Difference between revisions of "Team:DTU-Denmark/Results-choosing-organism"

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<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/3/3a/T--DTU-Denmark--results-species2.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 2: </b> - Growth of <i>S. commune</i> <i>Δsc3</i> on PDA 39g plates after 24, 48 and 72 hours respectively after inoculation.</p></figcaption>
 
<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/3/3a/T--DTU-Denmark--results-species2.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 2: </b> - Growth of <i>S. commune</i> <i>Δsc3</i> on PDA 39g plates after 24, 48 and 72 hours respectively after inoculation.</p></figcaption>
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<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/8/83/T--DTU-Denmark--choiceoforg-fig3.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 3: </b> - Fig.3. Growth of <i>A. oryzae</i> on rice to create bricks after 7 days of incubation at 28ºC.</p></figcaption>
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</p>
 
<p style="text-align:justify" >
 
<p style="text-align:justify" >
  
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This preliminary experiment indicated several species were interesting for our research, as they were able to grow in common media, producing mycelium that could form fungal bricks possibly of use for making fungal materials. After incubation at the following conditions: <i>S. commune</i> at 30ºC at light, <i>P. ostreatus</i> at 28ºC at dark and <i>A. oryzae</i> at 28 ºC at dark, only <i>A. oryzae</i> showed sporulation despite a similar growing speed. As the protoplastation and transformation protocol available to us relied on spores to produce the protoplasts <i>A. oryzae</i> seemed like the best choice of species to continue work on for the genetic engineering part. Furthermore, comparing the bricks it quickly became clear that <i>A. oryzae</i> produced the most coherent bricks (Figure 3), with the other species producing extremely brittle materials. This might be a feature of the substrates chosen for growth, as they were chosen based on species’  preference in terms of growth rate, so for <i>A. oryzae</i> it was rice and for <i>P. ostreatus</i> and <i>S. commune</i> it was saw dust. Addition of coffee grounds did nothing for the texture of the bricks but a mixture of rice and sawdust made the <i>A. oryzae</i> bricks harder. As shown in Table 1, once again it seemed that <i>A. oryzae</i> was the best choice for further work.
  
Furthermore, to successfully transform the species we tested the sporulation of the fungi under the conditions we researched in the literature. The presence of spores facilitates the generation of protoplasts from fungi cells, that can then be transformed.
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<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/thumb/9/98/T--DTU-Denmark--table1.png/1200px-T--DTU-Denmark--table1.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Table 1 </b> - Summary of the properties investigated according to every species. </p></figcaption>
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<p style="text-align:justify" >
After incubation at the following conditions: <i>S. commune</i> at 30ºC at light, <i>P. ostreatus</i> at 28ºC at dark and <i>A. oryzae</i> at 28ºC at dark, only <i>A. oryzae</i> showed sporulation.
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<br><br>
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This preliminary experiment showed that several species were interesting for our research, as they were able to grow in widely used media, and they produced mycelium that could form fungal bricks. In addition, only <i>A. oryzae</i> was able to sporulate. This was possible when cultured at 28ºC at dark for 5-7 days. Moreover, it is a well-studied species that are used in fermentation processes and has been engineered previously. Therefore, we decided to focus the research on transformation with genes of interest on <i>A. oryzae</i>.
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<br><br>
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In addition to being the only one to sporulate and to form coherent bricks (Figure 4), <i>A. oryzae</i> is a well-studied species that is used in fermentation processes and has been engineered previously. Therefore, we decided to focus the project on forming bricks and doing genetic engineering of genes of interest on <i>A. oryzae</i>.
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<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/f/f3/T--DTU-Denmark--incubator.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 4 </b> - Incubator containing the boxes used to grow the bricks.  </p></figcaption>
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Eventually, radiation tests were performed on <i>A. oryzae</i> and  <i>Ganoderma lucidum</i> (Figure 5). The irradiated samples were kept at a temperature of 20 degrees celsius, controls were prepared and set to grow at the same temperature. The irradiated samples got a combined dose of 63.85 mSv from 28.09.2018, 13.10 to 01.10.2018, 10.45. The irradiated samples had growth radii which were on average twice as large as the controls (Figure 6,7). These results are thought to be spurious, and the most likely candidate is that the sample room was kept at a higher temperature than 20 degrees. The primary result is thus that the fungi were able to grow, but it is unknown if the increased amount of radiation caused an increase in mutations.
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</p>
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<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/e/eb/T--DTU-Denmark--Radiationfig1.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 5 </b> - Agar plates inoculated with species of interest, placed at 4 m from the gamma radiation source at DTU Risø. </p></figcaption>
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<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/1/10/T--DTU-Denmark--Radiationfig2.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 6 </b> - <i>A. oryzae</i> growth after 3 days incubated under a gamma radiation dose of 63.85 mSv </p></figcaption>
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<p style="text-align:justify" >
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<p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2018/c/c1/T--DTU-Denmark--Radiationfig3.png" style="max-width: 100%;" > <figcaption><p style="text-align:center; font-size:14px;"><b>Fig. 7 </b> - <i>G. lucidum</i> growth after 3 days incubated under a gamma radiation dose of 63.85 mSv</p></figcaption>
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<p style="color:#000; font-size:14px;">(1) Flores, R. (2015). Plastic Alternatives: Exploring Mycelium as a Medium. Parsons The New School for Design<br><br>
 
