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2014 UBC iGEM

Human Practices

Overview

In an effort to identify need for our proposed we decided to examine environmental concerns facing the mining industry to determine whether our platform might be of any use to the industry.

The mining sector is vital to the local economy of British Columbia; however, local concerns have been raised with regards to the ability of the sector to be able to operate without jeopardizing the environment. Political and social tension at the interface of resource based industries and the environment has been growing since the Enbridge Northern Gateway pipeline was proposed in 2006.

Mount Polley

More recently, the Mount Polley Tailings pond dam ruptured on August 4th 2014 sending 8 million cubic meters of tailings material and 17 million cubic meters of water into Polley Lake and Quesnel Lake(6). Initially drinking water advisories were established for Polley Lake, Hazeltine Creek, Quesnel Lake, and the Quesnel River system to the Fraser River(1), further testing showed that the drinking water was safe and the ministry of environment did not expect wildlife to be affected(2). However, Quesnel lake is one of the biggest sockeye nurseries in the province and is vital to the local fishing industry (3). As many as 60 million young sockeye will hatch this spring in Quesnel lake and will depend on feeding in the lake to mature before they begin their migration, since heavy metals might remain in the lake for decades the impact on the Sockeye industry could be lasting (3). Many remain skeptical about the minister of environments claims that fish should not be effected for 2 reasons, first tissue sampling of the fish had not been carried out, and second, many reports from locals stated that salmon being caught appeared sick. (2,3) Such reports prompted several local Chiefs to close down their operations citing risk to human health (3). Distrust ran so deep within locals that many refused to consume tap water despite the drinking water ban being lifted on August 7th 2014(5).

Figure 1: An ariel image of the Mount Polley effluent spilling into Quesnel Lake (12)

The social, political, and environmental fallout from the mount Polley mine disaster could have significant implications for the industry and the local economy if environmental concerns are translated into policy that restricts the activity of the mine or increases overhead through heightened monitoring. In the days following the disaster members from political parties with strong environmental platforms such as the NDP and the Green Party made several visits to locals in the surrounding areas to hear their concerns. Furthermore, the clean up for the mount Polley Mine Disaster could cost anywhere between 50 and 500 million dollars (4), so there is economic precedent to prevent these disasters from occurring.

This unfortunate disaster highlights the growing public weariness regarding capability of the mining industry to operate while preserving the environment. In a province where similar fears have been able to dramatically slow the advancement of the Northern Gateway pipeline, these are concerns not to be taken lightly (7). However, such a disaster begs the question who’s to blame, should environmental protection and monitoring fall under the responsibility of the government or the industry. To better understand this we turn towards to legislative framework around the mining industry.

Legislation

Both the provincial government and the federal government regulate environmental impact in the mining industry (8). Though these bodies of legislation are meant to harmonize with each other, the provincial legislation differs from province to province and so each region falls under slightly different rules and guidelines for best practice. That being said, most of the enforcement comes from the federal acts such as the Canadian fisheries act, and the provincial acts geared towards protecting the environment (9). The Provincial mining acts on the other hand appear to serve as a set of guidelines towards best practice but are hardly enforced or policed. For example, the health and safety reclamation code under the B.C mining act includes provisions to protect and rehabilitate exploration and mining sites; though the language calls for the minimization of risk it does not set standards that need to be met, and thus is relatively ineffective (9). Other associations have set guidelines to direct the mining industry towards better practice but appear to do little, for instance the prospectors and developers association of Canada has a set of standards for exploration but these are completely voluntary, often not respected in the field (9).

Figure 2: Canadian Government Policies on Environment (2)

A closer examination of aspects of the federal environmental acts shows that while they offer stricter guidelines and policing, there are still loopholes that could be taken advantage of. The Metal Mining Effluent Regulations (under the federal Fisheries act) regulates 9 parameters of mine effluents but is restricted to PH and a variety of heavy metals; there appear to be no regulations for the limit or measurement of hydrocarbons or other toxins in effluents(10). The policing of these regulations seems to be lacking as well, in 2010 half of the 20 operating mines in B.C were exceeding effluent requirements and were not punished, several of these mines were having lethal effects on the trout and zooplankton populations (9).

Figure 3: Authorized Limits of Deleterious Substances (10)

Though there are loopholes and weaknesses in environmental legislation the overall trend since the 1900’s have been a steady increase in environmental legislation on the domestic and international stage (11).

Figure 4: International Environmental Agreements since 1900 (11)

This steady increase in environmental legislation is reflected by the steady increase in capital expenditure as well as ongoing expenditure within the Canadian mining sector over the past 8 years; the capital expenditure suggests growing investment in technology/practices to enable better protection in the future (12). More importantly it appears that the Canadian Mining industry, as well as Electric power generation and Oil and Gas extraction, is showing increased capital and ongoing expenditure on environmental things (12). This suggests that either out of requirement, or desire to be proactive the mining industry is spending more money on greener practices and might be interested in investing in new technologies that help minimize environmental impact.

Figure 5: Total Mining Industry Expenditure on Environmental Protection (12)

Figure 6: Mining Industry Expenditure on Environmental Protection as Percentage of Total Business Sector (12)

The Industry

To gain perspective we conducted an interview with Dr. John Thomspon, an expert in the mining space and a member of the genome BC board of directors. In our conversation with Dr. Thomspon we learned that in the mining industry environment is regarded not as competitive but as a common problem for the industry; “anything that can be done better is good for everyone”. Furthermore, the industry is in agreement that the amount of environmental legislature will increase and so will the expenditure to fulfill its requirements. This co-operative attitude and the predicted need to reduce impact suggest the mining industry would look favorably on technology that reduces environmental impact without harming yields.

