Posted

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

Posted

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.

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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.”

Posted

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!

FloridaAlgae_ExperimentCampaign

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

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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.

Posted

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

Posted

Monday, June 6

Monday morning got rolling with the attendance of ABE PhD student Dr. Andi Hodaj’s thesis defense regarding two-stage ditches as a tool to reduce nutrient loads. A two-stage ditch is a variation of a traditional agricultural ditch in which the banks are dredged to create floodplains, dissipating the energy of high-flow water and increasing interaction time between vegetation and water. Purdue’s two-stage ditch utilized in Dr. Hodaj’s was established in 2012 and drains 660 acres; it may be a possible implementation point for the project’s biological method.

two stage ditch enlargement

Above: An illustration of a two-stage ditch from thewhiteriveralliance.org

Additionally, primers arrived, and the Experiment project write-ups were finalized and proofed.

Tuesday, June 7

The Experiment campaign went live! Thank you to both Drs. Rickus and Solomon for endorsing the project, and to those who are project backers–your donations are greatly appreciated. See last week’s previous post for more information; the Experiment page can be found here. Work continued on both the spring publication and protein profiles for the wiki.

Wednesday, June 8

Formal lab meeting #1 was a success with the most highly prioritized goal for the upcoming week to find or generate relevant numbers for the project including necessary flow rates for a microbial fuel cell, an appropriate density of E. coli within it, etc. The rest of the afternoon was spent working on action items from the meeting and printing the spring publication, which is FINISHED.

Thursday, June 9

Team members Barrett Davis, Paige Rudin, and Suraj Mohan attended the Regional Clean Energy Innovation Forum held at Ross-Ade Stadium. Leading scientists from across the country gathered to discuss topics like energy storage, biomass and synthetic biology applications (a conversation that piqued the students’ interest), materials manufacturing, and more. The theme the team took away from the day is best summarized with the words of Purdue President Mitch Daniels during his opening remarks: “It’s only an innovation when it’s useful to someone.” How can new technology of nanowires and microbial fuel cells be integrated efficiently into established systems? Is it a cost-effective solution? Only time will tell, but the team is excited to find out.

Biomakers at Clean Energy Innovation Forum

Above: Barrett, Paige, and Suraj (left to right) pose for a picture at the 2016 Regional Clean Energy Innovation Forum

Friday, June 10

Happy birthday wishes to Barrett, as he celebrated his 20th birthday in the lab on Friday. In the best interest of keeping a sterile work environment, the team refrained from strewing confetti across the bench, although it would’ve been both fun and festive.

Dow AgroSciences generously donated various lab supplies to the iGEM workspace that the team was thrilled to pick up in Indianapolis on Friday morning. Thank you to Dr. Steve Evans, Mr. Mike Doody, and DAS administration for their support in realizing the dream of a self-sufficient, independent lab for the sole use of undergraduate iGEM students. With equipment, it is possible to operate without reliance upon the lab space of other Bindley Bioscience Center scientists, lending additional flexibility to the projects iGEMmers are able to complete.

Phosphorus genes arrived, and the team got to work on PCR amplification in the afternoon. This included resuspending IDT DNA gBlocks and using PCR to increase the amount of DNA present for transformation.

The Weekend

So diligent is this year’s team that several members completed additional PCR amplification and iGEM kit plate promoter transformations on Saturday and Sunday. After digestion and ligation, they did some gel electrophoresis, as well, running several different samples.

Posted

In an effort to raise funds for laboratory supplies, this year the Purdue iGEM team is launching a crowdfunding campaign on the Experiment website, a platform similar to GoFundMe and Kickstarter but exclusive to scientific endeavors. The fundraising goal is ambitiously set at $3,000, and the team would greatly appreciate any and all the help it can get. There is a short project description on the Experiment page in addition to a breakdown of how contributions will be invested, also featured below. Thank you for your support!
Experiment campaign budget breakdownWe-want-you-image

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Monday, May 30

Memorial Day was an optional day on the job, but the dedicated iGEM team put in an afternoon of work in Bindley. Practice transformations were successful–both GFP and RFP were apparently expressed, and growth on control plates was as expected. Practice minipreps were next on the agenda, which the interns also completed successfully in addition to some supply inventory.

Tuesday, May 31

Lists of supplies needed for various assays were assembled, and an assessment of necessary ordering was made, thus finalizing the functional assays to run for both nanowire and phosphorus genes. Additionally, brainstorming for an Experiment (crowd-funding for scientific research) campaign was completed.

