Team:UNITN-Trento/Project/CrustAway

From 2012.igem.org

(Difference between revisions)
Line 107: Line 107:
<div id="results" class="but"><img src="http://www.science.unitn.it/~igem/img/project/buttons/button_5.png" alt="" /><span class="title">Results</span></div>
<div id="results" class="but"><img src="http://www.science.unitn.it/~igem/img/project/buttons/button_5.png" alt="" /><span class="title">Results</span></div>
<div id="application" class="but"><img src="http://www.science.unitn.it/~igem/img/project/buttons/button_8.png" alt="" /><span class="title">Application</span></div>
<div id="application" class="but"><img src="http://www.science.unitn.it/~igem/img/project/buttons/button_8.png" alt="" /><span class="title">Application</span></div>
-
<div class="but" id="intro"><a href="https://2012.igem.org/Team:UNITN-Trento/Project/Terminators"><img src="http://www.science.unitn.it/~igem/img/project/buttons/button_16.png" alt="" /></a><span class="title">Terminators</span></div>
+
<div class="but" id="intro" style="position: relative; left: 40px;"><a href="https://2012.igem.org/Team:UNITN-Trento/Project/Terminators"><img src="http://www.science.unitn.it/~igem/img/project/buttons/button_14.png" alt="" /></a><span class="title" style="color: black;">Terminators</span></div>
<div class="clearfix"></div>
<div class="clearfix"></div>
Line 114: Line 114:
<div class="content" style="padding-left: 20px ;padding-right: 20px ;">
<div class="content" style="padding-left: 20px ;padding-right: 20px ;">
-
<div id="intro" class="chapter intro visible">
+
<div class="chapter intro visible">
-
<h3>INTRO</h3>
+
<h2 style="text-align: center;">INTRODUCTION</h2>
 +
<p>Have you ever noticed that ugly black crust found on precious monuments and statues? Here in Italy, we surely have it, and we’d like to find a way to return our monuments to their natural, beautiful state. <!-- <br/>The crusts in question are composed of a gypsum layer (i.e CaSO4-2H2O), that is the product of the reaction between calcite (i.e. CaCO3), the sulphur components of acid rain and atmospheric pollutants.--></p>
 +
<div style="width: 500px; margin: 0 auto;"><img style="width: 500px;" src="http://www.science.unitn.it/~igem/img/project/BlackCrustPolaroid.jpg" /></div>
 +
<p>Our idea is to create a bioremediation kit to help every sculptor, restorer, marble cutter or anyone interested in removing that anaesthetic and harmful black crust layer from their precious calcareous stones. A lot of chemical and mechanical approaches are already off the shelf, and someone also exploited in the past Sulfur Reducing Bacteria (SRBs) to eliminate the trapping gypsum matrix (Capitelli et al. 2007). </p>
 +
<p>However all of these methods show some weak points:
 +
<ol>
 +
<li>Chemical and mechanical methods are too invasive and they risk to damage the underlying and precious marble surface; We have met with experts in the restoration field and learned about the <a href="https://2012.igem.org/Team:UNITN-Trento/Art">criteria to define a good restoration</a>.</li>
 +
<li>Chemical methods have also health related risks. Workers, artists, restorers too often use chemicals to clean marble stones in unsafe conditions. We have met with one of the many local artists and reported our impressions on his methods to clean marble in the <a href="https://2012.igem.org/Team:UNITN-Trento/Art">Art & Science</a> section of our Wiki. </li>
 +
<li>Natural SRBs, which have been used in a few cases, instead need anaerobic conditions and they constitutively express the enzymes required for sulphur reduction, thus not leaving the choice to the operator to control the rate and amount of sulphur reduced.</li>
 +
</ol>
 +
As a valid alternative we propose an engineered E. coli capable of reducing the sulphuric gypsum matrix that should have the following advantages:
 +
<ol>
 +
<li>Work in <b>AEROBIC</b> conditions: this is a breakthrough in the field of SRBs!</li>
 +
<li>Should be <b>CONTROLLED</b> and <b>MODULATED</b> as needed.</li>
 +
<li>Should <b>NOT</b> be <b>INVASIVE</b> and work selectively against the gypsum matrix without touching the calcareous surface.</li>
 +
<li>Should be <b>CHEAP</b> and <b>EASY TO APPLY</b>. There will be no more need of expensive chemical and trained workers that have to work many hours to clean our statues and monuments.</li>
 +
</ol>
 +
</p>
-
<ul>
+
<p>To summarize, with our biological system we want to mix the strengths of all the available methods and eliminate their weak points to propose an infallible and very safe method to clean precious marble pieces!</p>
