Team:NJU-QIBEBT/team/Backgroud

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                     <li><a href="/Team:NJU-QIBEBT/wetlab/Notebook">Notebook</a></li>
                     <li><a href="/Team:NJU-QIBEBT/wetlab/Notebook">Notebook</a></li>
                     <li><a href="/Team:NJU-QIBEBT/wetlab/Parts">Parts</a></li>
                     <li><a href="/Team:NJU-QIBEBT/wetlab/Parts">Parts</a></li>
 +
                    <li><a href="/Team:NJU-QIBEBT/wetlab/cooperation"> Cooperation </a></li>
                 </ul>
                 </ul>
             </li>
             </li>
             <li class="menu"><a href="/Team:NJU-QIBEBT/humanPractice">HUMAN PRACTICE</a></li>
             <li class="menu"><a href="/Team:NJU-QIBEBT/humanPractice">HUMAN PRACTICE</a></li>
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             <li class="menu"><a href="/Team:NJU-QIBEBT/SAFETY">SAFETY</a></li>
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             <li class="menu"><a href="/Team:NJU-QIBEBT/SAFETY">ETHICS AND SAFETY</a></li>
             <li class="menu"><a href="/Team:NJU-QIBEBT/team">TEAM</a></li>
             <li class="menu"><a href="/Team:NJU-QIBEBT/team">TEAM</a></li>
             <li class="menu"><a href="/Team:NJU-QIBEBT/ACKNOWLEDGEMENT">ACKNOWLEDGEMENT</a></li>
             <li class="menu"><a href="/Team:NJU-QIBEBT/ACKNOWLEDGEMENT">ACKNOWLEDGEMENT</a></li>
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    <h1>Overview</h1>
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<h1>Background</h1>
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    <h3>The story of our E.coil
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<h2>Why we need biofuels
-
    </h3>
+
</h2>
-
     <p>Here is the story:
+
<h3>World needs energy!
 +
</h3>
 +
     <p>“The year 2013 saw an acceleration in the growth of global energy consumption, despite a stagnant global economy. Economic growth remained weak nearly everywhere and relative to recent history it was weaker in the emerging non-OECD economies. In line with that economic pattern, energy consumption growth was below average in the non-OECD, driven by China, and above average in the mature economies of the OECD, driven by the US. Emerging economies nonetheless continue to dominate global energy demand, accounting for 80% of growth last year and nearly 100% of growth over the past decade.
     </p>
     </p>
-
     <p>Long time ago, Clark Kent grew in the farm. While this summer, our E.coil grows in the LB. What is the difference between our E.coil and normal E.coli? Well, E.coil is super-E.coli! He has the power to produce much more fatty acids than his normal peers. How can that happen? After he “swallows” a plasmid containing all the special genes, he obtains the super power. On this magical plasmid, there are thioesterase, desaturases, fluorescence system and so on.
+
     <p> While consumption growth accelerated globally, it has remained below average – this is again, consistent with the weak global economic picture. Regionally, energy consumption growth was below average everywhere except North America. EU consumption continued to decline, hitting the lowest level since 1995 (despite economic growth of 35% over this period). ”[By Bob Dudley
 +
 Group Chief Executive and director of BP
 +
]
     </p>
     </p>
-
     <p>Thioesterase and fatty acid desaturase are key enzymes for free fatty acid (FFA) synthesis and unsaturated fatty acid production, respectively. They are both extensively spread in animals, plants and microorganisms. This time, we “borrow” the thioesterases from Umbellularia californica and Arabidopsis thaliana, use them to build this magical plasmid and equip our super-E.coli. Also, E.coli contributes to offering its own desaturase to the plasmid.
+
     <img src="https://static.igem.org/mediawiki/2014/5/59/022-qz.png">
 +
    <p>China’s Hong Kong skyline. China was the world’s largest producer and consumer of energy overall in 2013.
     </p>
     </p>
-
    <p>Besides that, our E.coil can produce the exact fatty acids we want. And this amazing power comes from different operon structures which regulate the expressions of corresponding thioesterases and desaturases. Thanks for them, we manage to produce various fatty acids in a controlled manner.
+
<h3>
 +
Oil will be exhausted!
 +
 