With regards to tailings ponds Dr. Thomspon informed us that there is very little environmental legislation governing them or instructing industry what to do with them. As a result tailings are often either buried or flooded, they are rarely remediated or re-mined for ore. Furthermore, governments won’t fund remediation unless the ponds are toxic. Given that mining companies spend millions of dollars on containing tailings, it would be beneficial for the industry to wield a technology that would allow them to re-mine tailings, thus reducing environmental impact and generating revenue. This concept is not foreign to the mining industry, in some cases when mineral prices sky rocket mining companies will invest in re-mining tailings ore for that given mineral, this is a practice that dates back to the earliest days of gold mining.

We propose that our platform of biological mineral separation would be attractive to the industry in addressing some of its environmental concerns while generating revenue. Coupled with our directed evolution system a variety of peptides could be used to extract many different minerals and possibly heavy metals. The industry has demonstrated a growing need to deal with environmental issues such as tailings through current image issues (Mount Polley), growing legislative restrictions and increasing environmental expenditures and our platform can offer a solution.

References

1) http://www.env.gov.bc.ca/eemp/incidents/2014/pdf/PSA_HealthAdvisory_MountPolley_20140805.pdf

2) http://www.env.gov.bc.ca/eemp/incidents/2014/pdf/Memo-QuesnelWaterQuality-DW-AL_20140807.pdf

3) http://www.theglobeandmail.com/news/british-columbia/mount-polley-tailings-spill-effects-could-last-for-decades/article20596892/

4) http://www.theglobeandmail.com/news/british-columbia/bc-further-rescinds-water-use-ban-near-mount-polley-mine-spill/article20024690/

5) http://www.desmog.ca/2014/08/12/residents-refuse-drink-water-despite-ban-lift-after-mount-polley-mine-disaster

6) http://www.env.gov.bc.ca/eemp/incidents/2014/mount-polley/#updates

7) http://en.wikipedia.org/wiki/Enbridge_Northern_Gateway_Pipelines

8) http://www.mining.bc.ca/our-focus/environmental-laws-regulations

9) http://www.miningwatch.ca/publications/introduction-legal-framework-mining-canada

10) http://laws.justice.gc.ca/eng/regulations/SOR-2002-222/page-17.html#h-51

11) http://www.eea.europa.eu/soer/europe-and-the-world/megatrends/environmental-regulation-and-governance-increasing

12) http://www5.statcan.gc.ca/olc-cel/olc.action?objId=16F0006X&objType=2&lang=en&limit=0

13) http://www.cbc.ca/news/canada/photos/mount-polley-mine-spill-an-aerial-view-1.2730436

Overview

As copper demand increases, efforts into finding new copper deposits have been recently on the decline. For years we have been surveying, large amounts of land and mining only the highest quality copper ores. These ores contain lower concentrations of arsenic (>0.2%), however, most of these resources have been mined and companies are now faced with using ores containing higher average arsenic concentrations. With 1% being the limit of most modern smelters, and the few smelters capable of smelting concentrates charging a premium for their service, new technologies will need to be developed to handle the increase in arsenic concentrations in an economically friendly manner.

Historical Copper Price

As indicated in Figure 1, prices of copper has been steadily increasing worldwide (1). As such, demand from mining companies for greater output has grown. Beyond just exploring new areas to mine, mining companies have to figure out how to maximize the output from their current land by re-extracting from the low grade copper ores.

Figure 1: Copper price for the past 25 year (1)

Current Global Mining Industry

According to SNL which provides global financial information on metal and mining, statistics (Figure 2) has shown that the global drilling activity in general has been declining gradually in the past 3 years, with the decreases in gold and copper as the most obvious (2). Such slowdown in drilling activity is due to the lack of investor funding for exploration (Figure 3). In fact in 2013, the amount of investment raised for exploration was lowered to levels not seen for a decade (2). The decrease in drilling activities can lead to stagnation in the industry’s medium- and long-term supply pipeline (2). As a result, copper producers may have to rely on current copper ores for extraction, most of which contain low level of copper.

Figure 2: Global Drilling Activity (2)

Figure 3: Significant Exploration-related Financings by Junior Companies, 2008-13 (3)

Copper Mining in Canada

Canada is the third largest copper producer in the world, after Chile and the USA. Copper mined in Canada is hosted in sulphide sources from volcanic and magnetic activity, and porphyry deposits. Copper is widespread in Canada and British Columbia is the largest copper-producing province, followed by Ontario and Quebec. Highland Valley Copper in British Columbia, owned by Teck Resources Limited, is the largest Copper mine in Canada (4).

Copper Extraction Vs Current Technological Limit

Due to more complex mineralogy and lower grade copper ores, arsenic content in copper concentrates has been stable since 2004, yet copper contained in concentrates has declined (Figure 4). The As/Cu ratio has increased by 40% since 2000 (Figure 5). Gradual depletion ore with low levels of arsenic is a growing concern within the copper industry (6); it leads to higher processing and environmental costs as the government has stringent environmental regulations particularly related to arsenic (5). As a result, this has been a concern for the miners and smelters.

