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Public Relations

Media Coverage

In order to spread the word about our sepsis diagnostic tool, we wrote a press release that provides an overview of iGEM, discusses the successes of last year’s team, and outlines what we are working on now. Members of our team then translated this into multiple languages including German, Bosnian, and Mandarin Chinese so that we could contact the hometowns of our team members who are international students. So far, we have been featured in two German newspapers and a St. Lucian newspaper. We also were featured in our school’s newspaper, the Campus Times.

Jeversches Wochenblatt

Campus Times

The Voice

NWZ (Nordwest-Zeitung)

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Social Media

Team Bio-Spire has been active on our Instagram, Twitter, and Facebook pages, where we post specific updates about what each subteam has been working on, called “Subteam Spotlights.” Additionally, we posted a series of informational posts about sepsis, which we translated into Hindi, French, German, Bosnian, Macedonian, Spanish, Russian, Romanian, and Chinese in order to expand their potential audience. Other posts include our weekly Facebook newsletter, member introductions, shoutouts to our sponsors, and information about different techniques and equipment our team has utilized in the lab. We also posted a series of synthetic biology facts to spread awareness of this scientific field. Additionally, we engage with other iGEM accounts through social media in order to learn more about their projects and facilitate collaborations.

Weekly Newsletters

In addition to our regular subteam updates, we have been releasing a weekly newsletter on Facebook in order to provide a more in-depth summary of what the team has accomplished during the past week. The newsletter is valuable for anyone looking to learn more about the science behind what we’re doing, or for groups looking to serve as potential sponsors for our project.

Hello and welcome to our first of many weekly updates! iGEM Team Bio-Spire has been working hard to get our project off the ground, and we’re excited to share what we’ve been busy with this week. In case you missed our intro post, our project is a wearable diagnostic device that will help to diagnose sepsis risk based on the levels of certain biomarkers found in sweat. Our team consists of several subteams, and we have been meeting both together and in small groups to develop our project. We have also had Zoom meetings with various experts on relevant topics, trained ourselves on useful software such as Benchling, and talked with other iGEM teams around the world to set up collaborations.

This week, the modeling team worked on dividing to conquer! First, we will have a couple modelers look into Shewanella metabolism. This bacterial species is one of the ways our wetlab subteam is considering reducing graphene oxide, and we want to know if overexpression of certain genes (that make it more efficient at the reduction) are harmful to the bacterium. Furthermore, we want to know if certain nutrients are key for the bacteria's reduction process--we want to feed them any chemical that will supercharge their desired function! A couple of us are investigating how to predict the number of functional groups left on our reduced graphene oxide using different reduction methods. These methods include overexpressing different genes in Shewanella as well as performing chemical (rather than biological) reduction. We are also planning what data to collect in a few experiments to translate the electrical signal our device measures into an estimated concentration of our biomarkers in sweat. And two of us have been learning more about fluids modeling to account for the fact that it takes time for our biomarkers to bind and dissociate from their aptamers, a process that has to occur as new sweat with a new biomarker concentration is constantly flowing over the sensor--tricky stuff!

Our hardware team sketched the design of a microfluidic part and did research on a variety of topics including protocols for making a microfluidic device, safe alternatives for sweat induction, how sweat is used to diagnose cystic fibrosis, and how iontophoresis is used for glucose monitoring.

The outreach and education team has been meeting with contacts about partnering with them to run educational science activities over the summer and during the school year. Additionally, we have finalized our list of activities and are writing up our lesson plans for them!

The policy and practice team has been doing lots of contacting physicians and sepsis specialists while also finalizing our ideation of human practices throughout the project. Similarly, the fundraising team has been talking with potential sponsors, working on a grant for our team, and getting our crowdfunding page up.

This week, the public relations team worked on preparing social media posts with information about sepsis, which we will also translate into some of the many languages that our team members speak. We also sent out our first press release to the media and engaged with other iGEM teams online. Our video team is working on the script and storyboard for a promotion video, and also a team intro video.