 +
</h3>
 +
 
 +
    <img src="https://static.igem.org/mediawiki/2014/d/d2/024-qz.png">
 +
    <p>*More than 100 years
     </p>
     </p>
-
     <p>Considering the strong power our super-E.coli processes, we do want to monitor its fatty acid producing progress. In this case, we design a fluorescence system composed of Transcriptional Regulatory Protein FadR to detect the concentration of fatty acids in the whole system.
+
     <p>♦less than 0.05%
     </p>
     </p>
-
     <p>In a word, by the ways listed above, we accomplish the switch between production of different kinds of fatty acids by applying different signals to operons, and we can obtain the real time production status of E.coli by fluorescence report.
+
    <img src="https://static.igem.org/mediawiki/2014/4/4c/025-qz.jpg">
 +
     <p>Total world proved oil reserves reached 1687.9 billion barrels at the end of 2013, sufficient to meet 53.3 years of global production, just 53.3 years.
     </p>
     </p>
-
     <h3>E.coil: Our responsibility to save the world!
+
     <img src="https://static.igem.org/mediawiki/2014/3/30/026-qz.jpg">
 +
    <p>Obviously, Middle East has the most.
 +
    </p>
 +
    <img src="https://static.igem.org/mediawiki/2014/7/72/027-qz.jpg">
 +
    <img src="https://static.igem.org/mediawiki/2014/b/b0/028-qz.jpg">
 +
    <p>Do a simple subtraction.
 +
        The production of the oil can’t meet the demands of Asia Pacific and North America’s daily use.
 +
    </p>
 +
    <img src="https://static.igem.org/mediawiki/2014/5/59/029-qz.jpg">
 +
    <p>This figure is more visualized.
 +
    </p>
 +
    <img src="https://static.igem.org/mediawiki/2014/7/71/030-qz.jpg">
 +
<br></br>
 +
<hr></hr>
 +
<br></br>
 +
<h3>Much more greenhouse gas!
 +
</h3>
 +
    <p>Crude oil prices keep increasing in the decades.
 +
        With the gas we released and the result of many other human activities, the world temperature has changed a lot in these years.
 +
    </p>
 +
    <img src="https://static.igem.org/mediawiki/2014/f/f9/031-qz.jpg">
 +
    <p>Monthly (thin lines) and 12-month running mean (thick lines or filled colors in case of Nino 3.4 Index) global land-ocean temperature anomaly, global land and sea surface temperature, and El Nino index. All have a base period 1951-1980.(from GISS Surface Temperature Analysis)
 +
    </p>
 +
    <img src="https://static.igem.org/mediawiki/2014/4/40/032.jpg">
 +
    <img src="https://static.igem.org/mediawiki/2014/9/92/033.jpg">
 +
<br></br>
 +
<hr></hr>
 +
<br></br>
 +
<h3>Let’s solve the problem!
 +
</h3>
 +
    <p>To meet continuing demand in the face of dwindling petroleum supplies while also curbing the release of greenhouse gases, we have two ways:
 +
        1. Emissions cap-and-trade
 +
        2. Renewable sources
 +
 
 +
    </p>
 +
        <h3>Renewable sources:</h3>
 +
        <p>Solar, wind, and biomass lead growth in renewable generation, hydropower remains flat.</p>
 +
 