Figure 4: As and Cu Content in Concentrate (5)

Figure 5: As/Cu Ratio in Concentrate (5)

According to the data provided by Teck, the largest mining company in Canada, arsenic content in copper concentrates is expected to double in the next 6-years. Thus, copper concentrates with high level of arsenic (>1% As) could enter the market. One thing to note is that copper concentrates with >1% As cannot be processed by standard smelting technology.

As shown in Figure 6, the arsenic smelting capacity is about 100,000 to 120,000 tonnes, yet with the increase in As content in Cu concentrates, the standard smelting technologies can no longer meet the demand of Cu processing. Technologies processing high Ar/Cu concentrates are available, yet they do not meet best-in-class environmental requirements. Therefore, new technologies and processes are necessary to maintain sustainable copper production from As-bearing Cu concentrates (>1 % As).

Figure 6: As Content in Cu Concentrate and Smelter’s As Capacity (5)

Technologies involving pyro-metallurgical pre-treatment are an option, yet they have certain restrictions and additional costs (6). Non-traditional methods that involves high pressure, high temperature or chemical agents could also add to the operation cost. Thus, our project aims for an easier solution that is much less energy demanding yet also environmental friendly.

References

1) http://www.infomine.com/investment/metal-prices/copper/all/

2) http://go.snl.com/P-MM-CM-140201-MicrositeReportDownloads_Request-SOTM-Mining--Explo.html

3) http://go.snl.com/P-MM-CM-140201-Q1MicrositeReportDownloads_RequestWET.html

4) http://copperinvestingnews.com/3381-copper-mining-in-canada.html

5) http://cesl.com/res/tc/documents/_ces_portal_meta/_portal_pages/cesl%20limited/downloads/a_sustainable_hydrometallurgical_process_ copper_deposits.pdf

6) Chen, C., Zhang, L., Jahanshahi, S. (2010) Thermodynamic Modeling of Arsenic in Copper Smelting Processes. Metallurgical and Materials Transactions B, Vol. 41B, pp.2010-1175.

Overview

After consultation with Mr. Sauve, from Teck Resources Limited, it became clear this technology had a place in the mining industry as a method of concentrating arsenic containing copper minerals before smelting. This will reduce the amount of concentrate that needs to be smelted in facilities capable of handling high arsenic concentrations, and reduce the associated costs.

Current Technology

Separation of copper from arsenic is not a new problem, it has been around for many years, and there are dozens of techniques and technologies that attempt to tackle this problem (1). Currently very few facilities are able to smelt copper with high concentrations of arsenic and those that can, generally use rather expensive techniques and charge mines a premium to use to smelt these high arsenic containing minerals (1). Many technologies are being developed and tested, to remove arsenic before or during smelting (1, 2, 3). However, many of these technologies are just coming online, with the goal of making smelting arsenic containing concentrates more accessible (1, 3).

Developing technologies

A majority of the new technologies for arsenic smelting will take more refinement and testing, however, they still may not meet the goal of providing an economic and simple technology that can easily be implemented in mines across the world. Many technologies, such as the CESL process developed by Teck and Aurubis, are planning to make smelting of arsenic rich ore (up to 4.7%) more accessible (2). However, until these technologies come online, mines are still charged a premium for smelting copper with >0.1% As, with prices skyrocketing after 0.5% As (1).

Our technology and place in the mining industry

Regardless of how long these technologies take to come online, reducing the volume of concentrate that reaches these smelters will always be more economically desired by mining companies. As such, UBC iGEM is developing a technology to simply and affordably separate non-arsenic containing copper bearing minerals (such as chalcopyrite), from arsenic containing copper bearing minerals (such as enargite). Traditional froth floatation techniques can already concentrate the arsenic containing copper up to 10-15%. However, currently the most common copper bearing mineral, chalcopyrite, and the most common arsenic containing copper bearing mineral, enargite, are notoriously difficult to separate via froth flotation (1, 4).

Our technique allows chalcopyrite to be selectively separated from enargite, and concentration of arsenic containing copper bearing minerals. Since the average ratio of chalcopyrite to enargite is over 100:1 (5), being able to remove the chalcopyrite and concentrate the enargite could greatly reduce the material mine’s need to send for smelter.

References

1) Taylor P et. al. (2014) “Treating high arsenic copper concentrates through pyrometallurgical processing”, Conference of Metallurgists Proceedings.

2) Bruce R et. all (2011) “Teck-Aurubis: An integrated mine to metal approach to develop high arsenic copper deposits using the CESL process”, CESL Publications.

3) Å. Holmström A., Hedström L., Lundholm K., Andersson M. , and L. Nevatalo L., “Partial Roasting of Copper Concentrate with Stabilisation of Arsenic and Mercury”

4) Curtis SB, Hewitt J, MacGillivray RTA, Dunbar WS, 2009. “Biomining with bacteriophage: Selectivity of displayed peptides for naturally occurring sphalerite and chalcopyrite.” Biotechnology and Bioengineering 102:644–650.

5) Mayhew K. Mean R. Lossin A. and Barrios P.,“A sustainable hydrometallurgical process to develop copper deposits challenged with high arsenic,”13th Internationl Congress expomin, 2014.

Overview

During this project we contacted four professionals who represent industrial and academic expertise on copper arsenic separation, caulobacter surface surface display proteins, and an expert on social applications for genetically modified organisms.