Last but not least, the wet lab team has been working on finishing the sequences that we plan to order from IDT. These are different genes implicated in the extracellular electron transfer pathways of S. oneidensis MR-1 (a type of bacteria known for its great reduction ability). We plan to overexpress them such that it can more efficiently reduce our graphene oxide. We have also been writing protocols so that we can go into lab as soon as all of our DNA comes.

We’ve had another productive couple of weeks as iGEM team BioSpire! First of all, the public relations team has been posting some facts about sepsis in a variety of different languages-- check out our Instagram (@ur.igem.2021) to see them! Our education team is finishing up videos for the Upward Bound college prep program and organizing age-appropriate science activities for the summer camps that we will be working with.

Our policy and practice team has been contacting physicians and sepsis specialists so that we can use their expertise to improve the design of our diagnostic device. Additionally, they have been finalizing the ideation of the human practices that we are employing throughout our project, including various ethical and social factors that come into play. Our fundraising team is starting to plan a 5k race fundraising event (stay tuned for more details!) and gathering sponsors for that. We are also continuing to work on our team’s promotional video, which is coming along nicely.

In the lab, we are working on synthesizing rGO (reduced graphene oxide) through different reduction methods and characterizing the products, as well as running asymmetric PCR reactions to synthesize single-stranded DNA aptamers, which we will eventually attach to rGO.

Our hardware subteam needed some rough estimates of what concentrations of biomarkers to expect in sweat in order to inform their circuit design--specifically, by how much to amplify the signal our device will detect--so the modeling team got to researching! Most data available in the literature reports the levels of our biomarkers in blood rather than sweat, but fortunately research suggests that the concentrations of our biomarkers are on the same order of magnitude in sweat as in blood. We did, however, have to do some digging to find the rough ranges not only for septic patients, but also for healthy controls and for patients in different positions on the clinical spectrum of sepsis because our device will be measuring signals for patients in all of these conditions. Our wiki design team has been finalizing the design of our team wiki page, which you can find here: https://2021.igem.org/Team:Rochester

And as always, message us or email us at uofr.igem@gmail.com to learn more about our project or to collaborate with Team Bio-Spire in any way.

Welcome to this week’s newsletter! Team Bio-Spire has been making some great progress in all aspects of our project; keep reading to learn more about what we do each day.

As mentioned before, our wetlab team is using ssDNA aptamers as our receptors for biomarkers, as they have highly specific binding. This past week, we managed to transform the plasmids with our aptamer sequences in E. coli cells, and we continued to improve the asymmetric PCR conditions, such that we can synthesize our receptors in high yield. We have also been working towards producing reduced graphene oxide (rGO) with our chassis microorganism Shewanella Oneidensis. This week we have transformed our S. Oneidensis. to overexpress genes involved in electron transport for reduction of graphene oxide (GO). We have overexpressed a few membrane proteins to increase the rate of reduction of our GO.

What is the ratio between our biomarkers in sweat and in blood? And how confidently can we predict that a patient is septic based on these biomarkers? To answer these questions, the modeling team has been scouring the literature and, this week, asking physicians who treat septic patients what kind of readout would be most useful. A warning when levels of a biomarker increase? A prediction about the likelihood a patient’s inflammation (measured by our biomarkers) is caused by sepsis or some other condition? We will fit our models and design our software based on the perspectives of these experts because we want to help medical professionals detect sepsis most effectively.

Our public relations is working on using social media to showcase some of the different projects our subteams are currently working on-- check out Instagram, Twitter, and Facebook for our Subteam Spotlight posts! Additionally, we are continuing to reach out to various media outlets and our team was recently featured in the newspaper Nordwest Zeitung from Tiana’s German hometown!

