Difference between revisions of "Team:Marburg/Human Practices"

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             agriculture in Germany <a style="padding: 0"
 
             agriculture in Germany <a style="padding: 0"
 
               href="https://www.bmel.de/DE/Landwirtschaft/Pflanzenbau/Gentechnik/_Texte/Gentechnik_Wasgenauistdas.html">
 
               href="https://www.bmel.de/DE/Landwirtschaft/Pflanzenbau/Gentechnik/_Texte/Gentechnik_Wasgenauistdas.html">
               (‘Gentechnik’, n.d.)</a>.
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               (‘Gentechnik’, n.d.)</a>.</p>
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             <b>Modern Methods in Breeding</b><br>
 
             <b>Modern Methods in Breeding</b><br>
 
             The traditional way of breeding, as explained above, although generating many domestic plants and animals,
 
             The traditional way of breeding, as explained above, although generating many domestic plants and animals,
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               Abstract?
 
               Abstract?
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                   of classical cyanobacterial research which lead to interesting discussions from which we gained a
 
                   of classical cyanobacterial research which lead to interesting discussions from which we gained a
 
                   lot of input. Furthermore, the leading experts of cyanobacteria offered talks where we learned how
 
                   lot of input. Furthermore, the leading experts of cyanobacteria offered talks where we learned how
                   to modify working on <i>Synechococcus elongatus</i>.<br>
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                   to modify working on <i>Synechococcus elongatus</i>.</p>
                  <br>
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                <p style="text-align: justify; margin-bottom: 1em;">
 
                   We were especially interested in the discussions about methods. We soon realized that the
 
                   We were especially interested in the discussions about methods. We soon realized that the
 
                   cyanobacterial scene has no standardized protocols for daily laboratory practices and they are also
 
                   cyanobacterial scene has no standardized protocols for daily laboratory practices and they are also
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                   concerned issues like standardized evaluation of light conditions. With our project for
 
                   concerned issues like standardized evaluation of light conditions. With our project for
 
                   standardizing growth conditions and providing a part collection we tackle these major issues for
 
                   standardizing growth conditions and providing a part collection we tackle these major issues for
                   scientists studying phototrophic organisms.<br>
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                   scientists studying phototrophic organisms.</p>
                  <br>
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                   Caused by our thrive for standardization as synthetic biologist, we decided to make a small study in
 
                   Caused by our thrive for standardization as synthetic biologist, we decided to make a small study in
 
                   the cyano community about standards in handling of cyanobacteria <b>[link standards in cyano
 
                   the cyano community about standards in handling of cyanobacteria <b>[link standards in cyano
 
                     community]</b>. Due to the results we know about the importance of our intention and will take
 
                     community]</b>. Due to the results we know about the importance of our intention and will take
                   the first step for creating a standard for working with cyanobacteria in synthetic biology.<br>
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                   the first step for creating a standard for working with cyanobacteria in synthetic biology.
                  <br>
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                   <img style="height: 50ex; width: 75ex"
 
                   <img style="height: 50ex; width: 75ex"
 
                     src="https://static.igem.org/mediawiki/2019/8/85/T--Marburg--JG_dif_media.png" alt="JG dif media">
 
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                     alt="JG dif media log">
 
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                     Fig.2 - Recording of the panelists in the middle of arguing with the viewers.
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                     Fig.1 - (Left) Growth of S. elongatus UTEX 2973 in different media. (Right) Growth of S. elongatus
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                    UTEX 2973 in different media (log-scale).
 
                   </figcaption>
 
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                   try to get hold of a spherical measurement device, as he assured us that this is the way to generate
 
                   try to get hold of a spherical measurement device, as he assured us that this is the way to generate
 
                   more accurate data, leading to a more reproducible setup - exactly what we were aiming for.<br>
 
                   more accurate data, leading to a more reproducible setup - exactly what we were aiming for.<br>
                  <br>
 
                  After acquiring such a device, we again implemented the feedback we got and measured growth curves.
 