-
<li>2nd: GET TOGETHER!! Cristina brought brownies!</li>
+
-
<li>9th: We started looking at some of the previous successful projects.</li>
+
<div class="internalLink" id="method"><a href="javascript:void(0);">READ MORE ABOUT OUR METHOD</a></div> <div class="clearfix"></div>
-
<li>16th: More on the old projects eating a fantastic Tiramisu from Giacomo.</li>
+
-
<li>23rd: Crash course on Synthetic Biology from Sheref and Cristina</li>
+
-
</ul>
+
-
<h3>APRIL</h3>
+
<h3>How does the black crust form?</h3>
 +
<p>One of the main factors in the formation of the black crust is the atmospheric pollution. The burning process of fossil fuels leads to an increase in the concentration of some acid gases in the atmosphere. In particular SO>su>2>/sub> when reacts with water induces the transformation of calcite (CaCO<sub>3</sub>, present in the stone substrate) into gypsum (CaSO<sub>4</sub> ·2H<sub>2</sub>O), which precipitates with inclusions of carbon particulate matter. Smog particles are also able to absorb gas pollutants on their surfaces, resulting in “dry deposition” of pollutant.</p>
 +
<div style="width: 500px; margin: 0 auto;"><img style="width: 500px;" src="http://www.science.unitn.it/~igem/img/project/BlackCrustFormation.jpg" /></div>
 +
<p>Black crusts are usually found on areas of the stone sheltered from rainfall, although still in presence of capillary water flowing through the pores. Calcium ions migrate to the surface of the stone during gypsum formation, leading to formation of cavities beneath the stone that weakens the stone’s integrity. The degradation process indeed affects both the stone conservation and appearance:
<ul>
<ul>
-
<li>13rd: Brainstorming. No more cakes?</li>
+
<li>When the formed gypsum is washed away it takes some of the stone particles with it, causing at first loss of detail, but eventually leading, again, to a loss of structural integrity.</li>
-
<li>16th: Brainstorming. Where is the cake?</li>
+
<li>In areas sheltered from rainwater, though, gypsum crusts remain. When combined with particulate matter from the atmosphere, gypsum creates the so called black crusts.</li>
-
<li>19th: It seems like everybody likes the idea proposed by Daniele. Remove the black crust from statues. We decided to look more specifically into these topics: A) how to dissolve the black crust, B) how to keep the &#8220;patina nobile&#8221; (calcium oxalate protective film) and C) how to kill biofilms, all to protect statues and marble monuments. Giacomo will look into secretion systems and Francesco suggested a photoinducible system. We have homework to do.</li>
+
-
<li>24th: Discussion on possible ways to achieve our goals. We looked into the mechanism of SRB for sulfate reduction.</li>
+
-
<li>27th: More ideas on the Black crust project based on a work of J.Keasling that Jason found in the literature. We are also thinking of having a side project for the characterization of deposited parts (RBS, promoters, terminators?). Each of us will further investigate the fesibility of the topics discussed on April 19th and will present a plan of work for next time.</li>
+
</ul>
</ul>
-
+
The composition of the black crust is heterogeneous and varies accordingly to the environment. The crusts found in big cities are rich in metals and carbonaceous particles, while the crusts of stoned found in a less urban environment are often characterised by the presence of microorganisms.
-
<h3>MAY</h3>
+
Although pollution has actually diminished during the last decades, the black crust problem is not been solved yet. It is thereby clear how these black crusts are a prominent issue in heritage material conservation and restoration, an issue that every remediator has to address.</p>
-
+
<div class="internalLink" id="method"><a href="javascript:void(0);">READ ABOUT OUR METHOD</a></div> <div class="clearfix"></div>
-
<ul>
+
-
<li>14th: Presentations and discussion on the investigated topics. Other PIs from CIBIO participated to the discussion too.</li>
+
-
<li>28th: The project is finalized: We will save the world one statue at time! We decided to drop the project on the formation of calcium oxalate and biofilm disruption. Perhaps next year team can look into it.</li>
+
-
</ul>
+
</div>
</div>
<div class="chapter method">
<div class="chapter method">
-
<h3>METHOD</h3>
+
<h2 style="text-align: center;">OUR METHOD</h2>
 +
<div style="width: 500px; margin: 0 auto;"><img style="width: 500px;" src="http://www.science.unitn.it/~igem/img/project/BacteriaNoInduction.jpg" /></div>
