Team:Cornell/notebook
Notebook
Week 1 (June 7 - June 13)
Wetlab
EcnB part extracted from A(ABEF) synthesized plasmids and purified. It was then ligated with H backbone (pSB1C3) and transformed. Had some issues growing cultures with ligations. We are excited to start cloning!
EcnB part extracted from A(ABEF) synthesized plasmids and purified. It was then ligated with H backbone (pSB1C3) and transformed. Had some issues growing cultures with ligations. We are excited to start cloning!
Drylab
Dry lab discussed and finalized a design as well as the dimensions for the fish tag. Parts were designed through SolidWorks in member’s own time.
Dry lab discussed and finalized a design as well as the dimensions for the fish tag. Parts were designed through SolidWorks in member’s own time.
Policy and Practices
We began searching for fish farm contacts, and started our YOURS mentorship program. We introduced our mentors to the kids and taught them about DNA and its importance.
We began searching for fish farm contacts, and started our YOURS mentorship program. We introduced our mentors to the kids and taught them about DNA and its importance.
Week 2 (June 14 - June 20)
Wetlab
Week one steps were redone. Started gel purifications instead of column purifications, so plasmids were re-cultured (pre-ligation). We had some issues with low DNA concentrations after gel purifications, so we increased amount of DNA used in digestions.
Flavo Subteam
The flavo subteam made cultures of two strains of Flavobacterium, and measured growth of bacteria with spectrophotometer. In addition, daily OD readings were taken to determine growth rate.
Week one steps were redone. Started gel purifications instead of column purifications, so plasmids were re-cultured (pre-ligation). We had some issues with low DNA concentrations after gel purifications, so we increased amount of DNA used in digestions.
Flavo Subteam
The flavo subteam made cultures of two strains of Flavobacterium, and measured growth of bacteria with spectrophotometer. In addition, daily OD readings were taken to determine growth rate.
Drylab
Dry lab continued with the CAD design of the fish tag. We also did research on a list of potentially compatible materials for the fish tag, including tubing, clamps, and syringes.
Dry lab continued with the CAD design of the fish tag. We also did research on a list of potentially compatible materials for the fish tag, including tubing, clamps, and syringes.
Policy and Practices
The YOURS kids got a tour of our lab and we taught them more about how DNA works in our body as the determining factor of our genetic characteristics. They were able to place their fingers on plates to “plate bacteria” and we showed them how to incubate the plates to help the bacteria grow. We helped them carry out an experiment that extracted DNA from strawberries and we showed them proper pipetting techniques. We also did a fun experiment with the kids with basic cooking ingredients to make a “volcano explode” to introduce chemical reactions.
We narrowed our search to a few fish hatcheries in the upstate New York region and began contacting them.
The YOURS kids got a tour of our lab and we taught them more about how DNA works in our body as the determining factor of our genetic characteristics. They were able to place their fingers on plates to “plate bacteria” and we showed them how to incubate the plates to help the bacteria grow. We helped them carry out an experiment that extracted DNA from strawberries and we showed them proper pipetting techniques. We also did a fun experiment with the kids with basic cooking ingredients to make a “volcano explode” to introduce chemical reactions.
We narrowed our search to a few fish hatcheries in the upstate New York region and began contacting them.
Week 3 (June 21 - June 27)
Wetlab
Internal (PstI) cut sites also found in AA & AE (switched to cutting the backbones and inserts with EcoRI and SpeI). AA+H (ZA) construct and AA+B (ZB) construct were sent for sequencing to verify the contents of the construct. The two primers added resulted in overlap, and sequencing was redone with one primer.
Flavo Subteam
Flavobacterium were re-plated, but they showed no growth after three days. Their growth is necessary to conduct ZOI (zone of inhibition) testing.
Internal (PstI) cut sites also found in AA & AE (switched to cutting the backbones and inserts with EcoRI and SpeI). AA+H (ZA) construct and AA+B (ZB) construct were sent for sequencing to verify the contents of the construct. The two primers added resulted in overlap, and sequencing was redone with one primer.
Flavo Subteam
Flavobacterium were re-plated, but they showed no growth after three days. Their growth is necessary to conduct ZOI (zone of inhibition) testing.
Drylab
We came up with and finalized the design of an applicator for the fish tag that improves upon the existing design. Parts were assembled through SolidWorks, and we planned to use the machine shop to build a metallic applicator.
