Difference between revisions of "Team:UofGuelph/Description"

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<body">
 
<body">
  
<h1 class="descHead">Project Design</h1>
+
<h1 class="descHead">Project Description</h1>
 
<img src="https://static.igem.org/mediawiki/2017/4/4a/T--
 
<img src="https://static.igem.org/mediawiki/2017/4/4a/T--
  
 
U_of_Guelph--gryphon.jpg" class="guelphImages">
 
U_of_Guelph--gryphon.jpg" class="guelphImages">
<h1 class="descSub">Whats the Deal with Beerstone?</h1>
+
 
 +
 
 +
<h1 class="descSub">What's the Deal with Beerstone?</h1>
 
<p class="descP">
 
<p class="descP">
 
Beerstone can form on any surface that comes into contact  
 
Beerstone can form on any surface that comes into contact  
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problem for brewers as long as beer has been  
 
problem for brewers as long as beer has been  
  
produced<sup>1, 2</sup>. The most problematic locations  
+
produced<sup>1,2</sup>. The most problematic locations  
  
 
for its formation are heat exchangers, fermentation  
 
for its formation are heat exchangers, fermentation  
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beerstone, into which nutrient-providing proteins often  
 
beerstone, into which nutrient-providing proteins often  
  
become entrapped<span class="super">6</span>. This allows  
+
become entrapped<sup>6</sup>. This allows  
  
 
for unwanted microbial growth and the formation of  
 
for unwanted microbial growth and the formation of  
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beer unsuitable for sale or consumption thus resulting in  
 
beer unsuitable for sale or consumption thus resulting in  
  
financial loss to the brewer<span class="super">7</span>.  
+
financial loss to the brewer<sup>7</sup>.  
  
 
<i>Lactobacillus</i> species in beer, in particular,  
 
<i>Lactobacillus</i> species in beer, in particular,  
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diacetyl in the beer, resulting in an unwanted ‘buttery’  
 
diacetyl in the beer, resulting in an unwanted ‘buttery’  
  
flavour<span class="super">7</span>. With the removal of  
+
flavour<sup>7</sup>. With the removal of  
  
 
beerstone, growth of these microbial contaminants will be  
 
beerstone, growth of these microbial contaminants will be  
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exposure burns of the eyes and skin, and corrosive damage  
 
exposure burns of the eyes and skin, and corrosive damage  
  
to surfaces<span class="super">2, 3, 8</span>. The use of  
+
to surfaces<sup>2, 3, 8</sup>. The use of  
  
 
these cleaning agents require long and frequent pauses in  
 
these cleaning agents require long and frequent pauses in  
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<i>Oxalobacter formigenes</i> is an anaerobic, Gram-
 
<i>Oxalobacter formigenes</i> is an anaerobic, Gram-
  
negative bacteria native to the human gut microbiota<span
+
negative bacteria native to the human gut microbiota<sup>5</sup>.  <i>O. formigenes</i> is a safe  
 
+
class="super">5</span>.  <i>O. formigenes</i> is a safe  
+
  
 
(biosafety hazard level 1) organism that relies solely on  
 
(biosafety hazard level 1) organism that relies solely on  
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oxalate as its source of energy, as well as its main  
 
oxalate as its source of energy, as well as its main  
  
source of carbon<span class="super">5, 9</span>.   
+
source of carbon<sup>5, 9</sup>.   
  
 
Metabolism of oxalate is accomplished by two enzymes,  
 
Metabolism of oxalate is accomplished by two enzymes,  
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Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A  
 
Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A  
  
Decarboxylase (OXC)<span class="super">5, 10</span>.  
+
Decarboxylase (OXC)<sup>5, 10</sup>.  
 