Scott Dunbar

Associate Professor, and head of UBC mining

Dr. Dunbar was one of our earliest collaborators who brought the issue of world-wide high quality copper ore depletion to our attention. We met with Dr. Dunbar three times, to refine our understanding of the problem, identifying the separation of chalcopyrite from enargite as an issue we could tackle and possibly solve. He also provided us with one of his most recent publications where it had been demonstrated that short peptide loops were capable of binding to chalcopyrite selectively. While they had previously been tested in phage, they haven’t been tried in more complicated systems such as bacteria. We would go on to use these loops as our principal method for attaching caulobacter to chalcopyrite.

Dr. John Smitt

Professor in Microbiology and Immunology at UBC

Dr. John Smitt is an expert in Caulobacter surface protein display systems. One of the issues presented to us by Dr. Dunbar was the limitations of expressing these chalcopyrite binding proteins in viruses. Expressing them in bacteria could yield a plethora of options to assist in the separation process. Dr. Smitt immediately suggested our usage of Caulobacter, an aquatic organism with a well-studied system of displaying proteins on its surface. During our eight meetings with Dr. Smitt we were able to develop a protocol to display our proteins on the surface of caulobacter.

Dr. Conor douglas

Post-Doctoral Fellow in UBC Science and Technology

Dr. Douglas is a sociologist that specializes in the societal effects of new discoveries in synthetic biological. Dr. Douglas assisted us in outlining potential problems and benefits our system could face, including biological containment, social stigma, and worker safety. During our two group discussions, and 3 meetings with him, we outlined and addressed some potential environmental and socio economic benefits and concerns relating to our project.

Paul Sauve

Process Engineer at Teck Resources Limted

Mr. Sauve is a specialist in Teck who works on strategies for dealing with copper containing high concentrations of arsenic. Our email correspondence with him over the duration of our project helped us outline and understand the various techniques and technologies available. Additionally, he assisted us in understanding techniques currently in development which deal with separating copper and arsenic. Furthermore, this allowed us to find our niche within the mining community. Mr. Sauve encouraged us to modify our design to allow the use of dead or alive caulobacter, as this would ease certain technological and logistical burdens for mining companies. This eventually turned into our exploration of coiled-coil proteins instead of gas vesicles for the separation component of our project.

The iGEM BioBrick registry has historically been a database for teams to browse and explore the parts available to them, to search for parts that aid in meeting their project goals, and to deposit parts that would serve the same purpose for the groups that would come after them. The iGEM registry is one of the defining features of iGEM it represents the accumulation of 10 years of knowledge and expertise within the synthetic biology community. As such, the maintenance, and structure of the registry is essential in preserving a decade of undergraduate research and in translating that work to the scientific community at large.

In designing our project we ran into problems navigating the registry, and with the performance of some parts form the registry; this drew us to investigate some of the inner workings of the registry. Furthermore, we felt that there was an unwritten consensus among iGEMers that the registry could use improvement, and any improvement in its ability to sort, manage, and track data would improve the speed and quality by which systems could be designed and implemented.

We began to question how reliable the information in the registry was, if annotation was automated (ie blast infrastructure), and if there were any patterns in the parts that were submitted that could lend clues to the problems we were encountering. The big question that drove our investigation was “are parts in the registry modified and optimized from year to year, or do teams submit a combination of brand-new and new/old composites every year with little optimization occurring”. In our mind, the optimization of parts over time represented an effective transfer, and building of knowledge from year to year, we believed this represented a form of expertise for a given part set that was desirable. In contrast parts submitted as chimeras of old and brand new parts did represent new knowledge but lacked the same level of expertise and was, in our mind, less desirable. In defense of this stance, a glance of the judging handbook over the last few years clearly shows an emphasis the production few parts with high quality characterization data, rather than submission of large quantities of poorly characterized parts; the judges have been pushing for greater expertise in igem projects and parts over the last few years. Before we can begin to address patterns lets take a quick look at how iGEM has grown over the years.

With humble beginnings in 2004 the number of teams participating has grown rapidly over the last ten years from 5 teams to 245 teams this year (Figure 1). In conjunction with this growth there has been a steady increase in the number of parts submitted each year (Figure 2).

Figure 1: Participation in iGEM

Figure 2: Part Submission

By hunting through the team websites and their addresses we were able to connect the parts they submitted with latitude and longitude coordinates, plotting these on a map of the world gives us a good indication of the global reach of iGEM as well as which regions/teams seem to contribute the most to the database (Figure 3. Appendix 1). Our data points to hotspots in the United States, Europe, and Asia. Furthermore, it appears that the most even distribution of densities occurs within the United States and Europe, where as Asia’s hot spots seem spread out but with each contributing a substantial amount to the registry. Producing a lot of parts is one thing but we wondered which teams were making the best parts, assuming that the more often a part has been used indicates better quality we were able to get a rough idea for which regions were producing the best parts. Obviously there would be a bias towards some of the earliest parts, promoters, RBS terminators; being deemed the highest quality but this was a good place to start. As seen in figure 4 the teams that produced the most parts happen to be the teams that produce the parts that are used the most.

figure 3

Figure 4

Figure 4 shows us what the total usage of parts produced by given locations is from the years 2007-2012, however, it does not shed light onto which parts from year to year constitute those numbers. We decided to look at all the composite parts submitted as team favorites each year, since we knew the part numbers for the components of the composite parts it was easy to then break the distribution down by year. What we found is that in every competition cycle since 2005 the most common used in these submissions were from the first competition cycle and from the year of the current competition (figure 5). Essentially, every year iGEMMERS build their favorites parts using the first parts placed into the registry and any new parts they created. Very few of the parts created between those years are used, suggesting that iGEMMERs are more interested in submitting new parts, (and obviously requiring promoters, Rbs, and terminators from the early years), and less interested in re-using parts from previous years.

