COVID

Mutation-mapping tool could yield stronger COVID boosters, universal vaccines

Anonymous — Tue, 10 Aug 2021 20:13:22 +0000

Mutation-mapping tool could yield stronger COVID boosters, universal vaccines Anonymous (not verified) Tue, 08/10/2021 - 14:13

Kelsey Simpkins

Researchers at CU Boulder have developed a platform which can quickly identify common mutations on the SARS-CoV-2 virus that allow it to escape antibodies and infect cells.

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Grad students and postdocs volunteer for campus COVID-19 population monitoring effort

Anonymous — Thu, 06 Aug 2020 16:09:31 +0000

Grad students and postdocs volunteer for campus COVID-19 population monitoring effort Anonymous (not verified) Thu, 08/06/2020 - 10:09

Jonathan Raab

A collection station outside of the Athletics Department on July 28. Photo courtesy Kristen Bjorkman.

CU Boulder is ramping up its ability to conduct COVID-19 monitoring analyses by enlisting volunteer graduate students and postdocs across campus, including several from the Department of Chemical and Biological Engineering.

Professors Leslie Leinwand, Roy Parker and Sara Sawyer, who have been playing important roles in CU Boulder’s COVID-19 testing strategy efforts, realized that making testing easily available on campus and monitoring asymptomatic students could help reduce the spread of disease.

“We are committed to making the CU Boulder community as safe as it can be and we believe that our best approach is to test and monitor as often as feasible,” Leinwand and Parker said in a joint statement.

“Studies have shown that a test every month or two weeks will be insufficient to stop or slow the spread of the virus infection. This will be an enormous effort requiring coordination of sample collecting and running monitoring tests from individuals at high risk of contracting or transmitting the virus.”

The testing plan will evolve as the situation changes and new technologies become available, but the contributions of the volunteers will remain important regardless.

“Critical to the success of this plan is the tremendous spirit of generosity in the form of volunteers among our graduate students, post-docs, staff and faculty to help us in this effort,” they said.

They approached Kristen Bjorkman, a postdoctoral researcher working in the Leinwand Lab of Molecular, Cellular, and Developmental Biology and the BioFrontiers Institute, to work on the all-volunteer monitoring program. Bjorkman now serves as the surveillance advisor and liaison for this effort and, recognizing the need for volunteers with the right experience and skill set for lab testing, put out a call to recruit students, postdoctoral researchers and faculty with life sciences backgrounds.

“We are fortunate to have expertise from multiple departments on campus as well as Medical Services to be able to formulate the safest, most efficient and most robust approach to sample collection, protocol validation and information security,” Bjorkman said. “Each volunteer is bringing a unique and valuable skill set with them. Some faculty already have decades of experience performing the exact molecular techniques in the lab that underlie the tests being deployed here.”

Testing process

[video:https://www.youtube.com/watch?v=THP-6oNvGJE]

Individuals to be tested as part of monitoring on campus—especially those judged to be at high risk of contracting or transmitting COVID-19—will self-collect their saliva in vials at outdoor collection stations. The saliva donors add a solution and seal and disinfect the vial.

Before the sample is ever opened, the collection station attendant—a volunteer graduate student or postdoc—will then boil the sample for at least 10 minutes to ensure that any virus present is rendered inactive. When the sample arrives at a specially prepared secure lab, the volunteers conduct molecular analysis on pools of these samples to determine if molecular signatures of the virus are present.

If one of these pools tests positive, the team will then work with Medical Services to get sample donors certified clinical testing, appropriate medical care and contact tracing as necessary.

The outdoor collection stations will be set up outside of the athletic training facilities to help test athletes and staff, who are being tested using pooled RT-PCR as well as an RT-LAMP assay developed in Sara Sawyer's lab. Collection tents will be present at all three student move-in events in August. Incoming students who have not already completed a PCR test within five days of move-in will be tested with the RT-LAMP screening tool and swabbed for a diagnostic PCR test to be run in the Wardenburg Clinic.

