Kamal Singh

Seeing the bigger picture through applied research projects

June 6, 2022 By Penquite, Cara (MU-Student) in Research Tags: applied science, basic research, biochemistry, Mizzou Research, research

Investigators at Bond LSC take steps to apply basic research

By Cara Penquite | Bond LSC

Yul Eum Song — Photo by Lauren Hines | Bond LSC

Scribbling in a lab notebook and planning experiments tucked between shelves of equipment, it’s easy to fixate on day-to-day lab operations. But scientists also face the challenge of finding how research can improve the world around us.

“The direction, the vision of the lab, ultimately comes from the principal investigator that bridges the research into applied directions,” said Jay Thelen, biochemistry professor and Bond LSC principal investigator

Despite the focus on basic research within the Bond LSC, many principal investigators choose to take their research to the next level with commercial partnerships.

Thelen’s lab researches ways to increase oil production in seeds and has three patents licensed to Yield 10 Bioscience, a sustainable crop innovation company who applies Thelen’s research to commercial crops. While seed oils like canola and soybean oil are known for their use in cooking, Thelen explains that increased production of these oils could play a larger role in sustainable fuel sources such as biodiesel and sustainable aviation fuel.

“We have to make more oil to balance out our need to eat it [and] our need to wean ourselves off of fossil fuels,” Thelen said. “To do that, we need to either plant more acres of oil seeds, or we have to raise the oil in existing oil seeds.”

Thelen researches enzymes with that potential application in mind. One is acetyl-CoA carboxylase, the enzyme which initializes the production of fatty acid chains found in plant oils.

“We’ve known this is an important enzyme, and we know that any tinkering you do with it has an impact on the oil production,” Thelen said. “In this case we’ve made new discoveries that permitted us to rationally engineer this enzyme to make it more active.”

Thelen suggests thinking of the enzyme as a “gatekeeper” to oil production which initializes the production of fatty acids and increases oil production. Thelen’s lab identified two different gene families that influence the activity of the enzyme in Arabidopsis and camelina plants. Yield 10 then applies these discoveries in other commercial plants.

While Thelen works closely with his commercial partner — having served on their scientific advisory board for three years and now stays in contact with Yield 10’s CEO to develop research projects — some labs stick with short-term arrangements.

Kamlendra Singh — assistant director of the Molecular Interactions Core at Bond LSC and Veterinary Pathobiology research assistant professor — studies HIV treatments. His lab identified a compound licensed by a commercial partner that targets the shell containing the virus’ genetic information.

Singh’s work in HIV started in 1994 with basic research investigating the enzyme that makes the viral DNA.

“I wasn’t into [studying] the drugs when I started working on HIV, I was mostly trying to understand how HIV enzymes works,” Singh said. “Once you know how the enzyme works, then you can target these enzymes for discovering the drugs.”

After years of studying how the enzyme works, Singh switched to HIV treatment. The first step to develop a treatment is to look for structures in the virus that the drug could potentially target to stop the viral replication. Singh targeted the shell around the virus’ genetic information known as the HIV capsid.

Building on previous research, Singh’s lab developed a compound able to bind the HIV capsid and prevent it from releasing the contained genetic information. Even with the licensing of his compound, Singh plans to continue researching ways to improve it.

“There are two reasons to keep working on it. One, well it’s my brainchild,” Singh said. “The second reason is as the company grows, we grow. We get more recognition and more funding. You can use it to [study] different viruses or use the same funding to improve upon it.”

While Singh plans to remain looking towards the applied side of his HIV research, he does not forget his roots in basic research.

“You have to put in time … [to] understand the system first, which is basic science, before you go to applied science,” Singh said.

Michael Roberts, a Chancellor’s Professor Emeritus of animal sciences and biochemistry who has had several patented projects, focuses on improving basic science projects and applies for patents if warranted.

“I don’t deliberately go into anything for commercial purposes,” Roberts said. “If I see something that I think does have commercial application, I’m happy to do it, but that is usually after you do [basic sciences].”

Whether starting a project with applications in mind or focusing on basic research, knowledge gained through research can be building blocks for the future.