Figure 5

Our next step was to preform a pairwise blast against all the parts in the registry to find matches then perform MSA for phylogeny tree generation, by filtering the known usage data we hooped to elucidate whether teams were improving upon existing parts. However, our finding showed an overwhelming number of parts composite parts that used the part of interest or a variant of that part and we were unable to determine if parts were being optimized over time. In the figure below, resembling a part of the larger phylogenetic tree, it is evident that there are many part variants. Thus we decided to take a closer look at how parts were distributed year by year.

We decided to trace the usage of a few of the most popular parts through the iGEM registry such as the LacI repressor and YFP. Using data collected from our own registry database we can show that these parts, and many more like them, tend to be picked up for a year or two by a given team and then dropped, however another team might use them in the next year (figure 6). This demonstrates the changing mindset of igem teams, they tend to avoid using the same parts year after year.

In the process of our extensive research towards our project’s feasibility in the mining industry, several uncertainties arose that may impact how effective our project will realistically be. With the ever-growing concern of genetically modified organisms (GMOs) in various parts of our everyday life, serious consideration was made to assess the possible impact our bacteria has once it exits its containment. We pursued various perspectives on the usage of GMOs, ones that we took into account when developing the design of our chalcopyrite-binding bacteria system. While much of project is still in the proof of concept stage, comprehensive analysis was conducted to ensure that our technology that would integrate with current mining techniques as seamless as possible.

Biosafety

During the search for our model organism, the issue of biosafety was brought up as an important criteria to our project. Any organisms with an ecologically invasive or pathogenic history were immediately disregarded. The most preferable models would be those that are naturally found within British Columbia, do not exhibit pathogenic traits and are extensively well researched. From those desired characteristics, we found Caulobacter crescentus to be an excellent model organism.

C. crescentus is commonly found in fresh water basins all throughout Canada and is profoundly studied in numerous laboratories. It is often a subject for studying the regulation of cell cycle and cell differentiation due to its ability to create two forms of daughter cells: a mobile “swarmer”cell form and a stationary “stalked” cell form (see Figure 1).

Figure 1 - the division of two cell types - “swarmer” cell (top) and “stalk” cell (bottom) (2)

There are two strains of C. crescentus: CB15, the wild-type microorganism, and NA100, the modified laboratory model. The main physiological difference between the two organisms are that the NA100 strain provides stalked and predivisional cells that can be physically separated from their swarmer cell predecessor, while the CB15 cell types cannot physically separate (1). Regardless of the strain, this organism is deemed non-pathogenic to other organisms, including humans. While there is no extensive research on the ecological interactions between C. crescentus and other microbes, its widespread use suggests a minimal effect on surrounding ecosystems.

As a preemptive measure against the risk of releasing live GMOs, one of our designs for our chalcopyrite-binding C. crescentus model eliminates the necessity of having live microbes in the mineral froth. The C. crescentus design involving coil-coiled proteins as a means to flocculate the bacteria-mineral complex together can be performed without any cells living in the solution. By not involving live cells in the actual chalcopyrite-enargite separation process, the risk of biocontamination is greatly reduced.

Industrial Setting

Although the usage of microorganisms in the mining industry has been well established for many years now, the deployment of a GMO into the mining environment is still a novel technique. Current biomining processes utilize microbial consortia involving many acidophilic, autotrophic iron- or sulfur-oxidizing prokaryotes (3). Most of these biomining practices integrate a natural metabolic system to extract the desired minerals. As such, they are generally well-studied and are predictable in their cellular behavior (3).

Concerns come up when integrating a genetically modified organism due to its possible complexity and uncertainty. When discussing with representatives in the mining industry, they feared that these chalcopyrite-binding bacteria would require different mediums to grow in and storage, different optimal solutions to bind and different protocols compared to those of the current consortia of microfauna. The main issue revolves around expending extra costs to create optimal environments specifically for these GMOs.

These concerns were heavily considered during the design process, especially when it came to the model organism itself. One characteristic of C. crescentus is that it can be easily grown in normal laboratory settings (37°C in agarose medium). Since our project only expresses surface proteins and an induced gas vesicle system, there are no major biological changes that would be specific to our project-specific organism. In addition, the chalcopyrite binding and the coil-coiled protein interaction do not require bioreactors or substantial changes in pressure or temperature; these bacteria can successfully collect the metal ores and flocculate immediately into a chalcopyrite-enargite solution. In actuality, our organism is very cost effective and affordable to both grow and utilize.

References

(1) Poindexter J. S. (1964) Biological properties and classification of the Caulobacter group. US National Library of Medicine.

(2) Berne et. al. (2010). A Bacterial Extracellular DNA Inhibits Settling of Microbial Progeny Cells Within a Biofilm. Molecular Microbiology.

(3) Rawlings D.E. and Johnson D.B. (2007) The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology.