A semester-long collection process is also planned, with weekly sampling and analysis of on-campus residents, student athletes and other individuals at high risk of contracting or transmitting COVID-19.

These efforts will happen in concert with daily wastewater monitoring of residence halls and select high-use buildings on campus, as targeting collection at these sites can occur as necessary.

ChBE graduate students step up

Get Involved

Graduate students or post-docs with a life sciences background affiliated with CU can volunteer to assist with the testing effort by contacting Kristen Bjorkman at bjorkmak@colorado.edu.

Zachary Baumer is a graduate student in Timothy Whitehead’s lab, which specializes in protein engineering and synthetic biology. Volunteering as a tester was a natural choice for him—and a source of inspiration.

“I am having trouble staying motivated in these weird times,” Baumer said. “But I believe this is important and purposeful, and that drive will carry over to my own research. I’m always looking to be part of something bigger than myself.”

Holly Coleman is an incoming graduate from the Missouri University of Science and Technology, about to begin her first semester as a graduate student here at CU.

“I volunteered because I want to help with the University's effort to monitor COVID on campus, and I thought my previous laboratory experience would be useful,” Coleman said. “I learned how to perform many biological assays during my undergraduate studies and internships.”

Ankur Sarkar of the Fox group works in a separate field, but volunteered to support CU and the Boulder community.

“Testing is known to help suppress infectious spread,” Sarkar said. “This effort is an opportunity to use my laboratory skills to meet a critical yet unmet need.”

Varsha Rao of the Anseth group likewise works in a field distinct from COVID-19 research, but has had a strong, ongoing interest in how the virus has spread in various countries.

“As a scientist and a member of the CU Boulder community, I feel really passionate and morally obligated to help out with the testing efforts in any way I can,” Rao said. “This opportunity sounded like the perfect way for me to use my scientific skills and knowledge to help the university open safely during a pandemic. I think engineering and research training forces you to make and justify decisions based on data. I can recognize why testing efforts are so important. They will allow us to better track and isolate COVID cases in a timely manner, providing the data necessary to quash outbreaks.”

Monitoring assays of those already on campus have already begun, helping the multifaceted team troubleshoot its processes and prepare to upscale its efforts when more students return in August.

Cross-campus collaboration

The developing COVID-19 testing and monitoring program has generated collaborations with students and faculty from a number of departments and units across CU Boulder, including Molecular, Cellular, and Developmental Biology; the Department of Biochemistry; the Department of Chemical and Biological Engineering; the Department of Psychology and Neuroscience and the BioFrontiers Institute.

The proposed pooled assays are being developed by the Parker Research Group. A rapid assay that will be used was developed by the Sawyer Lab. FDA approval for that test is being sought.

Additional support

Cresten Mansfeldt of The Department of Environmental Engineering and Sara Sawyer of MCDB and BioFrontiers developed wastewater monitoring programs and rapid screening tests, respectively.
Matt McQueen of Integrative Physiology and the Institute for Behavioral Genetics contributed to CU’s contact tracing capacity by training over 100 students.
Dan Larremore of Computer Science and BioFrontiers worked with Roy Parker to produce a study that confirmed the value of population testing and the importance of short turnaround time.
Gloria Brisson, Ann Mattson and the staff of Medical Services have continually provided expertise and are establishing a Public Health Clinic to specifically serve students who may have COVID-19.
Leisha Connors Bauer from Health Promotion is leading the contact tracing program through the Public Health Clinic, and has contributed numerous staff and student volunteers.

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Going remote offers challenges and new opportunities for young visiting scholars

Anonymous — Tue, 23 Jun 2020 19:52:07 +0000

Going remote offers challenges and new opportunities for young visiting scholars Anonymous (not verified) Tue, 06/23/2020 - 13:52

Jonathan Raab

The Young Scholars have frequently connected and collaborated remotely during the summer program. Photo courtesy Mason Lyons.

