Team:Cornell/Practices
Policy and Practices Overview
fishPHARM first started as an iGEM summer project, but has quickly evolved into an innovative start-up company with the potential for immediate commencement of commercial operations and a sustained impact in global aquaculture. We have engaged in several entrepreneurial endeavors to facilitate the growth of fishPHARM as not only a project in synthetic biology, but also as a local business venture capable of addressing BCWD globally. We have also partnered with a variety of fish hatcheries and research institutions in the New York State Finger Lakes Region to help move our discoveries beyond the lab bench and meet the demands of a growing consumer market. Through collaborations with these hatcheries, which battle with bacterial coldwater disease on a daily basis, we were able to both better understand the safety implications of deploying our product in an aquacultural setting and compare the economic costs of our product to those of current solutions. fishPHARM is designed directly with the needs of your everyday fish farmer in mind. By collaborating with our consumers, we aim to develop a product that is not only safe and effective, but also practical for treating BCWD in the real world.
Hatchery Collaborations
We were inspired to start fishPHARM after seeing the devastating effects of BCWD in the local fish hatcheries of New York State. Fish hatcheries in the Finger Lakes region constantly deal with BCWD, and we sought to aid the local fish farmers in a more personal way through fishPHARM.
fishPHARM is unique because no iGEM team has ever shared a collaboration with fish hatcheries and fish research units. We have collaborated with Bath, NY Hatchery, Rome, NY Hatchery, and the Cornell Biological Field Station in order to take fishPHARM from the lab bench to real-world implementation. We have received a plethora of feedback from fish farmers that has driven us to redesign and improve upon fishPHARM in order to develop the most efficient mechanism to treat BCWD. Our collaborations are detailed below.
Background: Bath Fish Hatchery, established in 1893, uses fish obtained from Cayuga Lake to produce roughly 86,000 pounds of rainbow, brown and lake trout annually [1]. The hatchery has had a tumultuous history, including a 1955 fire that leveled the main production facility, but remains an essential component of the New York aquaculture industry. The work the hatchery does ensures that the New York State Finger Lakes are teeming with fish during the annual angling season.
Collaboration: Cornell iGEM first toured Bath Hatchery over the summer, during which we were able to gain a behind the scenes look at how fish are bred and treated. Bob Sweet, a long-time employee at Bath Hatchery, spoke to us about how he had once seen BCWD kill up to 1000 fish/day at the hatchery. Sweet also brought to our attention the lack of real-time fish tank monitoring systems at Bath Hatchery that could be used to prevent diseases like BCWD. This inspired the team to develop Heimdall such that fishPHARM could not only treat BCWD, but prevent it as well.
Kenneth Osika, a Fish Culturist at Bath Fish Hatchery received our prototype and gave us feedback related to the application of the device. His responded that, “This applicator was too large for [his current] fish this size [5 inches long].You might have more luck with a smaller applicator that will produce only a small puncture wound.” After receiving his feedback, dry lab is working on reducing the diameter of the applicator, which can be done by having the applicator fit more snugly around the tag and using less metal overall to produce a narrower applicator.
Rome, New York State Hatchery
Background: The Rome Hatchery, located in the eponymous town in New York, has served the region for more than 75 years [2]. The hatchery is one of the state’s largest, with total production of brook and brown trout in excess of 160,000 pounds [1]. The hatchery provides fish to over 350 bodies of water, all of which are open to the public for recreational fishing.
Collaboration: We have also been in contact with Rome Hatchery, which houses a fish pathology lab that researches fish diseases such as BCWD. Andy Noyes, a fish pathologist at Rome Hatchery, spoke extensively with us about the devastating effects of BCWD on-site. He mentioned that the disease alone affects roughly 10-20% of fish at 8 out of 10 fish hatcheries in the area. We were able to better understand the process that fish farmers take to treat their fish through our conversations with Andy. Once our prototype was ready, we sent our device to Rome Hatchery for implementation, to gather feedback, and to improve upon the design of fishBIT.
Noyes was very supportive of the fishPHARM system and believed that the application of the fishBit to a few hundred adult fish could benefit several hundred thousand offspring.
“These [fishBIT] would be ideal for broodstock, where numbers of fish handled are only in the tens or hundreds. And brood should be the target group for something like this because 90% of our infections stem from vertical transmission (mom passes to the egg) … we [fish farmers] may all be using something like this someday.” After his feedback, we were inspired to redesign the prototype with a smaller fish tag for specific use with broodstock.