We came up with and finalized the design of an applicator for the fish tag that improves upon the existing design. Parts were assembled through SolidWorks, and we planned to use the machine shop to build a metallic applicator.
Policy and Practices
We continued the topic of DNA in bacteria with the YOURS kids by talking about antibiotic resistance and how we only want certain genes in our own experiments. The kids learned how to pipet and load something into a gel and watched as we showed them how we run gel electrophoresis experiments everyday.
We continued the topic of DNA in bacteria with the YOURS kids by talking about antibiotic resistance and how we only want certain genes in our own experiments. The kids learned how to pipet and load something into a gel and watched as we showed them how we run gel electrophoresis experiments everyday.
Week 4 (June 28 - July 4)
Wetlab
Had some issues growing cultures on plates. Most constructs had issues being cultured post-ligation and transformation.
Flavo Subteam
Flavobacterium was re-plated, but there was still no growth.
Had some issues growing cultures on plates. Most constructs had issues being cultured post-ligation and transformation.
Flavo Subteam
Flavobacterium was re-plated, but there was still no growth.
Drylab
Dry lab continued with the design of the applicator.
Dry lab continued with the design of the applicator.
Week 5 (July 5 - July 11)
Wetlab
We had to re-culture several plasmids (pre-ligation). We also received and made glycerol stocks of five new plasmids.
Flavo Subteam
Flavobacterium growth was tested on different types of plates to see if our plates were the issue causing lack of growth.
We had to re-culture several plasmids (pre-ligation). We also received and made glycerol stocks of five new plasmids.
Flavo Subteam
Flavobacterium growth was tested on different types of plates to see if our plates were the issue causing lack of growth.
Drylab
To market the product, the tag needs an appealing name. We brainstormed many potential ideas that may be useful in constructing a name. In addition, we researched specific tubing, clamps and other materials that we intend to utilize for the fish tag
To market the product, the tag needs an appealing name. We brainstormed many potential ideas that may be useful in constructing a name. In addition, we researched specific tubing, clamps and other materials that we intend to utilize for the fish tag
Policy and Practices
We moved on to the topic of proteins to start to relate what we were introducing to YOURS kids with our own project so they would understand the relevance of our research. After discussing the basic properties of proteins, we helped them carry out an experiment that separated proteins from different dairy products. The visual results helped them better understand how chemical reactions can change molecular structures.
We contacted Bath hatchery and set up a meeting time in July so that we could drive there and talk to representatives in person and our project in perspective of current solutions.
We moved on to the topic of proteins to start to relate what we were introducing to YOURS kids with our own project so they would understand the relevance of our research. After discussing the basic properties of proteins, we helped them carry out an experiment that separated proteins from different dairy products. The visual results helped them better understand how chemical reactions can change molecular structures.
We contacted Bath hatchery and set up a meeting time in July so that we could drive there and talk to representatives in person and our project in perspective of current solutions.
Week 6 (July 12 - July 18)
Wetlab
We cultured, ligated, and plated some of the new plasmids (A(LMNJKR) +H). We still had issues getting older plasmids past transformation stage.
Flavo Subteam
We determined that our plates (for the Flavobacterium) were the issue. We re-plated Flavobacterium on new plates(both strains).
We cultured, ligated, and plated some of the new plasmids (A(LMNJKR) +H). We still had issues getting older plasmids past transformation stage.
Flavo Subteam
We determined that our plates (for the Flavobacterium) were the issue. We re-plated Flavobacterium on new plates(both strains).
Drylab
Dry lab came up with the design of a box that can be used to market our products. We listed materials, dimensions, and designs that would make up our fish tag kit. For each kit, we intended to include 20 tags, one applicator, one gel vial, syringe and needle, along with an information booklet. Using oak tag, we started a physical copy of the box.
Dry lab came up with the design of a box that can be used to market our products. We listed materials, dimensions, and designs that would make up our fish tag kit. For each kit, we intended to include 20 tags, one applicator, one gel vial, syringe and needle, along with an information booklet. Using oak tag, we started a physical copy of the box.
Policy and Practices
Finally, we came a full circle and explained to the kids how bacteria can be potentially dangerous and helpful at the same time and how we can engineer their plasmids in ways to benefit other organisms. They learned about the ubiquitous nature of bacteria when they used cotton swabs to gather different bacterial samples from different areas in the building and let the samples grow overnight. Finally, we explained our own project’s goals and how we would be going to a hatchery the next week to see how farmers have to handle bacterial diseases that affect fish.