 +
    <img src="https://static.igem.org/mediawiki/2014/b/b5/034-qz-1.png">
 +
    <p>In the AEO 2013 Reference case, renewable generation increases from 524 billion kilowatt-hours in 2011 to 858 billion kilowatt-hours in 2040, growing by an average of 1.7 percent per year(Figure 83). Wind, solar, and biomass account for most of the growth. The increase in wind-powered generation from 2011 to2040, at 134 billion kilowatt-hours, or 2.6 percent per year, represents the largest absolute increase in renewable generation. Generation from solar energy grows by 92 billion kilowatt-hours over the same period, representing the highest annual average growth at 9.8 percent per year. Biomass increases by 95 billion kilowatt-hours over the projection period, for an average annual-increase of 4.5 percent.(from Annual Energy Outlook 2013)
 +
    </p>
 +
<br></br>
 +
<hr></hr>
 +
<br></br>
 +
    <h3>What we focus on is biomass!
     </h3>
     </h3>
-
     <p>With great power comes great responsibility. E.coil has the responsibility to produce fatty acids and save the world!
+
     <p>Biomass is biological material derived from living, or recently living organisms. It most often refers to plants or plant-based materials which are specifically called lignocellulosic biomass. As an energy source, biomass can either be used directly via combustion to produce heat, or indirectly after converting it to various forms of biofuel. Conversion of biomass to biofuel can be achieved by different methods which are broadly classified into: thermal, chemical, and biochemical methods.(from Wikipedia)
     </p>
     </p>
-
     <p>Since the mankind found the oil, our life has changed a lot. For example, we can fly in the sky like superman and we can move really heavy things just like superman. In short, oil is the essential chemical for multiple uses.
+
    <img src="https://static.igem.org/mediawiki/2014/e/ea/1234-qz.png">
 +
<br></br>
 +
<hr></hr>
 +
<br></br>
 +
<h3>Cellulosic or lignocellulosic biofuels:
 +
</h3>
 +
     <p>The utilization of plant structural polymer. It has two routes.
     </p>
     </p>
-
     <p>Q: Now that the oil is rather important, why we need fatty acid? I mean, why not sugar? What is Fatty acid?
+
     <p>Route1: Obtain some versatile intermediate such as 5- hydroxymethylfurfural and γ-valerolactone by a variety of chemical and biological process technologies
     </p>
     </p>
-
     <p>A: Fatty acid = Oil!
+
     <p>Route2: Following various pre-processing and pre-treatment steps, it utilizes enzyme cocktails to hydrolyze cellulose and hemicellulose polymers into sugar monomers or oligomers serving as feedstocks for any variety of microbial fermentation processes. Native metabolism or metabolic engineering of biochemical pathways enables the production of desired chemicals and fuels, for example, biomass-derived gasoline alternatives.
     </p>
     </p>
-
     <p>Fatty acids with different carbon chain length and saturation levels can be widely applied to industry, food, medicine and many other aspects. Most importantly, it is a very promising feedstock for the production of eco-friendly biodiesel. And this could be the potential power source to compensate for dwindling fossil energy.
+
     <p>Medium- and long-chain hydrocarbons can potentially serve as replacements for diesel, rendering them an attractive target for microbial production from lignocellulosic feedstocks. Unlike ethanol, the low water solubility of longer carbon chain-length hydrocarbons should result in reduced recovery costs and reduced toxicity in the fermentation broth due to phase separation. These hydrocarbons are also more likely to be compatible with existing transport and storage infrastructure and vehicle engines, and possess higher cloud points than biodiesel blends, enabling year-round usage in all climates. 
     </p>
     </p>
-
     <p> Relied on animal grease or plant oil currently, however, the processes of FFA production are restricted by seasonal, regional and many other factors. Besides that, the cost of producing is so high that it cannot be intensively industrialized. Given that, our super-E.coli emerges at this significant moment and take its obligation to save our world from energy crisis.
+
     <p>Two major biochemical pathways exist for production:
     </p>
     </p>
-
     <p class="se_title">So, let’s give it up for E.COIL!
+
     <p>The first pathway is the isoprenoid biosynthesis, where precursor molecules from central metabolism are used to generate isopentenyl diphoshate and its isomerized product, dimethylallyl diphosphate.
     </p>
     </p>
 +
    <p>The second pathway is fatty acid biosynthesis, for which acetyl-CoA (or rarely propionyl-CoA) serves as the precursor and for which long-chain. A number of natural products can also be generated through this pathway including free fatty acids (FFAs), phospholipids and di- and triacylglycerols, alkanes and olefins, fatty alcohols, methyl ketones, and esters of fatty acids.
 +
    </p>
 +
    <p>We chose E.coli as the host organism to develop a microbial conversion process of a target compound. Metabolic engineering offers the opportunity to genetically modify E.coli to optimize production of the naturally produced compound via single gene or entire pathway manipulation. Why we chose E.coli?
 +
    </p>
 +
<br></br>
 +
<hr></hr>
 +
<br></br>
 +
<h3>Why we chose E.coli?
 +
</h3>
 +
    <p>Because we have well-developed genetic engineering and synthetic biology tools; understanding of their metabolism, physiology, and gene regulation; and rapid and well-developed protocols for transformation and recombination, addition to its diversity of carbon utilization( eg. ability to readily metabolize pentose sugars) and rapid growth rate.
 +
    </p>
 +
    <h3>Reference:</h3>
 +
<div class="refer">
 +
    <p>1. EIA U S. Annual energy outlook 2013[J]. US Energy Information Administration, Washington, DC, 2013.
 +
</p>
 +
    <p>2. Lennen R M. Engineering Fatty Acid Overproduction in Escherichia coli for Next-Generation Biofuels[D]. UNIVERSITY OF WISCONSIN-MADISON, 2012.
 +
( http://depot.library.wisc.edu/repository/fedora/1711.dl:TILJIP5I5DABR82/datastreams/REF/content)
 +
</p>
 +
    <p>3. [BP Statistical Review of World Energy June 2014]
 +
(http://www.bp.com/content/dam/bp/pdf/Energy-economics/statistical-review-2014/BP-statistical-review-of-world-energy-2014-full-report.pdf)
 +
</p>
 +
    <p>4. National Aeronautics and Space Administration Goddard Institute for Space Studies (NASA GISS)
 +
(http://data.giss.nasa.gov/gistemp/)
 +
</p>
 +
    <p>5. Global Greenhouse Gas Reference Network
 +
(http://www.esrl.noaa.gov/gmd/ccgg/)
 +
</p>
 +
    <p>6. Lennen R M, Pfleger B F. Engineering Escherichia coli to synthesize free fatty acids[J].  Trends in biotechnology, 2012, 30(12): 659-667.
 +
( http://www.nature.com/nature/journal/v463/n7280/abs/nature08721.html)
 +
 +
</p>
 +
    <p>7. Zheng Y N, Li L L, Liu Q, et al. Optimization of fatty alcohol biosynthesis pathway for selectively enhanced production of C12/14 and C16/18 fatty alcohols in engineered Escherichia coli[J]. Microb Cell Fact, 2012, 11(11).
 +
( http://www.biomedcentral.com/content/pdf/1475-2859-11-65.pdf)
 +
</p>
 +
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Latest revision as of 03:41, 18 October 2014