                  One with cultures at 1500µE measured with a spherical device and one with 1500µE measured with a
 
                  planar device, where the measured intensities were converted to theoretically spherical values with a
 
                  conversion chart offered to us by Prof. Dr. Annegret Wilde from the University of Freiburg.<br>
 
 
                   <br>
 
                   <br>
 
                 </p>
 
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                 <p style="text-align: justify; margin-bottom: 1em;">
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                  After acquiring such a device, we again implemented the feedback we got and measured growth curves.
 +
                  One with cultures at 1500µE measured with a spherical device and one with 1500µE measured with a
 +
                  planar device, where the measured intensities were converted to theoretically spherical values with a
 +
                  conversion chart offered to us by Prof. Dr. Annegret Wilde from the University of Freiburg.<br>
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                  <br>
 
                   These experiments were a huge step in our project, as they heavily influenced the way we cultured our
 
                   These experiments were a huge step in our project, as they heavily influenced the way we cultured our
 
                   cyanobacteria, not only drastically improving their growth, but also clearly demonstrating how flawed
 
                   cyanobacteria, not only drastically improving their growth, but also clearly demonstrating how flawed
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                    purification using the Promegas Wizard® MagneSil® Plasmid Purification System.
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                   When the iGEM year started, we thought about how we could ease the work in the lab using our OT-2. We
 
                   When the iGEM year started, we thought about how we could ease the work in the lab using our OT-2. We
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                   pipette for up to 6 samples, as well as a protocol for the 8-channel pipette for up to 48 samples.<br>
 
                   pipette for up to 6 samples, as well as a protocol for the 8-channel pipette for up to 48 samples.<br>
 
                   <br>
 
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                    Fig.1 - Margarethe Schwarz visiting the iGEM team Marburg 2019 to watch the OT-2 perform a plasmid
 
                    purification using the Promegas Wizard® MagneSil® Plasmid Purification System.
 
                  </figcaption>
 
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                   We are very happy about this fruit bearing interaction, we think both sides profited from this
 
                   We are very happy about this fruit bearing interaction, we think both sides profited from this
 
                   cooperation in a big way.
 
                   cooperation in a big way.

Revision as of 22:29, 21 October 2019

H U M A N   P R A C T I C E S


Human Practices

Report on Genetic Engineering

Genetic engineering has been a hotly debated topic in politics as well as society in the past decades and still is today. Arguments like the nutrition of a growing world population due to a declining infant mortality rate or the loss of considerable areas of arable land due to erosion or pollution damage keep fueling the debate whether genetically modified organisms (GMO), especially crops, are needed to sustain the global demand for food. On the opposite, concerns have been raised concerning the potential adverse effects on human health and environmental safety. Besides the facts, part of the public debate is based around ethical questions and trust issues towards institutions and authorities. There have been studies and surveys carried out addressing many of these topics and additionally a diverse cluster of organisations and the media is bombarding the public with contrary statements. This report tries to give an overview on humanities relation to changing genetics, a brief summary of used methods, and gathers statements from scientists and authorities. It is meant as the motivational basis for this years Marburg iGEM team´s Public Engagement and Human Practice efforts.

History of Genetic Modification
Our ancestors had no conception of genetics but still were able to influence the genes of multiple organisms. It is a process known to everybody called artificial selection or selective breeding. Those individuals with the most desirable traits, like the biggest and most delicious fruits or the highest loyalty, is chosen to propagate and produce offspring. This process is repeated over several generations and the result is an organism with the selected traits. The dog, existing today in many #variations, is believed to be the organism our ancestors selectively bred first at around 32,000 years ago (Zimmer, 2013). And there are many more instances like corn which originates from a grass called teosinte with very few kernels (‘Evolution of Corn’, n.d.). However, this process is not considered GMO technology today. What we understand under genetic modification today can be traced back to the mid 1900´s when scientists discovered that genetic material can be transferred between different species (Avery, MacLeod, & McCarty, 1944), the structure of genetic material was identified as a double helix (Crick, Watson, & Bragg, 1954), the genetic code was deciphered (Nirenberg, Matthaei, Jones, Martin, & Barondes, 1963) and finally a DNA recombinant technology was described (Cohen, Chang, Boyer, & Helling, 1973). Only a few decades after these ground-breaking discoveries were made, the first genetically modified (GM) plants were produced in 1983, which were antibiotic resistant tobacco and petunia (Bevan & Chilton, 1982; Fraley, 1983; Herrera‐Estrella et al., 1983). Soon, the first GM plants were commercialized: in the early 1990´s China approved modified tobacco and in 1994 the United States Food and Drug Administration (U.S. FDA) approved the “FLAVR SAVR” tomato which was modified to have a longer shelf live by delaying ripening. Today numerous GM plants exist and are in use, covering popular fruits like papaya, melon and apple, flowers like roses, feed plants like sugar beet, vegetables like tomato, maize and potato and even cotton for clothes production (‘GM Crops List—GM Approval Database | ISAAA.org’, n.d.).