In the first reaction step, a Coenzyme A (CoA) is  
 
In the first reaction step, a Coenzyme A (CoA) is  
  
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ternary complex between the substrates and the enzyme,  
 
ternary complex between the substrates and the enzyme,  
  
resulting in an oxalyl-CoA complex<span class="super">5,  
+
resulting in an oxalyl-CoA complex<sup>5,  
 
+
10</span>.  The OXC enzyme then catalyzes a reductive
+
  
reaction in which formyl-CoA and CO2 are produced<span
+
10</sup>.  The OXC enzyme then catalyzes a reductive
  
class="super">5, 10</span>.  The FRC enzyme then cycles  
+
reaction in which formyl-CoA and CO2 are produced<sup>5, 10</sup>.  The FRC enzyme then cycles  
  
 
the CoA back to a new oxalate molecule to start the  
 
the CoA back to a new oxalate molecule to start the  
  
process again<span class="super">5, 10</span>.  Thiamine  
+
process again<sup>5, 10</sup>.  Thiamine  
  
pyrophosphate (TPP), Mg2+, acetate, and CoA are required  
+
pyrophosphate (TPP), Mg<sup>2+</sup>, acetate, and CoA are required  
  
for the reaction to take place<span class="super">5,  
+
for the reaction to take place<sup>5,  
  
10</span>.  The reaction mechanism for the breakdown of  
+
10</sup>.  The reaction mechanism for the breakdown of  
  
 
calcium oxalate by FRC and OXC can be shown by the  
 
calcium oxalate by FRC and OXC can be shown by the  
  
equations in Figure 1<span class="super">10</span>:
+
equations in Figure 1<sup>10</sup>:
 
<br><br>
 
<br><br>
 
</p>
 
</p>
  
<h1 class="descSub">Our Project Design</h1>
 
  
<p class="descP"> Here we will include information about
 
  
why we plan on doing our project the way we are, what our
+
<h1 class="descSub"><i>Oxalobacter formigenes</i> and the Breakdown of Oxalate</h1>
 +
<p class="descP">
 +
In nature, there are several bacteria whose metabolism involves the breakdown of oxalate, a process that could potentially be harnessed to remove beerstone buildup.  <i>Oxalobacter formigenes</i> is an anaerobic, Gram-negative bacteria native to the human gut microbiota<sup>5</sup>.  <i>O. formigenes</i> is a safe (Biosafety Hazard Level 1) organism that relies solely on oxalate as its source of energy, as well as its main source of carbon<sup>5,9</sup>.  Metabolism of oxalate is accomplished by two enzymes, Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A Decarboxylase (OXC)<sup>5,10</sup>. <br><br>
 +
In the first reaction step, a Coenzyme A (CoA) is transferred to oxalate by the FRC enzyme<sup>10</sup>.  It functions by forming a ternary complex between the substrates and the enzyme, resulting in an oxalyl-CoA complex<sup>5,10</sup>.  The OXC enzyme then catalyzes a reductive reaction in which formyl-CoA and CO<sub>2</sub> are produced<sup>5,10</sup>.  The FRC enzyme then cycles the CoA back to a new oxalate molecule to start the process again<sup>5,10</sup>.  Thiamine pyrophosphate (TPP), Mg<sup>2+</sup>, acetate, and CoA are required for the reaction to take place<sup>5,10</sup>.  The reaction mechanism for the breakdown of calcium oxalate by FRC and OXC can be shown by the equations in Figure 1<sup>10</sup>:<br><br>
  
plans are in some detail, and why we are doing what we
+
<img src="https://static.igem.org/mediawiki/2018/7/7d/T--UofGuelph--Descr1.jpeg" class="tmPhotoL" ><br>
 +
Figure 1: Reaction equations for the breakdown of oxalate by Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A Decarboxylase (OXC)<sup>10</sup><br><br>
  
are doing this year<br><br>To be, or not to be: that is  
+
Calcium oxalate is highly insoluble, due to the strong ionic bond between the calcium and oxalate ions.  The calcium oxalate forms a very strong lattice structure as a result of the high coulombic force between the ions<sup>11</sup>.  However, some solubility does occur, reaching an equilibrium with a low ion concentration. As oxalate is broken down into formic acid and CO<sub>2</sub> by the enzymatic process, more calcium oxalate must dissolve into solution in order to maintain equilibrium, as per Le Châtelier’s principle.<br><br></p>
  
the question:
 
Whether ’tis nobler in the mind to suffer
 
The slings and arrows of outrageous fortune,
 
Or to take arms against a sea of troubles,
 
And by opposing end them? To die: to sleep;
 
