11 weeks. 77 days. 1,848 hours. 110,880 minutes. 6,652,800 seconds. While not all spent in lab, these numbers represent the time of a summer spent learning, exploring, and discovering. At the conclusion of this week, the team’s full-time work in Bindley Bioscience Center will conclude as class begins after a brief respite. While there is still much to do, much has already been done. Now, the team is looking forward to the school year’s accomplishments as time continues ticking toward the Giant Jamboree in Boston at the end of October! A heartfelt thank-you to everyone who has supported this endeavor; it would not have been successful without you.

Summary of Lab Work

1. Development of theoretical genetic constructs for both phosphorus uptake and organic nanowire components of the project.

2. PCR amplification, digestion, ligation, gel electrophoresis, and transformation of individual M. phosphovorus genes into E. coli. Currently testing for functional characterization and protein expression.

3. In collaboration with the USDA National Soil Erosion Research Laboratory, construction of a prototype bioreactor from 5-gallon buckets, tubing, water filters, and an aquarium pump with complementary MATLAB model and silica beads for bioencapsulation.

4. Participation in InterLab study to standardize fluorescence units.

5. Collaboration discussions and activities with Exeter, Northwestern, UNL, UChicago, SVCE, and Rose-Hulman iGEM teams.

6. Human practices and outreach including fully-funded Experiment campaign, award of SYNENERGENE grant, a booth at the Wabash River Fest, media coverage, and a survey assessing knowledge of wastewater treatment practices that you can explore here if you haven’t already.

lab bench

Image courtesy of


Monday, July 25

Preliminary trials of testing for phosphorus using the lachat and the ICP-OES at the USDA National Soil Erosion Research Laboratory began. Both machines operate via spectrophotometry, comparing measured values to standard curves. The lachat measures orthophosphate, or soluble reactive phosphorus, while the ICP measures total phosphorus, the entirety of phosphorus contained in a sample. Corresponding with this endeavor, many bottles of Tris-HCl buffer, the media in which phosphorus-eating E. coli will be suspended, were created and autoclaved for future use.

Tuesday, July 26

The week continued by learning to make methanol-free bioencapsulation beads using the sol-gel method. A graduate student in the lab worked with team members to describe and demonstrate the protocol. After practice forming the beads, the team switched to a different method that could be more easily controlled and manipulated. E. coli were added to the beads to determine whether or not they would be able to survive within the structure.

Fluorescent Beads 1

Above: Shots of silica beads containing E. coli expressing green fluorescent protein, GFP, (left) and red fluorescent protein, RFP, (right) imaged under EVOS fluorescence microscope; the circled areas on the left indicate particularly bright spots where it can be reasonably inferred that a clump of E. coli is successfully producing GFP

Silica Beads 2

Above: Additional images of silica beads with E. coli expressing RFP (left) and GFP (right); the brightly-glowing RFP beads indicate RFP expression

Wednesday, July 27

Based on results from the lachat and ICP and the discovery that E. coli would not grow in the originally proposed Tris-HCl buffered solution, the measurement of phosphorus uptake protocol was modified after a productive meeting with advising scientists. Modified microbes will now be suspended in a minimal media solution whose components can be processed by both the sensitive lachat and ICP instruments. Prototype modeling progressed, with team member Barrett composing a 3D model to better-depict uptake system hardware. In the afternoon, a few team members also visited the West Lafayette Wastewater Treatment facility, where they learned about the local area’s methods for phosphorus removal featuring their newly-implemented chemical system.

3D Bioreactor

Above: Current bioreactor prototype with 2 5-gallon buckets, an aquarium pump, connective tubing, and 3 standard water filter chambers to house E. coli

Thursday, July 28

Additional trials of media and various water samples were run on both the lachat and ICP as team members were trained in their use. Colony PCR and sequencing to confirm the transformation of phosphorus genes into E. coli were also begun, with completion planned to coincide with the conclusion of next week.

Friday, July 29

Focus was placed on brainstorming possible development strategies of silica beads. Two components combine to make these beads: a sol phase and a buffer (Tris-HCl). The team has been trying to find the proper ratio of these two ingredients so beads solidify at an appropriate rate–too slowly, and an amorphous silica blob forms in the bottom of the mineral oil into which the beads drop; too quickly, and the mixture hardens inside the tubing through which it is dispensed. Cool temperatures slow the reaction, so the team has also tried completing the process in the cold room with mineral oil warmed on a hot plate, but to no avail. The current method involves the use of syringes to inject the two components into a small Y-shaped tube where they mix and then pass through a needle at the bottom to drop into mineral oil. According to calculations, 99,000 beads will be needed to fill a standard water filter canister; that’s a lot of drips!


