Research

Ocean microbes offer clues to environmental resilience

Susan Glairon — Fri, 16 May 2025 14:33:39 +0000

Ocean microbes offer clues to environmental resilience Susan Glairon Fri, 05/16/2025 - 08:33

Susan Glairon

A guide RNA strand, in purple, guides CRISPR to a DNA strand. Credit: Michelle Lehman/ORNL, U.S. Dept. of Energy

Andrew Hren, PhD student

Researchers at the University of Colorado Boulder and Oak Ridge National Laboratory have developed a new way to identify genetic changes that help tiny oxygen-producing microbes survive in extreme environments. The findings outline a new experimental approach for learning how microbes and other types of cells, including human cells, respond and adapt to environmental stress.

Their research, published in the Proceedings of the National Academy of Sciences, will also help scientists engineer faster-growing synthetic strains of microbes that could be used to develop new bio-derived fuels, chemicals and materials.

The multidisciplinary group of engineers and biochemists used a gene silencing system called CRISPR interference (CRISPRi) to turn down the activity of every gene in the genome of Synechococcus sp. PCC 7002, an ocean-dwelling cyanobacteria species. Cyanobacteria perform photosynthesis, much like plants.

鈥淏ecause these organisms produce a large share of the Earth's oxygen, understanding how they respond to a changing climate is critical,鈥� said Andrew Hren, a PhD student in the Fox Group and the paper鈥檚 first author.

The team explored how cyanobacteria responded to different light and temperature conditions found at various ocean depths. They discovered that making small changes in how certain genes are turned on or off can help the cells adapt better to extreme environmental conditions like heat, cold or drought.

Associate Professor Jerome Fox

"Our work shows how small genetic changes can yield large improvements in fitness when we push microbes to the edge of their comfort zone,鈥� said Jerome Fox, an associate professor of chemical and biological engineering at the University of Colorado Boulder and a co-lead author on the study with Carrie Eckert at ORNL, a former senior scientist fellow in the Renewable and Sustainable Energy Institute (RASEI). 鈥淥ur findings also highlight the value of using CRISPRi to turn the activity of genes down, but not off, as intermediate adjustments tended to provide the greatest survival advantage in extreme conditions.鈥�

The work was inspired by the late Jeff Cameron, an associate professor in the Department of Biochemistry and fellow at RASEI, Fox said.

鈥淛eff鈥檚 enthusiasm for cyanobacteria was infectious,鈥� Fox added 鈥淗e taught us everything we know and served as a critical resource on experimental design.鈥�

The researchers plan to continue studying cyanobacteria to further understand how the microbes absorb light and convert it into energy to develop new technologies鈥攕uch as engineered microbes that produce renewable chemicals and other useful products.

Researchers at the University of Colorado Boulder and Oak Ridge National Laboratory have developed a new method to identify genetic changes that help oxygen-producing microbes survive in extreme environments.

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How the tiger really got his stripes

Susan Glairon — Thu, 06 Feb 2025 15:53:35 +0000

How the tiger really got his stripes Susan Glairon Thu, 02/06/2025 - 08:53

Assistant Professor Ankur Gupta鈥檚 research on diffusiophoresis, where smaller particles move through a fluid, dragging larger particles with them, helps explain how this process may create clear biological patterns in nature, such as those seen on fish or a tiger's stripes.

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ChBE students make an impact at NCSU Future Leaders in Chemical Engineering symposium

Anonymous — Tue, 07 Dec 2021 07:00:00 +0000

ChBE students make an impact at NCSU Future Leaders in Chemical Engineering symposium Anonymous (not verified) Tue, 12/07/2021 - 00:00

Jonathan Raab

Students gathered for a photo after the symposium. Courtesy NCSU.

Students from the Department of Chemical and Biological Engineering presented their research as part of the competitive NC State University Future Leaders in Chemical Engineering symposium this past October. Three students from the department were recognized as awardees.

Michael Bibbey

Michael 鈥淕riff鈥� Bibbey is a senior chemical and biological engineering student working as an undergraduate researcher in the Cha Group. Bibbey presented his research on engineering novel photoactive protein therapeutics for improved chemotherapy efficiency and the inhibition of tumor growth.