Finally, we came a full circle and explained to the kids how bacteria can be potentially dangerous and helpful at the same time and how we can engineer their plasmids in ways to benefit other organisms. They learned about the ubiquitous nature of bacteria when they used cotton swabs to gather different bacterial samples from different areas in the building and let the samples grow overnight. Finally, we explained our own project’s goals and how we would be going to a hatchery the next week to see how farmers have to handle bacterial diseases that affect fish.
Week 7 (July 19 - July 25)
Wetlab
ZE construct was sequenced and stored as glycerol stock along ZK, ZO, ZA, and ZB. The glycerol stocks are for later use in ZOI testing.
Flavo Subteam
Flavobacterium plates displayed lawn growth that will be used for ZOI tests.
ZE construct was sequenced and stored as glycerol stock along ZK, ZO, ZA, and ZB. The glycerol stocks are for later use in ZOI testing.
Flavo Subteam
Flavobacterium plates displayed lawn growth that will be used for ZOI tests.
Drylab
Dry lab continued with construction of the box. In addition, fish tags were being printed using high resolution 3D printers.
Dry lab continued with construction of the box. In addition, fish tags were being printed using high resolution 3D printers.
Policy and Practices
We took the YOURS kids to the Bathe hatchery. We spoke to Bob Sweet who explained how they keep an eye on various conditions in the fish's environment through the use of chemicals. He talked to us about the fish they raise, the types of diseases the fish face such as ferunculosis, and the overall day-to-day things the hatchery has to worry about like maintenance. The YOURS students also learned about how the fish are raised and transported in detail and were allowed to feed the fish. We learned that the hatchery has chosen not to use fish tags and instead clips fish fins to keep track. Sweet’s opinion of the future for the fish/agriculture industry was that the environment would put greater stresses on wild fish and therefore depending on farm-raised fish would be beneficial in supplying the demand for more food in a world with a rising population. We were also directed to speak to Andy Norse at Rome Hatchery who was more aware of chemicals used to treat water to prevent diseases, and we followed up with a call on Monday to plan a Skype meeting with Andy.
On Saturday, Grace and Saie went to the local Ithaca’s Farmer’s Market to find locals with opinions about GMOs and fish farming for our Humans and SynBio Facebook page.
We took the YOURS kids to the Bathe hatchery. We spoke to Bob Sweet who explained how they keep an eye on various conditions in the fish's environment through the use of chemicals. He talked to us about the fish they raise, the types of diseases the fish face such as ferunculosis, and the overall day-to-day things the hatchery has to worry about like maintenance. The YOURS students also learned about how the fish are raised and transported in detail and were allowed to feed the fish. We learned that the hatchery has chosen not to use fish tags and instead clips fish fins to keep track. Sweet’s opinion of the future for the fish/agriculture industry was that the environment would put greater stresses on wild fish and therefore depending on farm-raised fish would be beneficial in supplying the demand for more food in a world with a rising population. We were also directed to speak to Andy Norse at Rome Hatchery who was more aware of chemicals used to treat water to prevent diseases, and we followed up with a call on Monday to plan a Skype meeting with Andy.
On Saturday, Grace and Saie went to the local Ithaca’s Farmer’s Market to find locals with opinions about GMOs and fish farming for our Humans and SynBio Facebook page.
Week 8 (July 26 - August 1)
Wetlab
ZG construct was sequenced and stored as glycerol stock. Started using Phusion PCR on all constructs that had not been biobricked (for increased yield).
Flavo Subteam
Attempted to sonicate ZA and ZB cultures, but they were only partially lysed. We also tried ZOI test on Flavobacterium plates (of both strains), with ZA, ZB, and Chloramphenicol and dH2O as controls.
ZG construct was sequenced and stored as glycerol stock. Started using Phusion PCR on all constructs that had not been biobricked (for increased yield).
Flavo Subteam
Attempted to sonicate ZA and ZB cultures, but they were only partially lysed. We also tried ZOI test on Flavobacterium plates (of both strains), with ZA, ZB, and Chloramphenicol and dH2O as controls.
Drylab
Dry lab outlined a comprehensive timeline for constructing business plan, fish tag testing, app design, and marketing. A feasibility analysis was conducted to assess the likelihood of fishPHARM in becoming a new startup. The app was intended to serve a preventative purpose.
In addition, we began researching sensors that could potentially complement the app.
