Difference between revisions of "Team:BUAP Mexico/Description"

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<h3>Motivation </h3>
 
<h3>Motivation </h3>
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<div align="center"><img style= "width:60%;"src="https://static.igem.org/mediawiki/2019/1/1d/T--BUAP_Mexico--Motivation.png"</div>
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<p>Recently the Puebla’s government approved a law to ban the use of plastics package as part of several action to decrease the negative impact caused by this material. On the other hand, Mexico city (cdmx) registered the highest air pollution levels in the last ten years, leading an environmental crisis which affects states around cdmx like Puebla, guerrero, tlaxcala and morelos. At first sight, this phenomena had a negative impact just in people living in this cities, however, based on this situation we decided to look for more information about the indirect effects on the environment and living organisms. Then, we noticed that we just saw the tip of the iceberg and this phenomenon has so many negative impacts but we had special interest in the ocean acidification which is one of the most unstudied and perhaps will be the most dangerous for the marine environment in the future. Then, as students of the faculty of Biological Sciences of the BUAP we decided to try to solve this problem and we looked for different projects that would be related and we found a lot of interesting ideas, but the most remarkable were the project from NCKU Tainan  and UESTC-China, they motivated us to try to solve this potentially dangerous problem at the same that we would be able to produce a beneficial material from this process. In our case  we decided to produce polyhydroxybutyrate (PHB) from the molecule causing the ocean acidification, the CO2.  
 
<p>Recently the Puebla’s government approved a law to ban the use of plastics package as part of several action to decrease the negative impact caused by this material. On the other hand, Mexico city (cdmx) registered the highest air pollution levels in the last ten years, leading an environmental crisis which affects states around cdmx like Puebla, guerrero, tlaxcala and morelos. At first sight, this phenomena had a negative impact just in people living in this cities, however, based on this situation we decided to look for more information about the indirect effects on the environment and living organisms. Then, we noticed that we just saw the tip of the iceberg and this phenomenon has so many negative impacts but we had special interest in the ocean acidification which is one of the most unstudied and perhaps will be the most dangerous for the marine environment in the future. Then, as students of the faculty of Biological Sciences of the BUAP we decided to try to solve this problem and we looked for different projects that would be related and we found a lot of interesting ideas, but the most remarkable were the project from NCKU Tainan  and UESTC-China, they motivated us to try to solve this potentially dangerous problem at the same that we would be able to produce a beneficial material from this process. In our case  we decided to produce polyhydroxybutyrate (PHB) from the molecule causing the ocean acidification, the CO2.  
 +
 
PHB might be used like a substitute of the plastic polymer, and it has the benefit to be biodegradable and ecofriendly, supporting in this way the government's efforts to avoid the use of plastic.</p>
 
