BioFrontiers

As pandemic spread, ‘I couldn’t just sit around’

Anonymous — Wed, 04 May 2022 23:02:14 +0000

As pandemic spread, ‘I couldn’t just sit around’ Anonymous (not verified) Wed, 05/04/2022 - 17:02

Catherine Arnold

After getting stuck in China, graduating PhD student pivoted research to help test for the COVID-19 virus without nasal swab

Stranded for the first two months of the COVID-19 pandemic at his family home in China, virus specialist Qing Yang was inspired to change his research direction, helping to create one of that pathogen’s first saliva tests.

The test was first deployed at the University of Colorado Boulder and around Colorado starting in the late summer of 2020 before being used elsewhere in the United States and Brazil.

Using data from the test, Yang and a research team published findings about asymptomatic COVID-19 in May 2021, concluding that a small number of individuals spread the disease.

Traveling to help fight COVID-19

Yang’s journey back to ��ý�Ļ��Ʒ in spring 2020 was delayed when the U.S. Embassy in China closed in response to the burgeoning pandemic. Sara Sawyer, one of his advisors and a professor of molecular, cellular and developmental biology, helped brainstorm a route back to Boulder, verifying in a letter to the U.S. Embassy that he was needed for important COVID research.

At the top of the page: Qing Yang examines samples of the rapid COVID-19 saliva test in the Sawyer Lab (Glenn Asakawa/��ý�Ļ��Ʒ). Above: Qing Yang is a graduating PhD student in molecular biology.

“I realized that working in such a related area, I couldn’t sit around,” said Yang, a graduating PhD candidate in molecular biology.

While in China, he used computational skills learned in his undergraduate studies to look at the dynamics of viral transmission and how more frequent testing could prevent the spread of the virus, he said.

In March 2020 he was able to exit to Thailand—staying there two weeks to get around travel limits from China during the early pandemic—and re-enter the United States in April 2020, after a brief stop in Canada.

Creating an important test

Back in Boulder, Yang and others in Sawyer’s research lab at the BioFrontiers Institute began looking at ways to reconfigure an existing rapid test method—previously used to diagnose dengue and other infection—to work without nasal swabs.

They created a test that uses saliva to produce answers in 45 minutes. Using very few materials, only pipettes (slender tubes for transferring liquid) and a heating source, their test was considered community deployable.

After ��ý�Ļ��Ʒ asked them to prepare the test for locations on campus, the team ran hundreds of samples to vet their system. Learning that test accuracy dropped when they scaled the testing, they spent several nights figuring out where the process went wrong and realized samples weren’t sealed well and evaporation was rendering results less accurate. Adding appendices to their paper, they showed how to troubleshoot step by step for accurate readouts.

Then the team worked to source materials for the test—a challenge during the early pandemic supply-chain slowdown—and deployed it on the ��ý�Ļ��Ʒ campus and elsewhere.

Yang and his colleagues published their findings about their test as well as the necessity for frequent testing.

Before the pandemic, Yang’s graduate work focused on finding host signatures (signs that a cell has been occupied by a pathogen) that signify an ongoing infection. This research was part of a project to find treatments for certain viruses. When the COVID pandemic started, he paused those investigations but has since returned to them.

In March 2020, he and a few colleagues co-founded the company Darwin Biosciences, which licenses the techniques in their test. With Darwin, they’re currently developing a handheld device that will detect host signatures in a saliva sample instead of pathogens, using the signatures as an indication of infection.

Previous viral research

As an undergraduate studying computer science and microbiology, Yang read the book The Hot Zone, about the origins of Ebola.

In the case of COVID response, everything accelerated; you immediately saw the outcome of your research being put into effect. That’s exciting.”

“I was fascinated by how researchers jump into these scenarios,” Yang said about why he chose to study viruses in graduate work.

He’s also intrigued by “how simple viruses are—and at the same time they can cause such traumatic consequences in public health and trigger such diverse human symptoms.”