With the COVID-19 pandemic hitting earlier this spring, the 2020 Young Scholars Summer Research Program had to go fully remote. But this year’s “visiting” students have been more than up to the challenge, adapting to the virtual program by learning new skills and connecting with research experts and engineering business leaders.

“It has been fantastic working remotely with the students,” program coordinator Associate Professor Timothy Whitehead said. “The students in the program are all engaged and ask careful and thoughtful questions during our Zoom chats.”

While over a dozen students typically participate in the 10-week program—with hands-on lab experience, classroom instruction, and field trips for outdoor recreation or to research facilities like NREL—five students are participating this year, conducting their research and attending a weekly workshop with faculty remotely.

Typically, the program offers visiting students the opportunity to enjoy Boulder and Colorado through outdoor activities and group outings.

“Our big draw—besides the world-class science and scientific environment—has been the city of Boulder and surrounding areas," Whitehead said. "It’s easy to recruit the top students to come here when they’ve spent a summer on Pearl or up in the foothills.”

While the program was unable to offer students these experiences this year, Whitehead and the participating faculty and staff quickly pivoted to weekly remote career development workshops and professional meetings over lunch.

“In recent weeks, students have met biotech scientists, nanotech company co-founders, graduate students and professors,” Whitehead said.

Two of the participating students are Mason Lyons of the University of Iowa and Alex Evenchik of the Massachusetts Institute of Technology.

Lyons is originally from La Motte, Iowa, and studies chemical engineering at the University of Iowa. He has interests in renewable energy and sustainability, including the history of the green movement and communication. A classmate recommended the program, and CU Boulder’s association with the National Renewable Energy Lab provided an additional incentive to apply.

“My research project aims to model an electrochemical cell, such as a hydrogen fuel cell, to calculate its overall efficiency using a voltage input which significantly increases the operating rate of the cell,” Lyons said. “I have learned about electrochemical cell reaction kinetics, equivalent circuit modelling, and how to solve these models in Matlab.”

While Lyons was looking forward to visiting Boulder in person, the program’s switch to a remote experience provided a new, challenging experience that expanded his skillset.

“I did not have any previous experience with modelling and computational experimentation, but it has been intriguing to learn how these techniques are used in conjunction with lab experiments,” Lyons said. “It has initially been hard to work for long periods of time because I am still working out the kinks for my Matlab code and incessantly am running into bugs. My mentor and I have had open and plentiful communications making troubleshooting easy on me.”

Alex Evenchik hails from Cambridge, Massachusetts and is majoring in materials science and engineering at MIT. While looking up professors who were conducting research at the intersection of materials science and biology, he connected with Assistant Professor C. Wyatt Shields IV, who recommended that he apply to the Young Scholars Summer Research Program.

“Beside Dr. Shields’ research, I was attracted to this program by the opportunity to spend a summer conducting research in a new environment so that I could broaden my view of research programs at different schools,” Evenchik said. Spending a summer in Boulder also appealed to him, but he has pressed on with his research despite not being able to visit in person.

“I’m using computational fluid dynamics software to give insight into and support the experimental design process of the PhD student I’m working with,” Evenchik said. “I’ve mainly been focusing my time on understanding the multi-physics software we are using, as well as looking more deeply into the fluid dynamics that describe the phenomena we are interested in utilizing.

"Although I haven’t been on campus, I still feel like the work I’m doing has a clear role in the lab’s objectives. Of course, not having the ability to interact daily and as easily work things out together makes the work more difficult, but daily meetings and the ability to call when needed has made the process relatively smooth.”

Whitehead sees two major takeaways for the “visiting” students.

“I hope that all students will have made a contribution in their host research laboratory, with the attendant dedication and persistence that takes,” Whitehead said. “Most of this year’s cohort had previous wet lab experience. I hope that the students now have a newfound appreciation for the excellent computational work done in the department.”

The Young Scholars Summer Research Program concludes in August.

The Young Scholars Summer Research Program went remote for 2020, but the students have been up to the challenge.