Background

Why we need biofuels

World needs energy!

“The year 2013 saw an acceleration in the growth of global energy consumption, despite a stagnant global economy. Economic growth remained weak nearly everywhere and relative to recent history it was weaker in the emerging non-OECD economies. In line with that economic pattern, energy consumption growth was below average in the non-OECD, driven by China, and above average in the mature economies of the OECD, driven by the US. Emerging economies nonetheless continue to dominate global energy demand, accounting for 80% of growth last year and nearly 100% of growth over the past decade.

 While consumption growth accelerated globally, it has remained below average – this is again, consistent with the weak global economic picture. Regionally, energy consumption growth was below average everywhere except North America. EU consumption continued to decline, hitting the lowest level since 1995 (despite economic growth of 35% over this period). ”[By Bob Dudley  Group Chief Executive and director of BP ]

China’s Hong Kong skyline. China was the world’s largest producer and consumer of energy overall in 2013.

Oil will be exhausted!

*More than 100 years

♦less than 0.05%

Total world proved oil reserves reached 1687.9 billion barrels at the end of 2013, sufficient to meet 53.3 years of global production, just 53.3 years.

Obviously, Middle East has the most.

Do a simple subtraction. The production of the oil can’t meet the demands of Asia Pacific and North America’s daily use.

This figure is more visualized.






Much more greenhouse gas!

Crude oil prices keep increasing in the decades. With the gas we released and the result of many other human activities, the world temperature has changed a lot in these years.

Monthly (thin lines) and 12-month running mean (thick lines or filled colors in case of Nino 3.4 Index) global land-ocean temperature anomaly, global land and sea surface temperature, and El Nino index. All have a base period 1951-1980.(from GISS Surface Temperature Analysis)






Let’s solve the problem!

To meet continuing demand in the face of dwindling petroleum supplies while also curbing the release of greenhouse gases, we have two ways: 1. Emissions cap-and-trade 2. Renewable sources

Renewable sources:

Solar, wind, and biomass lead growth in renewable generation, hydropower remains flat.

In the AEO 2013 Reference case, renewable generation increases from 524 billion kilowatt-hours in 2011 to 858 billion kilowatt-hours in 2040, growing by an average of 1.7 percent per year(Figure 83). Wind, solar, and biomass account for most of the growth. The increase in wind-powered generation from 2011 to2040, at 134 billion kilowatt-hours, or 2.6 percent per year, represents the largest absolute increase in renewable generation. Generation from solar energy grows by 92 billion kilowatt-hours over the same period, representing the highest annual average growth at 9.8 percent per year. Biomass increases by 95 billion kilowatt-hours over the projection period, for an average annual-increase of 4.5 percent.(from Annual Energy Outlook 2013)






What we focus on is biomass!