 +
<p>Our method exploits an engineered E. coli to reduce aerobically the sulphuric gypsum layer in a controlled and modulated manner. In 2001 the Keasling group has engineered bacteria to reduce sulphate aerobically and precipitate metals from water taking advantage of the production of sulfidric acid as one of the bioproducts of sulphur reduction. We took inspiration from this work and developed two new BioBrick devices directed to overproduce cysteine and then convert it to sulphide with the ultimate goal of dissolving the sulphate layer deposited on the blackened stones.</p>
 +
<h3>Who are the players?</h3>
 +
<div style="width: 500px; margin: 0 auto;"><img style="width: 500px;" src="http://www.science.unitn.it/~igem/img/project/CysE.jpg" /></div>
 +
<ul><li>CysE  is a Serine acetyltransferase that mediates conversion of L-serine to a precursor of L-cysteine in E.coli. More precisely we have used a mutant CysE (M256I) that has enhanced activity in that its enzymatic activity is less sensitive to feedback inhibition by cysteine.</li></ul>
 +
<div style="width: 500px; margin: 0 auto;"><img style="width: 500px;" src="http://www.science.unitn.it/~igem/img/project/CysDes.jpg" /></div>
 +
<ul><li>CysDes  is a Cysteine Desulfhydrase, first isolated in Treponema denticola, an anaerobic organism involved in periodontal diseases. It is an aminotransferase that converts cysteine into pyruvate, ammonia, and hydrogen sulphide.</li></ul>
-
<ul>
+
<h3>How do we control the expression of our devices?</h3>
-
<li>2nd: GET TOGETHER!! Cristina brought brownies!</li>
+
<div style="width: 500px; margin: 0 auto;"><img style="width: 500px;" src="http://www.science.unitn.it/~igem/img/project/BacteriaInduction.jpg" /></div>
-
<li>9th: We started looking at some of the previous successful projects.</li>
+
<p>The expression of CysE is controlled by an arabinose inducible cassette (our part BBa_K731201). Our composite device (BBa_K731030) is composed by araC –pBad, and strong RBS followed by M256I CysE.<br/>
-
<li>16th: More on the old projects eating a fantastic Tiramisu from Giacomo.</li>
+
The pBAD promoter is activated in the presence of L-arabinose. L-arabinose binds to the AraC protein and inactivates its inhibitory function, allowing the RNA polymerase to recognize the pBAD promoter and start the transcription of CysE.
-
<li>23rd: Crash course on Synthetic Biology from Sheref and Cristina</li>
+
</p>
-
</ul>
+
<p>CysDes was placed downstream of an IPTG inducible cassette (our part BBa_K731300). The expression of CysDes is therefore controlled by a system composed of: LacI (repressor protein) and a lacIq promoter followed by a strong hybrid promoter (Ptac), a Lac Operator and a strong RBS. Addition of IPTG inactivates the LacI repressor, thus allowing the expression of our gene of interest CysDes. </p>
 +
<p>The possibility of controlling simultaneously the expression of our two devices (i.e. by adding arabinose and/or IPTG) makes our system more <b>SAFE</b>, <b>CONTROLLABLE</b> and <b>MODULAR</b>.</p>
-
<h3>APRIL</h3>
+
<h3>How do we test the expression of our enzymes?</h3>
-
+
<p>We used the Gibson assembly method to create two sfGFP-tagged devices that were useful reporter to verify the expression of our genes.</p>
-
<ul>
+
<div style="width: 500px; margin: 0 auto;"><img style="width: 500px;" src="http://www.science.unitn.it/~igem/img/project/ConstructsGFP.jpg" /></div>
-
<li>13rd: Brainstorming. No more cakes?</li>
+
<div class="internalLink" id="results"><a href="javascript:void(0);">GO TO OUR RESULTS</a></div> <div class="clearfix"></div>
-
<li>16th: Brainstorming. Where is the cake?</li>
+
-
<li>19th: It seems like everybody likes the idea proposed by Daniele. Remove the black crust from statues. We decided to look more specifically into these topics: A) how to dissolve the black crust, B) how to keep the &#8220;patina nobile&#8221; (calcium oxalate protective film) and C) how to kill biofilms, all to protect statues and marble monuments. Giacomo will look into secretion systems and Francesco suggested a photoinducible system. We have homework to do.</li>
+
-
<li>24th: Discussion on possible ways to achieve our goals. We looked into the mechanism of SRB for sulfate reduction.</li>
+
-
<li>27th: More ideas on the Black crust project based on a work of J.Keasling that Jason found in the literature. We are also thinking of having a side project for the characterization of deposited parts (RBS, promoters, terminators?). Each of us will further investigate the fesibility of the topics discussed on April 19th and will present a plan of work for next time.</li>