Our fundraising team has been working on planning our 5k event and will soon begin publicizing it. Also, we are beginning to design our team merchandise, as well as the designs for the 5k t-shirts. Our video team has finished production on our promotional video that features facts about sepsis and our project, and we are working on translating the subtitles into a variety of different languages in order to increase accessibility.

Last week our outreach and education team taught some hands-on science lessons with summer camps at Nazareth University and RMSC. This week we will be adjusting our activities based on the student and counselor feedback we got from those camps, and we look forward to week two of working with Nazareth and RMSC. In terms of collaboration, Team Bio-Spire has been continuing to work with other iGEM teams on a variety of side projects.

Finally, our hardware team is planning to use an iterative casting-shrinkage procedure to make our microfluidic device. We are making a list of components and an exact protocol and we are hoping to do it next week. Since using FET biosensors is not the most optimal for rGO, we might invest in impedimetric or capacitive biosensors instead. This week, we will be working on designing micropillars, creating the sleeve/sock and electrode system design in Onshape, learning more about aptamers, and researching techniques to test rGO and microfluidics.

Welcome to this week’s newsletter! Team Bio-Spire has been doing the field of science proud this week, from going into the community to persevering through tricky experiments.

This past week, our Education team continued working with the Nazareth and RMSC summer camps, as well as running a live session with the students at Upward Bound. This week, we are looking forward to working with some troops from Girl Scouts of Western New York, as well as working with the Nazareth and RMSC summer camps.

Our inclusivity efforts continued this week, with our Policy and Practice team working with the Disabilities Office at UR to approve a 1 hour presentation mandatory for professors (like an orientation) focused on universal design. We met with a member of the autistic community at UR and the Disabilities Office director, who told us that the university has over 400 students registered with them as neurodiverse but that this is certainly an underrepresentation.

Hardware is working on manufacturing our first microfluidic device! Then, we will test it with a syringe and food colorings and see if we need to change capillary dimensions in COMSOL, a physics modeling software. To test our rGO, we will use silver conductive ink, and might use a 2-probe system that is available at a few labs on UR’s campus that are graciously willing to work with us! So far, we have an oscilloscope that we will likely use for measurements.

Our Modeling team’s Reduction Method Model seeks to answer two questions: 1) given a certain number of aptamers we want to attach, how many functional groups do we need to have left after reduction of our graphene sheet into rGO and 2) between chemical reduction, reduction with wild-type Shewanella, and reduction by Shewanella with various genetic modifications, which method gives us the desired degree of reduction? This week we worked on determining the specific surface area occupied on our graphene sheet by an aptamer. From there, we will use the bond length and how much space is taken up by oxygen bonds to subtract off the surface area of the oxygen groups. This will enable us to answer question 1!

This week, wetlab did PCRs for IL6, IL1b, TNFa, CRP with slightly different conditions. We are working on improving the binding assay: we will try smaller volumes first (we will test IL1b with the old PCR product), and will possibly re-test CRP and TNFa with the new protocol. Putting a hold on lactoferrin for now (since the biomarker is not here), we are hoping to attach aptamers to chemically reduced GO by the end of next week. We will work on how to test binding in that case.

We have been working with OSU on the children’s book to raise the awareness of sepsis in children and parents. Also we had a meeting with the SUNY-Oneonta team, and talked about collaboration on their hardware repository project and our hardware components.

Welcome to this week’s newsletter! Team Bio-Spire has been working hard to advance sepsis diagnostics, using data to distinguish it from other conditions and perfecting our device to measure its biomarkers!

Can we distinguish sepsis from other inflammatory conditions using biomarker levels? The research our modeling team has been doing over the last two weeks shows that may be hard--there is a lot of overlap in concentrations, depending on which paper you look at. So what readout will our device ultimately give? This week, modeling will investigate a bit of a pivot: rather than trying to specifically differentiate sepsis from common other causes of inflammation, we will potentially combine reported Sensitivity and Specificity values from published research because the latter quantity tells us how confident we can be that we aren’t diagnosing sepsis when the rise in biomarkers is really due to another cause. That way, our device could give a warning indication of potential sepsis, but associated with a level of diagnostic confidence based on these sensitivity and specificity values.