Interested in understanding more, he planned to use his two areas of study, computer science and biology, to mine data and conduct original research.

“Knowing that CU’s BioFrontiers Institute focuses on this type of collaboration, computation with biology, is part of why I chose Boulder for my graduate work,” said Yang.

After his CU graduation, Yang will work as a postdoctoral fellow at Fred Hutchison Cancer Center in Seattle, using computational research to determine how hosts respond to their first encounter with a virus. The work will involve collaboration with labs and museums in Mexico to look at the virus genetic sequences from archeological remains. In part, they’ll try to learn how past colonialism in Central America affects the distribution of viruses within the population and the disease outbreaks that have happened to Indigenous people.

Having his own opportunity to find solutions during a pandemic made him see the ways laboratory and computational research can be put into practice in the real world, said Yang.

“In the case of COVID response, everything accelerated; you immediately saw the outcome of your research being put into effect. That’s exciting. So is the fact that so many people stepped up and learned so many aspects of this virus.”

After getting stuck in China, graduating PhD student pivoted research to help test for the COVID-19 virus without nasal swab.

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Video: ��ý�Ļ��Ʒ experts give scientific update on COVID-19 pandemic

Anonymous — Fri, 17 Sep 2021 14:24:51 +0000

Video: ��ý�Ļ��Ʒ experts give scientific update on COVID-19 pandemic Anonymous (not verified) Fri, 09/17/2021 - 08:24

��ý�Ļ��Ʒ experts provide an update on the status of the delta variant in the United States, takeaways from the latest data on vaccines and breakthrough COVID-19 cases, and how the campus is approaching its sustainable response to the pandemic.

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Students may now pursue a minor in computational biology

Anonymous — Tue, 15 Jun 2021 19:19:50 +0000

Students may now pursue a minor in computational biology Anonymous (not verified) Tue, 06/15/2021 - 13:19

Tim Grassley

��ý�Ļ��Ʒ’s new minor combines disciplines like biology, computer science and mathematics

Undergraduates at the University of Colorado Boulder interested in biology and computer science used to have to find creative ways to blend their interests on their own. That changed when ��ý�Ļ��Ʒ launched a computational biology minor this past year.

At the top of the page: Printed out copy of the human genome (Adam Nieman/Flickr). Above: Maria Carilli, a ��ý�Ļ��Ʒ student.

The program offers interdisciplinary classes to undergraduates interested in the intersection of fields like biology, computer science and mathematics. This, in turn, allows students and researchers to develop new ways of understanding biological data, species’ behavior, the structure of genomes and other types of complex biological systems. The minor teaches students to approach biological questions using computational ways of thinking, such as simulating ecosystems using mathematical models.

The field offers opportunities to delve into specialized research of living organisms but also explores the way these findings fit into a wider understanding of biological systems. When communities consider trying to alter the behaviors of biological phenomena, like viruses, computational biology approaches can help leaders make informed decisions that predict outcomes of those choices.

Computational biology is extraordinarily relevant to some of the biggest questions and challenges we’re facing globally.”

“Computational biology is extraordinarily relevant to some of the biggest questions and challenges we’re facing globally,” says Kristin Powell, director of interdisciplinary education with the BioFrontiers Institute and associate director of the minor. “One thing that has come out of the last year is the pressing need for computational biology to study phenomena like the spread of COVID-19 and how we stop it.”

Creating a broad, interdisciplinary vision

The minor emerged from ��ý�Ļ��Ʒ’s interdisciplinary BioFrontiers Institute. Faculty had seen success in its graduate-level IQ Biology PhD program, but they wanted to address a growing gap in opportunities for undergraduates to learn about these innovative ideas.

Rather than follow the program designs of peer universities, which in many cases add some computer science coursework to a biology major or vice versa, ��ý�Ļ��Ʒ’s faculty opted to make the program as interdisciplinary, cross-departmental, cross-college and collaborative as possible.

