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@@ -16,7 +16,8 @@ Cytoplasmic Abundant Heat Soluble (CAHS) proteins in tardigrades are key players
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 As a first  part of this project, we aimed to stabilize *E. coli* cell-free systems using tardigrade proteins. For convenience and improved accessibility, we sought to produce the tardigrade proteins *in situ*, in the strain that is harboring the autolysate plasmid  \[4\]. As outlined above, previous work had shown that several lyoprotectant heat-soluble proteins from tardigrades protect proteins and living cells during desiccation. To our knowledge, it has not been attempted to protect cell-free expression systems with tardigrade proteins during desiccation or freeze drying, which we aimed to test in our project. Based on previous work by Boothby et al. (2017), where living  *E. coli* cells were stabilized and showed increased desiccation survival we reasoned that the same genes may help to improve the stability of cell-free systems.  the following tardigrade genes, originally stemming form *H. dujardini* \[1\] :
 
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 Following the method of Boothby et al.,(2017) the heat solubility characteristics of the tardigrade proteins were used to purify the proteins.  
 
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 Following purification we first quantified the protein concentration in the protein extracts and subsequently added the required amount to reach a total concentration of 0.5 mg/ml (figure 3; 4 a, b)  . This concentration was chosen based on the work of the TU-DELFT team in 2017, where this concentration and onwards was found to exhibit lyoprotectant effects on ß-galactosidase enzymes in solution.
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 To assess the capability of our tardigrade proteins to protect cell-free systems against the effects of desiccation we lyophilised lysate samples, where we had either expressed tardigrade genes *in situ* or where we added the proteins externally.  The samples were stored at room temperature for a time-frame of 2 weeks and rehydrated in the same volume that it was desiccated at.
 
@@ -76,6 +80,7 @@ To assess the capability of our tardigrade proteins to protect cell-free systems
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 As outlined in the [Engineering Page](https://2024.igem.wiki/tum-straubing/engineering),  we observed that while Gene 1 and Gene 2 demonstrated protective capabilities when produced internally, the externally supplemented proteins exhibited diminished protection(Figure 5). The storage buffer contains 50 mM NaCl - (more details in our [Protocols](https://static.igem.wiki/teams/5286/protocols.pdf)), so we hypothesized that there could be an inhibitory effect of the protein storage buffer on the lysate performance.
@@ -88,6 +93,7 @@ As outlined in the [Engineering Page](https://2024.igem.wiki/tum-straubing/engin
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 We found that an increased salt concentration does indeed inhibit the cell-free reaction. To counteract this we already started an additional protein purification protocol using the Panda-Pure protein purification kit supplied by our sponsor. 
@@ -102,6 +108,7 @@ As further validation we repeated the last experiment with biological replicates
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 Surprisingly, Gene 2 performed much better than in the previous assessment indicating variability between batches and the handling during the desiccation process.  
 In parallel, the same rehydrated lysate was used to start a reaction in PCR tubes for visualization using the Chemidoc System after 3 hours of incubation at room temperature.
@@ -114,6 +121,7 @@ In parallel, the same rehydrated lysate was used to start a reaction in PCR tube
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 Despite variance between experiments, gene 1 (CAHS107838) conferred the strongest desiccation tolerance (Figure 4 and 5). 
@@ -128,6 +136,7 @@ Building on these findings, we aimed to evaluate whether cell-free components co
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 Given that Lysate can be desiccated with low-cost vacuum desiccation we next sought to assess whether or not  the energy buffer can be stabilized using different lyoprotectants as well. For this we took inspiration from Guzman Chavez’s work where different concentrations of sugars were investigated for their lyoprotectant properties \[5\]. In this work they found an optimal concentration of 11.2 mM  for Maltodextrin and Lactose respectively which both exhibited desiccation protection effects as well as function as a potential additional energy source for the cell-free system . For Trehalose the same concentration we described previously was used, namely 0.54 M based on work from reference \[6\]. After low-cost vacuum desiccation the samples were left at room temperature for 1 week prior and resuspended in nuclease free water. 
 
@@ -139,6 +148,7 @@ Given that Lysate can be desiccated with low-cost vacuum desiccation we next sou
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 In alignment with past findings we found lactose and Maltodextrin  to exhibit strong desiccation protection abilities and the activity even surpassed the fresh energy buffer (Figure 10 ). This enhanced activity may be attributed to its ability to stabilize cellular components while simultaneously providing metabolic support, surpassing the protective effects observed in the fresh energy buffer.
 