After a successful week working with the Girl Scouts last week, our Outreach and Education team loved working with STEM girls ROC this Friday! As these camps slow down, we are shifting our focus to writing up such activities for our iGEM Wiki. We are also looking into making a synthetic biology activity book during the school year!

Our Policy and Practice team is planning a sepsis awareness Symposium for September, and our Collaboration team is interested in having a meet-up with other iGEM teams in the region to practice our presentations before the Jamboree! After a wonderful meeting with team Rio-UFRJ Brazil last Friday in which we received good advice on impedance measurement, we offered help to figure out drop casting on screen-printed electrodes, microfluidics, and 3D design using Onshape or COMSOL.

This week in wetlab we are working on optimizing conditions for binding assays. Yesterday, we tried 10x higher concentration for CRP and its aptamer. It did not work, so we decided to increase the concentration of aptamer by another multiple of 10. Will also increase the concentration of the biomarker (CRP) itself.

Hardware ran our first experiment last week! Our first 3D mold was twice the size of the original design in Onshape. Working with ReduceIt Mold did not work, since the capillaries in the 3D mold are too thin and we couldn’t get the compound out; it shrank though. We made another design in Onshape, printed the original size in Rettner Hall on campus, and will run the experiment again. If it works, we will test the flow using syringes and food colorings.

Finally, Fundraising is working on getting our 5k event approved and looking for donations of experiences or goods for our auction/raffle at the 5k. Please let us know if you—or a company you are affiliated with— have anything you’d like to donate to help support our team!

Welcome to another weekly newsletter! A lot of exciting things are happening with our project as the summer is winding down, and some of our team members have been taking well-deserved vacation time this month.

In terms of wetlab, we are continuing to produce aptamers via asymmetric PCR, and we’re almost ready to try Rolling Circle Amplification (RCA) for some of them, hoping that this will increase their affinity! This is an enzymatic process by which a short DNA or RNA primer is amplified to form a long single-stranded piece of DNA or RNA. Using asymmetric PCR, we were able to obtain mostly single stranded DNA, and we continued to test if our aptamers are able to bind to their target biomarkers. To produce rGO more efficiently, we have been amplifying certain genes that are part of the S. Oneidensis MR-1 electron transport pathway as well as the empty vector, in order to introduce sites that will allow us to clone these genes into Shewanella using Golden Gate technology. We will also be running more experiments with rGO in the coming days.

You know the saying about assumptions… but in Modeling, informed assumptions are key! Lactoferrin as a biomarker can help us distinguish various forms of inflammation from sepsis, which is overwhelming inflammation that is caused by infection, but we can’t find data on Lactoferrin levels in sepsis, exactly. Instead, we will look for data on Lactoferrin in specific forms of infection, but recognize this as a limitation of our model.

The education team is continuing to do outreach work with children in our community, and this week we visited a group of campers at the Rochester Museum and Science Center to teach them about genetics. The kids had fun using Punnett Squares and blood types to solve a murder mystery, and got creative in their guesses about who killed the Geico gecko.

More progress is being made on our team wiki this week as well, and each subteam is finalizing their writeup that will be featured on the page. The public relations team has been busy posting Subteam Spotlights highlighting this week’s work, and sharing some more information about the fascinating field of synthetic biology.

In the hardware subteam, we are experimenting with building our microfluidic device. We finished our first device last week but the 3D mold was made using a rigid material (ABS plastic), so instead we sent a new mold to be printed in a more flexible material. We will be running the new experiment on Friday. We plan to build our own potentiostat, which is a device that provides a voltage source to control the potential of an electrode. In order to achieve this, we found a group that fabricated their own low-cost potentiostat and reached out to them. We also placed orders for the items we need to build our circuit. Once we build a potentiostat, can use it to test impedance changes and also test if only the working electrode was modified.