Monday, July 18

In collaboration with Exeter, the team will be growing up last summer’s killswitch genetic construct under both aerobic and anaerobic conditions. To begin the week, they set up Dr. Rickus’s anaerobic chamber, which is a large, clear box with thick black gloves attached to reach into it–very mad science-y (example below). This week, culture growth will begin after air tanks to sustain the anaerobic culture arrive.

Anaerobic Growth Chamber

Example of an anaerobic chamber; image courtesy of

Tuesday, July 19

Mid-week discussion centered around using the sol-gel method to suspend E. coli in silica beads with which to fill containers external to the main containment area of the bioreactor. The bacteria will be immobilized within the matrix of silica fibers while phosphorus is still able to pass through, making this solution ideal for easy input and retrieval of E. coli from the bioreactor system. See the diagram below for an explanation of the method.


Infographic depicting the sol-gel procedure to form aerogel; image courtesy of

Wednesday, July 20

Wednesday’s focus was the development of a protocol for the quantification of phosphorus both intracellularly and extracellularly. It involved the creation of a guide for phosphorus on the Experiment page, so if you want to become familiar with the differences between total phosphorus, orthophosphate, and polyphosphate, feel free to check it out.

Thursday, July 21

The lab hosted Peter Oladipupo, a Mandela Washington Fellow, answering questions regarding the project as it relates to the generation of energy. It was enjoyable to hear his perspective and show him the progress being made. The day also brought continued research into the development of a model to both inform experimental decisions and make future predictions.

Friday, July 22

During the week, the team found out that IDT was unable to synthesize another nanowire gene, cancelling the order and decisively tabling the wet lab work for the nanowire side of the project for this competition cycle. So, full steam ahead with phosphorus. Nanowires will be revisited during the school year–strong side project potential!


Monday, July 11

After a successful weekend participating in the Wabash River Fest, the team jumped back into lab work, plating a new culture of Shewie, miniprepping a promoter for use with digestion the next day, and preparing glycerol stock cultures of successfully transformed parts. A bioreactor brainstorming session with USDA-NSERL staff Dr. Ashley Hammac, Stan Livingston, and Scott McAfee left team members enthused about the prototype to come later in the week. Additionally, the team met with representatives of the Purdue Foundry regarding the possibility of developing a business model for the phosphorus removal system. If lab work continues to go well, this may be something to pursue in the fall.

Bioreactor Sketch

Above: A preliminary sketch of proposed bioreactor design

Tuesday, July 12

Wet lab work consisted of the digestion and ligation of all three remaining phosphorus genes in preparation for transformations into E. coli. Mental effort for the day was directed toward understanding E. coli‘s Pho regulon, the system of genes that control phosphorus within the organism, in an effort to determine which specific sequences of DNA may be helpful to up-regulate in the synthetic microbes to greater improve their efficiency.

Wednesday, July 13

The bioreactor prototype was complete! Many thanks to the staff of the NSERL (National Soil Erosion Research Laboratory) for making it possible.

Bioreactor Prototype

Above: Bioreactor prototype, iteration 1

The prototype consists of two 5-gallon buckets, an aquarium pump and outflow tube to maintain constant water level and flow, and three separate ports around the base to channel water from the main reservoir into water filters that will eventually contain modified E. coli cartridges. Phosphorus is to be collected in these chambers, and effluent is controlled by the valves at the point where water flows from the filters. Further testing of the prototype will include the determination of the proper substrate to contain E. coli, optimum temperature and pH, and best water flow rate.

Thursday, July 14

Thursday morning began with celebration as all of the previous day’s transformations worked with multiple colonies appearing on every plate. Go, team! With all phosphorus genes successfully transformed, the team can now move forward with characterizing proteins. Along with this, some strains will be sent to other collaborating teams for characterization to confirm results.

Friday, July 15

Are synthetic biology terms sometimes confusing? Is scientific jargon difficult to understand? Look for explanation no further than the team’s newly-released glossary of synthetic biology and iGEM terms hosted on the Experiment page.

I'm Cultured

Does this joke make sense? If not, please check out the glossary!

With the new bioreactor prototype, several protocols needed to be written including a standard for measuring water flow and a process for system maintenance. The plan for the upcoming week is to characterize individual proteins and begin conducting tests to determine the optimal substrate for E. coli to inhabit in the bioreactor’s external chambers. Any thoughts on what to name the bioreactor? Tweet @PurdueBiomakers to let the team know what you think.