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Why developing a successful COVID-19 vaccine is only half the battle

Anonymous — Thu, 04 Jun 2020 18:15:38 +0000

Why developing a successful COVID-19 vaccine is only half the battle Anonymous (not verified) Thu, 06/04/2020 - 12:15

Kelsey Simpkins

A multidisciplinary team is working to build a pilot-scale system capable of producing 10,000 to 100,000 doses of COVID-19 vaccines per run that would be ready for use as human trials of vaccines begin in the next year.

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CU siblings share the science on pandemics with COVID-19 podcast

Anonymous — Wed, 20 May 2020 15:53:23 +0000

CU siblings share the science on pandemics with COVID-19 podcast Anonymous (not verified) Wed, 05/20/2020 - 09:53

Jonathan Raab

Listen to the Pandemic: Coronavirus Edition podcast

New episodes of the Kisslers' podcast air every week. The show can be found on a variety of podcast platforms.

Two College of Engineering and Applied Science alumni launched a new podcast earlier this year aimed at providing clear and accurate scientific information about the COVID-19 pandemic. If their collaboration seems natural, it is because they have more in common than degrees from CU Engineering—they also happen to be brothers.

Engineering alumni Mark and Stephen Kissler—alongside host and producer Matt Boettger—started the Pandemic: Coronavirus Edition podcast to share their expertise in medicine and mathematical modeling as applied to the ongoing COVID-19 crisis.

New episodes air weekly and feature the Kisslers’ commentary on topics relating to the crisis, from antibody testing efforts in Telluride, to mental wellness during social isolation, to health disparities along racial lines.

“It serves both as a science communication platform where we discuss an evidence-based approach to the news as well as a forum for us to discuss ways of staying grounded in the midst of the rapid changes in our lives that we are all experiencing,” said Mark Kissler (ChemEngr’10).

“It started out of an understanding that each of us brought a unique but complementary perspective and also that conversation and stories are often the best way to engage these types of complex issues.”

Mark, left, and Stephen, right connect on Zoom.

Mark serves as a clinician at the University of Colorado Hospital. He is also an instructor at both the CU School of Medicine and the College of Engineering and Applied Science through the Engineering Honors Program and the Herbst Program for Engineering, Ethics & Society.

“We had been thinking about respiratory pandemic pathogens for the past six or seven years,” said Stephen Kissler (ApMath‘13). “Matt Boettger brought us together for the podcast, looking to explore the human side of all this. How do we explore the different experiences in both the hospital and modeling worlds, and how do we construct our lives in this scenario?”

Stephen is an epidemiologist and postdoctoral fellow at the Department of Immunology and Infectious Diseases within Harvard’s T.H. Chan School of Public Health.

Sharing science in uncertain times

The Kisslers and Boettger set out to make the podcast accessible, with an eye toward using COVID-19-related news and topics to bring their medical and mathematical modeling expertise to bear.

“Our target audience was initially our friends and family,” Stephen said. “The point was to communicate in as an accessible and straightforward way as possible. We were thinking about things at the most fundamental level. What do these things mean for us, and how might we help the people that we know and love to understand them?”

It is no surprise that several episodes focus on pandemic-related events and issues in Colorado.

“We all grew up in and have very strong ties to Colorado,” Stephen said. “We weren’t sure this show would be for anyone other than our parents! But I also think that the best way to think about this pandemic is in a local context, although we always have to have an eye to the international context. The disease is spreading at a very local scale.”

The Kisslers said they also recognize a continuing need for direct communication from science and medical professionals as misinformation and political considerations color the narrative around the pandemic.

“One of the things that strikes me about the podcast medium is that we can have an informal tone and really approach an authentic dialogue in which we question one another, clarify things and come to an understanding,” Mark said. “I think that in my favorite podcasts—or lectures, or other educational experiences, for that matter—it is often the offhand remark that sparks a new understanding or a new way of looking at things.”

