td>
+            <td width="217">
+              <p>0.052499327</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Trp</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.00494474</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Phe</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.011192791</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Ile</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.004606983</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Leu</p>
+            </td>
+            <td width="208">
+              <p>0.00132329</p>
+            </td>
+            <td width="217">
+              <p>0.011335256</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Lys</p>
+            </td>
+            <td width="208">
+              <p>0</p>
+            </td>
+            <td width="217">
+              <p>0.038419982</p>
+            </td>
+          </tr>
+          <tr>
+            <td width="123">
+              <p>Pro</p>
+            </td>
+            <td width="208">
+              <p>0.025929325</p>
+            </td>
+            <td width="217">
+              <p>0.018145512</p>
+            </td>
+          </tr>
+          </tbody>
+        </table>
+        <p>
+          The total amount of proteinogenic amino acids in PCV#2 is 0.207 g per 100 g extract. In PCV#3 we have a
+          total amount of 0.339 g per 100 g extract. With the optimized protocol we were able to achieve 0.6 times
+          more proteinogenic amino acids per gram extract than before.&nbsp;&nbsp;&nbsp;
+        </p>
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+  </div>
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+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
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+            {
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+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
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+             */
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+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
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+        }
+      }
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+        plugins: {
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+             * stroke color, or array of colors
+             * @default: derived from borderColor
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+             */
+            lineWidth: 2 | '2px',
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+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
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+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
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+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    /* Dispendix Amplifikation */
+    var dispendixAGAamplifikation = document.getElementById('dispendixAGAamplifikation').getContext('2d');
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+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
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+            /**
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+             */
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+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
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+             */
+            absoluteValues: false
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+        }
+      }
+    });
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+    var HotScriptaseSchmelzkurveAGA = document.getElementById('HotScriptaseSchmelzkurveAGA').getContext('2d');
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+          xAxes: [
+            {
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+              },
+              ticks: {
+                maxTicksLimit: 10,
+                precision: 0
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+                display: true,
+                labelString: 'ddRn/dT'
+              },
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+              }
+            }
+          ]
+        },
+        plugins: {
+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            color: '#666',
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
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+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
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+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
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+             */
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+        }
+      }
+    });
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+        responsive: true,
+        scales: {
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+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'temperature [°C]'
+              },
+              ticks: {
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+                precision: 0
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+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'ddRn/dT'
+              },
+              ticks: {
+                min: -2,
+                max: 17
+              }
+            }
+          ]
+        },
+        plugins: {
+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            color: '#666',
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    var HotScriptaseSchmelzkurveCGG = document.getElementById('HotScriptaseSchmelzkurveCGG').getContext('2d');
+    window.myLine = new Chart(HotScriptaseSchmelzkurveCGG, {
+      type: 'line',
+      data: {
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+        ]
+      },
+      options: {
+        responsive: true,
+        scales: {
+          xAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'temperature [°C]'
+              },
+              ticks: {
+                maxTicksLimit: 10,
+                precision: 0
+              }
+            }
+          ],
+          yAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'ddRn/dT'
+              },
+              ticks: {
+                min: -2,
+                max: 17
+              }
+            }
+          ]
+        },
+        plugins: {
+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            color: '#666',
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    var HotScriptaseSchmelzkurveGAA = document.getElementById('HotScriptaseSchmelzkurveGAA').getContext('2d');
+    window.myLine = new Chart(HotScriptaseSchmelzkurveGAA, {
+      type: 'line',
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+          }
+        ]
+      },
+      options: {
+        responsive: true,
+        scales: {
+          xAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'temperature [°C]'
+              },
+              ticks: {
+                maxTicksLimit: 10,
+                precision: 0
+              }
+            }
+          ],
+          yAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'ddRn/dT'
+              },
+              ticks: {
+                min: -2,
+                max: 17
+              }
+            }
+          ]
+        },
+        plugins: {
+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            color: '#666',
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
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+              },
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+              }
+            }
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+        },
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+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
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+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
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+             */
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+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
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+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
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+             */
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+          }
+        }
+      }
+    });
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+    window.myLine = new Chart(HotScriptaseSchmelzkurveTGC, {
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+          }
+        ]
+      },
+      options: {
+        responsive: true,
+        scales: {
+          xAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'temperature [°C]'
+              },
+              ticks: {
+                maxTicksLimit: 10,
+                precision: 0
+              }
+            }
+          ],
+          yAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'ddRn/dT'
+              },
+              ticks: {
+                min: -2,
+                max: 17
+              }
+            }
+          ]
+        },
+        plugins: {
+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            color: '#666',
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    /* E.coli Amplifikation*/
+    var EcoliVergleichAGAAmplifikation = document.getElementById('EcoliVergleichAGAAmplifikation').getContext('2d');
+    window.myLine = new Chart(EcoliVergleichAGAAmplifikation, {
+      type: 'line',
+      data: {
+        labels: [
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+        ],
+        datasets: [
+          {
+            label: 'AGA E.coli BL21 wild type',
+            backgroundColor: window.chartColors.pink,
+            borderColor: window.chartColors.pink,
+            fill: false,
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+            errorBars: {
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+: { plus: 0.0, minus: -0.0 },
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+: { plus: 0.1836, minus: -0.1836 },
+: { plus: 0.195, minus: -0.195 },
+: { plus: 0.201, minus: -0.201 }
+            }
+          },
+          {
+            label: 'AGA E.coli BL21 with pRARE 2',
+            backgroundColor: window.chartColors.indigo,
+            borderColor: window.chartColors.indigo,
+            fill: false,
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+            errorBars: {
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+: { plus: 0.833, minus: -0.833 }
+            }
+          },
+          {
+            label: 'AGA E.coli Rosetta',
+            backgroundColor: window.chartColors.lightblue,
+            borderColor: window.chartColors.lightblue,
+            fill: false,
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+            errorBars: {
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+: { plus: 0.831, minus: -0.831 }
+            }
+          },
+          {
+            label: 'Negative control',
+            backgroundColor: window.chartColors.dark,
+            borderColor: window.chartColors.dark,
+            fill: false,
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+      options: {
+        responsive: true,
+        scales: {
+          xAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'Cycles [n]'
+              },
+              ticks: {
+                maxTicksLimit: 10,
+                precision: 0
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+          yAxes: [
+            {
+              scaleLabel: {
+                display: true,
+                labelString: 'dRn'
+              },
+              ticks: {
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+                max: 100
+              }
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+        },
+        plugins: {
+          chartJsPluginErrorBars: {
+            /**
+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    var EcoliVergleichAGGAmplifikation = document.getElementById('EcoliVergleichAGGAmplifikation').getContext('2d');
+    window.myLine = new Chart(EcoliVergleichAGGAmplifikation, {
+      type: 'line',
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+        datasets: [
+          {
+            label: 'AGG E.coli BL21 wild type',
+            backgroundColor: window.chartColors.pink,
+            borderColor: window.chartColors.pink,
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+            }
+          },
+          {
+            label: 'AGG E.coli BL21 with pRARE 2',
+            backgroundColor: window.chartColors.indigo,
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+            /**
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+             * @default: derived from borderColor
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+            /**
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+             */
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+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
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+             */
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+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
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+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    var EcoliVergleichCUAAmplifikation = document.getElementById('EcoliVergleichCUAAmplifikation').getContext('2d');
+    window.myLine = new Chart(EcoliVergleichCUAAmplifikation, {
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+        },
+        plugins: {
+          chartJsPluginErrorBars: {
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+             * stroke color, or array of colors
+             * @default: derived from borderColor
+             */
+            /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    /* E.coli Schmelzkurven*/
+    var EcoliVergleichAGASchmelzkurve = document.getElementById('EcoliVergleichAGASchmelzkurve').getContext('2d');
+    window.myLine = new Chart(EcoliVergleichAGASchmelzkurve, {
+      type: 'line',
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+             * @default: derived from borderColor
+             /**
+             * bar width in pixel as number or string or bar width in percent based on the barchart bars width (max 100%), or array of such definition
+             * @default 10
+             */
+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    var EcoliVergleichAGGSchmelzkurve = document.getElementById('EcoliVergleichAGGSchmelzkurve').getContext('2d');
+    window.myLine = new Chart(EcoliVergleichAGGSchmelzkurve, {
+      type: 'line',
+      data: {
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+            width: 10 | '10px' | '60%',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * lineWidth as number, or as string with pixel (px) ending, or array of such definition
+             * @default 2
+             */
+            lineWidth: 2 | '2px',
+            /**
+             * whether to interpet the plus/minus values, relative to the value itself (default) or absolute
+             * @default false
+             */
+            absoluteValues: false
+          }
+        }
+      }
+    });
+    var EcoliVergleichCUASchmelzkurve = document.getElementById('EcoliVergleichCUASchmelzkurve').getContext('2d');
+    window.myLine = new Chart(EcoliVergleichCUASchmelzkurve, {
+      type: 'line',
+      data: {
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Difference between revisions of "Team:Stuttgart/Results"