Tuesday, July 5

Returning from holiday, the team worked into the week with a couple of collaborative Skype calls. The first, Northwestern University, was in regard to co-hosting the iGEM North American Conference next summer. They are excited about the project and are looking into Chicago-area venues as the Purdue team investigates Indianapolis as a potential host city. Denny Luan, a founder of Experiment, the crowdfunding website utilized to raise money for lab supplies, spoke with the team on the day’s second call. An indication of Denny’s personality is given by the title of his groundbreaking study, “Qualitative survey of burritos in San Francisco.” He offered to assist with the iGEM wiki database, which is hugely exciting. Thank you for your enthusiasm, Denny!

Wednesday, July 6

Mid-week lab work consisted of transformations (ppgk was successful), PCR amplification, and gels. A reporter from local WLFI 18 TV news visited the lab, as well, and the story, related to Florida’s algal blooms, aired on the nightly news. Checked out the previous post for the link.

Florida algal blooms

Bloom in Lake Okeechobee, courtesy of NASA

Thursday, July 7

The team attended a presentation by Dr. Kevin King entitled “Production Agriculture and Environmental Targets: Can They Coexist?” He highlighted edge-of-field research aimed at quantifying the impacts of agricultural production practices and discussed potential management practices that might be used to reduce offsite nutrient transport, meeting established water quality targets. Additionally, the team is excited to announce that their submission for a SYNENERGENE Grant-Funded Collaboration proposal was selected! Collaboration with the Rathenau Institute will begin shortly.

Friday, July 8

After completing a survey designed to measure public perception of wastewater treatment methods, the team gathered supplies for outreach at the Wabash River Fest the following day. Existing gels were annotated and more were run as loose ends were tied up in the wet lab.

Saturday, July 9

Purdue iGEM hosted a booth at the Wabash River Enhancement Corporation’s (WREC) annual Wabash River Fest. It was great fun for all parties involved as passersby learned about DNA, built (and ate) their own licorice and marshmallow double helix models, and asked questions about synthetic biology and the phosphorus cycle. Young scientists tried their hands at pipetting, mixing colored water in eppendorf tubes.

Pipetting practiceWabash River Fest Instructing


Left: iGEM team members Paige Rudin and Bowman Clark interact with Wabash River Fest visitors, educating about DNA and its role in making us who we are

Right: Scientists in training demonstrate their pipetting prowess


Last night, the Experiment campaign reached and surpassed the funding goal of $3,000! Thank you to everyone who donated and spread news of the campaign. The team couldn’t have done it without you!

Funded Experiment Campaign

If you didn’t catch it live, the team was featured on local WLFI 18 TV last night! As the project is related to current Florida algal blooms, media picked it up and visited Bindley Bioscience Center. The team is excited to have shared their message with the community and hope the opportunity was beneficial for improving public perception of synthetic biology.


June 27 – July 1

This week, things are going to be shaken up a little bit. Here’s a quick summary of the goings-ons in short paragraph form:

The team visited Imagination Station in downtown Lafayette regarding the possibility of volunteering both this summer and continuing forward. Imagination Station is a museum with interactive exhibits; iGEM would assist by educating about synthetic biology. This would be a great opportunity for club community outreach, and we’re excited to launch this collaboration together.

Lab work continued with PCR amplification, gel electrophoresis, extractions, and transformations of phosphorus and nanowire genes.

Collaboration Skype calls with Exeter, the University of Chicago, and SVCE Chennai were successful. Exeter and UChicago are onboard to help with database entries and protein characterization, and SVCE will distribute a survey about wastewater management practices.

Through a meeting with Dr. Ron Semmel, a Monsanto scientist, the team acquired useful contacts and information regarding local phosphorus and nitrogen soil concentrations. Dr. Semmel concisely described his job: “They send me things. I try to kill them. If I can’t kill them, they go to market.”


Breaking news: this past week, Florida governor Rick Scott declared a state of emergency in several counties due to a toxic algal bloom. This is exactly the problem Purdue iGEM is working to solve! The so-called “miracle grow” of fertilizer, sewage, and manure pollution being added to water sources contains high concentrations of phosphorus, one of the nutrients contributing to algae growth. Check out more information with this CNN article.

You can be a part of the quest to remove icky green films from bodies of water across the nation by joining the team’s Experiment campaign. With a few days left to reach the $3,000 fundraising goal, the team needs your help to make dreams of clean water a reality!


Above background image courtesy of, algae-covered water near Florida’s Lake Okeechobee lowering tourism revenue and local morale


Monday, June 20

The week began with a strong focus on human practices as the team fleshed out 3 ideas. The first, iNAC, the iGEM North American Conference, was sparked by the observation that many more European than North American teams medal, and of those that medal, the proportion of golds is substantially higher for Europe. The concept is a “Going for Gold” event to facilitate better understanding of iGEM requirements, lab practices, and the constitution of a winning project. This event would take place in summer 2017, co-hosted in Chicago by Purdue and several other Midwest teams (in theory, anyway). In conjunction with iNAC, the team is hoping to host iNIC (iGEM Northern Indiana Conferenceto discuss the possibility of coordinating iNAC. If this event is pursued, it would be a day-long conference at the end of July.