鈥淚 was heavily involved in demonstrating the ability of our protein to slow the growth and spread of breast cancer,鈥� Bibbey said. 鈥淭his research is a big step in evaluating the efficacy of our modality, but more broadly it gives some important insight to the way bioconjugates may be able to induce cellular quiescence 鈥� a state of reversible growth arrest 鈥� in cancers.鈥�

Michael "Griff" Bibbey

As an attendee of the symposium, Bibbey enjoyed the opportunity to connect with his fellow undergraduate researchers and established faculty leaders in the fields of colloids, protein and pharmaceutical engineering and soft matter physics.

鈥淚 got to meet the brilliant young researchers who will be my colleagues for the rest of my career and made some great connections,鈥� he said.

Bibbey plans on continuing his research with the Cha Group on a tissue engineering project for his senior thesis. He is working alongside Sanheli Ganguly, a postdoctoral researcher, to develop a rapid, facile method for the DNA-mediated assembly of tissues. He recently co-authored a paper in Biotechnology & Bioengineering.

Bibbey will pursue a PhD in chemical engineering to enter a career in nanomedicine.

"Griff has shown tremendous potential as both a researcher and educator," said David Clough Professor Jennifer Cha. 鈥淥ver the past year or so, he has not only been doing experiments in my group which has led to him being a coauthor on a recently published article, he has been awarded several prestigious fellowships to intern at places such as Proctor and Gamble. Griff has been helping extensively in the classroom as a course assistant and TA. I see a very bright future for him in graduate school and beyond.鈥�

Shambojit Roy, a graduate student in the Cha Group, also shared praise for Bibbey.

鈥淚 have been mentoring Griff for the past year, and he is extremely enthusiastic and has a great attitude towards research,鈥� Roy said. 鈥淗e's a quick learner and has always shown interest in learning new things. I think he will do exceedingly well in graduate studies and research in general.鈥�

Carrie Bishop

Carrie Bishop is a senior chemical and biological engineering student working in the Anseth Research Group, which focuses on using biomaterial scaffolds in cell and tissue engineering.

For her presentation, she described the lab鈥檚 research into the cardiac disease Aortic Valve Stenosis (AVS) that causes abnormal blood flow through the heart.

Carrie Bishop

鈥淎 main part of the disease progression of AVS is that cells on the aortic valve undergo a phenotypic change that results in the valve becoming more stiff and calcific, but it is not fully understood why these changes occur,鈥� Bishop said. 鈥淭he Anseth Group has previously shown that we can use hydrogels 鈥� a type of biomaterial with a controllable stiffness 鈥� to better mimic healthy and diseased cellular environments.鈥�

Bishop said that this causes cells to undergo phenotypic change. The group investigated the epigenetic mechanics that appeared to control how the cells changed.

鈥淚 analyzed genomic sequencing data for RNA expression and the accessibility of distinct regions of chromatin to narrow down what genes might be causing the changes in cell expression based on changes in the mechanical environment,鈥� Bishop said. 鈥淎s a result of the overlaps between the differential expression of genes from healthy versus disease-like cells, we found four genes and numerous transcription factors that are implicated in this cellular transition, and therefore may be implicated in AVS.鈥�

The group is currently investigating the in vitro effects of those genes, which may result in pharmaceutical and therapeutic treatments that would obviate the need for invasive surgery procedures.

鈥淭hrough more than two years in my lab, Carrie has proven herself to be relentlessly curious, independent and unafraid to tackle new challenges,鈥� said Distinguished Professor Kristi Anseth.

鈥淐arrie is extremely motivated about doing research,鈥� said Dilara Batan, Bishop鈥檚 graduate student mentor. 鈥淪he is very self-motivated in learning new techniques and actively seeks additional challenges. She's well on her way to becoming an independent researcher.鈥�

Bishop greatly enjoyed the symposium experience.

鈥淭he symposium was fantastic. I was able to learn about a variety of other areas in chemical engineering research outside of CU Boulder,鈥� Bishop said. 鈥淚n addition to strengthening my presentation skills, it was great to be at an in-person poster session again, although it took a little getting used to.鈥�

Bishop thanked her mentors for their guidance, including Benjamin Carberry, Cierra Walker, Dilara Batan and Kristi Anseth.