PHB might be used like a substitute of the plastic polymer, and it has the benefit to be biodegradable and ecofriendly, supporting in this way the government's efforts to avoid the use of plastic.</p>
 +
 +
<h3>Abstract</h3>
 +
 +
<p>Nowadays the excessive production of CO₂ is causing a phenomenon called ocean acidification (OA) which combined with tons of plastics in the ocean are both main problems in the marine environment. Through genetically transformation, E. coli BL-21 bacterium will combine the capability of plants to get CO₂ from the marine environment (decreasing the OA) and the skill from some bacterium to degradate of vegetable waste in order to have sugar source. Both processes are vital in order to produce great pyruvate quantities to get polyhydroxybutyrate, which is used to produce bioplastics that could replace the prevailing polymer . For maintaining the Pyruvate production and photorespiration in the highest and lowest level, respectively we will design a system which works under anaerobic conditions and repress the aerobic metabolism using arcA protein and for measuring the pyruvate production we design a biosensor.</p>
 +
 +
<h3>Introduction<h3>
 +
<p>The greenhouse effect, produce by gases like CO₂, CH4, NxO, ozone, and water vapor, is a phenomenon that allows to maintain life as we know it, since if it does not exist, the average of temperature of the Earth will be -19°C approximately. This effect has been in equilibrium, since the earth, by itself, has biotic and abiotic mechanisms that allows decrease the amount atmospheric of these gases. On the biological side, we have that CO₂ plays a very important role in the ecosystems of the planet since, it is a metabolite produced by the most living beings as a secondary product of cellular respiration. On the other hand, it is the primary source of carbon for the production of sugars in photosynthesis. On the abiotic side, we have that the water bodies, specially oceans are capable to assimilate this gas, thereby reducing the atmospheric concentration and facilitating the access of marine organisms to this source.</p>
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 +
<div align="center"><img style= "width:40%;"src="https://static.igem.org/mediawiki/2019/7/7d/T--BUAP_Mexico--Introduction.png"</div>
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<p>However, since the beginning of industrial revolution, the use of machines that emit greenhouse gases increased significantly, this in combination with high rate of deforestation, which deprives the planet of its main terrestrial filters, has caused the concentration of atmospheric CO₂ pass through dramatic increases, since before this time, it has a range between 280 to 385 ppm and at the end of the 20th century it was estimated a range of 700 to 1000 ppm.</p>
 +
 +
<p>There is a growing scientific evidence that high absorption of CO₂ by the oceans, has occasioned an important increase in the average oceanic acidity in comparison with pre-industrial levels. According to Intergovernmental Panel on Climate Change (IPCC), continued CO₂ emissions in line with current trends, could make the oceans up to 150% more acidic in 2100 than they were at the beginning of the Anthropocene.</p>
 +
 +
<p>The CO2 that has been diffused in the water, reacts whith this molecule forming carbonic acid and a free hydrogen proton.The free hydrogen proton can react with the carbonate ion to produce bicarbonate.This reaction has profound impacts on biologic systems, since bicarbonate is considered a building block in the species calcification process, so a reduction in carbonate pool limits the growth of these organisms. With a reduce size the amount of food decreases and therefore the food-web is affected with the reduction of organisms of most aquatic species, that includes species of commercial value for human society and therefore ends up impacting in the economy.</p>
 +
 +
<p>Protons that do not react with free carbonate cause that pH of the medium to decrease and it has estimated that last 20 years the reduction is 0.1 pH units which can interpreted as a 26% increase water acidity. Carbonate ions are a basic building block of skeletons and shells for a large number of marine organisms including corals, seafood and marine plankton. Some of this smaller calcifying plankton are important source of food for higher marine organisms. Therefore, ocean acidification could have profound impacts in some of the most fundamental biological and geochemical processes of the sea in the coming decades.</p>
  
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<p>It is estimated that if the emission rate of this gas continues in this way, by the end of the century the acidity of the seas will have increased by 150%, levels that have not been experienced for more than 20 million years.</p>
  
 +
<p>In addition, acidification decreases the ability of ocean to absorb additional atmospheric CO₂, which implies that future CO₂ emissions lead to faster global warming, it is estimated that ocean absorb around 430 billion tons of atmospheric CO₂ or approximately a third of anthropogenic carbon emissions. This absorption has benefited humanity by reduce significantly the levels of greenhouses gases in atmosphere, thereby minimizing global warming.
 +
</p>
  
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<p>On the other hand, at the beginning of the years nobody imagined that plastic, which was supposed to be of great help for the development of human society given the versatility it possesses and therefore the variety of applications it can have, would have an opposite effect counterproductive in the environment, since in recent years the increase in the production of these synthetic polymers derived from petroleum has profoundly impacted the marine environment and the different species that inhabit it. The excessive production and poor regulation with this material has been such that the most dramatic case known is the new continent of garbage located in the Pacific Ocean, which is mainly composed of plastic. The main problem with these materials, in addition to the little regulation that exists in their production, is that they are petroleum-derived polymers that are chemically modified to obtain some characteristic of interest, so they have different properties from the polymers found in nature (such as cellulose, chitin, glycogen, etc.), this results in the degradation by microorganisms is very slow prolonging their life in the environment which leads to their accumulation. In Mexico, the annual consumption of plastics per inhabitant in 2005 was estimated at 49 kilograms. Of the total consumed, more than one million tons per year become waste. The presence of these plastics in the seas is variable, but there are reports of abundance of 3 to 5 kg/km^2, With records of up 30kg/km^2. in addition to this, the recycling rate is very low since of the 300 million tons produced annually in the country, only 3 % are recycled.</p>
  
