Category: Grant Stories

Articles about completed grants

Applying AI in Complex Macromolecular Modeling: A Difficult Challenge Realizing Beneficial Gains

AI is a hot topic these days, with engineers and scientists looking to adapt artificial intelligence (AI) technology into a variety of chemical, physical and materials applications. However, its use in predictions of kinetics and dynamics has not been studied as closely. This subject came to the fore at Mason’s Center for Simulation and Modeling in the form of a question, “Is AI capable of identifying meaningful patterns in the temporal behavior of solvated macromolecules?” This question is important because it is understood that chemical sciences combined with engineering the associated data will be critical for finding solutions for environmental pollution, healthcare, sustainable energy resources, and global warming. Learning how these processes occur at the molecular, nanometer, and mesoscopic scales — inspected through computational simulation — and analyzing how associated big datasets can play a fundamental role in tackling complex systems could prove valuable. This question prompted Professors Olga Gkountouna (then in the Department of Computational and Data Sciences at Mason) and Estela Blaisten-Barojas, the Director of Center for Simulation and Modeling sought a 4-VA@Mason grant to look more closely into the possibility.

With the grant in hand, but with the pandemic in full sway, Gkountouna and Blaisten-Barojas devised how the work on this important research could be conducted within the restrictions of the shutdown. They needed a bright, independent thinker who could be taught to take up this big question. The solution was found when they tapped (at the time) doctoral student James Andrews (pictured above with Blaisten-Barojas on an earlier assignment) to do the difficult research. Andrews had previously worked with Blaisten-Barojas on several projects leading to his doctoral dissertation, and both professors felt as though he would be up to the complex task.

Andrews dove into the project, exploring the ability of how three well established recurrent neural networks — ERNN, LSTM and GRU — could provide viable data models. “Basically, James worked on forecasting how and if a group of macromolecules in a solution are going to keep together as a cluster or not,” explains Blaisten-Barojas. “If we can analyze how the macromolecules are behaving, we can estimate a prediction of what will come in the future. It is an estimate of the future, similar to what is done with the weather.”

After much analysis, Andrews and the two PI’s concluded that the recurrent neural network architectures investigated generate data models which reproduce excellently the macromolecules fate in the solution in the short-term. In the long-term, the forecasts statistical distributions yielded time events with limited variability. However, the team was able to discern the parameters of when supervised machine learning serves as a viable alternative for long all-atom computer simulations.

Blaisten-Barojas adds that another important outcome of the research was the energy savings – both human and computational. “Predicting modeling saves hundreds of hours of computing time, which require a lot of energy. Indeed, the Office of Research Computing big computers would be crunching numbers and storing the many terabytes of space, for output that could be avoided. Having a reliable forecasting model predicting if it is worth continuing a simulation or if it is going to give results that are not expected is a highly desirable tool. With some information on the simulation future, one can plan ahead, stop, make changes, go in a different direction, or eventually continue the simulation. In a nutshell, our new decision-making tool aids the simulation practitioner to assess when long simulations are worth continuing.”

While the analysis was tedious and difficult, Blaisten-Barojas reports that Andrews found an outlet to keep up with the hard work – by leaning on peers in his research group. Andrews and three other doctoral students in the Computational Sciences and Informatics PhD program met virtually on Fridays during the pandemic to exchange their graduate research results, share comments, input, suggestions, and provide encouragement. “These meetings maintained a supporting and cheerful platform during the uncertain pandemic times,” notes Blaisten-Barojas.

The PhD study group: (From top) Scott Hopkins, Greg Helmick, Yoseph Abere.

Andrews’ hard work paid off, with a paper published in Chemical Science, the prestigious journal published by the Royal Society of London: “J. Andrews, O. Gkountouna and E. Blaisten-Barojas, “Forecasting Molecular Dynamics Energetics of Polymers in Solution from Supervised Machine Learning.”” The work has also been disseminated in arXiv, a preprint repository maintained by Cornell University and Zenodo, a database repository of codes and data maintained by CERN.

Another jewel in the crown for Mason’s Center for Simulation and Modeling, with some help from 4-VA@Mason.

Developing a Blood Test to Support Treatment of Surgically Induced Type I Diabetes

Starting Small. Finishing Big.

Happenstance brought Dr. Robin Couch’s Lab and research into the 4-VA network. Although he was aware of 4-VA@Mason’s Collaborative Research Grants, Couch hadn’t thought much about the program until he received a request from Dr. Mazhar Kanak of VCU. Kanak approached the Couch Lab and the Mason Metabolomics Facility, asking if it was possible to identify biomarkers in blood serum which will determine a patient’s suitability for an islet cell auto transplantation, a procedure applicable to patients that suffer from chronic pancreatitis, requiring the removal of the pancreas. Couch concluded that the 4-VA program could offer an opportunity to answer VCU’s call. Thus, he applied for, and subsequently received, a 4-VA@Mason grant.