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-In an effort to identify need for our proposed we decided to examine environmental concerns facing the mining industry to determine weather our platform might be of any use to the industry.
+In an effort to identify need for our proposed we decided to examine environmental concerns facing the mining industry to determine whether our platform might be of any use to the industry.
 <br><br>
 The mining sector is vital to the local economy of British Columbia; however, local concerns have been raised with regards to the ability of the sector to be able to operate without jeopardizing the environment. Political and social tension at the interface of resource based industries and the environment has been growing since the Enbridge Northern Gateway pipeline was proposed in 2006.
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+<h3>Overview</h3>
+<br><br>
+As copper demand increases, efforts into finding new copper deposits have been recently on the decline. For years we have been surveying, large amounts of land and mining only the highest quality copper ores. These ores contain lower concentrations of arsenic (>0.2%), however, most of these resources have been mined and companies are now faced with using ores containing higher average arsenic concentrations. With 1% being the limit of most modern smelters, and the few smelters capable of smelting concentrates charging a premium for their service, new technologies will need to be developed to handle the increase in arsenic concentrations in an economically friendly manner.
+<br><br>
 <h3>Historical Copper Price</h3>
 As indicated in Figure 1, prices of copper has been steadily increasing worldwide (1). As such, demand from mining companies for greater output has grown. Beyond just exploring new areas to mine, mining companies have to figure out how to maximize the output from their current land by re-extracting from the low grade copper ores.
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-<h3>Our Competitors</h3>
+<h3>Overview</h3>
+After consultation with Mr. Sauve, from Teck Resources Limited, it became clear this technology had a place in the mining industry as a method of concentrating arsenic containing copper minerals before smelting. This will reduce the amount of concentrate that needs to be smelted in facilities capable of handling high arsenic concentrations, and reduce the associated costs.
+<br><br>
+<h3>Current Technology</h3>
 Separation of copper from arsenic is not a new problem, it has been around for many years, and there are dozens of techniques and technologies that attempt to tackle this problem (1). Currently very few facilities are able to smelt copper with high concentrations of arsenic and those that can, generally use rather expensive techniques and charge mines a premium to use to smelt these high arsenic containing minerals (1). Many technologies are being developed and tested, to remove arsenic before or during smelting (1, 2, 3). However, many of these technologies are just coming online, with the goal of making smelting arsenic containing concentrates more accessible (1, 3).
 <br><br>
-A majority of the new technologies for arsenic smelting will take more refinement and testing, however, they still may not meet the goal of providing an economic and simple technology that can easily be implemented in mines across the world. Many technologies, such as the CESL process developed by TECH and Aurubis, are planning to make smelting of arsenic rich ore (up to 4.7%) more accessible (2). However, until these technologies come online, mines are still charged a premium for smelting copper with >0.1% As, with prices skyrocketing after 0.5% As (1).
+<h3>Developing technologies</h3>
+A majority of the new technologies for arsenic smelting will take more refinement and testing, however, they still may not meet the goal of providing an economic and simple technology that can easily be implemented in mines across the world. Many technologies, such as the CESL process developed by Teck and Aurubis, are planning to make smelting of arsenic rich ore (up to 4.7%) more accessible (2). However, until these technologies come online, mines are still charged a premium for smelting copper with >0.1% As, with prices skyrocketing after 0.5% As (1).
 <br><br>
+<h3>Our technology and place in the mining industry</h3>
 Regardless of how long these technologies take to come online, reducing the volume of concentrate that reaches these smelters will always be more economically desired by mining companies. As such, UBC iGEM is developing a technology to simply and affordably separate non-arsenic containing copper bearing minerals (such as chalcopyrite), from arsenic containing copper bearing minerals (such as enargite). Traditional froth floatation techniques can already concentrate the arsenic containing copper up to 10-15%. However, currently the most common copper bearing mineral, chalcopyrite, and the most common arsenic containing copper bearing mineral, enargite, are notoriously difficult to separate via froth flotation (1, 4).
 <br><br>
-Our technique allows chalcopyrite to be selectively separated from enargite, and concentration of arsenic containing copper bearing minerals. Since the average ratio of chalcopyrite to enargite is over 100:1 (5), being able to remove the chalcopyrite and concentrate the enargite could greatly reduce the material mine’s need to send for smelter.
+Our technique allows chalcopyrite to be selectively  separated from enargite, and concentration of arsenic containing copper bearing minerals. Since the average ratio of chalcopyrite to enargite is over 100:1 (5), being able to remove the chalcopyrite and concentrate the enargite could greatly reduce the material mine’s need to send for smelter.
 <br><br>
 <h3>References</h3>
@@ Line 188: / Line 203: @@
 <!-- ========================== Consultation PART ============================= -->
    <div class="tab-pane" id="hp4">
-<br><br>
+<h3>Overview</h3>
 During this project we contacted four professionals who represent industrial and academic expertise on copper arsenic separation, caulobacter surface surface display proteins, and an expert on social applications for genetically modified organisms.
+<br><br>
 <h3>Scott Dunbar</h3>
 Associate Professor, and head of UBC mining
@@ Line 223: / Line 239: @@
 <br><br>
    With humble beginnings in 2004 the number of teams participating has grown rapidly over the last ten years from 5 teams to 245 teams this year (Figure 1). In conjunction with this growth there has been a steady increase in the number of parts submitted each year (Figure 2).
-<img src="https://static.igem.org/mediawiki/2014/4/48/Partsubmissioninigem.png">
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/b/b9/Participationinigem.png">
+<h4>Figure 1: Participation in iGEM </h4>
+<img src="https://static.igem.org/mediawiki/2014/9/97/Participation.png">
+<br><br>
+<h4>Figure 2: Part Submission </h4>
+<img src="https://static.igem.org/mediawiki/2014/6/67/Parts_1.png">
 <br><br>
 By hunting through the team websites and their addresses we were able to connect the parts they submitted with latitude and longitude coordinates, plotting these on a map of the world gives us a good indication of the global reach of iGEM as well as which regions/teams seem to contribute the most to the database (Figure 3. Appendix 1). Our data points to hotspots in the United States, Europe, and Asia. Furthermore, it appears that the most even distribution of densities occurs within the United States and Europe, where as Asia’s hot spots seem spread out but with each contributing a substantial amount to the registry. Producing a lot of parts is one thing but we wondered which teams were making the best parts, assuming that the more often a part has been used indicates better quality we were able to get a rough idea for which regions were producing the best parts. Obviously there would be a bias towards some of the earliest parts, promoters, RBS terminators; being deemed the highest quality but this was a good place to start. As seen in figure 4 the teams that produced the most parts happen to be the teams that produce the parts that are used the most.
@@ Line 232: / Line 250: @@
 figure 3
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/c/c2/All_BBa_use_locations.png"style="height: 700px">
+<img src="https://static.igem.org/mediawiki/2014/9/9f/AllBBalocations.jpg.png" id="world_map_01">
 <br><br>
 Figure 4
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/c/c2/All_BBa_use_locations.png" style="height: 700px">
+<img src="https://static.igem.org/mediawiki/2014/c/c2/All_BBa_use_locations.png" id="world_map_01">
 <br><br>