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<div align="center"><img style= "width:60%;"src="https://static.igem.org/mediawiki/2019/6/65/T--BUAP_Mexico--Introduction3.png"</div>
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<p>Good regulation standards are necessary to help in the conservation of environment, however, removing plastic from our daily lives would seem an almost impossible task since it has permeated different social, economic and even cultural levels, so is important to search alternatives.</p>
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<h3>Abstract</h3>
 
<p>Nowadays the excessive production of CO₂ is causing a phenomenon called ocean acidification (OA) which combined with tons of plastics in the ocean are both main problems in the marine environment. Through genetically transformation, E. coli BL-21 bacterium will combine the capability of plants to get CO₂ from the marine environment (decreasing the OA) and the skill from some bacterium to degradate of vegetable waste in order to have sugar source. Both processes are vital in order to produce great pyruvate quantities to get polyhydroxybutyrate, which is used to produce bioplastics that could replace the prevailing polymer . For maintaining the Pyruvate production and photorespiration in the highest and lowest level, respectively we will design a system which works under anaerobic conditions and repress the aerobic metabolism using arcA protein and for measuring the pyruvate production we design a biosensor. </p>
 
  
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<h1>References</h1>
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<h3>Development </h3>
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<li>Mackey, K.R.M., J.J. Morris, F.M.M. Morel, and S.A. Kranz. 2015. Response of photosynthesis to ocean acidification. Oceanography 28(2):74–91,</li>
<p>To solve this problem we think of modifying a strain of E. coli to carry out the production of bioplastic from the CO₂ that is found in the marine environment; a high quality and low cost material can be a viable option to replace plastic polymers that generate negative impacts on the environment. This will be carried out in 3 modules: degradation, fixation and polymerization.
+
In the degradation module carbohydrates like xylose and glucose will be obtained from low-cost sources, such as the organic residues of sugarcane, this in order to provide sufficient raw material to the path of the pentose phosphate and to glycolysis. Both routes of vital importance since the first one provides ribulose 5-fostato and the second one 3PG (3-phosphoglycerate).
+
<li>Mollicaa, Nathaniel R.,  Guob, Weifu., Cohenb, Anne L., Huangc, Kuo-Fang., Fosterd, Gavin L., Donaldd, Hannah K and Solowe, Andrew R. (2017). Ocean acidification affects coral growth by reducing skeletal density. Proceedings of the National Academy of Sciences (Vol. 115, pp. 1754–1759).</li>
  </p>
+
   
 +
<li>Godbold JA, Calosi P. 2013 Ocean acidification and climate change: advances in ecology and evolution. PhilTrans R Soc B (Vol. 368, pp. 1-5).</li>
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<p>The fixation module will take the ribulose 5-phosphate molecule to produce ribulose 1,5-bisphosphate that will be used by rubisco to fix the CO₂ that acidifies the marine environment and thus obtain more 3PG molecules.</p>
 
 
<img src="https://static.igem.org/mediawiki/2019/6/64/T--BUAP_mexico--glycolysis.png" width=100% >
 
 
 
<p>The molecules of 3PG will be metabolized in the glycolysis for the final obtaining of pyruvate, which, in the polymerization module will be used to produce PHB's, molecules that can replace the plastic, being these low-cost and biodegradable.
 