“There was a fateful meeting in the biotech building where we got 10 faculty from across campus in the room and we asked, ‘If we designed a computational biology degree from the ground up, focusing on the most important ideas in the field, what would our ideal program look like?’” says Aaron Clauset, associate professor of computer science and faculty director of the minor. “‘How would it train young scholars for the next century of biological research?’ It was an inspiring meeting.”

Key support came from Robin Dowell, who is associate professor of molecular, cellular and developmental biology and a member of the BioFrontiers Institute's core faculty. Dowell’s research focuses on computational biology and uses an "antedisciplinary approach," whereby she "ignores boundaries between disciplines to follow this biological problem wherever it leads."

Top image: Kristin Powell, the director of interdisciplinary education with the BioFrontiers Institute, helped create this new minor. Middle image: Aaron Clauset, associate professor of computer science, also helped create this new minor. Bottom image: Robin Dowell, associate professor of molecular, cellular and developmental biology, was a key leader from the College of Arts and Sciences.

By the end, the team had a rough template for a computational biology minor. With the plan in hand, Powell, Clauset and Dowell began realizing the vision.

Launching the minor took about three years. Powell, Clauset and Dowell worked closely with a team to build an interdisciplinary curriculum and audits, establish the program’s administrative home in the Computer Science Department, determine how students gain access to coursework, decide who advised students and generate cross-college support.

“Each stage of launching an interdisciplinary program requires a lot of care,” notes Powell, “because the ultimate goal is to ensure that academic and administrative support enables undergraduates to seamlessly navigate an interdisciplinary education.”

Amplifying ��ý�Ļ��Ʒ’s remarkable opportunities

After launching in collaboration with the Computer Science Department, the program quickly gained interest from students across the university, many of whom had previously tried to bring together their interests in biology, computation and mathematics on their own.

One student, Maria Carilli, did not realize ��ý�Ļ��Ʒ had launched a minor in computational biology until she began researching graduate schools that focus on bioinformatics.

“One program that stood out to me, because I value interdisciplinary approaches to problems, was CU’s IQ Biology PhD program,” says Carilli. “I was put in touch with Dr. Kristin Powell, and she told me about that graduate program and then also about this really exciting opportunity that was just starting up, the computational biology minor.”

Enrolling opened opportunities for Carilli, who graduated in spring 2021 with majors in biophysics and music and a minor in computational biology, to learn a new coding language, study methods of thinking and apply many of the tools she had learned over her ��ý�Ļ��Ʒ academic experience.

She particularly enjoyed classes on biological networks, taught by Aaron Clauset, and statistical analysis of the human genome, taught by John Rinn. In both cases, students downloaded large data sets from publicly accessible databases to generate predictive algorithms and draw new conclusions.

“CU is so big and such a great research university, all of the departments are really strong,” says Carilli. “The interdisciplinary nature of computational biology is really well-served by CU.”

Carilli, who begins a PhD program in biochemistry and molecular biophysics at the California Institute of Technology in fall 2021, notes that, at first, the broad list of faculty and students’ majors, which span thirteen undergraduate majors and counting, was exciting but also intimidating. At the time, she was concerned she would have gaps in her skills that would put her at a disadvantage.

For those undergraduates who are hesitant about computational biology because of similar worries, she has this advice:

“Don't be afraid to explore things that you don't have experience in. That's the way you're going to learn and the way you're going to discover what you actually like and what you want to do.”

To enroll in the computational biology minor, students can submit a statement of interest and speak with Eva Lacy, the program’s undergraduate academic advisor.

The computational biology minor gained guidance and support from Robin Dowell and the Computational Biology Committee, Ken Anderson, Rhonda Hoenigman, Eva Lacy, Kim Noice, Mary Steiner, Beth Webb, Amber McDonnell, Eli Hallowell, Travis Torline, Lorenzo Rivas, the Computer Science Undergraduate Curriculum Committee, the College of Engineering and Applied Sciences Undergraduate Education Council, the BioFrontiers Institute and the many staff, faculty, deans and partner departments in the College of Arts and Sciences and the College of Engineering and Applied Science.

