Professional Activity and Scholarship Narrative: The overall goal of my research at the Department of Medical Microbiology and Immunology (MMI), University of Toledo (UToledo), is to understand how the host responds to viral infection. In this regard, my laboratory is focused on the type-I interferon (IFN) system, also known as the first line of defense against viruses. Over the past decade, my research was focused on how the key transcription factor interferon regulatory factor 3 (IRF3) functions to inhibit virus replication in cells and mice. Extensive studies from our research have revealed that IRF3, in addition to its role as a transcription factor, has non-transcriptional functions. Using complementary in vitro and in vivo models, we demonstrated that both transcriptional and non-transcriptional pathways contribute to the antiviral response of IRF3. Finally, we have also expanded the functions of IRF3 to non-viral disease models.

In the transcriptional pathway, IRF3, upon activation by virus infection, induces hundreds of antiviral genes, such as IFNs and IFN-stimulated genes (ISGs). The protein products of these ISGs inhibit specific stages of the viral life cycle, thereby inhibiting virus replication. Because a single ISG cannot inhibit all viruses, it is important to investigate virus-specific ISGs. Using high throughput screening approaches, we began to identify new viral restriction mechanisms of the host. We have isolated a subset of novel viral restriction factors, which we are testing on the replication of both RNA and DNA viruses, which are human pathogens. Some of the specific goals in this research area include: (a) Determine how the novel viral restriction factors inhibit viral infection: using paramyxo/pneumovirus (e.g., respiratory syncytial virus, human parainfluenza virus) and herpesvirus (e.g., HSV-1) infection models, we are studying how the newly identified factors inhibit these viruses in vitro, ex vivo and in vivo. These mechanisms are now also being tested in mouse models by using a mouse respiratory virus, Sendai virus, which belongs to the same virus family and causes a lethal infection in mice. (b) Investigate the molecular mechanisms of the newly identified viral restriction factors: we began to explore the molecular mechanisms of these newly identified restriction factors. A number of aspects are being examined: the ability to induce cell death, amplification of interferon responses, direct effect on the virus life cycle. Using the CRISPR/CAS9 approach, we are generating cells with the deletion of specific genes and the expression of mutants. Using TDRD7, a new antiviral ISG, isolated from the screen, we uncovered that autophagy inhibition is a novel antiviral mechanism of the IFN system (Subramanian et al. Plos Pathogens 2018, J Biol Chem 2020). The early studies of this project have been funded by a Scientist Development Grant (American Heart Association).

A major accomplishment of my research has been the discovery of a non-transcriptional pathway of IRF3, the RIG-I stimulated IRF3 mediated Pathway of Apoptosis (RIPA). In RIPA, IRF3 does not require its transcriptional activity but interacts with the pro-apoptotic protein BAX to trigger a direct apoptotic response in the virus-infected cells (Chattopadhyay et al., EMBO J 2010, Cell Cycle 2010, J Virol 2011, 2013). Specific proteins are required to trigger RIPA by virus-induced RIG-I activation. In recent studies, we demonstrated that a specific ubiquitination modification of IRF3 triggers RIPA (Chattopadhyay et al., Immunity 2016, Protein Cell 2017). Moreover, in the absence of induced antiviral genes, RIPA can protect mice against respiratory viral pathogenesis (Chattopadhyay et al., Immunity 2016). Using newly generated knock-in mice, our studies demonstrated that IRF3 can provide antiviral protection in the absence of its transcriptional activity. Moreover, the absence of RIPA leads to viral persistence (Peters, Chattopadhyay and Sen, J Virol 2008). Because the viruses often shut off the host protein synthesis machinery, it is critical to provide antiviral defense even in the absence of the induced antiviral genes. Some specific goals in this research area include: (a) Investigate novel regulators of RIPA: Because RIPA is a newly identified antiviral pathway, we are using various approaches to determine regulators of this pathway. We have shown earlier that the PI3 Kinase pathway negatively regulates this pathway (White, Chattopadhyay and Sen, J. Virol, 2011). We recently used a high throughput screen of the FDA-approved drug library and isolated a number of small molecule activators of RIPA (Glanz et al., Viruses, 2020). Some of these RIPA-activators, as expected, are potent antiviral agents. (b) Determine the non-transcriptional function of IRF3 to inhibit inflammatory responses: We recently collaborated with Laura Nagy (Cleveland Clinic) and investigated the role of non-transcriptional functions of IRF3 in liver diseases. Our collaborative studies showed that RIPA in specific cell types contributes to alcoholic liver diseases (J Hepatol 2019). Surprisingly, in non-alcoholic liver disease models, IRF3 inhibits the NF-kB functions to protect the host (Hepatol Comm 2019). We are now expanding the anti-inflammatory functions of IRF3 in other inflammatory disease models, including in viral inflammation. The studies of non-transcriptional pathways of IRF3 have been funded by R21 (NIAAA, Chattopadhyay, PI), an RO1 sub-award (NIAAA, Nagy, PI), and recently, an RO1 (NIAID, Chattopadhyay, PI).