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<img src="https://static.igem.org/mediawiki/2019/f/fc/T--BUAP_mexico--pyruvate.png"  width=60%>
 
 
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<h3>References </h3>
 
<p>
 
Baudel, Zaror C & C., D. A. (2005) Improving the value of sugarcane bagasse wastes via integrated chemical production systems: an environmentally friendly approach. Ind Crops Prod. 309-315.</p>
 
<p> Antonovsky et al., (2016). Sugar Synthesis from CO2 in Escherichia coli. (Cell 166, pp. 115–125)</p>
 
 
<p>Mackey, K.R.M., J.J. Morris, F.M.M. Morel, and S.A. Kranz. 2015. Response of photosynthesis to ocean acidification. Oceanography 28(2):74–91, http://dx.doi.org/10.5670/oceanog.2015.33.
 
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Latest revision as of 07:04, 14 December 2019

Motivation

Recently the Puebla’s government approved a law to ban the use of plastics package as part of several action to decrease the negative impact caused by this material. On the other hand, Mexico city (cdmx) registered the highest air pollution levels in the last ten years, leading an environmental crisis which affects states around cdmx like Puebla, guerrero, tlaxcala and morelos. At first sight, this phenomena had a negative impact just in people living in this cities, however, based on this situation we decided to look for more information about the indirect effects on the environment and living organisms. Then, we noticed that we just saw the tip of the iceberg and this phenomenon has so many negative impacts but we had special interest in the ocean acidification which is one of the most unstudied and perhaps will be the most dangerous for the marine environment in the future. Then, as students of the faculty of Biological Sciences of the BUAP we decided to try to solve this problem and we looked for different projects that would be related and we found a lot of interesting ideas, but the most remarkable were the project from NCKU Tainan and UESTC-China, they motivated us to try to solve this potentially dangerous problem at the same that we would be able to produce a beneficial material from this process. In our case we decided to produce polyhydroxybutyrate (PHB) from the molecule causing the ocean acidification, the CO2. PHB might be used like a substitute of the plastic polymer, and it has the benefit to be biodegradable and ecofriendly, supporting in this way the government's efforts to avoid the use of plastic.

Abstract

Nowadays the excessive production of CO₂ is causing a phenomenon called ocean acidification (OA) which combined with tons of plastics in the ocean are both main problems in the marine environment. Through genetically transformation, E. coli BL-21 bacterium will combine the capability of plants to get CO₂ from the marine environment (decreasing the OA) and the skill from some bacterium to degradate of vegetable waste in order to have sugar source. Both processes are vital in order to produce great pyruvate quantities to get polyhydroxybutyrate, which is used to produce bioplastics that could replace the prevailing polymer . For maintaining the Pyruvate production and photorespiration in the highest and lowest level, respectively we will design a system which works under anaerobic conditions and repress the aerobic metabolism using arcA protein and for measuring the pyruvate production we design a biosensor.

Introduction

The greenhouse effect, produce by gases like CO₂, CH4, NxO, ozone, and water vapor, is a phenomenon that allows to maintain life as we know it, since if it does not exist, the average of temperature of the Earth will be -19°C approximately. This effect has been in equilibrium, since the earth, by itself, has biotic and abiotic mechanisms that allows decrease the amount atmospheric of these gases. On the biological side, we have that CO₂ plays a very important role in the ecosystems of the planet since, it is a metabolite produced by the most living beings as a secondary product of cellular respiration. On the other hand, it is the primary source of carbon for the production of sugars in photosynthesis. On the abiotic side, we have that the water bodies, specially oceans are capable to assimilate this gas, thereby reducing the atmospheric concentration and facilitating the access of marine organisms to this source.

However, since the beginning of industrial revolution, the use of machines that emit greenhouse gases increased significantly, this in combination with high rate of deforestation, which deprives the planet of its main terrestrial filters, has caused the concentration of atmospheric CO₂ pass through dramatic increases, since before this time, it has a range between 280 to 385 ppm and at the end of the 20th century it was estimated a range of 700 to 1000 ppm.