Current numbers on GM crops
World
As stated above, many GM crops are relevant for food production today, be it indirectly for feed in production lines or directly as consumables. In 2018, 26 countries planted 191.7 million hectares worldwide with GM crops, which is an increase of 1% from 2017´s worldwide planted area. Accordingly, since its first commercialization in 1996 with 1.7 million hectares planted, GM crop area increased by an approximate 113-fold. The accumulated area planted with GM crops from 1996 to 2018 was 2.5 billion hectares. This makes biotechnology the fastest adopted crop technology in the world. Of the 193 member nations of the United Nations Organisation (UNO) 42 nations plus the European Union (EU) adopted GM crops, of which 26 countries (21 developing and 5 industrial) planted and 44 imported GM crops. The four major GM crops, namely soybeans, maize, cotton and canola, occupied 99% of the GM crop area (Figure 1). GM crops share in total crop area was 78% for soybeans, 76% for cotton, 30% or maize and 29% for canola. 42% of the global GM crop area was planted with stacked trait crops tolerant to various herbicides and pesticides. Around the world the GM crop area was unevenly distributed with the top five countries United States of America (USA), Brazil, Argentina, Canada and India planting 91% of the global GM crop area. In the EU, the two nations Spain and Portugal planted the GM crop MON810, which is an insecticide resistant maize, together covering 120.990 hectares. 95% of the area was planted by Spain. From 2017 to 2018 GM crop area in the EU has decreased by 8% from 131.535 hectares (Figure 2). Nevertheless the EU imported GM crops, roughly 30 million tons of soybean products, 10 million tons of maize and 2.5 million tons of canola originating from Argentina, Brazil and the USA. Since 1992, across the world 4.349 approvals to GM crops have been issued, of this being 2.063 for food, 1.461 for feed use and 825 for cultivation (‘ISAAA Brief 54-2018: Executive Summary | ISAAA.org’, n.d.).

GM crops 2018
Fig.1 - Area and adoption rate of GM crops (biotech crops) in 2018 worldwide.* GM sugar beets, potatoes, apple, squash, papaya and brinjal/eggplant. Adopted from ISAAA, 2018.
Global map
Fig.2 - Global map of GM (biotech) countries in 2018. Adopted from ISAAA, 2018.

Germany
In Germany, there is no more GM crop farming since 2012. GM maize has been planted last in 2008 (3.171 hectares, 0.15% of total maize area in Germany) and GM potatoes have been planted last in 2011 (2 hectares, 0.0008% of total potato area in Germany). GM crop area never made up more than 0.02% of land used by agriculture in Germany (‘Gentechnik’, n.d.).

Modern Methods in Breeding
The traditional way of breeding, as explained above, although generating many domestic plants and animals, is relatively slow and limited by the available traits individuals express. Modern breeding methods enhance the trait spectrum and the pace in which new traits can be discovered and implemented to crops or animals.

Plant Mutagenesis
As it is known that practical breeding depends on genetic variation plant mutagenesis expands the variability of traits. Variations found in nature do not represent the original spectra of spontaneous mutation due to the fact that they are recombining within populations and interacting with environmental factors. In the process of mutagenesis heritable changes occur in the genetic information induced by mutagenic agents called mutagens. These mutagens can be of chemical, for instance substances interacting with the DNA, or of physical origin, such as ionizing radiation (Oladosu et al., 2016). After using the mutagen on the crops, mostly seeds, seedlings or cell cultures from which single cells can be grown out, screening has to be done to see if changes in traits have been achieved by mutations. These mutations can be DNA double strand breaks, single base exchanges or alkylation of bases. In most cases, generated mutants are heterozygous, because the mutation happened in only one allele. Therefore the breeder needs to rear subsequent generations to evaluate recessive mutations. Selection then takes place in form of phenotypical, physical or molecular test to determine for instance plant height, earliness of maturity and biochemical composition. Mutagenesis breeding has impacted agriculture massively, with more than 3.300 entries to the Mutant Variety Database (‘Mutant Variety Database’, n.d.), covering all major food and feed crops.