Wednesday, June 1

Background research continued, and some ideas were tossed around concerning the official project theme for this year (more to come on that later). A meeting with Drs. Rickus and Solomon led to recommendations to practice with both the transmission electron microscope (TEM) and the process of electroporation for genome integration to prepare for performing these procedures later. Project write-ups for the Experiment campaign were completed, as was an application for a grant from SYNENERGENE for advanced human practices.

Thursday, June 2

The Experiment online crowdfunding platform was submitted for approval in the morning, and an order for both competent cells and primers was placed. Background research was again the main focus, and most team members concentrated their efforts on learning the ins and outs of both Shewe (Shewanella oneidensis) and tiny moon phosphorus-eaters (Microlunatus phosphovorus).

Friday, June 3

This week’s conclusion was easily one of its most exciting moments, as the team took a field trip to visit Drs. Chi-hua Huang and Ashley Hammac of the USDA National Soil Erosion Research Lab, who generously donated both their time and expertise to answer questions and allow the team to tour the facility. Analytical labs, rain-producing machines for the purpose of studying erosion patterns, bioreactors, and anaerobic growth chambers were among the cutting-edge technologies the team observed. Thank you, Dr. Huang and Dr. Hammac!

Word was received later in the afternoon that the Experiment proposal had been approved; the campaign launches June 9!

Posted

Monday, May 23

Day 1 on the job–the morning began with a tour of Bindley Bioscience Center for the new interns (Barrett, Caleigh, Emma, and Paige), during which Susan (the world’s best receptionist) kindly showed the fledgling researchers around and gave them the run-down on BBC do’s and don’t’s. The remainder of the day was spent working on gene design via Benchling, researching potential assays, and meeting with Drs. Rickus and Solomon. Important topics they raised included the importance of an experimental design plan, the need to begin with the basics (i.e. how do we know a protein is being expressed?) before delving into more complex issues of function, and gene design specifics.

Tuesday, May 24

Nine out of ten genes needed for luxury phosphorus uptake were ordered at the conclusion of Day 2! Throughout the day, genes were restructured for use with 3A Gibson Assembly protocol, and new constituent promoters were added (both sigma70 and sigmaS to arrest growth in P E. coli). Primer design began. Additionally, the hunt for assays continued for both phosphorus and nanowire constructs. Interns learned how to optimize codons using IDT both automatically and manually, checking for segments such as EcoRI, SpeI, XbaI, PstI, and HINDIII that should not be present in coding regions of constructs, as these sequences code for restriction sites.

Wednesday, May 25

A review of sterile technique and iGEM kit DNA extractions in the lab comprised a majority of the morning. Some golden rules of sterile technique: Always wipe down the lab bench with 70% ethanol before beginning; work as close to the flame as possible, as it creates a sterile “bubble”; and get into and out of pipette tip boxes as quickly as possible to keep them sterile. The autoclaving of new pipette tips and water was also used for demonstration purposes. Afternoon work consisted of continued definition of desired assays and design of nanowire genes.

Thursday, May 26

The creation of ready-to-use plates was the focus of lab work on Thursday. Interns followed an existing protocol to make plain LB agar, LB agar with ampicillin, and LB broth, culminating in the pouring and storing of too many plates to count. Caleigh, Sean, Suraj, and Paige took a field trip to the West Lafayette Waste Management facility to speak with Sara Peel of the Wabash River Enhancement Corporation (WREC) and Angela Andrews of the City of Lafayette Water Pollution Control. It was discovered that the facility is newly permitted for phosphorus removal; however, a chemical method as opposed to a biological one will be implemented August 1 for both political and financial reasons. The up-front cost for chemical treatment was less than for biological treatment, which made it the optimal choice for the time being, but the facility plans to switch to biological treatment as soon as it has the funds to do so, as this will be more cost-effective longterm. The team plans to return to the plant sometime in July to receive a full tour and collect wastewater samples to be used for testing.

wabash

 

Featured above is an overview of the Wabash River with the West Lafayette Wastewater Treatment Facility circled in red

Friday, May 27

Brainstorming for both background content for the official iGEM project wiki and a project timeline were completed in addition to an establishment of a protocol for completing lab notebooks. A Work Breakdown Structure (WBS) and Gantt Chart were constructed to record timeline information. Practice transformations of GFP and RFP kit plate parts were completed by the interns throughout the day. The conclusion of a successful first week!