Biomass is biological material derived from living, or recently living organisms. It most often refers to plants or plant-based materials which are specifically called lignocellulosic biomass. As an energy source, biomass can either be used directly via combustion to produce heat, or indirectly after converting it to various forms of biofuel. Conversion of biomass to biofuel can be achieved by different methods which are broadly classified into: thermal, chemical, and biochemical methods.(from Wikipedia)






Cellulosic or lignocellulosic biofuels:

The utilization of plant structural polymer. It has two routes.

Route1: Obtain some versatile intermediate such as 5- hydroxymethylfurfural and γ-valerolactone by a variety of chemical and biological process technologies

Route2: Following various pre-processing and pre-treatment steps, it utilizes enzyme cocktails to hydrolyze cellulose and hemicellulose polymers into sugar monomers or oligomers serving as feedstocks for any variety of microbial fermentation processes. Native metabolism or metabolic engineering of biochemical pathways enables the production of desired chemicals and fuels, for example, biomass-derived gasoline alternatives.

Medium- and long-chain hydrocarbons can potentially serve as replacements for diesel, rendering them an attractive target for microbial production from lignocellulosic feedstocks. Unlike ethanol, the low water solubility of longer carbon chain-length hydrocarbons should result in reduced recovery costs and reduced toxicity in the fermentation broth due to phase separation. These hydrocarbons are also more likely to be compatible with existing transport and storage infrastructure and vehicle engines, and possess higher cloud points than biodiesel blends, enabling year-round usage in all climates. 

Two major biochemical pathways exist for production:

The first pathway is the isoprenoid biosynthesis, where precursor molecules from central metabolism are used to generate isopentenyl diphoshate and its isomerized product, dimethylallyl diphosphate.

The second pathway is fatty acid biosynthesis, for which acetyl-CoA (or rarely propionyl-CoA) serves as the precursor and for which long-chain. A number of natural products can also be generated through this pathway including free fatty acids (FFAs), phospholipids and di- and triacylglycerols, alkanes and olefins, fatty alcohols, methyl ketones, and esters of fatty acids.

We chose E.coli as the host organism to develop a microbial conversion process of a target compound. Metabolic engineering offers the opportunity to genetically modify E.coli to optimize production of the naturally produced compound via single gene or entire pathway manipulation. Why we chose E.coli?






Why we chose E.coli?

Because we have well-developed genetic engineering and synthetic biology tools; understanding of their metabolism, physiology, and gene regulation; and rapid and well-developed protocols for transformation and recombination, addition to its diversity of carbon utilization( eg. ability to readily metabolize pentose sugars) and rapid growth rate.

Reference:

1. EIA U S. Annual energy outlook 2013[J]. US Energy Information Administration, Washington, DC, 2013.

2. Lennen R M. Engineering Fatty Acid Overproduction in Escherichia coli for Next-Generation Biofuels[D]. UNIVERSITY OF WISCONSIN-MADISON, 2012. ( http://depot.library.wisc.edu/repository/fedora/1711.dl:TILJIP5I5DABR82/datastreams/REF/content)

3. [BP Statistical Review of World Energy June 2014] (http://www.bp.com/content/dam/bp/pdf/Energy-economics/statistical-review-2014/BP-statistical-review-of-world-energy-2014-full-report.pdf)

4. National Aeronautics and Space Administration Goddard Institute for Space Studies (NASA GISS) (http://data.giss.nasa.gov/gistemp/)

5. Global Greenhouse Gas Reference Network (http://www.esrl.noaa.gov/gmd/ccgg/)

6. Lennen R M, Pfleger B F. Engineering Escherichia coli to synthesize free fatty acids[J]. Trends in biotechnology, 2012, 30(12): 659-667. ( http://www.nature.com/nature/journal/v463/n7280/abs/nature08721.html)

7. Zheng Y N, Li L L, Liu Q, et al. Optimization of fatty alcohol biosynthesis pathway for selectively enhanced production of C12/14 and C16/18 fatty alcohols in engineered Escherichia coli[J]. Microb Cell Fact, 2012, 11(11). ( http://www.biomedcentral.com/content/pdf/1475-2859-11-65.pdf)