Dry lab outlined a comprehensive timeline for constructing business plan, fish tag testing, app design, and marketing. A feasibility analysis was conducted to assess the likelihood of fishPHARM in becoming a new startup. The app was intended to serve a preventative purpose.
In addition, we began researching sensors that could potentially complement the app.
Week 9 (August 2 - August 8)
Wetlab
We successfully sequenced and glycerol stocked ZR, ZL, and ZJ constructs. There were some weird results on gels of other constructs, possibly due to mutations in the backbone (H). We also started cloning MBP with Z constructs to stabilize the Ecn-B peptides since they were likely being degraded in the cell.
Flavo Subteam
Chloramphenicol ZOI control didn’t work. We attempted ZOI test with ampicillin instead for positive control data.
We successfully sequenced and glycerol stocked ZR, ZL, and ZJ constructs. There were some weird results on gels of other constructs, possibly due to mutations in the backbone (H). We also started cloning MBP with Z constructs to stabilize the Ecn-B peptides since they were likely being degraded in the cell.
Flavo Subteam
Chloramphenicol ZOI control didn’t work. We attempted ZOI test with ampicillin instead for positive control data.
Drylab
Meeting addressed fundamental parts of a business plan. Members conducted research into various aspects of the aquaculture industry, consumer behavior, and finances in order to construct a comprehensive business plan.
Meeting addressed fundamental parts of a business plan. Members conducted research into various aspects of the aquaculture industry, consumer behavior, and finances in order to construct a comprehensive business plan.
Policy and Practices
iGem members Sachi and Saie presented at the The Summer Institute for Life Sciences (SILS) symposium. SILS is a program of the Office of Undergraduate Biology (OUB) at Cornell that invited undergraduates to present their summer research activities. These iGem members were able to talk about our research this summer with fishPharm.
iGem members Sachi and Saie presented at the The Summer Institute for Life Sciences (SILS) symposium. SILS is a program of the Office of Undergraduate Biology (OUB) at Cornell that invited undergraduates to present their summer research activities. These iGem members were able to talk about our research this summer with fishPharm.
Week 10 (August 9 - August 15)
Wetlab
At this stage, Z(A,B,E,G,J,K,L,O,R) constructs have been biobricked. Continued using Phusion PCR for MBP + Z constructs. There were some smearing issues with MBP on gels (for ligation).
Flavo Subteam
We began to use terramycin for ZOI control testing since other antibiotics did not have visible results.
At this stage, Z(A,B,E,G,J,K,L,O,R) constructs have been biobricked. Continued using Phusion PCR for MBP + Z constructs. There were some smearing issues with MBP on gels (for ligation).
Flavo Subteam
We began to use terramycin for ZOI control testing since other antibiotics did not have visible results.
Drylab
Members designed potential business cards along with labels for the flavocide gel vials. The app development process is moving along smoothly.
Members designed potential business cards along with labels for the flavocide gel vials. The app development process is moving along smoothly.
Week 11 (August 16 - August 22)
Wetlab
We attempted Gibson Assembly with MBP-TEV insert and H (pSB1C3) backbone as an alternative cloning mechanism. The longer sequence will increase EcnB peptide stability.
We also received synthesized plasmids from DNA 2.0 with all EcnB inserts from biobricked Z constructs and MBP-TEV (not in pSB1C3).
We attempted Gibson Assembly with MBP-TEV insert and H (pSB1C3) backbone as an alternative cloning mechanism. The longer sequence will increase EcnB peptide stability.
We also received synthesized plasmids from DNA 2.0 with all EcnB inserts from biobricked Z constructs and MBP-TEV (not in pSB1C3).
Drylab
Dry lab continued with the design of labels and business cards. App development is proceeding without hurdles. The business plan was finalized.
Dry lab continued with the design of labels and business cards. App development is proceeding without hurdles. The business plan was finalized.
Week 12 (August 23 - August 29)
Wetlab
We had issues with growing cultures for Gibson plates. This was likely due to poor selection on antibiotic plates, possibly due to antibiotic degradation. We removed inserts from synthesized plasmids and started cloning procedures into pSB1C3.
We had issues with growing cultures for Gibson plates. This was likely due to poor selection on antibiotic plates, possibly due to antibiotic degradation. We removed inserts from synthesized plasmids and started cloning procedures into pSB1C3.