“Science is simple. Even the most applied research project has its genesis in basic biology and basic research,” Thelen said.

Read more about how MU research leads to patents, inventions and licensing at https://research.missouri.edu/news/leveraging-mizzou-discoveries.

How a pandemic spreads

July 16, 2021 By Roger Meissen in Research Tags: COVID-19

COVID-19 analysis looks at variant spread

Saathvik Kannan, Kamal Signh, and Austin Spratt — Saathvik Kannan, Kamal Singh, and Austin Spratt, worked together at Bond LSC to identify new SARS-CoV-2 variants. | photo by Davis Suppes, Bond LSC

By Davis Suppes | Bond LSC

Variants of the virus that causes COVID-19 continue to plague the world with spikes in infection, keeping the current pandemic from being fully controlled as Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections remain unmanageable in some parts of the world.

Researchers at Bond Life Sciences Center and the University of Nebraska Medical Center (UNMC) have been conducting research on mutations in four new variants, B.1.1.7, B.1.351, P.1 and CAL.20C. These evolving variants appear to be more infectious and transmissible than the original Wuhan-Hu-1 virus.

It all started with a new spike in infections of a variant of SARS-CoV-2 in the UK. Despite a slowdown in infections due to precautions of masks and lockdowns, the new spike meant something about the virus had changed.

“Our goal was to find out where these variants are distributed, and how they are migrating,” said Kamal Singh, Assistant Director Molecular Interactions Core, and scientist at Bond LSC. Singh was a corresponding author on the paper and has been at Bond LSC for 12 years.

Their work showed completely different mutations in these variants based on regions, but also where variants have common lineage. That commonality can be seen between the CAL.20C and B.1.351 variants.

While related to each other, they also developed different mutations.

“B.1.1.7 was more infectious and was able to spread to more people. It slowly dominated and that’s what happened in the United States as B.1.1.7 is now the dominant variant of SARS-CoV-2 in the US,” said Saathvik Kannan, a co-author. Kannan is going to be a 10th grader at Columbia’s Hickman High School this fall but works under Singh at Bond LSC as a computer programmer and researcher.

Once they identified the related COVID-19 variants, they wanted to trace their migration. This allows them to see where the mutations are being carried and which regions have a more dense number of infections. The prevalence of variants was key in identifying where they were moving.

Their analysis looked at certain mutations in each variant to see how they were related, why some sequences have mutations that others don’t and tried to determine how they evolved from their original sequence.

By comparing the structure of each virus, they were able to illustrate how the related mutations moved state by state across the country.

Sankey diagram variant CAL.20C US.jpg — This Sankey diagram for variant CAL.20C in the United States.They aligned the first-known CAL.20C sequences from each state then grouped the sequences based upon the date collected and closely their structures matched, with cut-offs of 96, 94, 93, 92, 91 and 90 percent compared with the previous group.

“It is pretty clear that some states have a higher homology match, which helps us see a pretty linear trend of migration from the Western states to the East in the United States,” said Austin Spratt, a computer science senior and lead author on the paper. Spratt has worked under Singh at Bond LSC for two years.

The study cautions that the sequences of viruses are being deposited at an unprecedented rate, so it is possible that some conclusions may change as more sequences of variants become available.

“These variants are continuously evolving and complex in nature, but a proper understanding of what makes each variant unique, its genetic makeup and its interaction with host proteins is critical to developing the most effective vaccine,” said co-corresponding author Siddappa Byrareddy, Professor & Vice-Chair of Research, in the Department of Pharmacology & Experimental Neuroscience, at the University of Nebraska Medical Center. “Not only will this help us to design better vaccines now, but greatly help us to be prepared to deal with more mutant variants in the future.”

Although analysis indicates that mutations only in one variant do not reflect evolution of it, these genetic mistakes may increase infectiousness of a particular variant

The short period of time, volume of variants and limited travel around the world all point to a greater infectivity than the original (Wuhan-Hu-1) virus. Recent deadly surges in India caused by variant B.1.617.2 or the Delta variant will soon be added to their analysis to further understand the COVID-19 pandemic.