Genetic Engineering
This term is used to describe methods which alter the genetic makeup of an organism using DNA recombinant technology. This technology resorts to enzymatic tools called restriction enzymes. These cut the DNA site specific and can thereby isolate genetic constructs coding for desirable traits. When gene(s) are introduced into an organism this can be achieved either directly or indirectly. The direct approach utilizes a method called microparticle bombardment (Sanford, 1990). Developed in the 1980´s, engineered DNA is coated on microparticles of either gold or tungsten and then shot with high velocity at the target organism using high pressure helium gas. The DNA fragments can then be incorporated into the organism’s genetic material. There are other direct methods such as electroporation or microinjection but particle bombardment is the most effective. The indirect approach makes use of a vector: the soil bacterium Agrobacterium tumefaciens naturally infects plants and alters its hosts genome via a plasmid called Ti-plasmid. This plasmid can be engineered to carry genes coding for a desired traits instead of its natural genes for infection. With the development of a method called CRISPR/Cas9 and other variants genetic engineering in plants got much easier (Cong et al., 2013; DeMayo & Spencer, 2014; Ran et al., 2013). This system is found in bacteria where it serves as a defence mechanism against viruses. The endonuclease is guided to its target cutting site via a guide mRNA where it induces a double strand break (DBS). The DBS can be repaired in two distinct ways. Non-homologous end joining leads to a small deletion while homologous recombination allows for the integration of donor DNA into the endogenous DNA. Thereby, the CRISPR method allows for small alteration or hole gene insertions at target sites.
At this point it may be appropriate to introduce the two terms “cisgenic” and “transgenic”. While “transgenic” refers to organisms in which genetic material outside the species boundary, originating from a donor organism which is sexually incompatible to the engineered organism, has been inserted.“Cisgenic” on the contrary describes genetic modifications within the boundaries of sexual compatibility. Therefore, cisgenic plants are similar to traditionally bred plants (Schouten, Krens, & Jacobsen, 2006). The most obvious example of transgenic plants are the many varieties of so called “Bt” crops. Standing for Bacillus thuringiensis, into these plants a gene from the bacterium was integrated which leads to the production of a crystal protein that is toxic to specific pest insects (‘Insecticidal Plants’, 2015).

Opinions on GMOs
There are many scientific publications evaluating specific GMO traits towards the environment and health safety. Additionally many reviews exist summarizing GMO effects to a much broader scale possible here (Bawa & Anilakumar, 2013; Nicolia, Manzo, Veronesi, & Rosellini, 2014; Snell et al., 2012; Zhang, Wohlhueter, & Zhang, 2016). In many of these, authors conclude that the application of GMO offers great opportunities but still has to be carried out with precautions. A simple “yes” or “no” cannot be given (Zhang et al., 2016). Still, due to the partly contradictory evidence, it cannot be said there is a consensus among scientists, according to Hilbeck et al., 2015.

Benefits of GM crops
Humanity faces several challenges in the coming decades. Among them are the increasing world population, a decrease of arable land or the bottleneck of traditional breeding methods (Zhang et al., 2016). To all of these, GMOs pose a genuine answer. The easiest way to produce more food for a growing population is to increase productivity by earlier maturity, easier harvesting, processing and cultivation. Adding to that, if we resorted to organically producing todays yields, humanity would need to cultivate an additionally 3 billion hectares, which is the equivalent to the size of two South America’s (‘Time to call out the anti-GMO conspiracy theory – Mark Lynas’, n.d.). But food also needs to become nutritious. A good example here is “Golden Rice” (Ye et al., 2000), which produces a precursor of vitamin A. The deficiency of vitamin A is estimated to kill more than half a million children under the age of 5 each year (Black et al., 2008) and cause another half million irreversible cases of childhood blindness (Humphrey, West, & Sommer, 1992).

