The Nucleus of an Expanding Science

by | Dec 18, 2014

From blood clotting to Alzheimers and clean water, MCB faculty members are frequently involved in cross campus, interdisciplinary and even visionary efforts involving both highly translational projects and those that are deeply fundamental.

Illinois School of Molecular and Cellular Biology magazine December 2014

Benito Mariñas, professor of civil and environmental engineering, had a problem. He was part of an effort to provide clean water to communities in East Africa, but the range of contaminants was vast. Diarrhea from unsafe drinking water is an enormous global health burden. Many contaminants cause chronic diarrhea, which leads to numerous health problems and is one of the leading causes of death in children under five-years old.  One contaminant Mariñas was wrestling with was adenovirus, which was very resistant to low pressure UV disinfection, a common technique that worked for other viruses.

Wanting to better understand the challenge, he sought out MCB professor Joanna Shisler, professor of microbiology, who, he learned, worked with adenovirus. Could she help him with this problem, he wondered?

“Benito wanted to be able to measure what was going on with the virus when it was being disinfected,” says Shisler, who agreed to help.

Thus began a seven-year (so far) collaboration that has begun, not only to address some of Mariñas’s questions, but also to train “very unique people” with experience in molecular biology, engineering and global health issues, says Shisler. So far Shisler and Mariñas have trained five students together and published four papers on their collaborative work.

Thanks to Shisler’s in-depth understanding of the complex biology of viruses, the team is slowly making progress in determining how to neutralize viruses and also how to determine if they have been neutralized. One grand challenge in the field is how do you detect an active, intact virus versus the individual parts that are no longer a unit.

Current methods can identify the genome and the protein elements of the virus, but it can’t tell if they are together, and thus infectious, or if they were separated, at which point they are no longer infectious.

One approach involves an effort by Yi Lu, professor of chemistry, to design an aptamer to recognize an entire virus particle. Aptamers are single-stranded RNA, and very long molecules. Lu is trying to design one that will recognize an entire virus particle. Lu is trying to find an aptamer that would bind to the intact virus particle but not the disinfected particle.

“The grand vision here is that we know how adenoviruses are inactivated; we know on a molecular level and what we’re doing is developing a new technology so we can detect infectious particles in the water supply,” says Shisler. Once they do that they can start asking the question, “is the disinfection system effective?”

Ultimately, Shisler and her colleagues hope to develop a product that can detect contaminants, that is accepted by the community, and perhaps could be a source of jobs or micro-businesses. Madhu Viswanathan, a professor of business, who studies how groups in the lowest socioeconomic stratus make decisions, is lending his expertise to the project, as well.

This project is one of three large cross-campus projects recently funded by the University’s Institute of Sustainability, Energy, and Environment.

“I’ve learned an aspect of public health I wouldn’t have without this collaboration,” reflects Shisler. “Helping communities alone has been really rewarding, but we’re also training different levels of students who become more broadly trained, who can put pieces of information together for new solutions.”

“It is highly likely that any hardcore molecular biosciences project on campus will involve MCB faculty,” says Steve Sligar, professor of biochemistry and director of MCB.

Sometimes, as in the case with Shisler, a researcher on campus will approach an MCB member with a question. In other cases, MCB faculty have had problems for which they seek out engineers, computer analysts or physical scientists for solutions.

In addition, as scientists seek to answer more and more complex questions, the need to collaborate with people who have different areas of expertise becomes essential.

“When you employ a certain methodology in isolation, even though it may be very powerful, you are very limited in scope, but when you combine it with other methodologies, other ways of looking at the same problem from different angles you have a great chance to make significant contributions,” says Emad Tajkhorshid, professor of biochemistry, biophysics and computational biology. He should know, since he collaborates with countless colleagues across (and beyond) campus.

One undertaking that is resulting in significant contributions involves understanding how cell membranes and membrane proteins work. Jim Morrissey, professor of biochemistry, had done ground-breaking functional studies on blood clotting, and how blood-clotting proteins interact with membranes for much of his career. But understanding the detailed protein-membrane interactions underlying experimental observations often presents a real challenge because 1) they are exceedingly complex, 2) the membrane is very difficult to work with and 3) the necessary high-resolution techniques have not existed until now.

When fellow biologist Steven Sligar developed the “nanodisc” technology, Morrissey realized it could help him in his efforts. Nanodiscs are 10-nanometer-long slices of cell membrane, stabilized by a protein that encircles it like a disc.

“Membrane proteins are extremely difficult to study because if you remove them from the cell membrane, they become inactive, they aggregate like scrambled eggs, and they die,” says Sligar.

Meanwhile, Chad Rienstra, professor of chemistry, had developed a way to use solid-state NMR (SSNMR) to answer structural questions about larger molecules, including membrane proteins that standard NMR cannot. This technology also promised to advance the understanding of cell membranes and could be used to understand how the lipid portion of membranes, in particular, interacts with membrane proteins.

This is precisely the kind of interdisciplinary undertaking in which cell biologists are essential, says Martha Gillette, professor of cell and developmental biology.

“To really ask the best questions about a complex system you need to be steeped in how that system works. In that sense biologists are critical to the growth and development of not only the campus but the whole enterprise of bringing technology to bear on living things,” Gillette says.

Morrissey also collaborates with Tajkhorshid, who is a bit of a hybrid. A member of the biochemistry department, he has two PhDs, one in pharmaceutical chemistry and one in biophysics. He loved chemistry in his pharmacy program and became interested in computer science, moving into computational chemistry. Soon he realized that there were much more exciting areas in computational biology where he could work with functional  macromolecules, such as channels, transporters and receptors.