<p style="color:#000; font-size:14px;">(1) Flores, R. (2015). Plastic Alternatives: Exploring Mycelium as a Medium. Parsons The New School for Design<br><br>
 
(2) van Wetter, MA., Wösten, HA., Sietsma, JH., Wessels, JG. (2000). Hydrophobin gene expression affects hyphal wall composition in Schizophyllum commune. Fungal Genet Biol. 2000 Nov;31(2):99-104.<br><br>
 
(2) van Wetter, MA., Wösten, HA., Sietsma, JH., Wessels, JG. (2000). Hydrophobin gene expression affects hyphal wall composition in Schizophyllum commune. Fungal Genet Biol. 2000 Nov;31(2):99-104.<br><br>
(3) Sanchez, C. (2010). Cultivation of Pleurotus ostreatus and other edible mushrooms. Appl Microbiol Biotechnol. 2010 Feb;85(5):1321-37.<br><br>
+
(3) Sanchez, C. (2010). Cultivation of Pleurotus ostreatus and other edible mushrooms. Appl Microbiol Biotechnol. 2010 Feb;85(5):1321-37.
(4) Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends in Genetics Vol.25 No.2.<br><br>
+
<br><br>(4) Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends in Genetics Vol.25 No.2.
(5) Machida, M., Asai, K., Kikuchi, H. (2005). Genome sequencing and analysis of <i>Aspergillus oryzae</i>. Nature volume 438, pages 1157–1161</p>
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<br><br>(5) Machida, M., Asai, K., Kikuchi, H. (2005). Genome sequencing and analysis of <i>Aspergillus oryzae</i>. Nature volume 438, pages 1157–1161
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<br><br>(6) Matt W. (2016) How Bad is the Radiation on Mars? Universe Today. https://www.universetoday.com/14979/mars-radiation1/. Accessed October 15, 2018.
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<br><br>(7): Dartnell, L. R., Desorgher, L., Ward, J. M., & Coates, A. J. (2007). Modelling the surface and subsurface martian radiation environment: implications for astrobiology. Geophysical research letters, 34(2).
 +
<br><br>(8): Simonsen. Lisa C. Zeitlin, Cary. (2017) Briefing to NAC HEO/SMD Joint Committee Meeting “Mars Radiation Environment – what have we learned?”, https://www.nasa.gov/sites/default/files/atoms/files/mars_radiation_environment_nac_july_2017_final.pdf
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Revision as of 23:43, 17 October 2018

Choice of organism

Growing conditions between fungal species can vary, depending on how they grow in nature. Factors could be temperature, amount of light and the substrate, among other things. With the goal of growing fungal biobricks, a selection of the species used for our research needed to be done.

Choice of organism

Pleurotus ostreatus, Aspergillus oryzae and Schizophyllum commune were initially researched. First, S. commune has been investigated and used for the generation of bricks by the company Ecovative Design (1), which we collaborated with. In addition, S. commune also allowed us to study genes affecting the structure of mycelium, by using mutants as ΔSC3. This strain is characterized by a lack of SC3 gene, responsible for the production of hydrophobins. Hydrophobins are small proteins present in filamentous fungi that have the ability to repel water and create a coating in hydrophobic surfaces (2).

Secondly, P. ostreatus is a common edible mushroom also known as oyster mushroom that has been widely cultivated. In addition to having a strong mycelium, it is used in industrial processes and mycoremediation. (3).

Additionally, A. oryzae has been used for fermentation processes for at least 2000 years (4). In addition, its genome has been sequenced (5), being an optimal choice for the generation of a genetic toolbox.

On the other hand, as our project involved an eventual growth of fungi in Mars, the species used would ideally be able to grow under Mars’ conditions. Besides temperature, radiation is a key element to consider. $\alpha$- and $\beta$-radiation are fairly easily blocked, so even though there is an increased background radiation on Mars (6), the primary concern will be the increased levels of $\gamma$-radiation, since this type of radiation can penetrate very thick walls and inhibit growth of fungi or bacteria (7). To simulate the background gamma-radiation dose that fungi would receive on Mars, which is in the range of 12 rads/year (8), A. oryzae together with another fungal species, Ganoderma lucidum were exposed to this level of radiation during the first three days of growth. The results suggested that the radiation did not inhibit the growth of any of the species.