In addition, my laboratory is also engaged in other collaborative projects within and outside of the UToledo. In collaboration with Travis Taylor, Associate Professor (MMI, UToledo) we are studying the pro-viral role of TRAF proteins in tick-borne flavivirus replication (iScience 2019). This project is currently funded as an RO1 with my role as a co-investigator (NIAID, Taylor, PI). We are collaborating with Bina Joe, Professor and Chair (Physiology and Pharmacology, UToledo), and Jason Huntley, Associate Professor (MMI, UToledo) on an R21 grant (NIAID, Joe, PI; my role is a co-investigator) to investigate COVID-19 pathogenesis in a hypertensive rat model. We are collaborating with Dr. Ritu Chakravarti, Assistant Professor (Physiology and Pharmacology, UToledo), to study the role of 14-3-3 family of proteins in inflammatory signaling pathways (PNAS, 2020, Front Immuno, 2019). We have been collaborating with Laura Nagy (Cleveland Clinic), a world leader in the biology of liver diseases, on various projects related to the role of IRF3 in liver diseases. These projects have already yielded several publications and NIH grants. Recently, my laboratory is collaborating with other state universities of Ohio in state-wide monitoring of SARS-CoV-2 gene copies in wastewater. It has been shown that SARS-CoV-2 viral RNA can be shed in the feces of COVID-19 patients. The viral RNA can be detected as a leading indicator of the community spread. We are funded (Chattopadhyay, PI) by the Ohio Department of Health and US EPA to test the viral RNA levels in the wastewater samples collected from various wastewater treatment plants in Ohio. The increased viral RNA levels are immediately reported to the local health departments to enforce restrictions within the community.

The research in my laboratory at UToledo has been funded continuously by national, regional, and local grants. I moved to the UToledo in 2016 with a 3-year American Heart Association-funded Scientific Development Grant ($231,000, 2015-2019), which helped me set up my laboratory. This award was a perfect start to my independent career and supported a high throughput screen of antiviral ISGs against paramyxovirus replication. During the second year into my tenure at UToledo, I secured an R21 grant from NIAAA, National Institutes of Health ($402,937, 2018-2021). This award was a successful product of my collaborative studies with Laura Nagy, a world leader in the area of hepatic diseases and innate immunity, to study how non-transcriptional IRF3 activities regulate alcoholic liver diseases. The collaborative projects with Laura Nagy also helped me with an RO1 sub-award (Nagy, PI) from NIAAA/NIH ($117, 881, 2019-2022). These awards helped me build my research program at UToledo and recently helped me obtain my first RO1 award by NIAID/NIH ($2,207,000, 2021-2026). This award will help uncover new non-transcriptional functions of IRF3 in regulating virus-induced inflammatory responses. Recently, my laboratory has also been involved in a state-wide project to monitor SARS-CoV-2 gene copies in the wastewater of various parts of Ohio. This project has been funded ($478,195, 2020-2021) by the Ohio Department of Health and US EPA and has been continued by CDC/OSH ($656,518, 2020-2021). In addition, my work has been funded by local awards from the Medical Research Society ($50,000, 2020-2022) and the UToledo research office ($9,300, 2020-2021). In addition, I am a co-investigator on an RO1 grant (Taylor, PI) by NIAID/NIH ($1,950,000, 2020-2025) to study tick-borne virus infection and pathogenesis. I serve as a co-investigator on an R21 grant (Joe, PI) by NIAID/NIH ($424,875, 2021-2023), to study COVID-19 pathogenesis in a newly-generated hypertensive rat model. I also serve as a co-investigator on an Ohio Department Health award ($200,258, 2020-2021, Chakravarti, PI) to evaluate the SARS-CoV-2 gene copies in the wastewater collected from various dormitories in the UToledo campus. Overall, since joining UToledo, I have secured a total of $4,152,831 from various grants as a PI and $2,946,182 on grants as a co-investigator. In addition, my research activities are also supported by UToledo start-up funds.

I have been the recipient of numerous awards for my contribution to research at local, national, and international levels. Some of the most prominent include Milstein Young Investigator Award by the International Society for Interferon and Cytokine Research (ISICR) in 2010 and Boltzmann Award by the European Cytokine Society in 2008. I have been the recipient of the Early Career Faculty Grant by the American Association of Immunologists in 2017, 2019, and 2020. At the university level, I was the only nominee selected by the university for submission of the Edward Mallinckrodt Jr Foundation Grant proposal in 2016. I was one of the three finalists for the Medical Research Society research award in 2018 and 2019. I was the recipient of the Medical Research Society award in 2019 for investigating novel antiviral drugs for respiratory virus infection. Recently, I received the 2021 President’s Award for Excellence in Creative and Scholarly Activity, UToledo, and the Dean’s Award for New Investigator Research Excellence for 2021, UT-COMLS.