Bishop is working on a senior thesis project with the Anseth Research Group, as well as applying to graduate schools and exploring employment opportunities in the bioengineering and computational biology sectors.

Cyrus Haas

Cyrus Haas is a senior chemical and biological engineering student working in the Whitehead Research Group. Haas presented research on a new method to identify SARS-CoV-2 escape mutations.

Cyrus Haas

鈥淎n escape mutation occurs when SARS-CoV-2 mutates, preventing the immune defenses that humans have developed from fighting back against the virus,鈥� Haas said. 鈥淭his can have a significant impact on vaccine and monoclonal antibody treatment efficacy. The rise of new SARS-CoV-2 variants like Delta show that variants with escape mutants are already seen in circulation.鈥�

Haas said these variants can lead to higher infection rates and more severe cases of COVID-19.

鈥�The research provides a complete experimental pipeline for identifying potential escape mutations before they are seen in circulation,鈥� Haas said. 鈥淢y specific work focused on developing software that could be used to compile experimental DNA sequencing data and run a statistical analysis to identify the potential escape mutations.鈥�

鈥淐yrus is an incredibly bright and talented undergraduate,鈥� said Associate Professor Timothy Whitehead. 鈥淗e has already been a co-author on two published papers, which is an outstanding achievement for an undergraduate researcher. He has been able to make contributions in my lab both computationally as well as experimentally.鈥�

Haas credited Irene Francino-Urdaniz for leading the research project and developing the experimental pipeline. He also thanked postdoctoral associate P.J. Steiner for help with writing the software and Whitehead for his guidance and mentorship.

鈥淭his was the first in-person setting where I was able to share the research I worked on with other peers, graduate students and faculty,鈥� Haas said.

鈥淭here were many other students from the symposium that were presenting important research and it was a great place to meet other chemical engineers from around the country. I鈥檓 excited for the opportunity to stay connected with these peers and potentially work with them in the future.鈥�

Haas is applying to graduate school to pursue a PhD in chemical and biological engineering, with a focus on protein engineering and synthetic biology.

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Kaar joins team using NSF grant to develop "on-demand, on-site" mRNA creation

Anonymous — Tue, 21 Sep 2021 19:43:41 +0000

Kaar joins team using NSF grant to develop "on-demand, on-site" mRNA creation Anonymous (not verified) Tue, 09/21/2021 - 13:43

Jonathan Raab

COVID-19 vaccines are just the beginning for mRNA-based therapies; enabling a patient鈥檚 body to make almost any given protein could revolutionize care for other viruses, like HIV, as well as various cancers and genetic disorders. However, because mRNA molecules are very fragile, they require extremely low temperatures for storage and transportation. The logistical challenges and expense of maintaining these temperatures must be overcome before mRNA therapies can become truly widespread.

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Anseth, Sprenger among recipients of AB Nexus grants

Anonymous — Thu, 27 May 2021 18:54:55 +0000

Anseth, Sprenger among recipients of AB Nexus grants Anonymous (not verified) Thu, 05/27/2021 - 12:54

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Shields Lab receives NIH grant to help quickly diagnose fungal infections

Anonymous — Tue, 18 May 2021 17:48:29 +0000

Shields Lab receives NIH grant to help quickly diagnose fungal infections Anonymous (not verified) Tue, 05/18/2021 - 11:48

Jonathan Raab

A prototype of the pipette tip is seen trapping silicone particles under stimulation from an acoustic standing wave.

The Shields Lab has received an NIH Exploratory/Developmental Research Grant Award (R21) to develop a specialized pipette to isolate and prepare fungal biomarkers for study.