Cornell Biological Field Station
Background: The Cornell Biological Field Station in Bridgeport, New York is an extension of Cornell University that participates in a government-funded effort to better understand fisheries and aquaculture, with a focus on Oneida Lake and other bodies of freshwater in the state of New York. The station was developed to analyze aquatic population dynamics in Oneida Lake as well as to conduct biological research in many of the surrounding natural aquatic ecosystems and fisheries in upstate New York [3].
Collaboration: Thomas E. Brooking, an aquatic animal employee at the Cornell Biological Field Station, was able to try out our prototype and has given us more insight on the effectiveness of fishBIT. He found the fish tag component to be fairly flexible and prone to yieldig under stress when it came to tagging fish with tougher skin. He believed that the “the barb needed some reinforcement to be less brittle.” We took this feedback into account by modifying our prototype design to be more durable.
Economic Analysis
Oxytetracycline (branded as Terramycin) costs roughly $0.70/gram. Since the total amount of antibiotic required for a 10-day treatment is 25 g/100 lbs, treatment of a fish stock with Terramycin costs about $0.025 per dollar of fish [4]. However, Terramycin is already becoming obsolete as a treatment protocol due to the rapid formation of resistant strains [5]. While the antibiotic may appear cost effective, it cannot be relied upon as a long-term solution due to the rise of antibiotic resistance. Bacterial tolerance of chemotherapeutic agents could obligate fish farmers to use more potent antibiotics, which could have undesirable side effects on their stock. Furthermore, the evolutionary capability of Flavobacterium to overcome antibiotics suggests that reliance on such agents in the future is a questionable proposition.
Our tag consists of three core components: an on/off clamp, medical-grade tubing and 3-D printing material. Given that the clamps are $.23 each, the requisite tubing is $.21 a tag and the printing material is $1.40/tag, the total material cost per tag is $1.83 [6]. This translates to about $.13 per dollar of fish. While this may seem like a nontrivial amount, fishPHARM guarantees users a peace of mind that Terramycin simply cannot match. fishPHARM’S EcnB peptide is biodegradable as well as, and thus does not pose the same environmental and health risks that antibiotics do.
It is clear that the negative consequences of Flavobacterium psychrophilum infection are acute. As reported by the New York Department of Environmental Conservation, an epizootic of BCWD once infected 25% of lake trout raised in New York State hatchery raceways [7]. Given the inedibility of infected salmonids, the organism has the potential to reduce the financial yield of a salmon population from $7/lb to $4.90/lb in this scenario. Since roughly 2.4 million tons of salmon are produced by aquaculturists each year, even a small incidence of BCWD would have dire economic ramifications.
Environmental Impact
EcnB is naturally found in the human gut genome and thus not a hazard to human health. The benign nature of the treatment protocol we have devised provides distinct advantages over oxytetracycline, an antibiotic used to treat BCWD, because abuse of such chemotherapeutic agents fosters resistance among targeted pathogens [8]. In fact, a study conducted between 1994 and 1998 among Danish trout farms recorded an oxytetracycline resistance rate of between 60 and 75 percent of Flavobacterium colonies sampled [9].
Furthermore, fishPHARM has the potential to be a more reliable, enduring solution, as it would be more difficult for Flavobacterium psychrophilum to develop any evolutionary countermeasures to such a system. It should be further noted that agents such as amoxicillin have uses in medicine, and that encouraging the development of strains resistant to such drugs could have deleterious consequences for human health.
Comprehensive Risk Assessment
Overview
It is tempting as scientists to think that we can treat risk assessment as we would treat any other scientific protocol - that with a few key steps and critical considerations, we will always end up with the right answer. However, assessing risk, particularly for environmental projects, is not that simple. Thinking about potential impacts and risks often turns up more questions than answers, and it is difficult to know where to start. For this reason, we have employed three approaches to risk assessment. The first was developed by Cornell’s Environmental Health and Safety Department, pertaining specifically to work with recombinant organisms. The next was developed by the Environmental Protection Agency as a general environmental risk assessment and modified by both the Woodrow Wilson Center and our team for use on our synthetic biology project. Finally, we strived to embody the design principles set forth by the Presidential Commission for the Study of Bioethical Issues. Each approach has its limitations, but all of them have helped to inform our project design, research practices, and considerations for further development of our project.