Today, with his 4-VA project complete and yielding very promising results, Couch has emerged as an unabashedly enthusiastic cheerleader for the possibilities of collaborative research across the Commonwealth. “Here in Virginia, we’re doing some very cutting-edge research, between UVA, Virginia Tech, JMU, VCU and all the other schools,” says Couch, “the state has really invested a lot of money at these institutions; but we’re all doing something a little bit different. Therefore, it’s imperative that we support collaborations between the institutions to maximize our dollars so we’re not duplicating efforts.”

Couch, an Associate Professor in Mason’s Chemistry and Biochemistry Department reflects on why he believed it was possible to develop a test to meet VCU’s needs. Couch details the comprehensive testing done in the Mason Metabolomics Facility, noting, “Unlike most bloodwork — where you just are looking at a targeted analysis of say a single glucose test – in our lab, we can look at thousands of different features and do a comparison.”

Specifically, Kanak — whose position titles include Assistant Professor; VCU School of Medicine, Department of Surgery, Division of Transplant Surgery; and Director of the Pancreatic Islet Cell Transplant Lab – wanted some insight into predicting which patients would be good candidates for an islet cell auto transplantation.

When the pancreas is removed, so is the body’s ability to produce insulin. Through islet cell transplantation however, the body can generate insulin and avoid surgically induced Type I diabetes. Yet this procedure is only effective in 25-50 percent of patients who have a pancreatotomy. Kanak postured, could a blood test serve as a predictor of successful surgery? Couch thought it was possible.

Challenges Ahead.

Islet cell auto transplantation is conducted during the surgery to remove the pancreas. The patient’s specific pancreatic cells that normally produce insulin (Islet cells) are extracted, cleansed, and returned into the patient. The islets then embed themselves onto the liver and resume their function releasing insulin. Because the islets are the patient’s own, there is no auto rejection.

Kanak carefully collected bloodwork from nine different pancreatotomy patients at various time points — before the patient underwent surgery, at several stages during the surgery, and then after the surgery – and sent them to Couch for analysis.

Then the pandemic hit. The analysis Couch envisioned possible looked possibly impossible. Labs were shut down. Students were sent home. Faculty couldn’t conduct research. The blood samples sat frozen in the lab. For months and months.

Then, when labs began to open back up, there were explicit restrictions on who could be in the lab and how many people could be in the lab. Several students originally designated to work on the project moved on to other life choices with the long break. Fortunately, Couch had a more than suitable fallback plan. He was able to rely on Mason Metabolomics Facility Lab Co-Director Dr. Allyson Dailey, who stepped in to handle the research. “I was able to run all the samples and then assisted with data analysis,” says Dailey.

Sample processing is quicker than data analysis, notes Couch. So, when the lab got back to work following the shutdown, considerable time was spent doing an exhaustive analysis of what features in the bloodwork most correlated with surgical outcomes. Dailey concluded that of the 2,500 features found, there were only six metabolites identified as predictors of outcome. A big breakthrough for the team.

“Now we don’t need to look at 2,500 metabolites, we only need to look at six — and we can ignore all of the other ones,” Couch points out. “Going forward, we can focus our study and our attention only on those six and it makes it much easier to process the data. Now, it won’t be so time consuming.”

With the important groundwork done, Couch believes they can take this research to the next level. “This is a great pilot scale investigation,” says Couch. Next stop? Getting a grant application into the National Institutes of Health, to seek funding for a clinical study with hundreds of participants — ensuring the biomarkers are validated.

Importantly, Couch thinks there actually could be much more to the research. He wonders, if it is possible to identify the successful candidates for islet cell auto transplantation; is there a future where this procedure could be valuable for all Type I diabetes patients? “Is it feasible to engineer out the problems and then make it successful for everybody?” Couch asks. “Hopefully,” he answers.

Couch and Dailey reflect on the research and its outcome. Concludes Couch, “None of this would have happened if it wasn’t for the 4-VA funds. We would have never had access to those samples, and we would never have done the research if it wasn’t for this program that fosters that collaborative environment. We’ll get further faster with this type of collaboration. It’s one thing to fund individual islands (schools) with equipment and personnel, but to make a bridge between the islands, it really makes a big difference.”

Bringing Technology to Public Good

Mason and JMU “Engineers” Project for Hard-of-Hearing Community

When a proposal to fund a project entitled “Toward T-Shaped Graduates: A Joint Capstone Program at the Nexus of Mechanical Engineering and Science and Technology Policy” arrived at the 4-VA@Mason office, it was quickly apparent that it would check more than a few 4-VA boxes – creating an interdisciplinary, wholistic approach for education which utilizes technology for societal good. As it turns out, the 4-VA Advisory Board agreed, and a grant for the research was extended.