鈥淲e aim to create a pipette that is functional and ergonomic to isolate multiple fungal biomarkers鈥攊ncluding antibodies and antigens鈥攆rom blood and prepare them for downstream analysis,鈥� said Assistant Professor C. Wyatt Shields IV. 鈥淥ur hope is that this technology will improve the convenience and value of serodiagnoses鈥攄iagnoses derived from blood serum and other bodily fluids.鈥�

The grant was made through the National Institute of Allergy and Infectious Diseases for the group鈥檚 project 鈥淎coustofluidic Pipette for Rapid Serodiagnosis of Candida Infection.鈥�

There is a growing need for technology that can assist researchers and medical professionals studying invasive fungal diseases present in the blood, as current methods of diagnosis require up to three days. This process often involves giving patients antibiotics as a precaution, which is ineffective against fungal infections and can cause additional complications.

鈥淢aking a user-friendly pipette to capture and purify these biomarkers could shorten the timeline required for a positive readout and add value to current clinical practices for detecting invasive fungal diseases,鈥� Shields said.

The NIH grant is expected to catalyze new developments in the project, which the group has been working on for about a year.

鈥淢y group has a deep interest in biointerfacing and responsive particles,鈥� Shields said. 鈥淭he technology we are developing leverages a class of silicone particles that binds to specific biomarkers and compresses when exposed to an acoustic standing wave. Together, these features allow our particles to undergo efficient trapping in an acoustic standing wave, which is central to our core innovation.鈥�

Shields hopes to leverage the pipette technology to target difficult-to-study and deadly pathogens, both fungal and non-fungal. He also hopes to extend the technology to include an in-line fluorescence inspection module to create a point-of-care device that can be used in clinical settings.

鈥淭his project combines topics in colloid and interface science, biorecognition, immunology and medical device engineering,鈥� Shields said. 鈥淥ur department has abundant resources and expertise in each of these areas, which will greatly benefit our efforts.鈥�

The Shields Lab has received an NIH Exploratory/Developmental Research Grant Award (R21) to develop a specialized pipette to isolate and prepare fungal biomarkers for study.

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Developing efficient, dynamic windows for comfort and climate change research appears in Nature Energy

Anonymous — Thu, 29 Apr 2021 16:23:49 +0000

Developing efficient, dynamic windows for comfort and climate change research appears in Nature Energy Anonymous (not verified) Thu, 04/29/2021 - 10:23

Jonathan Raab

See the technology in action

[video:https://vimeo.com/540396286]

Researchers from the Department of Chemical and Biological Engineering and the Materials Science and Engineering Program are among the authors of 鈥淧olymer inhibitors enable >900鈥塩m² dynamic windows based on reversible metal electrodeposition with high solar modulation鈥� which appeared in the April issue of the highly prestigious science journal Nature Energy.

Dynamic windows that feature adjustable tint controls provide the ability to reduce the carbon footprint of buildings by regulating the flow of light and heat passing through the glass. These windows can be of benefit to the environment, reduce heating and cooling costs and provide an increased level of comfort for building occupants.

The primary roadblock to the widespread implementation of this technology has been developing an affordable, scalable and fast-acting color-neutral tinting. The researchers behind the new paper believe their method of depositing responsive metal films may overcome this obstacle.

"These windows have the widest range of light transmission and most neutral color of any dynamic window technology,鈥� said Professor Michael McGehee. 鈥淲ith their potential for low cost, I think they are destined to have a huge impact on the window industry. They will save energy and make building spaces much more pleasant."

Their findings demonstrate that reversible metal electrodeposition鈥攗sing polymer inhibitors鈥攃an effectively deposit responsive metal films in dynamic windows to reduce and reflect the passage of heat and light in under three minutes. This process increases the efficiency, uniformity, affordability and durability of the windows.

鈥淭here鈥檚 been tremendous activity around dynamic windows for decades but the existing technology has yet to really impact people鈥檚 lives,鈥� said Michael Strand, one of the paper鈥檚 authors, who also wrote a blog post elucidating their research. 鈥淥ur latest work is validation that what we have is truly exciting. It鈥檚 been a long road to get to where we are today with an even greater journey ahead, but we are eager to bring this technology to people all over the world."

The faculty from CU Boulder collaborated with researchers from the National Renewable Energy Laboratory, the University of Nevada - Reno and Stanford University.

Researchers from the Department of Chemical and Biological Engineering and the Materials Science and Engineering Program are among the authors of 鈥淧olymer inhibitors enable >900鈥塩m2 dynamic windows based on reversible metal electrodeposition with high solar modulation鈥� which appeared in the April issue of the highly prestigious science journal Nature Energy.