 Figure 4 shows us what the total usage of parts produced by given locations is from the years 2007-2012, however, it does not shed light onto which parts from year to year constitute those numbers. We decided to look at all the composite parts submitted as team favorites each year, since we knew the part numbers for the components of the composite parts it was easy to then break the distribution down by year. What we found is that in every competition cycle since 2005 the most common used in these submissions were from the first competition cycle and from the year of the current competition (figure 5). Essentially, every year iGEMMERS build their favorites parts using the first parts placed into the registry and any new parts they created. Very few of the parts created between those years are used, suggesting that iGEMMERs are more interested in submitting new parts, (and obviously requiring promoters, Rbs, and terminators from the early years), and less interested in re-using parts from previous years.
 <br><br>
 Figure 5
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/0/0e/2006.png"
+<img src="https://static.igem.org/mediawiki/2014/thumb/6/6b/Y_total_fav_parts.png/800px-Y_total_fav_parts.png">
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/1/1a/2007.png"
+Our next step was to preform a pairwise blast against all the parts in the registry to find matches then perform MSA for phylogeny tree generation, by filtering the known usage data we hooped to elucidate whether teams were improving upon existing parts. However, our finding showed an overwhelming number of parts composite parts that used the part of interest or a variant of that part and we were unable to determine if parts were being optimized over time. In the figure below, resembling a part of the larger phylogenetic tree, it is evident that there are many part variants. Thus we decided to take a closer look at how parts were distributed year by year.
+<br><br>
+<img src= https://static.igem.org/mediawiki/2014/thumb/9/98/BBa_E0030_phylo.png/800px-BBa_E0030_phylo.png>
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/4/4d/2008.png"
+<img src= https://static.igem.org/mediawiki/2014/9/93/BBa_E0020_phylo.png>
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/5/5f/2009.png"
+We decided to trace the usage of a few of the most popular parts through the iGEM registry such as the LacI repressor and YFP. Using data collected from our own registry database we can show that these parts, and many more like them, tend to be picked up for a year or two by a given team and then dropped, however another team might use them in the next year (figure 6). This demonstrates the changing mindset of igem teams, they tend to avoid using the same parts year after year.
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/d/d7/2010.png"
+<img src= https://static.igem.org/mediawiki/2014/d/dd/BBa_C0012_year_hist.png>
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/b/b4/2011.png"
+<img src= https://static.igem.org/mediawiki/2014/1/1b/BBa_C0040_year_hist.png>
 <br><br>
-<img src="https://static.igem.org/mediawiki/2014/4/48/2012.png"
+<img src= https://static.igem.org/mediawiki/2014/4/4c/BBa_C0062_year_hist.png>
 <br><br>
+<img src= https://static.igem.org/mediawiki/2014/8/8f/BBa_E0030_year_hist.png>
+<br><br>
+</div>
+<!-- ================== END Data mining PART ================================= -->
+<!-- ========================== GMO PART ============================= -->
+  <div class="tab-pane" id="hp6">
+<br><br>
+In the process of our extensive research towards our project’s feasibility in the mining industry, several uncertainties arose that may impact how effective our project will realistically be. With the ever-growing concern of genetically modified organisms (GMOs) in various parts of our everyday life, serious consideration was made to assess the possible impact our bacteria has once it exits its containment. We pursued various perspectives on the usage of GMOs, ones that we took into account when developing the design of our chalcopyrite-binding bacteria system. While much of project is still in the proof of concept stage, comprehensive analysis was conducted to ensure that our technology that would integrate with current mining techniques as seamless as possible.
+<br>
+<h3>Biosafety</h3>
+During the search for our model organism, the issue of biosafety was brought up as an important criteria to our project. Any organisms with an ecologically invasive or pathogenic history were immediately disregarded. The most preferable models would be those that are naturally found within British Columbia, do not exhibit pathogenic traits and are extensively well researched. From those desired characteristics, we found Caulobacter crescentus to be an excellent model organism.
+<br><br>
+C. crescentus is commonly found in fresh water basins all throughout Canada and is profoundly studied in numerous laboratories. It is often a subject for studying the regulation of cell cycle and cell differentiation due to its ability to create two forms of daughter cells: a mobile “swarmer”cell form and a stationary “stalked” cell form (see Figure 1).
+<h4>Figure 1 - the division of two cell types - “swarmer” cell (top) and “stalk” cell (bottom) (2)</h4>
+<img src="https://static.igem.org/mediawiki/2014/0/09/Hellooooo.jpg">
+<br><br>
+There are two strains of C. crescentus: CB15, the wild-type microorganism, and NA100, the modified laboratory model. The main physiological difference between the two organisms are that the NA100 strain provides stalked and predivisional cells that can be physically separated from their swarmer cell predecessor, while the CB15 cell types cannot physically separate (1). Regardless of the strain, this organism is deemed non-pathogenic to other organisms, including humans. While there is no extensive research on the ecological interactions between C. crescentus and other microbes, its widespread use suggests a minimal effect on surrounding ecosystems.
+<br><br>
+As a preemptive measure against the risk of releasing live GMOs, one of our designs for our chalcopyrite-binding C. crescentus model eliminates the necessity of having live microbes in the mineral froth. The C. crescentus design involving coil-coiled proteins as a means to flocculate the bacteria-mineral complex together can be performed without any cells living in the solution. By not involving live cells in the actual chalcopyrite-enargite separation process, the risk of biocontamination is greatly reduced.
+<br><br>
+<h3>Industrial Setting</h3>
+Although the usage of microorganisms in the mining industry has been well established for many years now, the deployment of a GMO into the mining environment is still a novel technique. Current biomining processes utilize microbial consortia involving many acidophilic, autotrophic iron- or sulfur-oxidizing prokaryotes (3). Most of these biomining practices integrate a natural metabolic system to extract the desired minerals. As such, they are generally well-studied and are predictable in their cellular behavior (3).
+<br><br>
+Concerns come up when integrating a genetically modified organism due to its possible complexity and uncertainty. When discussing with representatives in the mining industry, they feared that these chalcopyrite-binding bacteria would require different mediums to grow in and storage, different optimal solutions to bind and different protocols compared to those of the current consortia of microfauna. The main issue revolves around expending extra costs to create optimal environments specifically for these GMOs.
+<br><br>
+These concerns were heavily considered during the design process, especially when it came to the model organism itself. One characteristic of C. crescentus is that it can be easily grown in normal laboratory settings (37°C in agarose medium). Since our project only expresses surface proteins and an induced gas vesicle system, there are no major biological changes that would be specific to our project-specific organism. In addition, the chalcopyrite binding and the coil-coiled protein interaction do not require bioreactors or substantial changes in pressure or temperature; these bacteria can successfully collect the metal ores and flocculate immediately into a chalcopyrite-enargite solution. In actuality, our organism is very cost effective and affordable to both grow and utilize.
+<br><br>
+<h3>References</h3>
+(1) Poindexter J. S. (1964) Biological properties and classification of the Caulobacter group. US National Library of Medicine.
+<br><br>
+(2) Berne et. al. (2010). A Bacterial Extracellular DNA Inhibits Settling of Microbial Progeny Cells Within a Biofilm. Molecular Microbiology.
+<br><br>
+(3) Rawlings D.E. and Johnson D.B. (2007) The microbiology of biomining: development and optimization of mineral-oxidizing microbial consortia. Microbiology.
+<br><br>
 </div>
    </div>
 </div>
-<!-- ================== END Data mining PART ================================= -->
+<!-- ================== END GMO PART ================================= -->
 <!-- ================== END TABS ========================== -->