Their research was published in the paper ‘Evolution, Correlation, Structural Impact and Dynamics of Emerging SARS-CoV-2 Variants’ in the “Computational and Structural Biotechnology Journal” on June 19, 2021.
Funding provided by: Bond LSC, Swedish research Council, American Lung Association, National Institute of Dental and Craniofacial Research in collaboration with Prof. Gary Weisman of the Bond Life Sciences center.

Beyond the Vaccine

September 25, 2020 By Lauren Hines in Research Tags: COVID-19, virology

Lucas Woods from the Weisman lab watches lung cancer cells and oral epithelial cells grow. | photo by Lauren Hines, Bond LSC

By Lauren Hines | Bond LSC

Vaccine development remains a central goal to get the current COVID-19 pandemic under control. While vaccines are highly vital in the fight against the current pandemic, what if scientists could prevent the virus from entering cells altogether? Researchers at Bond Life Sciences Center are working to do just that and, so far, they’re the only ones at Mizzou on the case.

For the Gary Weisman lab, that starts with their study of a family of purinergic receptors which are found on the plasma membrane of cells. Molecules outside the cell bind to receptors and serve as signals to trigger an action, whether it’s transporting something into a cell, alerting its defenses or initiating programmed cell death. The specific receptors they study sound off one of the first alarms to alert host immune cells when a cell is damaged.

Weisman, Bond LSC principal investigator and Curators’ Distinguished Professor of biochemistry, noticed that the spike protein in the virus that causes COVID-19, SARS-CoV-2, shares an amino acid sequence — arginylglycylaspartic acid or RGD — with one of the receptors his lab studies named, P2Y2.

“So, we had this one niche that no one I think has followed,” Weisman said. “Even though people understand RGD sequences are important for protein to protein interactions, and possibly viral entry, no one has looked at this with respect to coronaviruses.”

While ACE2, a plasma membrane receptor, serves as the primary cell-surface receptor for SARS-CoV-2 binding, a potential role for the RGD sequence in the spike protein is to bind to alternate receptors and subsequently enhance viral infectivity.

“We postulated that if there was a way to use our receptor, it might be to block the entry of the virus,” Weisman said. “The virus can’t replicate on its own. It has to get inside the cell to be replicated, so if we prevent the entry, we can potentially stop the infections.”

They found plasma membrane receptors like ACE2 and P2Y2 all share this sequence that binds to other cell-surface receptors called, integrins. The lab is currently exploring ways to block these pathways without blocking other functions.

Few other labs have made this connection because RGD is not known to be present on many of the membrane receptors. In addition, the Weisman lab already has the supplies and connections to study these receptors.

“We, as the lab, have been studying this receptor and this family of receptors for so long that if there is a lab that has the tools and the knowledge to answer this question, I definitely think that is us,” said Kevin Muñoz Forti, Ph.D. candidate for the department of biochemistry.

Kevin Muñoz Forti is doing cell culture work in “the hood,” which is a space used to prevent researchers and other outside factors from contaminating the cells. | photo by Lauren Hines, Bond LSC

The lab partners with Kamal Singh, assistant director of the Molecular Interactions Core at Mizzou and associate research professor in the department of veterinary pathobiology, who works with viruses in a way that won’t infect workers.

Singh achieves this by using look-alikes, or pseudovrises, of the spike protein on SARS-CoV-2. To the cell, this mimics the outer shell of SARS-CoV-2, but is not contagious.

Even though the Centers for Disease Control and Prevention and Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, expect a vaccine soon, this work is for the long run.

“I can guarantee you this isn’t the last coronavirus that will come up,” Singh said. “There will be many because it has been kind of periodic lately. Coronaviruses have been emerging, so the research done in collaboration with Gary’s lab will definitely be available for… future coronaviruses.”

Coronaviruses are a family of viruses which may cause respiratory illness in humans. The most recent diseases, before COVID-19, caused by previous coronaviruses were Severe Acute Respiratory Syndrome (SARS) from 2002 and Middle East Respiratory Syndrome (MERS) from 2012. Severe Acute Respiratory Syndrome Coronavirus 2 is the virus that causes COVID-19.