No more; and by a sleep to say we end
 
The heart-ache and the thousand natural shocks
 
That flesh is heir to, ’tis a consummation
 
Devoutly to be wish’d. To die, to sleep;
 
To sleep: perchance to dream: ay, there’s the rub;
 
For in that sleep of death what dreams may come
 
When we have shuffled off this mortal coil,
 
Must give us pause: there’s the respect
 
That makes calamity of so long life;
 
For who would bear the whips and scorns of time,
 
The oppressor’s wrong, the proud man’s contumely,
 
The pangs of despised love, the law’s delay,
 
The insolence of office and the spurns
 
That patient merit of the unworthy takes,
 
When he himself might his quietus make
 
With a bare bodkin? who would fardels bear,
 
To grunt and sweat under a weary life,
 
But that the dread of something after death,
 
The undiscover’d country from whose bourn
 
No traveller returns, puzzles the will
 
And makes us rather bear those ills we have
 
Than fly to others that we know not of?
 
Thus conscience does make cowards of us all;
 
And thus the native hue of resolution
 
Is sicklied o’er with the pale cast of thought,
 
And enterprises of great pith and moment
 
With this regard their currents turn awry,
 
And lose the name of action.–Soft you now!
 
The fair Ophelia! Nymph, in thy orisons
 
Be all my sins remember’d.</p>
 
  
<h1 class="descSub">Future Development</h1>
+
<h1 class="descSub">Creating a Biological System to Aid in the Breakdown of Oxalate</h1>
<p class="descP"> Here we will write about our plans for  
+
<p class="descRef">  
 +
Overall given dangers, time and costs to the brewing industry involved in the removal of beerstone, we propose to investigate the use of FRC and OXC for the safe and efficient breakdown of beerstone from brewing equipment. Aside from the production and characterization of FRC and OXC to be used as subsequent treatment on calcium oxalate (and related compounds such as sodium oxalate), we hope to develop a biological system as a form of beerstone treatment. In a cell system, oxalate is brought in by an oxalate-formate antiporter (OxIT) and converted to CO<sub>2</sub> and formyl-CoA. Formyl-CoA is reused by FRC as a CoA donor in a subsequent reaction and released from the cell as formate by OxIT5 (Figure 2). <br><br>
 +
Utilizing <i>S. cerevisiae</i>, we can transform the episomal plasmid pD1218 into w303α that replaces the MATα pheromone secretion system with our genes of interest (frc, oxc) The OxIT antiporter will also be cloned into our plasmid system to allow for the presence of an alternative energy generation system with both FRC and OXC working to facilitate the breakdown of oxalate. The metabolic activity of w303α will be characterized with a modified Minimum Inhibitory Concentration Assay in which yeast will be grown in varying concentrations of C<sub>2</sub>CaO<sub>4</sub> . After 48 hours, the levels of oxalate in solution will be measured using a Calcium Oxalate Dissolution Kit (Trinity Biotech).<br><br>
  
the future of this project and what direction we plan on
+
<img src="https://static.igem.org/mediawiki/2018/4/40/T--UofGuelph--Descr2.jpeg " class="tmPhotoL" ><br>
 +
Figure 2. Metabolic pathway of oxalate degradation illustrating the OxIT antiporter<sup>5</sup><br><br>
 +
</p>
  
heading. <br><br>To be, or not to be: that is the
 
  
question:
 
Whether ’tis nobler in the mind to suffer
 
The slings and arrows of outrageous fortune,
 
Or to take arms against a sea of troubles,
 
And by opposing end them? To die: to sleep;
 
No more; and by a sleep to say we end
 
The heart-ache and the thousand natural shocks
 
That flesh is heir to, ’tis a consummation
 
Devoutly to be wish’d. To die, to sleep;
 
To sleep: perchance to dream: ay, there’s the rub;
 
For in that sleep of death what dreams may come
 
When we have shuffled off this mortal coil,
 
Must give us pause: there’s the respect
 
That makes calamity of so long life;
 
For who would bear the whips and scorns of time,
 
  
<h1 class="descSub">References</h1>
 
<p class="descRef"> Rose, D. This is a test (2017). Sci.
 