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 ##           **Optimizing the Energy Solution for Low-cost Access** 
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 One major hurdle standing in the way of accessible cell-free systems is the costly energy buffer constituting roughly 50 % of the total reaction costs \[7\]. Therefore one aim of our project is to identify an alternative energy buffer mix that significantly reduces the costs of cell-free systems contributing to their accessibility. We initially conducted a cost analysis based on the canonical energy buffer mix published in Sun et al. (2013) reseach paper which represents a standard state-of-the-art formulation \[8\]. For this, we looked at current prices for each component and calculated the price per millimole as well as the cost per milliliter reaction volume based on the quantity that has to be added to the energy mix (see [Protocols](https://static.igem.wiki/teams/5286/protocols.pdf) and Fig. 13).
 
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 ### Replacement of the Nucleotide Source
 
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 To assess the effect of the substitution of nucleotides, we kept all other components of the canonical energy buffer \[8\]. The measurement was conducted in technical duplicates with Lysate generated from the bacterial autolysate strain and a sfGFP reporter constructed under the control of a strong, constitutive bacteriophage lambda promoter (P70) \[BBa\_K2411000\].
  
@@ -208,6 +222,7 @@ To assess the effect of the substitution of nucleotides, we kept all other compo
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 Results from this experiment showed no severe effect of substitution of NTPs on the overall cell-free reaction activity (Figure 15). As the energy balances and fluxes will change with each substitution, the effects of NTP substitution were studied again for each alternative energy constituent.
 
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 #### **Replacing Amino Acids with Tryptone**
 
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  In our experiment, tryptone performed comparably to the canonical energy buffer containing amino acids (see Fig. 17). Consequently, this component was integrated into our workflow for subsequent optimization. 
 
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 Surprisingly, the replacement of amino acids with yeast extract resulted in three times as high of an activity than the canonical energy buffer (Figure 18). This is in disagreement with the findings of Nagappa et al. (2022) where the yeast extract variants performed less than the standard buffer \[10\].
 
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 The resulting fluorescence was found to be lower than the standard energy buffer, potentially indicating an energy limitation resulting from yeast extract amino acid supplementation. It may be hypothesized that the yeast extract and tryptone do not cover the amino acid demand fully, necessitating their synthesis using native enzymes. This reduces the energy phosphate pool by increasing the demand of NTPs. However, the differences were insignificant indicating that the replacement of NTPs and amino acids could be conducted simultaneously.
 
@@ -331,6 +350,7 @@ In previous work, 3-PGA was substituted with maltodextrin along with HMP as a ph
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 Maltodextrin is broken down via phosphorylation using HMP as a phosphate donor, producing glucose-1-phosphate, which enters glycolysis to generate ATP. Coenzymes like NAD and CoA enhance ATP regeneration and inorganic phosphate (iP) recycling, while lactate and acetate are produced as waste (Fig. 22) \[13\]. To avoid phosphate buildup, which hampers protein synthesis, Swartz's team explored phosphate-free energy sources like glucose and pyruvate, improving ATP regeneration through glycolysis (source, Swartz's team). Pyruvate can generate ATP without phosphate accumulation, and glucose is a cost-effective alternative to phosphate-based compounds.
 
@@ -352,6 +372,7 @@ Maltodextrin is broken down via phosphorylation using HMP as a phosphate donor,
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 The Maltodextrin-based energy solution was found to gradually generate energy in contrast to the canonical one. The kinetics of sfGFP production were slower and the reaction did not reach saturation within the time-frame we analyzed (Fig.23). After 10 h, the maltodextrin sample surpassed the fluorescence of the sample with standard buffer, potentially outperforming the canonical energy buffer in the long run. Similar observations were made in a repeat experiment (Fig. 24). 
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@@ -371,6 +392,7 @@ The Maltodextrin-based energy solution was found to gradually generate energy in
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 These results indicate that maltodextrin may be used as a potential replacement for 3-PGA, especially if speed of protein production is not a concern.
 
@@ -397,6 +419,7 @@ Another component of the energy buffer that we sought to replace was Coenzyme A
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 As there was no previous literature outlining the substitution of CoA in cell-free systems, we initially decided to supplement calcium-D(+)-pantothenate (CAS Nr. 137-08-6) in equimolar quantities to CoA (0.24 mM). 
 
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  Baseline correction was performed by subtracting the group  minimum value from each data point and removing background fluorescence from a negative control without template. Error bars represent the standard deviation for n=2 samples.
 
@@ -435,6 +459,7 @@ Following discussions with our core team member Mara Valverde Rascón, a former
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 To our surprise, we found that even water from the Danube river showed reasonable activity upon rehydration, presenting the real possibility of our prototype being used in point of care applications such as the surveillance of water sources using biosensors (Fig. 28). 
 
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 Baseline correction was performed by subtracting the group  minimum value from each data point and removing background fluorescence from a negative control without template. Error bars represent the standard deviation for n=2 samples. 
 
 We found that despite the processing of lysate with a small table top centrifuge the overall lysate activity was the same, potentially indicating a potential application for prototyping.