“We can challenge each other, we can ask each other questions, we can clarify right on the spot," Stephen said. "That sort of mimics what is going on in the community everyday. We’re trying to collectively come to what the truth and the reality of the situation is. It’s never been more important than it is now for the common person to evaluate different sources of information coming in because they have a direct bearing on our lives. The podcast has allowed us to contribute to those conversations in ways that we wouldn’t have been able to otherwise.”

Those contributions have been well-received thus far, as the podcast has generated a steady stream of positive feedback from those within and without the scientific community, they said.

“The most meaningful comment for me was from a couple awaiting their first child, who said that it helped alleviate some of their anxiety and provide a touchpoint for good information,” Mark said. “Another listener said that it helped concretely influence the ways that he and his household were social distancing.”

Bringing CU’s engineering mindset to medicine and mathematical modeling

Mark and Stephen credit their foundational education as CU engineers with the success they have found in their respective fields.

Mark Kissler was the class of 2010 Silver Medal Award winner for the college, a Boettcher Scholar and a member of the Engineering Honors Program. After graduating from CU, he went on to earn his master’s in narrative medicine from Columbia University and his medical degree at Baylor Medical School. He returned to Colorado to complete his residency at CU Anschutz.

“Engineering seems to me to be a great preparation for medical training,” Mark said. “So much of medicine is about understanding how to break down problems, to think analytically, and to keep both the small and the large picture before you at all times.

“I can't overstate the importance of engagement in the humanities that are uniquely available through the Herbst program, which propelled me into narrative medicine and continue to inform the ways that I engage with patients and colleagues. It's that sense of the technical motivated by and situated within a larger context that still motivates my teaching and work as a clinician.”

Stephen earned the Outstanding Undergraduate of the College Award when he graduated in 2013 with a BS/MS. He participated in both the Engineering Honors and Global Engineering programs. After graduation, he became a Gates-Cambridge Scholar and earned his PhD at Cambridge University.

“The education and the overall experience that I got at CU was absolutely world-class,” Stephen said. “Applied Math had exceptional instruction and mentorship. Anne Dougherty took a personal interest in each of her student's progression. She was very attuned with what each student wanted to do with lives and careers. There was a constant stream of opportunity that she made sure was open to us.

“The training I got at CU was rigorous and practical. I did my PhD at the University of Cambridge, where the students were able to solve mathematics problems to a remarkable degree. But when it came to solving a research problem—the spread of a pandemic, for example—it was much more difficult for them than it was for me. That was training that I got at CU that is remarkably rare. Courses are so project-based and oriented toward this paradigm of mathematics as a tool for thinking very clearly about the world.”

Stephen credits the Engineering Honors Program for inspiring him to use mathematics in truly practical, humanized ways.

“I’m studying a pandemic now, and there is certainly something to be said about the mathematics of pandemics. But this is also a human thing. I need to be able to understand who I am in the context of the outbreak, and in the context of social responsibility and a deep commitment to help people,” he said.

As a graduate of the Department of Chemical and Biological Engineering, Mark Kissler has some advice for aspiring engineering students interested in a career in medicine.

“Don't underestimate the importance of breadth of experience, both intellectually and personally,” he said. “We are urged from so many places to do things because they are good for the application, because they are the type of experiences that will ‘look good’ in the future. But freeing yourself from those secondary, external motivators and approaching opportunities that will allow you to ask better, more authentic questions about what you uniquely have to offer the world—I think that's the best preparation for the real work in these fields.”

Two brothers who are alumni of the College of Engineering and Applied Science bring their expertise to a popular COVID-19 podcast.

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From Bryant lab to London, alumna’s educational journey led her to the fight against COVID-19

Anonymous — Tue, 28 Apr 2020 17:35:30 +0000

From Bryant lab to London, alumna’s educational journey led her to the fight against COVID-19 Anonymous (not verified) Tue, 04/28/2020 - 11:35

Jonathan Raab

Anna Blakney, a third-generation alumna of the Department of Chemical and Biological Engineering, is among the researchers working to develop a vaccine for the COVID-19 virus at Imperial College London.