+
-
</ul>
+
-
+
-
<h3>MAY</h3>
+
-
+
-
<ul>
+
-
<li>14th: Presentations and discussion on the investigated topics. Other PIs from CIBIO participated to the discussion too.</li>
+
-
<li>28th: The project is finalized: We will save the world one statue at time! We decided to drop the project on the formation of calcium oxalate and biofilm disruption. Perhaps next year team can look into it.</li>
+
-
</ul>
+
</div>
</div>
<div class="chapter results">
<div class="chapter results">
-
<h3>RESULTS</h3>
+
<h2>RESULTS</h2>
-
<ul>
+
-
<li>2nd: GET TOGETHER!! Cristina brought brownies!</li>
+
-
<li>9th: We started looking at some of the previous successful projects.</li>
+
-
<li>16th: More on the old projects eating a fantastic Tiramisu from Giacomo.</li>
+
-
<li>23rd: Crash course on Synthetic Biology from Sheref and Cristina</li>
+
-
</ul>
+
-
+
-
<h3>APRIL</h3>
+
-
+
-
<ul>
+
-
<li>13rd: Brainstorming. No more cakes?</li>
+
-
<li>16th: Brainstorming. Where is the cake?</li>
+
-
<li>19th: It seems like everybody likes the idea proposed by Daniele. Remove the black crust from statues. We decided to look more specifically into these topics: A) how to dissolve the black crust, B) how to keep the &#8220;patina nobile&#8221; (calcium oxalate protective film) and C) how to kill biofilms, all to protect statues and marble monuments. Giacomo will look into secretion systems and Francesco suggested a photoinducible system. We have homework to do.</li>
+
-
<li>24th: Discussion on possible ways to achieve our goals. We looked into the mechanism of SRB for sulfate reduction.</li>
+
-
<li>27th: More ideas on the Black crust project based on a work of J.Keasling that Jason found in the literature. We are also thinking of having a side project for the characterization of deposited parts (RBS, promoters, terminators?). Each of us will further investigate the fesibility of the topics discussed on April 19th and will present a plan of work for next time.</li>
+
-
</ul>
+
-
+
-
<h3>MAY</h3>
+
-
+
-
<ul>
+
-
<li>14th: Presentations and discussion on the investigated topics. Other PIs from CIBIO participated to the discussion too.</li>
+
-
<li>28th: The project is finalized: We will save the world one statue at time! We decided to drop the project on the formation of calcium oxalate and biofilm disruption. Perhaps next year team can look into it.</li>
+
-
</ul>
+
</div>
</div>
<div class="chapter application">
<div class="chapter application">
-
<h3>APPLICATION</h3>
+
<h2>APPLICATION</h2>
-
<ul>
+
-
<li>2nd: GET TOGETHER!! Cristina brought brownies!</li>
+
-
<li>9th: We started looking at some of the previous successful projects.</li>
+
-
<li>16th: More on the old projects eating a fantastic Tiramisu from Giacomo.</li>
+
-
<li>23rd: Crash course on Synthetic Biology from Sheref and Cristina</li>
+
-
</ul>
+
-
+
-
<h3>APRIL</h3>
+
-
+
-
<ul>
+
-
<li>13rd: Brainstorming. No more cakes?</li>
+
-
<li>16th: Brainstorming. Where is the cake?</li>
+
-
<li>19th: It seems like everybody likes the idea proposed by Daniele. Remove the black crust from statues. We decided to look more specifically into these topics: A) how to dissolve the black crust, B) how to keep the &#8220;patina nobile&#8221; (calcium oxalate protective film) and C) how to kill biofilms, all to protect statues and marble monuments. Giacomo will look into secretion systems and Francesco suggested a photoinducible system. We have homework to do.</li>
+
-
<li>24th: Discussion on possible ways to achieve our goals. We looked into the mechanism of SRB for sulfate reduction.</li>
+
-
<li>27th: More ideas on the Black crust project based on a work of J.Keasling that Jason found in the literature. We are also thinking of having a side project for the characterization of deposited parts (RBS, promoters, terminators?). Each of us will further investigate the fesibility of the topics discussed on April 19th and will present a plan of work for next time.</li>
+
-
</ul>
+
-
+
-
<h3>MAY</h3>
+
-
+
-
<ul>
+
-
<li>14th: Presentations and discussion on the investigated topics. Other PIs from CIBIO participated to the discussion too.</li>
+
-
<li>28th: The project is finalized: We will save the world one statue at time! We decided to drop the project on the formation of calcium oxalate and biofilm disruption. Perhaps next year team can look into it.</li>
+
-
</ul>
+
</div>
</div>