Drylab
A enlarged fishBIT tag model was 3D printed for display purposes. Sensor design for the app was started. We began looking into various tests that could be done to test the durability of our tag, including but not limited to tensile testing and wind tunnel testing.
A enlarged fishBIT tag model was 3D printed for display purposes. Sensor design for the app was started. We began looking into various tests that could be done to test the durability of our tag, including but not limited to tensile testing and wind tunnel testing.
Week 13 (August 30 - September 5)
Wetlab
We encountered issues with getting past ligation stage with synthesized plasmid inserts and H backbone.
To confirm EcnB expression, several SDS-PAGEs were done on constructs without stabilizing proteins to use for Western blots (to see their expression) and later ZOI assays.
We encountered issues with getting past ligation stage with synthesized plasmid inserts and H backbone.
To confirm EcnB expression, several SDS-PAGEs were done on constructs without stabilizing proteins to use for Western blots (to see their expression) and later ZOI assays.
Drylab
Business plan was reviewed by a professor with expertise in the area. Additional tags were printed, and samples were sent to prospective customers for feedback.
Business plan was reviewed by a professor with expertise in the area. Additional tags were printed, and samples were sent to prospective customers for feedback.
Policy and Practices
We sent our prototype of the fishBit to Rome Fish Hatchery and the Cornell Biological Field Station for feedback. We hope to use any advice and critiques to update our fishBit to fit the industry’s needs in the best way possible.
We sent our prototype of the fishBit to Rome Fish Hatchery and the Cornell Biological Field Station for feedback. We hope to use any advice and critiques to update our fishBit to fit the industry’s needs in the best way possible.
Week 14 (September 6 - September 12)
Wetlab
A Gibson construct (MJ) was successfully sequenced. Western blots showed possible expression of ZG and ZR, but not ZJ, though we didn’t have a positive control because it did not survive past the lag phase.
Switched focus to getting expression from all biobricked Z constructs and MJ to use in ZOI assays.
A second set of constructs (ZG, MJ, ZQ, ZT) were set up for western blots.
A Gibson construct (MJ) was successfully sequenced. Western blots showed possible expression of ZG and ZR, but not ZJ, though we didn’t have a positive control because it did not survive past the lag phase.
Switched focus to getting expression from all biobricked Z constructs and MJ to use in ZOI assays.
A second set of constructs (ZG, MJ, ZQ, ZT) were set up for western blots.
Drylab
Dry lab finalized plans for testing fishBIT. App design and sensor designs continue smoothly.
Dry lab finalized plans for testing fishBIT. App design and sensor designs continue smoothly.
Policy and Practices
iGem members Grace, Casey, and Rishabh attended the Sciencenter Building with Biology event where they helped enthusiastic science-lovers on a Saturday morning learn how to spread plates, demonstrated the possibilities of 3D printing, and simulated rearranging genes with legos.
iGem members Grace, Casey, and Rishabh attended the Sciencenter Building with Biology event where they helped enthusiastic science-lovers on a Saturday morning learn how to spread plates, demonstrated the possibilities of 3D printing, and simulated rearranging genes with legos.
Week 15 (September 13 - September 19)
Wetlab
The second set of western blot revealed expression of ZG, MJ, and ZT. ZG was taken to be the positive control based on previous western blot. A series of ZOI disk diffusion assays were set up at the Cornell Vet School to test the efficacy of our BioBrick constructs.
The second set of western blot revealed expression of ZG, MJ, and ZT. ZG was taken to be the positive control based on previous western blot. A series of ZOI disk diffusion assays were set up at the Cornell Vet School to test the efficacy of our BioBrick constructs.
Drylab
Dry lab tested the durability of fishBIT using agar gel samples and dead fish samples. In a hydraulics lab, fishBIT was tested for its resistance to current turbulence.
Dry lab tested the durability of fishBIT using agar gel samples and dead fish samples. In a hydraulics lab, fishBIT was tested for its resistance to current turbulence.
Policy and Practices
We sent our prototype of the fishBit to Bath Fish Hatchery. That same week, both hatcheries and the field station were able to give us valuable critiques including their opinion on the size of our product, the ease of application, and even encouraged us to continue with what they believed to be a valuable contribution to improvement of the fish industry.
We sent our prototype of the fishBit to Bath Fish Hatchery. That same week, both hatcheries and the field station were able to give us valuable critiques including their opinion on the size of our product, the ease of application, and even encouraged us to continue with what they believed to be a valuable contribution to improvement of the fish industry.