“These are really, really fascinating machines,” he says.

Tajkhorshid’s group does computer simulations in which they use computational biology to help understand how atoms move on such short timescales that can’t be measured experimentally. His group provides testable hypotheses.

“I really love to look at molecules and understand them,” says Tajkhorshid. “Every time I see an interesting problem I jump on it.  My main goal is to apply these computational techniques to exciting biomolecular problems and to advance our understanding of the microscopic world in and around us.”

At the time that Tajkhorshid heard about Morrissey’s work, Tajkhorshid’s group had been doing computer simulations on cell membranes that were about the size of the nanodiscs. He realized that he could run simulations of the binding of blood clotting proteins to membranes. 

More recently, this membrane team has expanded to include Ryan Bailey, professor of analytical chemistry. Bailey has developed a micro ring technology that can measure the binding affinity and rate of binding of the protein with the membrane. 

Morrissey says when physical scientists, such as Bailey and Rienstra, collaborate with biologists, their expertise can be more effectively brought to bear on important problems.

“Chemists and engineers who collaborate with biophysicists enjoy bringing their expertise to bear, but blood clotting is a very mature field, it’s very hard to enter,” he says. “By working with us, we can tell them what very important questions there are and then they can bring their expertise to bear. Biology is their future. Although they are world class in their field, they also need biologists to identify the most important biomedical questions to focus on.”

These collaborations have been enormously fruitful. The team has joint lab meetings every other week and has published 18 papers together. They have also competed successfully for multiple NIH grants.

“It’s one of the most exciting things I’ve ever done,” says Morrissey, of this set of new approaches to a well-established field. “Working with mathematicians, biophysicists, chemists, and enzymologists we can make much faster progress and new ideas, which create a deeper understanding and fundamental insights into membrane functions.”

“Nobody else is really studying these protein-membrane interactions at the level we are, with so many complementary techniques,” adds Tajkhorshid.

This multidisciplinary approach is laying the groundwork for new therapies for blood clotting diseases and disorders, like hemophilia and thrombosis. Using these approaches will help them understand why, for example, factor VII binds stronger or weaker compared to other coagulation factors and how they can change that behavior to improve current therapies.

Gillette is leading an equally ambitious collaborative project that will explore the dynamic brain – “how it remembers, enables us to move or be moved, to awake and sleep each day of our lives,” as she says.

The team, which includes Jonathan Sweedler, professor of chemistry, Gabriel Popescu, professor of electrical and computer engineering, and John Rogers, professor of materials science and engineering, intends to examine how neurons in the brain are activated in response to experiences, in order to see how they cause behavioral changes and subsequent activities of the neurons, also known as brain plasticity. In order to do this, the team will develop and use newly created, complementary technologies that will non-invasively control, measure, and analyze brain network dynamics and change in real time.

Gillette is very optimistic that these tools hold tremendous promise for identifying the signatures of neural activity that generate complex behaviors, insights not previously possible.

One technique, developed by Popescu, is a non-invasive, non-labeling imaging method that reveals differences in optical densities within the cell. For example, the nucleus is revealed as a crater because of spatial differences in its optical density.

“These are novel imaging technologies that you can’t buy,” says Gillette.

Popescu’s technique will be further developed so that he can image, not single cells, but slices of brain where all the connectivity is laid down by developmental processes and see how they are functioning in real time, thanks to Rogers’s transparent tattoo-like electrodes and sensors and Sweedler’s analytical techniques to measure peptides. Gillete, the neurophysiologist, brings the intellectual glue that will orchestrate the approaches and interpret the outcomes to advance brain science.

“I’m really proud of this project,” says Gillette. “It wouldn’t have happened except for two things. Everyone involved is very innovative and very collegial. You have to put your ego down and be willing to work with the group, and all the people we’re collaborating with are like that. That’s the future: working across disciplines.”

Dan Llano’s interests in the brain have led, in his case, to the clinic, where he ferrets out how aging and Alzheimer’s affect the auditory system, as well as how language and cognitive dysfunction arises from stroke.

“We are studying how brains process various kinds of sounds using a range of techniques including imaging, electrophysiology, and computational work,” says Llano, professor of medical and molecular integrative physiology and full-time faculty member with the Beckman Institute’s NeuroTech group.

Llano has a very successful collaboration with Taher Saif, professor of mechanical science and engineering, who has had a longstanding interest in the mechanical properties of neurons. For example, Saif determined that even tiny perturbations in the mechanical tension of neurons can substantially change neuronal activity.

Llano has preparations of brain slices in his lab that he puts on micro-devices built by Saif that exert tiny forces on the portions of brain tissue.  He then uses optical imaging to measure how populations of brain cells respond to these forces.

“There are many clinical conditions where mechanical forces are extremely important, for example, brain tumors, traumatic brain injury, and hydrocephalus, all stretch brain cells and nobody has any idea how that affects brain function,” says Llano.

The collaboration was initiated by one of Saif’s graduate students, Anthony Fan, who knew Llano’s group was using optical imaging. Fan thought that might be a good way to measure the impact of stretching across a population of neurons instead of a single neuron at a time.

Saif and Fan, are experts at making micro-devices, such as the one that can stretch a single neuron. Llano is using that device for another project, for which they are submitting a collaborative grant.

This combination of experimental biology with new techniques in computation and imaging is where the future lies.

And, as biologically based research becomes more and more highly collaborative, MCB is a natural magnet — the nucleus even, of an expanding science.

Book cover of MCB, The Nucleus of an Expanding Science

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