This project asked students from James Madison University and Mason to consider how technology can be applied to solve challenges that include both technological and policy components. Through trans-institutional partnerships, students were challenged to innovate outside of their disciplinary backgrounds by collaborating across programs. They were guided by four faculty advisors from a range of fields — engineering, biotechnology, political science, and communications. As the lead PI Dr. Jeffrey Moran explains it, “T-shaped graduates are those that represent both a depth (the stem of the capital letter ‘T’) and breadth (top of ‘T’) of expertise.”

Moran sought to task students with the goal of addressing public needs; this often means tackling problems that straddle boundaries between disciplines. Moran noted that today’s environment calls for a new type of student and professional – an individual who is skilled in transcending disciplinary silos to address undertakings that do not fit into a single, specific category.

Mason student and team lead Kyle Hall called the project assignment complex and challenging. “It was so broad and open, it was hard to know where to begin,” Hall says. That, along with the shutdown brought on by the pandemic, the team (naming themselves ‘Level 6’ — see below) was prevented from meeting in person with the JMU students or with policymakers (as originally intended) to discuss the project. Nevertheless, they forged ahead armed with research confirming that the deaf and hard-of-hearing community were often hampered by their disability when driving.

Looking toward the future of autonomous vehicles (AV), the team settled on creating an alert system for an AV to support hard-of-hearing adults as they rode in an AV.

Their first assignment would be to learn more about the specific needs of the population. Fortunately, Hall notes, the JMU group had experience in theory and research reports and were able to provide the necessary foundation to begin project development. Additionally, because the JMU team also had experience in research involving human subjects, they were able to obtain permission from an institutional review board to start the study almost immediately.

Following the JMU start, the Mason team procured a golf cart to function as the prototype vehicle for the project, and they launched on a series of technological modifications to alert the ‘driver’ to activities around the vehicle.

First, the students created an alert system using a 360-degree microphone mounted in the cart. The microphone, linked to a Raspberry Pi (a small onboard computer), reads sounds in the immediate area. Using machine learning approaches, the system detects 10 different sounds that signal the need for increased caution, including an ambulance, fire engine and police siren, honking horn, construction work, people yelling, children playing, and dogs barking. The process was sometimes time-consuming – as is typical for machine learning, the system had to be “trained” to recognize these sounds, sometimes taking up to 100 hours for the network to learn one sound. When one of the 10 noises is detected, a seat cushion outfitted with a haptic sensor vibrates to let the driver know that a hazard is nearby. The driver is then prompted to read a tablet screen on the dashboard which identifies the noise.

One additional piece of instrumentation outfitted in the vehicle is a camera installed on the ceiling, which is pointed at the driver’s forehead and can read body temperature. Although not solely relevant to deaf users, the team anticipated that body temperature checks will be widely considered the norm for ridesharing in the post-COVID-19 era.

This labor-intensive systems creation and testing was undertaken in a workshop located on the Science and Technology campus in Manassas, where the group met most Friday afternoons during the spring semester. There, Hall says, they each focused on specific elements of the technology, but worked together to ensure a seamless final product. (In one positive outcome of the general switch to virtual learning due to the pandemic; a JMU student on the team, who was living at home in Northern Virginia taking online classes, was able to join the Mason team in person in Manassas.)

“This project allowed the advisors and students to tackle complex, multifaceted problems for the public good while building a great relationship with our colleagues at James Madison, which will continue in the future,” says Moran. “And the students far exceeded our expectations for finding creative solutions to difficult problems, especially during this complicated year and with such an open-ended project.”

Nathan M. Kathir, Associate Professor & Director of Senior Projects in the Department of Mechanical Engineering Projects agrees, “A primary objective of the mechanical engineering program’s senior design course, also known as the capstone program, is to enrich the educational experience of senior-level students with a real-world engineering experience. Mason’s six students on the Team level-6 experienced much more than that.” Kathir continues, “In the program’s five-year history, they were the first team to collaborate with those outside of Mason and they did that despite restrictions due to Covid-19 throughout the year. In a T-shaped graduate manner, not only they used their technical expertise, but they also excelled on other areas such as collaboration, communication, partnering with external stakeholders, managing risks, and planning for unknowns.”

Hall and Moran foresee that this project could be the beginning of a true legacy project, augmented by students in the future, adding modifications for communities with vision or mobility issues. “I can see that this project could continue to build great things,” notes Moran.

Meet the Level 6* Team

Although each member of the team focused on specific and separate modifications for the vehicle, it was a group effort to bring the total technology to fruition.

Josh Ogden — devised the technology for the camera.

Paul Cipparone — formulated the haptic cushion.

Jeorge del Carpio Arispe — focused on the touch screen.

Oliver Lopez — worked on CAD modeling.

Raizel Clemente — handled all communications, purchases for items and materials.

Kyle Hall — organized the project and insured deadlines were met and wrote all the reports.

*The Level 6 name is a nod to the ratings of AVs – as a Tesla is considered Level 3, highly autonomous cars are Level 5 — this team’s development of technical modifications is Level 6.