Latest revision as of 23:29, 21 October 2019

Project

Results

qRT-PCR for the relative quantification of specific tRNA-species

References

tRNA quantification of rare codons in V. natriegens with reverse transcription and the use of ‘GreenMasterMix without ROX’

Outlook

Growth curves Vibrio natriegens

Results

Cloning of tRNA fragments into pSB1C3

Cloning of tRNA fragments into ptRNA_backbone via BioBrick Cloning

Cloning of tRNA fragments into ptRNA_backbone via Gibson Assembly

Isolation of Vibrio natriegens DSM 759 genome chr.1 and amplification of tRNAs

Cloning of tRNA fragments (amplified from Vibrio natriegens DSM 759 genome) into ptRNA_backbone via BioBrick Cloning

Cloning of tRNA fragments (amplified from Vibrio natriegens DSM 759 genome) into ptRNA_backbone via NEBuilder HiFi DNA Assembly

Cloning of tRNA fragments (amplified from Vibrio natriegens DSM 759 genome) into ptRNA_backbone via Gibson Assembly

Outlook

References

Transformation of pRARE into Vibrio natriegens

Mutagenesis of sfGFP

Media based on algae: first tests determining important substrates

Medium based on LB

Medium without tryptone

Autolysis in combination with bead-milling results

Free amino acid estimation with rFAN assay

Anthrone assay to Determine Soluble Carbohydrate Concentration

References

Results: Cell wall disruption of C. vulgaris and C. sorokiniana

CDW correlation of algae Chlorella vulgaris Results

CDW-OD correlation by dilution Results

Results preliminary Chlorella vulgaris extraction methods (FACS analysis)

Conclusion:

Growth Curves of various bacteria in PhyCoVi Medium

Sugar HPLC Results

Amino acid HPLC Results