Revision as of 22:04, 17 September 2012

Crust Away

Crust Away


Introduction
Our Method
Results
Application
Terminators

INTRODUCTION

Have you ever noticed that ugly black crust found on precious monuments and statues? Here in Italy, we surely have it, and we’d like to find a way to return our monuments to their natural, beautiful state.

Our idea is to create a bioremediation kit to help every sculptor, restorer, marble cutter or anyone interested in removing that anaesthetic and harmful black crust layer from their precious calcareous stones. A lot of chemical and mechanical approaches are already off the shelf, and someone also exploited in the past Sulfur Reducing Bacteria (SRBs) to eliminate the trapping gypsum matrix (Capitelli et al. 2007).

However all of these methods show some weak points:

  1. Chemical and mechanical methods are too invasive and they risk to damage the underlying and precious marble surface; We have met with experts in the restoration field and learned about the criteria to define a good restoration.
  2. Chemical methods have also health related risks. Workers, artists, restorers too often use chemicals to clean marble stones in unsafe conditions. We have met with one of the many local artists and reported our impressions on his methods to clean marble in the Art & Science section of our Wiki.
  3. Natural SRBs, which have been used in a few cases, instead need anaerobic conditions and they constitutively express the enzymes required for sulphur reduction, thus not leaving the choice to the operator to control the rate and amount of sulphur reduced.
As a valid alternative we propose an engineered E. coli capable of reducing the sulphuric gypsum matrix that should have the following advantages:
  1. Work in AEROBIC conditions: this is a breakthrough in the field of SRBs!
  2. Should be CONTROLLED and MODULATED as needed.
  3. Should NOT be INVASIVE and work selectively against the gypsum matrix without touching the calcareous surface.
  4. Should be CHEAP and EASY TO APPLY. There will be no more need of expensive chemical and trained workers that have to work many hours to clean our statues and monuments.