Putting the History of Higher Education Under a Microscope

While the Council for the Advancement of Higher Education Programs (CAHEP) considers the history of higher education a required knowledge area, and it is often a core course in higher education programs nationally, Mason’s Kelly Schrum, PhD, recognized that the class is rarely taught by historians and often lacks a focus on the critical thinking, research, and digital literacy skills essential for success in the rapidly changing higher education workplace.

When Schrum, a historian and associate professor of higher education, discussed this disconnect with colleague Chase Catalano, PhD, at Virginia Tech (VT), they saw that within this challenge there was an interesting opportunity: Create a history of higher education course at Mason and VT that is founded on historical thinking and research skills. Students could work collaboratively on digital research projects that draw on university archives locally and nationally. Moreover, they could build on this work to create an open educational resource (OER) on the history of higher education.

Schrum developed a plan, and then turned to 4-VA@Mason to seek a Collaborate Research Grant for her project entitled, “Reimagining the History of Higher Education in the Digital Age.” Subsequently, Schrum and Catalano received 4-VA funding to help get the project off the ground and, joined by Sophia Abbot, a doctoral student at Mason, they got to work.

Abbot, who has previously been involved with faculty development and has studied student-faculty partnerships in teaching, plays several integral roles in the project. The first is determining the current teaching landscape in higher education. To that end, Abbot and Mason sophomore, Kelly Tcheou, sent out surveys to instructors involved in teaching the history of higher education around the country to determine the specific subject areas included in their courses.

Along with Schrum and Catalano, Abbot implemented a new primary source learning activity for their courses this past fall. While Schrum and Catalano supported students in the selection of their research topics and their analysis of primary historical sources, Abbot helped students translate their research to the digital space as they developed online learning activities for their peers. Abbot shares the example of one student’s research which looked at the history and the language of the Pell Grant. The student gained a deeper understanding of how the language used in the original legislation resulted in who was able to gain access to the grants over the years; and who was not. “Their research is doing exactly what we’d hoped… students are empowered to take historical thinking into their work,” says Abbot. “When students create historical narratives — learning the context and history of the sources — they can look back at sources and understand the impact of the history of higher education on colleges and universities today.”

Additionally, Abbot introduces students to the opportunity to share their work on the primary source website the team is building. Here, Abbot acts as a liaison between the Mason and VT students and faculty. “Because I am not in an evaluation role, I am able to make sure that students understand that sharing – or not sharing — their work is completely optional and will not affect their grade. I’m there to communicate the importance of consent,” she notes.

Assisting Abbot with the website is Carolyn Mason who graduated from Mason in December with BA in anthropology and plans to begin a PhD program in anthropology in the fall. Mason identifies primary sources related to higher education including a university’s founding, student life, academics, and campus culture and uploads them to the website. She is also collecting a list of university archives that house historical documents related to their institution.

At the conclusion of the history courses, Abbot returns to interview students on both campuses to determine their thoughts about the class and their decision regarding sharing their work on the website. She has interviewed 12 students and collected 19 student projects from both campuses.

While the project is still in its infancy, it has already generated a lot of attention. The prototype website https://higheredhistory.gmu.edu/ presents more than 100 primary sources. Over 60 history of higher education instructors have responded to the invitation to share their teaching practices. And the team has piloted their primary source learning activity in two different higher education graduate courses (Fall 2020) and recruited a third course to pilot the activity (Spring 2021).

“We were delighted to have the ability to enrich the study of higher education, offer our students the opportunity to develop asynchronous online learning activities, and promote collaboration across institutions,” explains Schrum. “Already, we have had great results.”

Abbot, Schrum, and Catalano presented initial findings at the Conference on Higher Education Pedagogy in February.

“This project has been a wonderful exercise in collaboration and research,” concludes Schrum. “In fact, it has caught the eye of our colleagues at several additional 4-VA schools who are interested in partnering with us on this in the future. We are also looking at the development of a workshop on this for instructors in the history of higher education. There may be more to come!”

Virginia Food Systems Leadership Institute: From Concept to Course

4-VA@Mason takes great pride in being the catalyst for hundreds of impactful research projects and innovations in higher education. This is achieved via micro grant seed funding for Collaborative Research Grants; supporting projects that encourage cooperation between partner schools within the state and capitalize on the strengths of each school.

However, a new milestone was reached in this effort this spring — as one such grant team partnership morphed from a multi-year, thoughtful, wholistic, statewide Collaborative Research project to another of 4-VA’s foundational endeavors, Shared Courses. The Shared Course concept has its roots in the 4-VA commitment to identify and deliver top tier courses between partner schools, thus saving the costs involved in bringing unique classes to fruition on each campus.