Finally, our collaboration team is putting the finishing touches on a comprehensive academic journal article that will be sent in as part of a collaboration with the Maastricht iGEM team in the Netherlands. We are also working with Ohio State University to create a children’s book that educates kids about sepsis and how it can be prevented and treated. We also met with the TU Delft team (also from the Netherlands) and discussed aptamer and circuit design while learning about each other’s projects.

Hello and welcome to another edition of our team newsletter! Our wetlab team has been running more PCRs, Quantiflors, and agarose gels to express and quantify our aptamers, as well as producing and testing the rGO that we will be using in our device. As wetlab gets close to attaching our aptamers to rGO, we take a step closer to a model that is key for our device to produce a readout: a calibration curve to translate the electrical property measured by the device into a predicted concentration of each biomarker in the sweat it’s exposed to. Once we have rGO with aptamers attached, we will expose them to a variety of sweat mimic solutions containing known concentrations of each biomarker and measure the resulting impedance across our graphene sheets. Then we will perform regression analysis on the resulting data.

The wiki team is preparing to start adding content to the wiki as teams start submitting their write ups. We’ve also been working on adding a few new features to our wiki, like a custom loading screen. Our hardware is also coming along nicely, and we plan to run another experiment using a more flexible material. The PDMS was curing for 24 hours, but ended up leaking out through our mold. To remedy this, we will go back to using ABS plastic. For the potentiostat, we got all of the necessary materials and are still waiting for our circuit board to arrive. We also have electrodes and will work on modifying them using drop casting.

Our fundraising team is working hard planning a fundraising event (stay tuned!), and our outreach team is still working with summer camps and planning to do outreach in both a nursing home and a prison to bring synthetic biology education to both groups. We are in collaboration with a variety of other iGEM teams working on a Sepsis Symposium event to share the knowledge of medical professionals, sepsis survivors, and other scientists which is very exciting. In September, we all plan to walk, run, or bike a mile to raise money for the Sepsis Alliance as part of their Sepsis Superhero fundraiser, so be on the lookout for posts regarding that event. And last but not least, we are putting the finishing touches on our children’s book about sepsis that we are working on with Ohio State’s team.

Thanks for reading and we hope you are following along with our Subteam Spotlight posts as well on our social media accounts. As always, feel free to reach out with any questions or resources that could be of interest to Team Bio-Spire.

We are back with another update from Team Bio-Spire! The past few weeks have been busy as we adjust to another semester of classes, but we are still full steam ahead in all aspects of our project. Our wetlab team is finishing up expressing and analyzing our DNA aptamers using amplification methods such as PCR and RCA, and finalizing our protocol for attaching them to reduced graphene oxide (rGO) using thermal evaporation. We also performed sequencing on the E. coli that was used to transform our aptamers, and performed biobrick transformations using Shewanella bacteria.

To inform the wet lab team on what concentration of aptamers to use for attachment to rGO, the modeling team is working on a model which predicts how many and what type of functional groups remain on the rGO, depending on the degree of reduction. This was done using mathematical modelling in R and rGO characterization data from many papers in literature. The model will then predict what concentrations of aptamers should be used for optimal attachment to rGO, which is what we are currently working on. We are trying to find what is the volume occupied by functional groups and how much physical space aptamers need to attach.

Our hardware team is currently planning to test fluid flow in our microfluidic device using food coloring. This way, we will see if we get a desired fluid flow in channels, or if we need to change parameters in the COMSOL software and make a new device.They are also modifying the working electrode of a screen-printed electrode by drop casting a solution of GO and drying it with N2 flow. They wiill then test if the modification of the surface of the electrode worked by using either a multimeter or oscilloscope and checking whether current decreases.