“It’s really an incredible opportunity,” Blakney said. “As scientists, what we are really in it for is the joy of discovery—but also being able to impact human health.”

Blakney was the College of Engineering and Applied Science’s class of 2012 Silver Medal Award winner and went on to earn her PhD in bioengineering from the University of Washington. Currently she is the Marie Sklodowska-Curie Post-Doctoral Research Fellow at Imperial College London.

Blakney works in Professor Robin Shattock’s lab within the Department of Infectious Disease. She is part of a research group that has been developing a vaccine platform for almost four years—one that uses self-amplifying RNA that is derived from an alpha virus and encapsulated in lipid nanoparticles. When delivered to a cell, this RNA makes copies of itself, resulting in a high amount of protein and antigen expression—meaning dosages can be dozens or hundreds of times smaller than usual.

"This is highly useful for outbreak scenarios, because it means we can make a higher number of doses from the same batch size of RNA, which is advantageous when we're trying to make millions of doses quickly," Blakney said. “We were planning on going into clinical trials later this year, but with the spread of coronavirus becoming a global pandemic, we were well-poised to be able to pivot and focus on making this vaccine."

Research into a potential vaccine for COVID-19 at Imperial College is an international effort between the Shattock lab, Acuitas Therapeutics of Vancouver and TriLink Biotechnologies in California. The Shattock lab has seen its research staff reduced from 30 to eight due to social distancing measures—with those remaining working on the vaccine.

Her research group is preparing the vaccine for a succession of upcoming clinical trials. If they go well, the vaccine would be available next year. What remains to be seen is how often the vaccine will need to be modified and re-administered, like the yearly flu shot.

“It will depend on how long the immunity from the vaccine lasts—one year, five years, or does it last a lifetime?” Blakney explained. “But it also depends on how successful we are in limiting the spread of the virus, and whether it is able to hide in viral reservoirs—and whether we will see seasonal outbreaks.”

As the only trained engineer among a team of immunologists, her perspective helps bring fresh ideas to her group’s problems.

“The engineering perspective is one of coming in with this iterative design mindset of testing something, changing it, and really trying to understand the system. I think that’s pretty unique to engineering training, and I think that’s a really valuable skill set.”

Blakney credits a summer camp-style outreach program at CU for seeding her interest in bioengineering. As a high school student, she attended this program one summer, spending four days in the dorms and participating in various engineering-related activities. One such event was a lecture and demonstration concerning polymers by Professor Kristi Anseth. This presentation inspired Blakney to attend CU to become a chemical engineer.

“I’ve always had a real interest in impacting human health. I find it really fascinating—especially making tools to help prevent diseases,” Blakney said.

It was her education at CU that helped prepare her for just such a career in medical research.

“Majoring in chemical engineering is one of the best undergrad majors you can do, that’s what I tell everybody,” she said. “It gives you this unique way of thinking critically, but you also have a problem-solving sort of outlook. It’s really challenging and makes you think about how to make things work.”

As an undergraduate, Blakney worked as a researcher in Professor Stefanie Bryant’s lab.

“Stefanie was an amazing mentor for me,” Blakney said. “She was truly my inspiration for deciding to go into research. I know from my experiences with her that I wanted to lead a research group and become an independent researcher. It set me up perfectly to know what my next step was going to be."

Bryant would frequently meet with Blakney one-on-one, which was a rare commitment for a faculty member to make with an undergraduate. The two still keep in contact, often seeing one another at conferences prior to the pandemic.

For biomedical research, having an engineering background helps her think through the challenges associated with scaling up the production of treatments.

“Vaccine development at a lab scale is easy to do, but when you think about scaling it up to make five million doses, that’s really a chemical engineering problem,” she said.

“No matter what you’re developing in the bio field, there is a need for chemical engineers and their skill set.”

An alumna of the Department of Chemical and Biological Engineering is at the forefront of international COVID-19 vaccine research.

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