To summarize, with our biological system we want to mix the strengths of all the available methods and eliminate their weak points to propose an infallible and very safe method to clean precious marble pieces!

How does the black crust form?

One of the main factors in the formation of the black crust is the atmospheric pollution. The burning process of fossil fuels leads to an increase in the concentration of some acid gases in the atmosphere. In particular SO>su>2>/sub> when reacts with water induces the transformation of calcite (CaCO3, present in the stone substrate) into gypsum (CaSO4 ·2H2O), which precipitates with inclusions of carbon particulate matter. Smog particles are also able to absorb gas pollutants on their surfaces, resulting in “dry deposition” of pollutant.

Black crusts are usually found on areas of the stone sheltered from rainfall, although still in presence of capillary water flowing through the pores. Calcium ions migrate to the surface of the stone during gypsum formation, leading to formation of cavities beneath the stone that weakens the stone’s integrity. The degradation process indeed affects both the stone conservation and appearance:

  • When the formed gypsum is washed away it takes some of the stone particles with it, causing at first loss of detail, but eventually leading, again, to a loss of structural integrity.
  • In areas sheltered from rainwater, though, gypsum crusts remain. When combined with particulate matter from the atmosphere, gypsum creates the so called black crusts.
The composition of the black crust is heterogeneous and varies accordingly to the environment. The crusts found in big cities are rich in metals and carbonaceous particles, while the crusts of stoned found in a less urban environment are often characterised by the presence of microorganisms. Although pollution has actually diminished during the last decades, the black crust problem is not been solved yet. It is thereby clear how these black crusts are a prominent issue in heritage material conservation and restoration, an issue that every remediator has to address.

OUR METHOD

Our method exploits an engineered E. coli to reduce aerobically the sulphuric gypsum layer in a controlled and modulated manner. In 2001 the Keasling group has engineered bacteria to reduce sulphate aerobically and precipitate metals from water taking advantage of the production of sulfidric acid as one of the bioproducts of sulphur reduction. We took inspiration from this work and developed two new BioBrick devices directed to overproduce cysteine and then convert it to sulphide with the ultimate goal of dissolving the sulphate layer deposited on the blackened stones.

Who are the players?

  • CysE is a Serine acetyltransferase that mediates conversion of L-serine to a precursor of L-cysteine in E.coli. More precisely we have used a mutant CysE (M256I) that has enhanced activity in that its enzymatic activity is less sensitive to feedback inhibition by cysteine.
  • CysDes is a Cysteine Desulfhydrase, first isolated in Treponema denticola, an anaerobic organism involved in periodontal diseases. It is an aminotransferase that converts cysteine into pyruvate, ammonia, and hydrogen sulphide.

How do we control the expression of our devices?

The expression of CysE is controlled by an arabinose inducible cassette (our part BBa_K731201). Our composite device (BBa_K731030) is composed by araC –pBad, and strong RBS followed by M256I CysE.
The pBAD promoter is activated in the presence of L-arabinose. L-arabinose binds to the AraC protein and inactivates its inhibitory function, allowing the RNA polymerase to recognize the pBAD promoter and start the transcription of CysE.

CysDes was placed downstream of an IPTG inducible cassette (our part BBa_K731300). The expression of CysDes is therefore controlled by a system composed of: LacI (repressor protein) and a lacIq promoter followed by a strong hybrid promoter (Ptac), a Lac Operator and a strong RBS. Addition of IPTG inactivates the LacI repressor, thus allowing the expression of our gene of interest CysDes.

The possibility of controlling simultaneously the expression of our two devices (i.e. by adding arabinose and/or IPTG) makes our system more SAFE, CONTROLLABLE and MODULAR.

How do we test the expression of our enzymes?

We used the Gibson assembly method to create two sfGFP-tagged devices that were useful reporter to verify the expression of our genes.

RESULTS

APPLICATION