“This is the virus that causes COVID-19 or SARS-CoV2,” said Lucas Woods, Weisman research lab manager. “If this type of research were to have been investigated during the first coronavirus epidemic, there might have been some type of lead on the type of work we’re doing… so, absolutely this work will be useful after a vaccine or treatment is available.”

Looking ahead, the study has two years of funding from the American Lung Association in addition to grants from the National Institutes of Health. The Weisman lab hopes to eventually make it to clinical trials, but the road from basic research to clinical trials is long and arduous.

“What’s on our side, at least for the future, is that with some of these pathways we’re looking at, there are already available drugs that target these particular pathways,” Woods said.

These pathway-blocking drugs aren’t approved for humans yet, but this research could facilitate clinical scientists to test the safety of these or related drugs in humans.

The Weisman lab’s research of P2 receptors can be applied to many systems in the body and other diseases. This also allows for more ways to receive grants to fund studies longer. Along with the COVID-19 studies, they study P2 receptors in diseases that affect salivary glands.

Cheikh Seye, Mizzou professor of biochemistry, studies vascular diseases that relate to the receptors studied by the Weisman lab. Seye understands that one of the complications of COVID-19 in humans is vascular related.

“I mean there’s a lot of interaction between the vasculature and other systems, so it doesn’t stay with the salivary gland,” Seye said. “It’s all interconnected, so that’s why we need to have a multi-dimensional approach.”

In addition, the lab has found commonalities between oral and lung epithelial tissue that may contribute to COVID-19.

While this study has quite a bit of potential, it’s a long way away from seeing practical results.

“All the people in the lab have confidence because they have been successful on their own doing this before,” Weisman said. “So, it’s just another challenge, but we know how to get the answers, we have the tools and we’re optimistic that we’ll find out something.”

Researchers working on this study include Gary Weisman, Kamal Singh, Lucas Woods, Cheikh Seye, Jean Camden and Kevin Muñoz Forti.

#IAmScience: Kamlendra Singh

February 27, 2020 By Jerome Duggan in #IAmScience Tags: HIV, virology

By Jerry Duggan | Bond LSC

Kamal Singh was in the town of Allahabad in his native India, preparing for competitive exams to become a government official. As he craned his head to the left, he saw a highly respected official getting berated by an arrogant and disrespectful political leader. While Singh always knew that, in these positions, one was under the government’s thumb to an extent, that incident was what sealed the deal for him and made him realize he did not want to spend his life simply taking orders and being subject to verbal abuse by corrupt politicians.

It was at that moment — roughly 30 years ago — he decided he wanted to dedicate his life to something more personally fulfilling: research.

Singh was raised in a small village in rural India. While his primary and high school education came from a military school, he obtained a Master’s degree in physics from Agra University, in Agra, the city where Taj Mahal is located. Still, Singh thought he wanted to work as a public official until that incident served as the last straw. After that, he decided to complete his graduate degree in quantum physics, and committed fully to a life in academia.

That led him to cross the Atlantic in 1994 when he moved to the U.S. and joined Rutgers New Jersey Medical School. He realized that now was his chance to focus on a different area of science that he had always been fascinated with: biochemistry.

“I taught myself everything from scratch in New Jersey,” he said. “I had always wanted to work with DNA polymerase, and I felt like now was my chance to really get involved with that.”

Over the span of 15 years in New Jersey, he occupied a number of positions including postdoctoral fellow, instructor and assistant professor. His work transitioned from research related to DNA polymerase to his current focus on Human Immunodeficiency Virus (HIV) and other viruses including Foot-and-Mouth Disease Virus, SARS and MERS coronaviruses.

That’s where Singh’s story came to Mizzou where he arrived in Jan. 2009. While he has always been highly motivated and driven by collaborations, the bread and butter of his work for more than a decade has come at the Bond LSC focused on HIV.

The goal of Singh’s HIV-focused research, in a nutshell, is to find drugs that bind to the active site of the enzymes that replicate HIV, thereby blocking the spread of the disease. According to Kyle James Hill, a postdoctoral student working in Dr. Singh’s lab, the function of his research is twofold: to better inform human understanding of the viral life cycle and to help identify novel targets of drug identification to potential treatments.