  
Awesome. 28-29 </p>
 
  
<div class="sponsor">
+
<h1 class="descSub">References</h1>
<p class="footer-links" style="text-align:center!
+
<p class="descRef">
 +
1. guelph.ca. Annual & Summary Water Services Report. (2017). at <​http://guelph.ca/wp-content/uploads/AnnualandSummaryWaterServicesReport.pdf​> <br>
 +
2. morebeer.com. Removing & Preventing Beerstone Buildup. (2014). at https://www.morebeer.com/articles/removing_preventing_beerstone​<br>
 +
3. Gemmel, M. The removal and prevention of beerstone. (2017). at ​http://www.beerlab.co.za/blogs/news/the-removal-and-prevention-of-beer-stone​<br>
 +
4. Alavi, Z. I. & West, D. B. Proposed Method for the Quantitative Determination of Oxalate in Beer and Wort. ​American Society of Brewing Chemists Journal ​41, 24-27 (1983)<br>
 +
5. Stewart, C. S., Duncan, S. H. & Cave, D. R. Oxalobacter formigenes and its role in oxalate metabolism in the human gut. ​FEMS Microbiology Letters ​230, 1-7 (2004)<br>
 +
6. Johnson, D. & Swanson, H. D. A Look at Biofilms in the Brewery. (2000). at ​http://www.birkocorp.com/brewery/white-papers/biofilms-a-look-at-biofilms-in-the-brewery/​<br>
 +
7. Paradh, A. D., Mitchell, W. J. & Hill, A. E. ​Occurrence of Pectinatus and Megasphaera in the Major UK Breweries. ​Journal of the Institute of Brewing​ 117, 498-506 (2011)<br>
 +
8. worksafe.vic.gov.au. Cleaning - Using caustic cleaners. (n.d.). at https://www.worksafe.vic.gov.au/__data/assets/pdf_file/0014/14531/HSS0094_-_Cleaning_-_Using_caustic_cleaners.pdf <br>
 +
9. atcc.org. ​Oxalobacter formigenes ​Allison ​et al.​ (ATCC® 35274TM). (2016). At​https://www.atcc.org/products/all/35274.aspx#documentation​<br>
 +
10. Sidhu, H. ​et al​. ​DNA sequencing and expression of the formyl coenzyme A transferasegene, frc, from​ Oxalobacter formigenes​. ​Journal of Bacteriology ​179, 3378-3381 (1997) <br>
 +
11. Arnott, H., J., Pautard, F. G. E. & Steinfink, H. Structure of Calcium Oxalate Monohydrate. ​Nature​ 208, 1197-1198 (1965)
 +
</p><br>
  
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<h1>Design</h1>
 
<p>
 
Design is the first step in the design-build-test cycle
 
 
in engineering and synthetic biology. Use this page to
 
 
describe the process that you used in the design of your
 
 
parts. You should clearly explain the engineering
 
 
principles used to design your project.
 
</p>
 
 
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<h3>What should this page contain?</h3>
 
<ul>
 
<li>Explanation of the engineering principles your team
 
 
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<li>Discussion of the design iterations your team went
 
 
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Latest revision as of 01:37, 8 December 2018

Project Description

What's the Deal with Beerstone?

Beerstone can form on any surface that comes into contact with beer and wort (unfermented beer) and has been a problem for brewers as long as beer has been produced1,2. The most problematic locations for its formation are heat exchangers, fermentation vessels, aging tanks, kegs, and beer dispense lines. Beerstone is comprised of a combination of precipitated calcium oxalate and entrapped beer polypeptides3. Oxalate enters the brewing process from the cereal grains and hops used to make beer4. Oxalate is present in the form of aqueous oxalic acid which is a corrosive, highly oxidized compound that has strong chelating activity5. These oxalate ions are soluble in both wort and beer, allowing them to combine with calcium ions to form calcium oxalate4. Calcium ions enter the brewing process through the water, grains and water- correction salts4. Calcium oxalate precipitates out of solution upon formation, and is one of the most insoluble metallo-organic compounds with a low solubility4. In a geographic region with high calcium levels in the drinking water, such as Guelph, Ontario, this can lead to up to 165g of calcium oxalate building up in a single 1000L batch of beer1. This precipitation can happen either during the brewing or bottling processes, or after the beer has been bottled depending on when the calcium oxalate formation occurs4. The point during the process at which calcium oxalate forms is dependent on temperature, time, pH and ion concentration4. If calcium oxalate forms after filtration, or if all calcium oxalate crystals are not filtered out of the beer, haze and sediment may form4. In addition, calcium oxalate crystals can cause over-foaming during filling or when a pressurized container such as a can or bottle is opened4.