Environmental Health and Safety (EHS)
Cornell’s Environmental Health and Safety Department lays the groundwork for determining safe research practices on campus, and greatly informed our own safety protocols. They specifically suggested the following risk assessment criteria for researchers working with recombinant organisms.
- Formation – The creation of a genetically-altered micro-organism through deliberate or accidental means. For our purposes, our modified organism was altered intentionally, thus we know all of the donor organisms and the recipient organism are not hazardous.
- Release – The deliberate release or accidental escape of some of these microorganisms in the workplace and/or into the environment. Our product consists of naturally found peptides and not the genetically modified organism itself that essentially stays in the laboratory setting so the the surrounding environment will not have to deal with any release of microorganisms.
- Proliferation/Competition/Establishment – The subsequent multiplication, genetic reconstruction, growth, transport, modification and die-off of these micro-organisms in the environment, including possible transfer of genetic material to other micro-organisms. The inclusion of the ecnB gene in our organism severely impedes growth, so even if our organism was to escape the lab into the environment, it couldn’t survive. Also, the ecnB gene has to be expressed so the organism wouldn’t be any different in that sense from other strains naturally found.
- Effect – The subsequent occurrence of human or ecological effects due to interaction of the organism with some host or environmental factor. Ideally, our cells would not have an effect on the environment or any other host as they are constrained to the laboratory setting. However, if there were to be a leak somewhere in the lab, the largest concern would be if another organism were to somehow take up DNA lost from our cells. This would require a naturally competent bacterial strain to come across a leak that yields an intact plasmid, and the plasmid would have to be able to replicate. In all likelihood, in the absence of selective pressure, the plasmid would actually be deleterious to the cell due to toxicity of the EcnB peptide.[10]
Comprehensive Environmental Assessment
The EPA’s Comprehensive Environmental Assessment (CEA) is a tool to allow scientists to broaden their perspectives by incorporating the experiences, expertise, and concerns of diverse stakeholders. CEA differs from traditional methods of risk assessment by recognizing that risk assessment is fundamentally a decision-making process in which scientists, experts, and the public should be engaged in transparent dialogue. The goal is to evaluate limitations and tradeoffs to arrive at holistic conclusions about the primary issues that researchers should be addressing in their research planning.
The Woodrow Wilson International Center for Scholars in Washington, D.C., recently launched efforts to lay out a framework to apply CEA to synthetic biology. This groundbreaking project set out to assess the CEA approach’s relevance to synthetic biology, in anticipation of the growing demand for synthetic biology-based solutions to global issues. They arrived at the conclusion that scientists should focus on some major areas of risk assessment: altered physiology, competition and biodiversity, evolutionary prediction/gene transfer. In the past, using this framework has helped to uncover its limitations and the ways in which we could improve our own approach to environmental risk assessment. [11,12,13]
Altered Physiology: We synthesized new proteins that are originally found in E. coli, but we induced them at a higher rate. The proteins are involved with osmoregulation, so the toxins would cause E. coli to lyse itself if the regulation somehow goes out of control. Thus, we found that the growth rate of our engineered cells was severely impaired due to the toxicity of EcnB.
Competition and Biodiversity: Since our cells never leave the laboratory environment and only the EcnB peptides enter the fish, the issue of competition is not as relevant as it would be for other projects. Our engineered plasmids cause our cells to be not as able to compete in the natural environment as the cells would grow too slowly and other bacteria would outcompete them. These new cells would not have time and resources to form their own niche.
Evolutionary Prediction/Gene Transfer: There is not likely to be a consequence when it comes to evolutionary prediction as there would be low evolutionary pressure for the bacteria to keep the plasmid in absence of the antibiotics. Furthermore, the cells with the engineered plasmids would be retained in the laboratory setting. Moreover, if EcnB gets more aggressive as a toxin, it would just lyse the cells before the culture has the chance to proliferate. The issue of gene transfer is not relevant and not likely since we are limited to and working in the laboratory setting when handling bacterial cells.