Kyle James Hill works on a bacterial transformation in Dr. Singh’s lab.

More precisely, Singh’s work is focused on enzymes/proteins that serve particular functions for the virus after the virus enters human body. Most enzymes have a suffix of -ase, and what comes before the suffix generally states the function of a given enzyme. For example, protease has to do with proteins, specifically the breakdown of proteins into smaller proteins or other subunits. Enzymes can have a positive function such as promoting growth and generation of muscle tissue, or a negative function, such as what happens when HIV highjacks their function for its own benefits. The HIV infection, in turn, weakens a person’s immune system and lowers his/her her ability to fight disease, in this case AIDS. Each enzyme has an active site, or a region where its specific function is carried out. All research that deals with enzymes, therefore, must center on what goes on at the active site.

Singh’s HIV-focused research is centered specifically on three HIV enzymes: reverse transcriptase, integrase and protease. Reverse transcriptase catalyzes reverse transcription: that is, the formation of DNA from an RNA genome of HIV. Reverse transcriptase converts RNA genome of HIV into DNA.

HIV then uses another enzyme called integrase to insert viral DNA into the genetic framework of the host cell. This allows the virus to further embed itself in what was once a healthy cell. A third enzyme called protease breaks down long proteins into smaller functional proteins, and these smaller proteins then combine with the genetic material of HIV to infect another cell.

The practical application of Singh’s work is that it is focused on moving research toward tangible results that physicians, in turn, can use to better diagnose and treatment plans for patients. Singh’s current lab work focuses most of all on finding drugs that are able to work to treat HIV patients from different parts of the world.

Singh became interested in investigating why certain drugs designed to treat HIV in the developed world, have less effect on the particular strains of HIV that exist in low- and middle-income countries. To help him with this process, Singh developed a collaboration with scientists at the renowned Karolinska Institutet in Stockholm, Sweden. Singh is also an Associate Faculty member at Karolinska.

While HIV infects people all over the world, there are actually many different strains of the virus, and some strains are more abundant in particular regions of the world. According to Singh, there are 10 subtypes of the virus, and more than 100 hybrid or combined types of it. Some drugs treat a particular subtype better than others. If a given drug does not work to treat a particular subtype, then it is useless in terms of treating patients that are infected with that strain of the virus. According to Singh, most drugs produced in the U.S. treat HIV subtype B, which is most prevalent in the developed world. However, patients in many other parts of the world, such as India, South Africa and Brazil are infected with subtype C of the virus. Singh says that 95% of patients in India are infected with subtype C.

“Because these patients are infected with a different strain of the virus, they, in many cases, do not respond to the type of drugs that are traditionally given to patients in the developed world,” he said. “Our job is figuring out why they don’t respond to that particular drug, and then coming up with something that can more effectively treat them.”

This practical application of his work is what’s most rewarding to Singh. His lab is able to provide concrete results that physicians then apply when making decisions about how to best treat their patients. Based on Singh’s work, physicians can better determine which type of drug would most likely effectively treat patients infected with a specific subtype of the virus, also considering the specific set of genetic variations and mutations that the patient may have. It is in this way that Singh’s work makes a very real difference in the world, and that is ultimately what keeps him so passionate about his work.

“To be able to apply what I work on in the lab and see it at work in real patients is very rewarding for me,” he said. “I am able to see the entire process unfold, starting with the very basic biochemistry all the way to direct application to the patients. Seeing that I’m making a real difference means everything to me.”

Bond Life Sciences Center adds Molecular Interactions Core as a new research hub

February 16, 2018 By Roger Meissen in Research Tags: Molecular Interactions Core

Tom Quinn, director of the Molecular Interactions Core, and others demonstrate equipment for its Jan. 24 open house. | Photo by Katelyn Brown, Bond LSC

By Katelyn Brown | Bond LSC

For researchers, the shape of molecules gives insight into how cells, viruses and other macromolecular interactions take place.

Getting a clear view of that structure is the hard part, and the new Molecular Interactions Core (MIC) at the Bond Life Sciences Center will now give researchers from many different disciplines one place where state-of-the-art equipment are available for them to use to further science.