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Multi-program PhD candidate first author on cardiac fibrosis-based paper

Anonymous — Mon, 26 Apr 2021 16:26:18 +0000

Multi-program PhD candidate first author on cardiac fibrosis-based paper Anonymous (not verified) Mon, 04/26/2021 - 10:26

Josh Rhoten

Cierra Walker, a PhD candidate in the both the Materials Science and Engineering Program and Interdisciplinary Quantitative Biology Program at CU Boulder is the first author on a new paper in Nature that explores what happens to cells after a heart attack.

Titled 鈥淣uclear Mechanosensing Drives Chromatin Remodelling in Persistently Activated Fibroblasts鈥� and appearing in Nature Biomedical Engineering, Walker said the paper will help doctors and researchers better understand and treat damage after cardiac fibrosis develops.

鈥淎fter a heart attack, your heart cells gets stiffer. This is known as cardiac fibrosis and it reduces the heart鈥檚 ability to function properly,鈥� she said. 鈥淔ibrosis impacts the cell operation within your heart, causing the cells to further promote fibrosis progression or 鈥榓ctivation.鈥� So a major goal for doctors and researchers is to reverse the cell's activation and help the cells return to normal.鈥�

Walker added that 鈥� in the paper 鈥� the team was able to show that the cells in question are 鈥渟tuck鈥� in an activated state through changes in their DNA accessibility (epigenetics). 鈥淲e identified that we could reverse these activated cells to normal cells by treating them with particular small molecules,鈥� she said.

Walker is part of the Anseth Lab in the Department of Chemical and Biological Engineering and the Leinwand Lab in the BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology. She said she has always been interested in heart biology and research, making this a fun project to work on.

鈥淗eart disease is the number one cause of death in developed countries, so it is amazing to me that there are still no treatments for cardiac fibrosis. I think this type of research is incredibly important for improving treatment options for people with heart disease,鈥� said.

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Spike protein mapping could lead to more effective COVID-19 vaccine boosters and therapies

Anonymous — Thu, 25 Mar 2021 15:38:11 +0000

Spike protein mapping could lead to more effective COVID-19 vaccine boosters and therapies Anonymous (not verified) Thu, 03/25/2021 - 09:38

Jonathan Raab

This research is in pre-print online:

As millions of people around the world receive vaccines to halt the spread of COVID-19, mutated variants of the virus continue to appear, challenging the efficacy of mass vaccination programs and social distancing.

New research from the Sprenger and Whitehead groups aims to identify and map common mutations in 鈥淪pike鈥� proteins鈥攖he proteins that allow the virus to enter and infect cells. This would provide researchers with a roadmap to anticipate and counteract the development of future SARS-CoV-2 strains with effective vaccines and vaccine boosters.

The collaborative research combined the Sprenger group鈥檚 expertise in computational methods to study how antibodies interact with viral proteins with the unique technological capabilities of the Whitehead group.

鈥淲e identified common Spike mutations for certain antibodies that are elicited during natural infection from the virus,鈥� said Associate Professor Timothy Whitehead. 鈥淭hese mutations may emerge in lineages after population vaccination, and a prospective knowledge of these mutations may allow us to develop better vaccine boosters and therapies against SARS-CoV-2.鈥�

The researchers utilized a genetically engineered strain of yeast, which expressed portions of the viral Spike proteins along its surface. They created mutant variations of the Spike proteins and studied their ability to go unrecognized by antibodies鈥攅ssentially modeling the potential mutations of SARS-CoV-2.

Irene Francino Urdaniz

"Molecular simulations can provide unique insight into the mechanisms by which the identified Spike mutations allow SARS-CoV-2 to escape pressure by the immune system,鈥� said Assistant Professor Kayla Sprenger. 鈥淲e observed common escape mechanisms from multiple neutralizing antibodies with the same germline gene origins, which may have important implications for future SARS-CoV-2 immunotherapeutics."

Whitehead credits one of his graduate students, Irene Francino Urdaniz, with leading the effort in his lab.