Deposits of beerstone provide protection and nutrients for bacteria to grow due to the porous surface of the beerstone, into which nutrient-providing proteins often become entrapped6. This allows for unwanted microbial growth and the formation of biofilms upon the beerstone, for example, species of the genera Pectinatus and Megasphaera. These microorganisms cause beer spoilage, products with reduced shelf-life, off-flavours and sour tastes, rendering the beer unsuitable for sale or consumption thus resulting in financial loss to the brewer7. Lactobacillus species in beer, in particular, causes high turbidity which manifests as a hazy appearance in the liquid. It also causes a high level of diacetyl in the beer, resulting in an unwanted ‘buttery’ flavour7. With the removal of beerstone, growth of these microbial contaminants will be prohibited, improving brew quality and reducing downstream processing.

Beerstone is difficult to remove for several reasons. Calcium oxalate is extremely insoluble in both hot and cold water, meaning that the use of harsh chemicals is currently required for effective methods of removing beerstone. These involve caustic or other harsh cleaners which are dangerous to work with due to the potential for exposure burns of the eyes and skin, and corrosive damage to surfaces2, 3, 8. The use of these cleaning agents require long and frequent pauses in production which lower the efficacy of the brewing process. Additionally, the equipment required to utilize these caustic chemicals and the chemical disposal requirements are costly and potentially environmentally damaging.

Oxalobacter formigenes and the Breakdown of Oxalate

Oxalobacter formigenes is an anaerobic, Gram- negative bacteria native to the human gut microbiota5. O. formigenes is a safe (biosafety hazard level 1) organism that relies solely on oxalate as its source of energy, as well as its main source of carbon5, 9. Metabolism of oxalate is accomplished by two enzymes, Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A Decarboxylase (OXC)5, 10. In the first reaction step, a Coenzyme A (CoA) is transferred to oxalate by the FRC enzyme10. It functions by forming a ternary complex between the substrates and the enzyme, resulting in an oxalyl-CoA complex5, 10. The OXC enzyme then catalyzes a reductive reaction in which formyl-CoA and CO2 are produced5, 10. The FRC enzyme then cycles the CoA back to a new oxalate molecule to start the process again5, 10. Thiamine pyrophosphate (TPP), Mg2+, acetate, and CoA are required for the reaction to take place5, 10. The reaction mechanism for the breakdown of calcium oxalate by FRC and OXC can be shown by the equations in Figure 110:

Oxalobacter formigenes and the Breakdown of Oxalate

In nature, there are several bacteria whose metabolism involves the breakdown of oxalate, a process that could potentially be harnessed to remove beerstone buildup. Oxalobacter formigenes is an anaerobic, Gram-negative bacteria native to the human gut microbiota5. O. formigenes is a safe (Biosafety Hazard Level 1) organism that relies solely on oxalate as its source of energy, as well as its main source of carbon5,9. Metabolism of oxalate is accomplished by two enzymes, Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A Decarboxylase (OXC)5,10.

In the first reaction step, a Coenzyme A (CoA) is transferred to oxalate by the FRC enzyme10. It functions by forming a ternary complex between the substrates and the enzyme, resulting in an oxalyl-CoA complex5,10. The OXC enzyme then catalyzes a reductive reaction in which formyl-CoA and CO2 are produced5,10. The FRC enzyme then cycles the CoA back to a new oxalate molecule to start the process again5,10. Thiamine pyrophosphate (TPP), Mg2+, acetate, and CoA are required for the reaction to take place5,10. The reaction mechanism for the breakdown of calcium oxalate by FRC and OXC can be shown by the equations in Figure 110:


Figure 1: Reaction equations for the breakdown of oxalate by Formyl Coenzyme A Transferase (FRC) and Oxalyl-Coenzyme A Decarboxylase (OXC)10

Calcium oxalate is highly insoluble, due to the strong ionic bond between the calcium and oxalate ions. The calcium oxalate forms a very strong lattice structure as a result of the high coulombic force between the ions11. However, some solubility does occur, reaching an equilibrium with a low ion concentration. As oxalate is broken down into formic acid and CO2 by the enzymatic process, more calcium oxalate must dissolve into solution in order to maintain equilibrium, as per Le Châtelier’s principle.