��ý�Ļ��Ʒ’s new minor combines disciplines like biology, computer science and mathematics

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New COVID-19 test returns results in 45 minutes, without nasal swab

Anonymous — Tue, 28 Jul 2020 17:09:31 +0000

New COVID-19 test returns results in 45 minutes, without nasal swab Anonymous (not verified) Tue, 07/28/2020 - 11:09

��ý�Ļ��Ʒ researchers have developed a rapid, portable, saliva-based COVID-19 test able to return results in 45 minutes.

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Arthritis, autoimmune disease discovery could lead to new treatments

Anonymous — Mon, 20 Nov 2017 21:56:38 +0000

Arthritis, autoimmune disease discovery could lead to new treatments Anonymous (not verified) Mon, 11/20/2017 - 14:56

��ý�Ļ��Ʒ researchers have discovered a potent, drug-like compound that could someday revolutionize treatment of autoimmune diseases by inhibiting a protein instrumental in prompting the body to start attacking its own tissue.

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Two distinguished profs recognized as top inventors

Anonymous — Mon, 20 Feb 2017 23:38:32 +0000

Two distinguished profs recognized as top inventors Anonymous (not verified) Mon, 02/20/2017 - 16:38

Roni Dengler

Leslie Leinwand and Chris Bowman named fellows of the National Academy of Inventors

University of Colorado Boulder Distinguished Professors Leslie Leinwand and Chris Bowman have been named fellows of the National Academy of Inventors (NAI).

Leinwand is chief scientific officer of the BioFrontiers Institute and professor in the Department of Molecular, Cellular and Developmental Biology, and Chris Bowman is the James and Catherine Patten endowed chair of the Chemical and Biological Engineering Department.

A nonprofit organization founded in 2010, the National Academy of Inventors aims to acknowledge academic innovators who hold U.S. patents that benefit society.

Election to NAI fellow status is “the highest professional distinction accorded solely to academic inventors who have demonstrated a prolific spirit of innovation in creating or facilitating outstanding inventions that have made a tangible impact on quality of life, economic development and welfare of society,” the NAI states.

Bowman and Leinwand’s research and innovations do just that.

Leslie Leinwand

“Since I started my career as an academic scientist, I’ve always wanted to treat or cure genetic diseases; that’s been my passion right from the start,” says Leinwand, whose lab researches genetic heart and skeletal muscle diseases.

She made progress toward this goal with her first patent, which outlined a new way for scientists to secure a fundamental protein found in muscles. With this ability, they could then make progress toward understanding how mutations in the protein, and others it interacts with, might lead to disease.

“My first patent was quite special to me,” she says. “We were trying to develop some assays that are now translating to therapies.”

Since then, she has been awarded three other patents and co-founded two biotech companies based on technologies developed in her lab, including a mouse model of hypertrophic cardiomyopathy, a genetic heart disease that is a common cause of sudden death in athletes.

Leinwand presented these mice to the scientific community as a test bed for drugs that might treat the disease. One of the companies she co-founded, MyoKardia, now develops small molecules and uses these mice to test the effectiveness of compounds that are now in clinical trials to treat the disease.

“It’s flattering to be named a fellow,” says Leinwand. “It’s nice for CU, and I’m happy about it.”

Bowman, who’s been awarded close to a dozen patents, is likewise flattered to be named to this year’s NAI fellows class.“It’s a very big honor,” he says. “To be recognized in that way, particularly by your peers, is incredibly nice.”

Bowman’s research combines engineering and material science with organic chemistry “to address problems that couldn’t be addressed otherwise.”

“We try to design new materials that enable properties or capabilities that the material wouldn’t have otherwise,” says Bowman.