The third idea is in regards to the Great North American Skype Series (G-NASS), a “Skype roulette” to foster inter-team communication. There would be a goal of 20 teams participating in a couple of 30-minute calls. More to come soon.

iNAC flyer

Above: Mock-up flyer for the iGEM North American Conference, coming 2017

Tuesday, June 21

Tuesday morning kicked off with the digestion of phosphorus genes for ligation later that afternoon. Researchers met with Dr. Tommy Sors, Bindley Bioscience Center’s Chief Liaison, regarding the use of equipment for Western blot protocols and an overview of the project. He commented on its ambitious scope, quoting Wes Jackson: “If your life’s work can be accomplished in your lifetime, you’re not thinking big enough.”

Wednesday, June 22

Modeling commenced with Mark Aronson, former iGEM president and current advisor who Skyped the team from New York. A working bioreactor model is top priority, with layers of complexity to be added as experimental data is collected. Phosphorus genes were again transformed into competent cells, and newly-received plasmids resuspended after transport.

Thursday, June 23

Transformed phosphorus cells were inoculated, several colonies taken from LB agar plates and suspended in LB broth with ampicillin to incubate overnight. All phosphorus genes also underwent PCR amplification. An afternoon Skype call with the University of Exeter in England topped off the day as teams exchanged greetings, project synopses, and ideas for future collaboration.

Friday, June 24

A Shewanella oneidensis culture, generously donated by Argonne National Laboratory, arrived amidst great celebration on Friday morning. This Shewie will serve as a basis of comparison for E. coli expressing organic nanowires. The team was busy in the lab making and running gels for phosphorus and re-transforming phosphorus genes after Thursday’s inoculations proved less than satisfactory. The University of Nebraska–Lincoln Skyped in the afternoon, which was especially relevant as they are tackling a similar wastewater treatment dealing with nitrogen and nitrate remediation. A rewarding end to a productive week.


Monday, June 13

Most significantly this week, team members hosted Molecular Agriculture Summer Institutes (MASI) high school students in the lab as they worked with Emma on completing InterLab protocols [InterLab is an iGEM-wide study working to establish a consistent unit of measurement for fluorescence; experimentation and measurement is completed using GFP.] The transformations completed over the weekend proved successful–the positive RFP control exhibited growth, while there was no growth on the negative control. Transformed cells were inoculated and plates parafilmed for short-term storage. PCR was completed for 3 phosphorus genes whose gel electrophoresis analyses were unclear when attempted over the weekend. Wiki design was also discussed to get this critical project element up and running ASAP.

Tuesday, June 14

Lab work for Tuesday included the mixing of gels for later electrophoresis, the miniprep of promoters that were PCR’ed previously, and continued InterLab transformations.

Wednesday, June 15

Meeting day! Highlights of this week’s meeting include a discussion of the utilization of mass spectroscopy to complete proteomic profiles, the wastewater analytics tools possibly available to us through the generosity of Dr. Ashley Hammac and the USDA National Soil Erosion Research Lab, and the idea to replicate a study upregulating E. coli genes related to phosphorus uptake and storage as a basis of comparison to engineered strains. Via Skype, the team established a collaboration agreement with Rose-Hulman Institute of Technology’s iGEM team, aiding them with fluorescent microscopy in exchange for help characterizing some proteins.

In the afternoon, several team members volunteered with the Wabash River Enhancement Corporation (WREC) by aiding in the upkeep of a rain garden in Lafayette designed to use plants to stop pollutants from infiltrating the Wabash. Water flows off the roof of site buildings (Oakland Elementary), and nutrients (such as phosphorus) are captured by plant roots. This garden needed some weeding and re-planting to be in tip-top shape again.

Oakland Elementary Rain Garden WREC Rain Garden

Above left: Rain garden at Oakland Elementary School in Lafayette, IN

Above right: iGEMmers Bowman Clark, Paige Rudin, and Hana Kubo (left to right) hard at work planting grasses

Thursday, June 16

Team members were busy in the lab completing transformations of phosphorus genes, more PCR, autoclaving, and inoculation of transformed InterLab genes. Excitement of the day was a discussion of hosting a conference for other iGEM teams–stay tuned for more to come.

Friday, June 17

Gel electrophoresis, inoculations of transformations from yesterday, and the production of more LB agar plates with ampicillin closed out the week in Bindley Bioscience Center. Additionally, here’s an update on the Experiment crowdfunding campaign in the form of an advertisement to be featured on news screens across campus. Thank you to everyone who has aided our cause!

Experiment campaign update