Risks of GM crops
GMOs pose risks to its consumer as do crops deriving from traditional breeding. Major risks are toxicity, allergenicity and genetic hazards emerging from the inserted or altered gene itself, the expressed protein, products of the metabolism, pleiotropic effects or the disruption of natural genes in the organism (Zhang et al., 2016). There have been reports on the strong allergenicity of “Starlink” maize, which is directly connected to the inserted gene from Bacillus thuringiensis (Bravo, Gill, & Soberón, 2007; Sanchis, 2011; Tabashnik, 1994; Werth, Boucher, Thornby, Walker, & Charles, 2013). Also, GM crops can have an adverse ecological influence. For example, the weed species Amaranthus palmeri did evolve a glyphosate resistance after years of glyphosate use on resistant cotton fields (Gilbert, 2013). Another possibility is the fact, that insect resistant crops infer with ecological food webs by shifting predator prey ratios. Moreover, targeted pests might decline and primary minor pest become major issues (Bawa & Anilakumar, 2013; Snow & Palma, 1997).

Statements from Authorities
The Public Acceptance of Agricultural Biotechnologies (PABE) project revealed a range of questions concerning rather institutional considerations of the public, such as who is befitting from GMO use, by whom consequences have been evaluated, if authorities have enough power to regulate large companies and why the public has not been better informed about their use (Marris, 2001). For this reason, an overview of institutional statements might be appropriate.
The European Commision (EC) published the book “A decade of EU-funded GMO research”. Within this endeavor more than 200 million Euro of research grants were spent to evaluate GMO´s in areas such as environmental impact, food safety, biomaterials and biofuels and risk assessment and management. It conclusively states: “The main conclusion to be drawn from the efforts of more than 130 research projects, covering a period of more than 25 years of research, and involving more than 500 independent research groups, is that biotechnology, and in particular GMOs, are not per se more risky than e.g. conventional plant breeding technologies.” (Publications Office of the European Union, 2010)
The National Academy of Sciences founded by the U.S. Congress summarize in their comprehensive report, that large numbers of animal feeding studies provided reasonable evidence that animals were not harmed by food derived from GM crops, although admitting some studies were not designed optimal. Furthermore, long-term data in livestock health before and after GM crop introduction did not show adverse effects associated with the crops. And at last, epidemiological data on cancer and human health over time was revised but no substantiated evidence was found that GM crops are less safe than foods from non-GM crops. (Read "Genetically Engineered Crops, n.d.)
The British Royal Society states the following to the question “Is it safe to eat GM crops?” on its website: “Yes. There is no evidence that a crop is dangerous to eat just because it is GM. There could be risks associated with the specific new gene introduced, which is why each crop with a new characteristic introduced by GM is subject to close scrutiny. Since the first widespread commercialisation of GM produce 18 years ago there has been no evidence of ill effects linked to the consumption of any approved GM crop.” Before new GM foods are permitted to the market a variety of test has to be completed and the results are used by the authorities to determine the safety of the GM product, making “new GM crop varieties at least as safe to eat as new non GM varieties, which are not tested in this way.” (‘Is it safe to eat GM crops?’, n.d.)

Conclusion
As biologists, using genetic engineering methods every single day, they are quite natural to us. Nevertheless, we are confronted with the public debate too. Having experienced the public aversion towards GMO ourselves and having red about the many proposed justifications against it we realized that a direct exchange between the public and experts from all fields as well as diverse interest groups might provide a good common ground for an open discussion. In this way we hoped the perspective of being indoctrinated reflected my public studies might be avoided.


N I N A
S C H E E R


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P L A N T   M A R K E T


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P A N E L D I S C U S S I O N


Our team has organized a panel discussion to see how experts from various fields and the regional population feel about green genetic engineering.


Integrated Human Practices

C Y A N O
B I O T E C H


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P R O F. D R.
A N N E G R E T   W I L D E


Cultivation expertise from leading cyano scientist Prof. Wilde

D O U L I X


Another justification for real case use for our colony picking project.

S T A N D A R D I Z A T I O N
I N   C Y A N O   C O M M U N I T Y


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C Y A N O
C O N F E R E N C E   2 0 1 9


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E X P E R T   O N   C Y A N O S
J A M E S   G O L D E N


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O P E N T R O N
+   K E O N I


One of the earlier inspiration for our colony picking project.

P R O M E G A


Automating plasmid purification protocol with the OT-2.