Chris Bowman

Many of these new materials are dental restoratives, like cavity fillings and teeth sealants. His lab also works on so-called “smart” materials that respond when exposed to light or when heated up as well as on developing materials that solidify faster or are stronger than existing materials. These innovations could prove useful for micro- and nanotechnology applications in wound healing.

Although, he says he’s not sure he deserves the recognition, he’s grateful for the work the NAI does.

“Having the NAI advocating on behalf of creativity and invention and helping our government to understand the various issues [of licensing technology] will be valuable,” says Bowman.

Others are happy to laud his work for him.

"Chris has had enormous impact in polymer science research, as a department chair, for his outstanding teaching and mentorship, for starting and leading the Materials Science and Engineering Program, in starting new companies and in inventing and developing new technologies," department chair Charles Musgrave said in a press release.

"His election to the NAI specifically recognizes Chris as a world leader among academic inventors."

Bowman and Leinwand join 175 leaders of academic invention named 2016 fellows in December and will be inducted as part of the Sixth Annual Conference of the NAI at the John F. Kennedy Presidential Library and Museum in Boston, Mass. on April 6.

Assembled each year, a selection committee evaluates fellows for election. This year’s committee included 19 members, encompassing NAI fellows, recipients of U.S. national medals, National Inventors Hall of Fame inductees, members of the National Academies and senior officials from the U.S. Patent and Trademark Office, among others.

The National Academy of Inventors Fellows program includes 757 fellows worldwide. Together, the fellows hold “more than 26,000 issued U.S. patents and have generated more than 8,500 licensed technologies and companies, and created more than 1.1 million jobs with more than $100 billion in revenue generated based on their discoveries,” according to the 2016 NAI Activities Report.

Leinwand and Bowman join chemical and biological engineering Professor Kristi Anseth, elected in 2015, and former electrical and computer engineering Professor Kristina Johnson as NAI fellows.

University of Colorado Boulder Distinguished Professors Leslie Leinwand and Chris Bowman have been named fellows of the National Academy of Inventors (NAI).

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$1.1 million grant funds ��ý�Ļ��Ʒ research into next-generation vaccines

Anonymous — Mon, 07 Nov 2016 18:03:33 +0000

$1.1 million grant funds ��ý�Ļ��Ʒ research into next-generation vaccines Anonymous (not verified) Mon, 11/07/2016 - 11:03

The University of Colorado Boulder has received a $1.1 million grant from the Bill & Melinda Gates Foundation to develop next-generation vaccines that require no refrigeration and defend against infectious diseases with just one shot.

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Scientist develops new way to look at a cellular shapeshifter

Anonymous — Thu, 27 Oct 2016 19:29:31 +0000

Scientist develops new way to look at a cellular shapeshifter Anonymous (not verified) Thu, 10/27/2016 - 13:29

Loren Hough has won a New Investigator Maximizing Investigators’ Research Award from the National Institutes of Health to further vital research in the field of biophysics, specifically the behavior of tubulin, a protein involved in many life processes.

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Yeast gene rapidly evolves to attack viruses, researchers find

Anonymous — Thu, 06 Oct 2016 22:43:37 +0000

Yeast gene rapidly evolves to attack viruses, researchers find Anonymous (not verified) Thu, 10/06/2016 - 16:43

Humans have used Saccharomyces cerevisiae yeast in baking, brewing and winemaking for millennia. New research from the University of Idaho and ��ý�Ļ��Ʒ reveals another way that yeast species can help our species: by demonstrating how viruses interact with their hosts, and how hosts may evolve to fight back.

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Innovator Award winner brings to light the electrical changes in cells

Anonymous — Tue, 04 Oct 2016 22:42:28 +0000

Innovator Award winner brings to light the electrical changes in cells Anonymous (not verified) Tue, 10/04/2016 - 16:42

Emilia Costales

Electric voltage powers life: Human brains use electrical transients to process every thought, and every heartbeat arises from voltage changes in heart cells.