The policy and practice team is working on planning a Sepsis Awareness symposium for September 18th that features medical professionals speaking on sepsis, and we have invited other iGEM teams to join as well. They are also researching the treatment of sepsis in other places, and we have reached out to iGEM teams across the world to hear how it is handled in their countries.

We are finishing up writing and editing the wiki writeups for each subteam, which will be posted in order to document all aspects of our project. Our fundraising team is planning a virtual 5k fundraising event, and we have developed team shirts that we will be receiving soon! The collaboration team is finalizing work on our children’s book project with Ohio State, which has allowed us all to showcase our creative sides.

Finally, the public relations team is continuing to document our progress on social media, and recently did an interview with the Campus Times here at Rochester-- keep an eye out for our feature! We have also joined the Sepsis Superhero challenge hosted by the Sepsis Alliance, which will allow us to raise money for their organization by pledging to walk, run, or bike a mile and receive donations from family and friends. Thanks for reading and supporting our team’s efforts to create a better way to diagnose sepsis!

A lot has been going on this week for iGEM Team Bio-Spire! Tomorrow is our Sepsis Symposium, which we have been working hard to plan and advertise. If you’d like to sign up to hear talks from medical professionals, sepsis advocacy experts, and iGEM teams, see our most recent post for the link and QR code!

We are finalizing our writeups for the wiki site, which will give a great overview of all the work we have done and allow the judges to determine how well we have fulfilled the judging requirements. If you’re interested in seeing the type of medals that teams can win, check out the Medal Criteria at the bottom of this page: https://2021.igem.org/Judging/Medals

Our education team visited the Highlands at Pittsford this week, a local senior living community, and gave a presentation on our project. We received a lot of engaging questions from the residents there and enjoyed getting to share our work with them! Our public relations team is currently working on a social media post series with information about some of the techniques we use in lab, such as PCR and Raman Spectroscopy. Next weekend, our team will be participating in the Sepsis Superhero challenge, and we will run, bike, or walk a mile to suport the mission of the Sepsis Alliance. Please consider donating so that we can reach our goal!

Our collaboration team is now taking feedback and performing revisions for the children’s book on sepsis that we are working on with the Ohio State iGEM team-- it’s coming along nicely! If you work with children or have kids in the 7-10 age range, let us know if you’d like to preview our story and give feedback! We are also working on a webinar collaboration for other iGEM teams to share their lab expertise.

Our video team is working on creating a video that summarizes everything we’ve been working on, and our fundraising team is planning our virtual fundraiser 5k event which will be announced soon. We also have team logo T-shirts in the works.

The modeling team used curve fitting in Python to obtain equations for converting sweat concentration to plasma concentration! We’ll be able to find the equation to convert resistance to sweat concentration once we are able to measure the resistance for known concentrations of our biomarkers exposed to our prototype sensor. For the CRP and Lactoferrin biomarkers we have to assume a 1:1 ratio from sweat to plasma because there is nothing in the literature, which is reasonable based on our research. Our software team is currently looking at Labview software to run the software for our device.

Our hardware team performed more testing on the microfluidic device by injecting dyes at different rates to simulate sweat flow. Now, they are waiting for feedback from modeling and will work on printing the electrode cover for incorporating electrodes into the microfluidics. Regarding the potentiostat, we build the circuit daughter board and connected it with Arduino, which we will use to write code.

Finally, in wetlab we ran PCR and a 2.5% agarose gel binding assay on our aptamers. We next need to attach the aptamers to our rGO, continue RCA to amplify the aptamers, and then test the functionality! Thanks to everyone who is following our project and supporting it in any way, we appreciate it!

Sepsis Superhero Challenge

In order to raise money for the Sepsis Alliance, a foundation that works for sepsis advocacy and awareness, our team participated in their Sepsis Superhero Challenge. Several team members ran, biked, or walked a mile during the last week of September, and family and friends donated to the cause on our team page. Through this initiative, we were able to raise over $200 for the Sepsis Alliance!

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