The project crossing this boundary is the Virginia Food System Leadership Institute (VFSLI), which found its footings at a 4VA-funded symposium in 2015 at the Smithsonian-Mason School of Conservation in Front Royal. There, interested faculty were brought together from Virginia Tech, University of Virginia, James Madison University and George Mason University. Also attending the symposium were campus dining services personnel and sustainability managers. They discussed avenues to harness the intellectual, human, and economic capital of colleges and universities to foster the emerging food economy in Virginia.

“Immediately, we saw a lot of synergy. We had a passionate group of folks involved in all areas of food — producers, delivery partners, and consumers.” says Kerri LaCharite, PhD, Assistant Professor in Mason’s Department of Nutrition and Food Studies. “What’s more, we also recognized the need to support small-to medium-sized growers by helping them access institutional markets — a real boost for Virginia’s rural economy.”

In April of 2016, again under the 4-VA banner, a second symposium convened more than 40 Virginia food system stakeholders including farmers and processors; distributors and Aramark and Sodexo representatives (food service vendors at Virginia colleges); and faculty from the four schools. Their focus was to increase university sourcing of Virginia-grown food.

In 2018, the leaders of this effort from the four 4-VA schools developed an intensive four-week class which was piloted at the Smithsonian-Mason School of Conservation. It was an instant success.

Mason Nutrition and Food Studies graduate student Kelly Kogan attended the course. “This course was a fantastic chance to really immerse myself in the complex and changing chain of food delivery systems in Virginia,” Kogan said. “I also loved the mix of students who attended. We were graduates and undergraduates representing five schools.”

This year, the latest breakthrough is the course: NUTR 626 Food Systems — a fully online, asynchronous, and synchronous, class offered through 4-VA Shared Courses program. It will run Monday through Friday May 24 through June 17 with synchronous sessions 12-1 pm and 5-6:30 pm. Although Mason’s LaCharite and UVA’s Tanya Deckla Cobb will take the lead, the teaching will be divided between all the schools – including Tech’s Kim Niewolny and Michael Broderick from JMU. This year, this top team is joined by former Virginia Secretary of Agriculture Basil Gooden, currently a visiting scholar at VCU.

(Part of the VFSLI team on a recent call: Clockwise from top right: Kerri LaCharite, Basil Gooden, Michael Broderick and Tanya Deckla Cobb.)

“This is a one-of-a-kind class which could only have been developed through a true collaborative effort,” explains LaCharite. “Each school contributed something vital to the project, and we are the better for it. But, without the 4-VA funding, this would never have happened. We’ve gone from a concept to a reality which will benefit students – and, subsequently, food system sustainability, farmers, schools, and businesses throughout Virginia.”

4-VA@Mason Grant Provides Rich Research Opportunity

Expectations for 4-VA@Mason’s grants include thoughtful, impactful research; statewide collaboration with partner universities; and experiential learning opportunities for students. However, the 4-VA@Mason story grows stronger when that learning opportunity gets elevated to supporting post graduate work.

Over the past two years, students in Haw Chuan Lim’s lab at Mason’s Science and Technology campus have contributed to the work done on Dr. Lim’s 4-VA grant “High-throughput bee pathogen survey: Combining expertise in pollinator biology, bioinformatics and genomics to yield insight into pollinator health.” They looked deeply at whether the presence of managed or feral honeybees, with their large colony sizes, influences pathogen populations of native bees (bumble and mason bees).

To do this, Lim’s students — including master’s candidate David Lambrecht — collected bees across 10 sites around Northern Virginia and analyzed pathogen strains – viruses/fungi — using high-resolution genotyping techniques. They partnered with UVA’s T’ai Roulston, who is appointed to Blandy Experimental Farm, along with landowners and farmers of the Virginia Working Landscape project. The resulting research will be important as beekeepers and farmers navigate the continuing loss of bee colonies.

That research was the foundation of Lambrecht’s master’s thesis “Prevalence and Cross Infection of Eukaryotic and RNA Pathogens of Honeybees, Bumble Bees, and Mason Bees” which he recently defended via Webex during the Coronavirus shutdown. “This 4-VA opportunity gave me a chance to research honeybees and other pollinators important to our ecosystem,” explains Lambrecht. “The results provide some guidance for successfully supporting their populations.”

Armed with his new MS, Lambrecht is off to join the ranks of the Environmental Protection Agency, where he will intern and help with gene editing regulations.

“At 4-VA, we’re always proud of the research opportunities and resulting outcomes we have to show,” noted 4-VA@Mason Campus Coordinator Janette Muir, “but when we get to combine research and collaboration with these types of prospects for our students — that’s a great success!”

Mason’s Center for Simulation and Modeling “Scales Up” with 4-VA Partner ODU

Of the 21 iterations of the definition of the word ‘scale’ in the Oxford Dictionary, one is particularly applicable to the latest 4-VA grant project “Scalable Molecular Dynamics;” that is: “the full range of different levels of people or things.” This definition illustrates both the scope of the research and the collaborators involved in the effort.