Traditional measurements of voltage inside cells involve scientists making tiny wires and impaling cells, exactly the way one could measure voltage flowing through a copper wire. However, due to the small size and fragile nature of cells, it has been technically impossible to measure voltage in neurons in a high throughput manner.

Joel Kralj, assistant professor in molecular, cellular and developmental biology and a University of Colorado BioFrontiers Institute faculty member, became interested in measuring cellular voltage as a postdoctoral researcher and developed a protein-based sensor that converts changes in voltage to changes in fluorescence, finally bringing to light the electrical changes in cells.

“The fact that we can convert changes in voltage to something visible allows us to make movies showing these biological processes,” says Kralj, “And because it’s really easy to take a movie, we now have a way of collecting vast amounts of voltage data without a physical connection to the cell, which is faster and easier.”

Kralj recently won a New Innovator Award from the National Institutes of Health for his work on voltage in neurons. According to the NIH, the New Innovator Award supports “unusually innovative research” from young investigators like Kralj.

Joel Kralj in the lab.

The NIH gives out only about 50 of these awards per year. The program is meant to support creative researchers doing high-risk, high-impact science — a description that Kralj easily matches.

As part of this award, Kralj will receive $1.5 million to support his research, and the New Innovator Awards allow more flexibility in spending than most grants. He plans to spend the grant money to develop automated microscopy hardware that will be capable of measuring neuronal voltage from hundreds to thousands of conditions.

Kralj is joining Andrew Goodwin, assistant professor of chemical and biological cngineering, as ��ý�Ļ��Ʒ’s only New Innovator awardees.

To study neurons, Kralj plans to focus on the approximately 20,000 proteins that transmit genetic information to find out how each protein affects voltage in neurons. This intensive process will involve removing a single protein in each measurement to see how its removal impacts the cell.

Kralj will then create a database that includes the effects each of the 20,000 proteins on the electrical changes in neurons—changes that lead to neurological diseases like epilepsy and Amyotrophic Lateral Sclerosis, or ALS.

“I am hoping that our sensors, and the database we’re creating, will help us identify the full complement of proteins essential for normal function, and also how their absence might give rise to disease. The New Innovator Award is going to give me the flexibility to follow a lead in this research,” says Kralj.

For more on the BioFrontiers Institute, see http://biofrontiers.colorado.edu.

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BioFrontiers

As pandemic spread, ‘I couldn’t just sit around’

Traveling to help fight COVID-19

Creating an important test

Previous viral research

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Video: ��ý�Ļ��Ʒ experts give scientific update on COVID-19 pandemic

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BioFrontiers

As pandemic spread, ‘I couldn’t just sit around’

Traveling to help fight COVID-19

Creating an important test

Previous viral research

Related Articles

Video: ����������ý�Ļ���Ʒ experts give scientific update on COVID-19 pandemic

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Students may now pursue a minor in computational biology

Creating a broad, interdisciplinary vision

Amplifying ����������ý�Ļ���Ʒ’s remarkable opportunities

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New COVID-19 test returns results in 45 minutes, without nasal swab

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Arthritis, autoimmune disease discovery could lead to new treatments

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Two distinguished profs recognized as top inventors

Leslie Leinwand and Chris Bowman named fellows of the National Academy of Inventors

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$1.1 million grant funds ����������ý�Ļ���Ʒ research into next-generation vaccines

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Scientist develops new way to look at a cellular shapeshifter

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Yeast gene rapidly evolves to attack viruses, researchers find

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Innovator Award winner brings to light the electrical changes in cells

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Video: ��ý�Ļ��Ʒ experts give scientific update on COVID-19 pandemic

Amplifying ��ý�Ļ��Ʒ’s remarkable opportunities

$1.1 million grant funds ��ý�Ļ��Ʒ research into next-generation vaccines