There is a growing scientific evidence that high absorption of CO₂ by the oceans, has occasioned an important increase in the average oceanic acidity in comparison with pre-industrial levels. According to Intergovernmental Panel on Climate Change (IPCC), continued CO₂ emissions in line with current trends, could make the oceans up to 150% more acidic in 2100 than they were at the beginning of the Anthropocene.

The CO2 that has been diffused in the water, reacts whith this molecule forming carbonic acid and a free hydrogen proton.The free hydrogen proton can react with the carbonate ion to produce bicarbonate.This reaction has profound impacts on biologic systems, since bicarbonate is considered a building block in the species calcification process, so a reduction in carbonate pool limits the growth of these organisms. With a reduce size the amount of food decreases and therefore the food-web is affected with the reduction of organisms of most aquatic species, that includes species of commercial value for human society and therefore ends up impacting in the economy.

Protons that do not react with free carbonate cause that pH of the medium to decrease and it has estimated that last 20 years the reduction is 0.1 pH units which can interpreted as a 26% increase water acidity. Carbonate ions are a basic building block of skeletons and shells for a large number of marine organisms including corals, seafood and marine plankton. Some of this smaller calcifying plankton are important source of food for higher marine organisms. Therefore, ocean acidification could have profound impacts in some of the most fundamental biological and geochemical processes of the sea in the coming decades.

It is estimated that if the emission rate of this gas continues in this way, by the end of the century the acidity of the seas will have increased by 150%, levels that have not been experienced for more than 20 million years.

In addition, acidification decreases the ability of ocean to absorb additional atmospheric CO₂, which implies that future CO₂ emissions lead to faster global warming, it is estimated that ocean absorb around 430 billion tons of atmospheric CO₂ or approximately a third of anthropogenic carbon emissions. This absorption has benefited humanity by reduce significantly the levels of greenhouses gases in atmosphere, thereby minimizing global warming.

On the other hand, at the beginning of the years nobody imagined that plastic, which was supposed to be of great help for the development of human society given the versatility it possesses and therefore the variety of applications it can have, would have an opposite effect counterproductive in the environment, since in recent years the increase in the production of these synthetic polymers derived from petroleum has profoundly impacted the marine environment and the different species that inhabit it. The excessive production and poor regulation with this material has been such that the most dramatic case known is the new continent of garbage located in the Pacific Ocean, which is mainly composed of plastic. The main problem with these materials, in addition to the little regulation that exists in their production, is that they are petroleum-derived polymers that are chemically modified to obtain some characteristic of interest, so they have different properties from the polymers found in nature (such as cellulose, chitin, glycogen, etc.), this results in the degradation by microorganisms is very slow prolonging their life in the environment which leads to their accumulation. In Mexico, the annual consumption of plastics per inhabitant in 2005 was estimated at 49 kilograms. Of the total consumed, more than one million tons per year become waste. The presence of these plastics in the seas is variable, but there are reports of abundance of 3 to 5 kg/km^2, With records of up 30kg/km^2. in addition to this, the recycling rate is very low since of the 300 million tons produced annually in the country, only 3 % are recycled.

Good regulation standards are necessary to help in the conservation of environment, however, removing plastic from our daily lives would seem an almost impossible task since it has permeated different social, economic and even cultural levels, so is important to search alternatives.

References

  • Mackey, K.R.M., J.J. Morris, F.M.M. Morel, and S.A. Kranz. 2015. Response of photosynthesis to ocean acidification. Oceanography 28(2):74–91,
  • Mollicaa, Nathaniel R., Guob, Weifu., Cohenb, Anne L., Huangc, Kuo-Fang., Fosterd, Gavin L., Donaldd, Hannah K and Solowe, Andrew R. (2017). Ocean acidification affects coral growth by reducing skeletal density. Proceedings of the National Academy of Sciences (Vol. 115, pp. 1754–1759).
  • Godbold JA, Calosi P. 2013 Ocean acidification and climate change: advances in ecology and evolution. PhilTrans R Soc B (Vol. 368, pp. 1-5).