While orchestrating a variety of other projects and programs at Mason’s Center for Simulation and Modeling (CSM) located in the College of Science, lead PI Dr. Estela Blaisten-Barojas took on one more when she applied for and received the 4-VA grant. Blaisten-Barojas was interested in undertaking a serious study of predictive computational and simulation-based approaches in chemical and materials sciences combined with engineering approaches. This study is central to finding innovative solutions for environmental pollution, healthcare, sustainable energy resources, global warming, and ways of fighting terrorism, crucial to both Virginia’s and the nation’s competitiveness in science and engineering.

Blaisten-Barojas consults with team member James Andrews

To launch and deliver “Scalable Molecular Dynamics” a full-throttled balancing act was necessary, Blaisten-Barojas called in her colleague Dr. Robert Handler from the Mechanical Engineering department at Volgeneau and Dr. Eric Weisel, Executive Director, Virginia Modeling, Analysis, and Simulation Center (VMASC) at Old Dominion University, a 4-VA partner school. Then, she added a number of talented students, including Gideon Gogovi, Scott Hopkins and James Andrews, to her 4-VA team. Each brought countless hours of research to the project – enhancing both the collective mission and their personal portfolios.

Blaisten-Barojas was interested in testing computational techniques for scaling up various aspects of a molecular simulation in which a large molecule is solvated or flows in a viscous solvent. Specifically, they studied the atomistic behavior of the polymer polyacrylamide, or PAM. This polymer, when immersed in gel-type solvents, is used for the separation of proteins, an important component in bio detection.

The team’s research identified several interesting and notable characteristics regarding the structure and energetics of PAM in implicit and explicit solvents – as team members studied the chain shape and the diversity of coiling and twists of the polymer in the various solvents. The researchers noted closely the changes in shape from an elongated spaghetti string to a more football-like object. Importantly, based on what they learned, they were able to make some scaling up predictions about how big structures can grow. This new understanding is valuable for efficiently controlling the performance of devices based on molecular components.Once the project got moving, the full range definition of scalability was set in motion. In fact, the simulations were so complex that they reached the maximum allowed in Argo, Mason’s centralized research computing cluster.

Gideon Gogovi presents at the ACS convention

Scott Hopkins at the poster presentation

Already, two conference presentations have been made based on the research – a talk and a poster at the recent American Chemical Society (ACS) Mid Atlantic Research Meeting; two journal papers are in submission.

Blaisten-Barojas notes that although the research, results and dissemination have been gratifying, it was the new-found relationship with the VMASC which capped the full range of different levels of people and subjects concept. “This is a very important first step,” Blaisten-Barojas notes. “We now know who they are and they know who we are. I know that if they see possibilities in some of their initiatives, they will knock on our door first and we will do the same.”

Hard Work, Partnerships and a 4-VA Grant: Producing Big Results in IPF Research

(L to R) Geraldine Grant, Charlotte Nigg, Jorge Fernandez Davila, Honoria Riley, Ganit Pricer, Michelle Devlin, Luis Rodriguez

Like any cutting-edge research team, the undergrad and grad students assembled in Dr. Geraldine Grant’s molecular and cell biology lab at George Mason’s Science and Technology Campus knew that in order for their project to be successful they needed a few things to break their way. Specifically, for their 4-VA grant “Prognostic Noninvasive Biomarker Investigation of Induced Sputum and Peripheral Blood in IPF” (Idiopathic Pulmonary Fibrosis), they would need a lot of science, a touch of luck, a drop of art, and more than a little bit of help from their friends.

Their goal was ambitious: Identify biomarkers that would help track the diagnosis and progression of the disease as well as the efficacy, if even detected, of medical treatment. The goal would be a tall order for this difficult-to-diagnose and difficult-to-treat lung condition which affects more than 200,000 people in the U.S alone.

IPF is a progressive, fatal lung disease that is survived by few patients three to five years after diagnosis. With IPF, patients experience severe scarring (fibrosis) of the lungs for an unknown reason. Over time, the scarring gets worse and it becomes difficult for the patient to take in a deep breath and inhale enough oxygen to fill the lungs.

Long-time Grant Lab member and part of the initial team writing the 4-VA@Mason proposal, Dr. Luis Rodriguez explains, “Diagnosing IPF is a difficult task. Most of the time, diagnosis is simply a continuing series of elimination testing. Doctors back into the diagnosis because it was determined that it’s not A, B, or C.” What’s more, Rodriguez points out, “The disease can present in a number of different ways and the only standard for diagnosis confirmation is a sample from the lungs, but through that, the patient is at critical risk.”

However, tackling the diagnosis was just a part of the Grant lab challenge. Treating the disease can also prove problematic, as it can progress slowly or rapidly and the efficacies of treatment are difficult to determine. With few therapeutic options, little to no systematic tracking of treatment, and a wide range of patient responses to said treatment, the work was cut out for the team.