Bioethics:
We designed our project in accordance with the ethical principles identified by the Presidential Commission for the Study of Bioethical Issues (2010). Our primary motive is to better stabilize our source of food by fighting a disease that is often harmful economically to communities and physically detrimental to many species of fish and the animals that rely on these fish as much as we do. We have also demonstrated responsible stewardship by considering the environmental implications of our project. The ecological impact of placing our genetically modified strain in water would be minimal because our filtration system will not allow bacteria to escape, and we have structured our future directions around risk management for the future. In addition, our project is an intellectually responsible pursuit: it cannot foreseeably be used to cause people harm. In the spirit of democratic deliberation, we launched our Humans & SynBio campaign, to get people thinking and talking about the ethics of synthetic biology. Our proposed system would be easy, cost-effective, and potentially usable on a global scale. Additionally, the modularity of our platform allows it to be adapted to the needs of different communities, in order to best serve global populations and environments.[14]
Limitations and Future Directions:
We have learned from our studies that there needs to be more education about synthetic biology, as many people are not fully aware of this field. In addition, it would be helpful to have a comparison of opinions before and after we discuss what synthetic biology is. In order to make our human practices assessments more effective, we would need to have a broader sample size of people taking surveys and answering our questions. Because we live on a fairly liberal university campus with a constituency that socioeconomically slants towards the upper-middle class, our answers may be biased. However, if we were to interview a much larger and diverse sample size, our survey results would be more informative.
Risk assessment can constantly be improved upon. It would be interesting to know what versions of our project, within our portfolio of future ideas and applications, would be the most widely used and accepted. Could we use other materials/gels to make our FishBit more biodegradable? Would other industries be interested in using this tag system to treat other animals that face other diseases?
References
[1] Fish Hatcheries A Look at DEC Fish Hatcheries. (2015). Retrieved August 15, 2015.
[2] Getchonis, J., & Mills, E. (2007). The History of the Cornell University Biological Field Station. Retrieved August 1, 2015.
[3] Faisal, M., Schulz, C., Loch, T., Kim, R., Hnath, J., & Whelan, G. (2013). Current Status of Fish Health and Disease Issues in the Laurentian Great Lakes: 2005-2010. Great Lakes Fishery Policy and Management: A Binational Perspective, 2nd Edition, 259-302. Retrieved August 1, 2015, from aquaticanimalhealth.msu.edu/CurrentStatusofFishHealthandDiseaseIssuesintheLaurentianGreatLakes2005-2010.pdf
[4] Wegmans. (2015, September 1). Retrieved September 1, 2015.
[5] Barnes, M., & Brown, M. (2011). A Review of Flavobacterium Psychrophilum Biology, Clinical Signs, and Bacterial Cold Water Disease Prevention and Treatment. The Open Fish Science Journal, 4, 40-48.
[6] Schache, J. (1983). Coldwater Disease. A Guide to Integrated Fish Healthcare Management in the Great Lakes Basin, 83(2), 193-197.
[7] Global aquaculture production of salmonid species in tonnes 1950-2010 as reported by FAO. (2012, April 1). Retrieved September 22, 2015.
[8] Kerry, J., Hiney, M., Coyne, R., NicGabhainn, S., Gilroy, D., Cazabon, D., & Smith, P. (1999). Fish feed as a source of oxytetracycline-resistant bacteria in the sediments under fish farms. Aquaculture, 131(1-2), 101-113.
[9] Barnes, M., & Brown, M. (2011). A Review of Flavobacterium Psychrophilum Biology, Clinical Signs, and Bacterial Cold Water Disease Prevention and Treatment. The Open Fish Science Journal, 4, 40-48.
[10] Cornell Environmental Health and Safety. (2014). Biological Safety Levels 1 and 2 Written Program. Available from https://securepublish.ehs.cornell.edu:8499/LabSafety/biological-safety/biosafety-manuals/Biological_Safety_Levels_1_and_2_Manual.pdf
[11] Dana, G. V., Kuiken, T., Rejeski, D., & Snow, A. A. (2012). Synthetic biology: Four steps to avoid a synthetic-biology disaster. Nature, 483. doi:10.1038/483029a
[12] Presidential Commission for the Study of Bioethical Issues. (2010). New directions: The ethics of synthetic biology and emerging technologies. Washington, D.C.: PreDana, G. V., Kuiken, T., Rejeski, D., & Snow, A. A. (2012).
[13] Synthetic Biology Project. (2011, July 28). Comprehensive Environmental Assessment and Its Application to Synthetic Biology Applications. Retrieved from http://www.synbioproject.org/events/archive/cea/
[14] Synthetic biology: Four steps to avoid a synthetic-biology disaster. Nature, 483. doi:10.1038/483029asidential Commission for the Study of Bioethical Issues.