鈥淲hen the pandemic started, we saw the opportunity to apply techniques mastered by the Whitehead lab to make a contribution,鈥� Francino Urdaniz said.

鈥淲e set up a system to test how well antibodies neutralize SARS-CoV-2 by displaying the S RBD on the yeast cell鈥檚 surface. Early in the process, we had the extraordinary opportunity to collaborate with Brandon Dekosky鈥檚 lab and the Vaccine Research Center to characterize a newly discovered neutralizing antibody with our platform.鈥�

鈥淔rancino Urdaniz developed the genetically engineered yeast strain and discovered how to screen for mutations on the Spike protein that result in loss of antibody efficacy,鈥� Whitehead said. 鈥淪he is a Balsells fellow and represents the fantastic students we are able to recruit from the best universities in Europe.鈥�

Other institutions involved in the work include University of Kansas, The Scripps Research Institute, the International AIDS Vaccine Initiative, Columbia University and the NIH Vaccine Research Center.

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Growing a better, more affordable solar cell from perovskite

Anonymous — Tue, 02 Mar 2021 16:36:28 +0000

Growing a better, more affordable solar cell from perovskite Anonymous (not verified) Tue, 03/02/2021 - 09:36

Jonathan Raab

Cross-sectional SEM image of the spin-coated MAPbI₃ film processed from DMF precursor solution (annealed for 5 s at 100 掳C) on a PTAA-covered ITO glass substrate.

While solar panels have traditionally used silicon-based cells, researchers are increasingly looking to perovskite-based solar cells to create panels that are more efficient, less expensive to produce and can be manufactured at the scale needed to power the world.

Perovskite materials have properties that indicate they may be well-suited for energy applications like batteries and solar cells. They are synthetically 鈥済rown鈥� in films for such applications. One of the fundamental questions related to their production, however, is whether they can be grown from the top down or bottom up. Each has significant impacts on how the films function.

In 鈥淐rystallization in One-step Solution Deposition of Perovskite Films: Upward or Downward?鈥� published in Science Advances in January, Professor Michael F. Toney and his research partners describe a process of top-down growth, leading to a broader understanding of how to produce cells that are more efficient and stable while being less expensive than traditional silicon-based cells.

鈥淭he potential exists for the perovskite family to supplant silicon as the primary material involved in solar energy production,鈥� Toney said. 鈥淲e鈥檙e attempting to understand how to make good, quality films for perovskite solar cells. But it was unclear whether starting at the top and going down or starting at the bottom and going up was the best method.鈥�

Toney credits his collaborator on this project Professor Jinsong Huang of the University of North Carolina at Chapel Hill as one of the key researchers behind this effort. This collaboration was made possible from the Department of Energy-funded Center for Hybrid Organic Inorganic Semiconductors for Energy (CHOISE).

Perovskite solar cells are on the way to commercialization after tremendous demonstration of excellent efficiencies and stabilities, Huang said.

鈥淥ne critical question to be answered next is whether the lab-scale, nail-sized cells can be scaled up to one-to-two-square-meter modules while still keeping their efficiency and stability,鈥� he said. 鈥淭o answer this, the critical step to take is to understand how perovskite films are grown so that its uniformity can be well controlled, which results in better module efficiency and stability.鈥�

Huang believes this research will help engineers refine the process to increase efficiency and drive down costs of perovskite modules.

Toney鈥檚 interest in the subject began about a decade ago, over lunch with CU Boulder Professor Michael McGehee. McGehee convinced Toney to investigate the perovskite class of materials as a possible replacement for silicon in solar cell production.

Toney describes the study of compound metal halide perovskites as being in its infancy, as opposed to silicon, which has been under study and in use for decades.

鈥淔or metal halide perovskite, the properties are quite different from silicon, so at a high level we鈥檙e trying to understand, what are these properties?鈥� Toney said. 鈥淲e鈥檙e learning more about the constituent atoms and molecules that control those properties. We鈥檙e asking: how do we tune the properties to create something that is useful for society?鈥�

This research was completed in collaboration with researchers at CU Boulder, the National Renewable Energy Laboratory, the Department of Energy鈥檚 CHOISE program and at Stanford University.

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