First, they needed data, and a reliable stockpile at that. Their objective was to get a large sample of patients suffering with the disease and to extract RNA. The next step would be to correlate the RNA with the current status of each patient’s disease, which included precise measurements of two important criteria: 1. How they breathe in and out, and 2. How far they can walk in six minutes.

That’s when they called on their first partner in the grant project, Northern Virginia’s INOVA Hospital and Dr. Steve Nathan. INOVA has long been a recognized care and treatment center for IPF and has a history of successful lung transplants for IPF patients. Through INOVA, the Grant team wanted to build that necessary data set to track, if possible, the measurements of disease progression. Nathan and the clinic were all in.

With a base of 40 patients in Nathan’s province, the Grant team got to work – monitoring, measuring and capturing data. The process was long and tedious, and they encountered their share of difficulties. One such roadblock meant refining mitochondria sensors in the patient blood samples measuring changes in oxygen that, in turn, captured the progression of the disease and the effectiveness of the treatment. Their perseverance paid off, however, with a statistically significant reliable data set. (Which, Rodriguez points out, continues to grow and provide valuable information.)

Their next task, then, was to analyze said data in a meaningful and productive way. That’s when they called in their second partner Dr. Norou Diawara, of the Math Department at 4-VA partner school Old Dominion University. Diawara has vast experience and expertise in the field of Biostatistics, which fit the bill for the Grant project.

All efforts paid off with noteworthy results, as the research identified gene signatures that indicated what patients responded to treatment and those that didn’t – a giant leap forward in their medicine.

What’s more, Rodriguez notes, is that the initial grant has spawned a cadre of further opportunities including OSCAR undergraduate students continuing the analysis of the data set, and grants submitted to NIH, as well as to NSF for a grant on the biology of mitochondria. The project has also been featured in several poster presentations. One such notable presentation was at the Pulmonary Fibrosis Foundation Summit in September, a convocation of the leaders of research and treatment of Pulmonary Fibrosis, where the poster ranked in the Top 10.

(L to R) Durwood Moore, Ganit Pricer, Honoria Riley, Brieann Sobieski, Geraldine Grant, Michelle Devlin

“The 4-VA grant got this ball rolling,” concludes Rodriguez, “and we’ve progressed a long way from the start of this effort. However, I can see this initial research continuing to produce important results for years to come.”

4-VA Grant Supports State STEM Summit

More than 140 leaders from Virginia’s K-12 and higher education institutions, out-of-school providers, the private and business sectors, and state officials and institutions joined together recently to begin the work of developing a blueprint for a statewide STEM network. This structure will be the basis for creating cross sector pedagogies providing Virginia’s youth access to a learning environment which will allow them to grow important skills to engage in science, technology, engineering, and mathematics from PreK – 16. “Virginia’s STEM Summit” was hosted by Virginia Commonwealth University and sponsored through a grant from 4-VA. The project was developed by a group 4-VA schools – VCU, Virginia Tech, George Mason, James Madison, and University of Virginia in coordination with the Virginia Department of Education and the Office of the Governor.

Governor Ralph Northam has charged Virginia’s STEM leaders with the job of creating an infrastructure, with input from all stakeholders, for the newly-appointed Virginia STEM Education Commission. The strategic plan is due next year.

As 4-VA grant team member and Associate Director of the Center for Educational Networks and Impacts at Virginia Tech Susan Magliaro, explained, “Our goal today is to provide a well woven tapestry of information from our STEM leaders.”

Left to Right, Padhu Seshaiyer (Mason), Leland Melvin and Kelly Knight (Mason)

The day-long conference began with a keynote address from retired NASA astronaut, materials science engineer, educator, and former NFL wide receiver Leland Melvin. Melvin shared with the audience how STEM education necessitates an open mind, perseverance, and personal support in order to be successful. George Mason University’s PI on the project, Dr. Padmanabhan Seshaiyer noted, “Leland was the perfect kick-off for our conference. He clearly illustrated that STEM doesn’t have to be stuffy or difficult to understand, it’s a hands-on experiential learning opportunity which can open doors for all of our students, and especially our minority or underserved students. It can bring projects and process to life.”

Other Mason participants in this 4-VA summit included members with diverse backgrounds and expertise in STEM including Dr. Rebecca Jones, Ms. Kelly Knight, Dr. Karen Lee, Dr. Kammy Sanghera and Ms. Kerin Hilker-Balkissoon.

The conference also included a panel discussion addressing some of the more difficult obstacles to overcome while implementing STEM programs, presented by a range of leaders from the business, education and policy arenas. Each highlighted best practices developed by state or local school boards from around the country. The consensus was that successful existing ecosystems in STEM were developed by building a culture which welcomed all stakeholders, and where the resulting guidelines represented a convergence of values and practices.

Following the panel discussions, attendees joined together to hammer out the framework for such ecosystems based on their professional backgrounds.