Dr. Kamal Singh is excited that goal is being realized.

One of the 10 MU’s core facilities that serve scientists’ needs, the MIC specifically provides training, advising and shared equipment for researchers to take a closer look at molecules.

That’s where Dr. Singh comes in.

He serves as the Assistant Director of the MIC and oversees the day-to-day operations of the facility. Dr. Singh makes sure the machines are operational, communicates with researchers interested in using the facility, trains those who do not yet know how to use the equipment and gives guidance as well as collaborative feedback on things like computer-assisted drug design — his specialty.

The humming of machines is the first thing noticed when walking into the MIC. These instruments allow you to look at 3-dimensional models of the molecules like HIV enzymes or view protein crystals under a microscope before diffracting light through them. It’s a lab where miniscule pieces of life become big and important.

Dr. Mark McIntosh, the vice chancellor of research for all UM system campuses, had the idea to create the MIC.

“It was Dr. McIntosh’s vision to bring everything together; which includes structural biology, molecular interactions, particle size, zeta potential, mass of the nanoparticles, etc. He also wanted to bring peptide synthesis here to have everything at one central location,” Dr. Singh said.

Understanding structure at the molecular level helps scientists figure out how reactions happen, how molecules fit together and serve as signals and how pathogens can invade cells, among other possibilities.

“I’m hoping that we can really facilitate structural and molecular research on campus — structural determination and molecular interactions — and really push boundaries of the current state of the field,” said Dr. Tom Quinn, the Director of the MIC.

Dr. Quinn hopes the state-of-the-art equipment will allow the MIC to be a resource for both research faculty and students to be on the cutting edge in their fields.

Dr. Ritcha Mehra-Chaudhary and Dr. Fabio Gallazzi work within the MIC and provide their expertise. Dr. Mehra-Chaudhary works with X-ray crystallography, dynamic light scattering and custom protein expression, while Dr. Gallazzi is an expert in custom peptide synthesis. Their work can be important for understanding drug design to combat viruses and cancers.

The MIC started with one machine, an X-Ray Diffractometer, in room 442 of the BLSC. It took six months to collect the different machines from different departments in the campus, but in December the MIC became fully operational. The MIC team celebrated with an open house on Jan. 24, 2018.

“It’s kind of crowded, but it’s good,” Dr. Singh said. “We have invited everyone, mainly researchers, but also undergrads. The entire university is welcome to come see what we have. The idea is the advancement of science in our school.”

The MIC won’t only be beneficial for campus researchers, but also researchers from all over and undergrad students who are eager to learn the details of molecular interactions and learn how to use core facilities.

There are many exciting and new technologies in the MIC that will interest outside researchers, according to Dr. Quinn. One of these is the nanodisc technology that Dr. Mehra-Chaudhary works with. This technology allows researchers to study membrane proteins outside of something bigger, like a cell, while also keeping them in a functional and native structural state. The nanodisc project is part of collaboration between the MIC and the Electron Microscopy Core to allow researchers to get high resolution structures of membrane proteins.

While affordable, outside and campus researchers must also pay a price to use the facilities to cover consumables, instrumentation maintenance and staff.

“We definitely want to at least break even. I don’t know how long it will take to get there. However, the major goal is to support the scientists on campus and facilitate their research,” Dr. Singh said.

Bringing this support to campus also means supporting future scientists. Dr. Singh has three undergraduate students working with him who are learning how to use the advanced technology, and he helps to train many more from all different departments.

The goal is to one day expand the MIC to a point where all molecular interactions facilities can be at one place.

“There are certain techniques we don’t have, and I hope that in the future we will get them. We hope to provide all modern techniques to the university community in coming years. Not only linked to that room, we want to expand it,” Dr. Singh said.

Dr. Quinn agrees, and he hopes that as researchers come and use the core. In the process the core can understand future needs and where the research is moving to see what new technology under their umbrella could be added to keep supporting the scientists.

The MIC is a big step for the MU research community, and staff is hopeful that it will continue to grow and produce life-altering research.