Results

In the first experiment, the species were seeded at 3 different concentrations of MEA (47,5 g, 50 g and 52,5), PDA (19,5 g, 39 g and 58,5 g) and YPD. Thereafter, growth pictures were taken every 24 hours and the size of the fungal colonies was compared. In addition, different growth conditions (temperature and light) were tested for each of the species. S. commune was incubated 30ºC at light and 27ºC at light, P. ostreatus at 28ºC at dark and 25ºC at light, and A. oryzae at 28ºC at dark and 30ºC at dark.

In addition, we also investigated the growth of a mutated S. commune strain ,ΔSC3.

Fig. 1: - Growth of A. oryzae on PDA 58.5g (A), S. commune on PDA 39g (B) and P. ostreatus on PDA 19.5g (C) plates after 24, 48 and 72 hours respectively after inoculation.

S. commune, P. ostreatus and A. oryzae grew at a similar rate on all media. However, the mutant strain of S. commune, Δsc3, was able to grow only at PDA 39 g (Figure 2).

Fig. 2: - Growth of S. commune Δsc3 on PDA 39g plates after 24, 48 and 72 hours respectively after inoculation.

Fig. 3: - Fig.3. Growth of A. oryzae on rice to create bricks after 7 days of incubation at 28ºC.

This preliminary experiment indicated several species were interesting for our research, as they were able to grow in common media, producing mycelium that could form fungal bricks possibly of use for making fungal materials. After incubation at the following conditions: S. commune at 30ºC at light, P. ostreatus at 28ºC at dark and A. oryzae at 28 ºC at dark, only A. oryzae showed sporulation despite a similar growing speed. As the protoplastation and transformation protocol available to us relied on spores to produce the protoplasts A. oryzae seemed like the best choice of species to continue work on for the genetic engineering part. Furthermore, comparing the bricks it quickly became clear that A. oryzae produced the most coherent bricks (Figure 3), with the other species producing extremely brittle materials. This might be a feature of the substrates chosen for growth, as they were chosen based on species’ preference in terms of growth rate, so for A. oryzae it was rice and for P. ostreatus and S. commune it was saw dust. Addition of coffee grounds did nothing for the texture of the bricks but a mixture of rice and sawdust made the A. oryzae bricks harder. As shown in Table 1, once again it seemed that A. oryzae was the best choice for further work.

Table 1 - Summary of the properties investigated according to every species.

In addition to being the only one to sporulate and to form coherent bricks (Figure 4), A. oryzae is a well-studied species that is used in fermentation processes and has been engineered previously. Therefore, we decided to focus the project on forming bricks and doing genetic engineering of genes of interest on A. oryzae.

Fig. 4 - Incubator containing the boxes used to grow the bricks.

Eventually, radiation tests were performed on A. oryzae and Ganoderma lucidum (Figure 5). The irradiated samples were kept at a temperature of 20 degrees celsius, controls were prepared and set to grow at the same temperature. The irradiated samples got a combined dose of 63.85 mSv from 28.09.2018, 13.10 to 01.10.2018, 10.45. The irradiated samples had growth radii which were on average twice as large as the controls (Figure 6,7). These results are thought to be spurious, and the most likely candidate is that the sample room was kept at a higher temperature than 20 degrees. The primary result is thus that the fungi were able to grow, but it is unknown if the increased amount of radiation caused an increase in mutations.

Fig. 5 - Agar plates inoculated with species of interest, placed at 4 m from the gamma radiation source at DTU Risø.

Fig. 6 - A. oryzae growth after 3 days incubated under a gamma radiation dose of 63.85 mSv

Fig. 7 - G. lucidum growth after 3 days incubated under a gamma radiation dose of 63.85 mSv

(1) Flores, R. (2015). Plastic Alternatives: Exploring Mycelium as a Medium. Parsons The New School for Design

(2) van Wetter, MA., Wösten, HA., Sietsma, JH., Wessels, JG. (2000). Hydrophobin gene expression affects hyphal wall composition in Schizophyllum commune. Fungal Genet Biol. 2000 Nov;31(2):99-104.

(3) Sanchez, C. (2010). Cultivation of Pleurotus ostreatus and other edible mushrooms. Appl Microbiol Biotechnol. 2010 Feb;85(5):1321-37.

(4) Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends in Genetics Vol.25 No.2.

(5) Machida, M., Asai, K., Kikuchi, H. (2005). Genome sequencing and analysis of Aspergillus oryzae. Nature volume 438, pages 1157–1161

(6) Matt W. (2016) How Bad is the Radiation on Mars? Universe Today. https://www.universetoday.com/14979/mars-radiation1/. Accessed October 15, 2018.

(7): Dartnell, L. R., Desorgher, L., Ward, J. M., & Coates, A. J. (2007). Modelling the surface and subsurface martian radiation environment: implications for astrobiology. Geophysical research letters, 34(2).

(8): Simonsen. Lisa C. Zeitlin, Cary. (2017) Briefing to NAC HEO/SMD Joint Committee Meeting “Mars Radiation Environment – what have we learned?”, https://www.nasa.gov/sites/default/files/atoms/files/mars_radiation_environment_nac_july_2017_final.pdf