Longtime STEM proponent Amy Sabarre, Director of STEM Education for the Harrisonburg City Schools, observed, “I’ve been involved with the development of a core curriculum for STEM in the Commonwealth for years, and this Summit has been a long time coming. But, we’re here now, and we’re making great strides.”

Concurrently, newer stakeholders see the same bright future. Says Makerspace coordinator at William and Mary, Jonathan Frey, “Makerspaces have been growing and evolving at a dramatic pace throughout the world. What was once a location for tinkerers to play with technology has now become an impactful community engineering center both in academia and the private sector. Here in the Commonwealth there are dozens of makerspaces and it’s time to coordinate collaboration throughout Virginia. The 4-VA STEM Summit offers an opportunity for introduction and collaboration between such efforts from the peaks of Appalachia to the sands of the eastern shore.”

The day concluded with a group effort to integrate the work created at each roundtable into a viable framework for the Commonwealth. The conclusions will provide the basis for the STEM ecosystem build out and will be forwarded to the Virginia’s STEM Education Commission.

(Research + Collaboration) = (Important Results in the Lab + Successful Career Outcomes)

The science would not be easy. There were going to be long days and nights in the lab, countless tests to run and techniques to be tweaked. But the end game was intriguing; identify opportunities to affect modifications in the Francisella proteome, a bacterium categorized as a class “A” bioterrorism agent. Unlike its cousin, the more well-researched E. coli bacteria, many aspects of the Francisella proteome are not fully understood. Due to its potentially virulent nature, it is important to research and document the biochemistry of this organism in order to develop new therapies or vaccines.

While the van Hoek lab at the Mason Sci-Tech campus has been studying Francisella since 2005, they were interested to learn more about post-translational modifications (PTMs) – changes undergone by the protein when certain chemical groups are added. Specifically, Dr. Monique van Hoek, a professor in the School of Systems Biology, with a joint appointment to the National Center for Biodefense and Infectious Diseases at Mason, was interested in how the Francisella bacterium changes the activity of its proteins with the addition of the acetyl chemical group. Although van Hoek had years of experience in Francisella research, for this particular project she recognized that while her lab could make the protein/peptide samples, it was necessary to run a thorough molecular analysis of the samples to measure acetylation. That, she saw, could be done through a collaboration with another 4-VA partner university – Virginia Commonwealth, in their Chemical and Proteomics Mass Spectrometry Core Facility. It was that connection which paved the way for yet another groundbreaking 4-VA research project – “Critical post-translational modifications of the Francisella proteome.”

As van Hoek explains, not only did the research produce results, the grant also had a positive effect on students in her lab and faculty at VCU. “Real lives were changed — two great students graduated and went on to get good jobs,” notes van Hoek. The first student, Ekaterina (Kate) Marakosova, was a Ph.D. student at Mason who began the project with van Hoek working with the more virulent forms of Francisella. “Kate started on this project with me and developed techniques to identify protein acetylation. Kate has since gotten her doctorate and gone on to get a great job at the Food and Drug Administration,” says van Hoek. “Alex Ii is now working as a laboratory technician with me,” adds van Hoek. “In May, Alex defended her Master’s on another aspect of this project ‘Acetylation as a regulatory mechanism of chitinase activity in Francisella tularensis subsp. novidica.’”

Ii came to the van Hoek lab after starting her degree at VCU in Bioinformatics. “Once I got into this lab, I realized I really liked the work,” says Ii. “When I first started here, I was working with Kate and immediately jumped into the project. We were coming in at 5:00 am and often didn’t leave until 8:00 pm. The sample preparation was difficult, and we had to do a lot of troubleshooting, but it was worth it!” Ii was not only all in for the lab work, but with anything else that needed to be done, even driving samples to the lab in Richmond late at night.

van Hoek also notes that her collaborator at VCU, Dr. Kristina Nelson, points to the project in furthering her own research. Nelson received a 4-VA Complementary Grant for her part in the project. “With the complementary funding, we were able to purchase standards and columns in order to ensure that the instrument was operating at peak performance, to give the best data possible,” explains Nelson. “It was fascinating to be able to visualize the changes in the protein acetylation profile.”

“The new collaboration with Kristina was certainly another positive outcome of the 4-VA grant,” says van Hoek.

In addition to furthering the education and professional tracks of those on the project, the research was fruitful. The team has identified multiple Francisella proteins that are acetylated and look to be important in Francisella’s ability to infect hosts. To share the research, a poster was presented at the American Society for Microbiology meeting on biofilms and the manuscript has been submitted for potential publication.

While van Hoek notes there is still much more to be investigated with regard to the Francisella bacterium, which causes human disease in the US and in Europe, she credits the 4-VA@Mason grant for delivering these important results, and making such positive effects on the people and the science. van Hoek continues to study important questions of Francisella biology, such as which proteins are secreted by this bacterium and how they are exported. In fact, van Hoek and Nelson are now at work on another 4-VA collaborative research project on this very subject “Secreted Proteins of Francisella – a new understanding.” Stay tuned!