Team:British Columbia/HumanPractices

From 2014.igem.org

Latest revision as of 03:59, 18 October 2014

Human Practices

Overview

Mount Polley

Figure 1: An ariel image of the Mount Polley effluent spilling into Quesnel Lake (12)

Legislation

Figure 2: Canadian Government Policies on Environment (2)

Figure 3: Authorized Limits of Deleterious Substances (10)

Figure 4: International Environmental Agreements since 1900 (11)

Figure 5: Total Mining Industry Expenditure on Environmental Protection (12)

Figure 6: Mining Industry Expenditure on Environmental Protection as Percentage of Total Business Sector (12)

The Industry

References

Overview

Historical Copper Price

Figure 1: Copper price for the past 25 year (1)

Current Global Mining Industry

Figure 2: Global Drilling Activity (2)

Figure 3: Significant Exploration-related Financings by Junior Companies, 2008-13 (3)

Copper Mining in Canada

Copper Extraction Vs Current Technological Limit

Figure 4: As and Cu Content in Concentrate (5)

Figure 5: As/Cu Ratio in Concentrate (5)

Figure 6: As Content in Cu Concentrate and Smelter’s As Capacity (5)

References

Overview

Current Technology

Developing technologies

Our technology and place in the mining industry

References

Overview

Scott Dunbar

Dr. John Smitt

Dr. Conor douglas

Paul Sauve

Figure 1: Participation in iGEM

Figure 2: Part Submission

Biosafety

Figure 1 - the division of two cell types - “swarmer” cell (top) and “stalk” cell (bottom) (2)

Industrial Setting

References