Creating a Biological System to Aid in the Breakdown of Oxalate

Overall given dangers, time and costs to the brewing industry involved in the removal of beerstone, we propose to investigate the use of FRC and OXC for the safe and efficient breakdown of beerstone from brewing equipment. Aside from the production and characterization of FRC and OXC to be used as subsequent treatment on calcium oxalate (and related compounds such as sodium oxalate), we hope to develop a biological system as a form of beerstone treatment. In a cell system, oxalate is brought in by an oxalate-formate antiporter (OxIT) and converted to CO2 and formyl-CoA. Formyl-CoA is reused by FRC as a CoA donor in a subsequent reaction and released from the cell as formate by OxIT5 (Figure 2).

Utilizing S. cerevisiae, we can transform the episomal plasmid pD1218 into w303α that replaces the MATα pheromone secretion system with our genes of interest (frc, oxc) The OxIT antiporter will also be cloned into our plasmid system to allow for the presence of an alternative energy generation system with both FRC and OXC working to facilitate the breakdown of oxalate. The metabolic activity of w303α will be characterized with a modified Minimum Inhibitory Concentration Assay in which yeast will be grown in varying concentrations of C2CaO4 . After 48 hours, the levels of oxalate in solution will be measured using a Calcium Oxalate Dissolution Kit (Trinity Biotech).


Figure 2. Metabolic pathway of oxalate degradation illustrating the OxIT antiporter5

References

1. guelph.ca. Annual & Summary Water Services Report. (2017). at <​http://guelph.ca/wp-content/uploads/AnnualandSummaryWaterServicesReport.pdf​>
2. morebeer.com. Removing & Preventing Beerstone Buildup. (2014). at https://www.morebeer.com/articles/removing_preventing_beerstone​
3. Gemmel, M. The removal and prevention of beerstone. (2017). at ​http://www.beerlab.co.za/blogs/news/the-removal-and-prevention-of-beer-stone​
4. Alavi, Z. I. & West, D. B. Proposed Method for the Quantitative Determination of Oxalate in Beer and Wort. ​American Society of Brewing Chemists Journal ​41, 24-27 (1983)
5. Stewart, C. S., Duncan, S. H. & Cave, D. R. Oxalobacter formigenes and its role in oxalate metabolism in the human gut. ​FEMS Microbiology Letters ​230, 1-7 (2004)
6. Johnson, D. & Swanson, H. D. A Look at Biofilms in the Brewery. (2000). at ​http://www.birkocorp.com/brewery/white-papers/biofilms-a-look-at-biofilms-in-the-brewery/​
7. Paradh, A. D., Mitchell, W. J. & Hill, A. E. ​Occurrence of Pectinatus and Megasphaera in the Major UK Breweries. ​Journal of the Institute of Brewing​ 117, 498-506 (2011)
8. worksafe.vic.gov.au. Cleaning - Using caustic cleaners. (n.d.). at https://www.worksafe.vic.gov.au/__data/assets/pdf_file/0014/14531/HSS0094_-_Cleaning_-_Using_caustic_cleaners.pdf
9. atcc.org. ​Oxalobacter formigenes ​Allison ​et al.​ (ATCC® 35274TM). (2016). At​https://www.atcc.org/products/all/35274.aspx#documentation​
10. Sidhu, H. ​et al​. ​DNA sequencing and expression of the formyl coenzyme A transferasegene, frc, from​ Oxalobacter formigenes​. ​Journal of Bacteriology ​179, 3378-3381 (1997)
11. Arnott, H., J., Pautard, F. G. E. & Steinfink, H. Structure of Calcium Oxalate Monohydrate. ​Nature​ 208, 1197-1198 (1965)


University of Guelph iGEM 2018