Before joining the University of Toledo in 2016, I worked in various positions, from the postdoctoral fellow, research associate, and project staff, at Lerner Research Institute (LRI), Cleveland Clinic. I began my postdoctoral career in the laboratory of Dr. Indira Sen, Department of Molecular Cardiology (LRI), and received extensive training in biochemistry and cell biology. I was involved in investigating the role of proteolysis of angiotensin-converting enzyme (ACE), a key player in controlling blood pressure. These studies led to the phase of my research career in the laboratory of Dr. Ganes Sen, a world leader in the area of innate antiviral immunity in the Department of Molecular Genetics and Virology, LRI. My initial goal was to continue my biochemical findings of ACE research in the transgenic mouse models. These early results were productive and also helped me transition to a side project, which eventually turned into the most exciting journey of my research career. In a vibrant research group, I found all the tools to mature into an independent investigator and developed several projects in the area of innate antiviral host defense. Using complementary model systems, we extensively studied a viral apoptotic pathway mediated by IRF3. These projects were instrumental in developing and building my interest in the area of innate immunity. My role in these projects was supported by a number of NIH grants (Sen, PI). Along with developing these projects, I got the opportunity to work with several collaborators and mentors, who have played and are still playing critical roles in my research career. Before starting my postdoctoral research at Cleveland Clinic, I did my graduate and undergraduate studies in various parts of India. I did my BS in Chemistry and MS in Biochemistry at Calcutta University, where I was exposed to basic biochemistry and molecular biology concepts and research projects. After finishing my MS, I moved to the Indian Institute of Technology, Delhi, a premier research and educational institute in India, to pursue my graduate studies in Biotechnology. As a graduate student, I was exposed to a wide range of research projects starting from basic biotechnology, biochemical engineering, plant and mammalian cell cultures, fermentation and chromatography technologies, etc. My research project was to isolate the naturally synthesized derivatives of an anticancer drug podophyllotoxin, a secondary metabolite produced by the cell culture from an Indian medicinal plant. The cell culture-derived compounds were HPLC-purified and tested on human cancer cells for the inhibition of cell proliferation. In addition to graduate research, I got an opportunity to work on an industrial project sponsored by Biocon, a leading biopharmaceutical company in India, based on my encouraging results.

Overall, I have the training, expertise, and motivation necessary to lead my research team to accomplish our research goals. I have assembled an excellent group of mentors, and team members that include the graduate, undergraduate and medical students, postdoctoral fellows, research technologists, and expert collaborators, to continuously elevate our research standards.

Teaching Narrative: I am deeply involved in teaching since I began my career as an Assistant Professor at the University of Toledo in 2016. I became an integral part of the Clinical Virology course for the University of Toledo College of Medicine and Life Sciences (UT-COMLS) medical students. For the last five years, I have been teaching a wide range of topics from basic virology to virus-mediated human diseases. For the annual Infectious Disease curriculum, I’m involved in teaching nine contact teaching hours (out of a total of eighteen hours of Clinical Virology) for the first year of the MD class. During 2016-2017, I was involved in teaching the 2nd-year MD students (INDI783, Immunity and Infection course). In the new curriculum, from 2017 onwards, I am involved in teaching the 1st-year MD students (INFD780, Infectious Diseases course). In the last five years, my student evaluations have been excellent, in the range of 4.2-4.6 out of 5 (please see my evaluations), which continuously exceeds my expectation. I take the feedback from the students seriously and update my lecture contents appropriately. The key elements of my teaching success so far are my motivation, excitement, engagement, sincerity, and passion for effectively delivering the complex topic. I make a sincere effort to respond to my students’ doubts and queries without wasting any time.

I am also involved in teaching graduate-level courses for master’s and doctoral students. Currently, I serve as a Course Director for the Advanced Microbiology course offered to the second-year MS and PhD students in the MMI research track. In this role, I coordinate with the faculty instructors for teaching various advanced bacteriology and virology contents. I also teach in this course and received positive feedback from my students. In addition, I teach a first-year graduate class on pathogen-activated transcription factors for the Cellular Signaling course. My students perform very well, and I receive excellent feedback for my role (please see my graduate evaluations). I also participate as a faculty moderator for the track-specific journal club course, about two classes every year.

I was also interested in contributing to undergraduate teaching; however, this was challenging in the College of Medicine, where we do not have any undergraduate students. However, I found a way to be involved in undergraduate teaching by participating in a research credit course, the Directed Research in Human Health Sciences (INDI4000, Directed Research in Human Health Sciences, 1 credit/semester). I had two students who have been taking this course continuously for the last 2-3 years. These students participate in laboratory research and journal club. The students get exposure to high-quality research by interacting with the research students and staff in the lab. One of these students has recently got accepted into the MD program at the UT-COMLS. Moreover, these students also got an opportunity to be involved as a co-author in a recently published review article. I feel satisfied by engaging these students in basic biomedical research.

I have been involved in teaching junior and senior students from the local high school. The students participate in summer research programs and get early exposure to biomedical research. So, far I have supervised two high school students, and one of these students was a co-author in a paper from our group. One of these students has been placed at the University of Pennsylvania.

As a research mentor, I am involved in supervising the masters and doctoral students, postdoctoral fellows, research associates, and research technicians in my laboratory. So far, I have completed mentoring one MS and one PhD student since I joined the UT-COMLS in 2016. In addition, currently, I am mentoring a third-year PhD and a second-year MD/PhD student. I have also mentored twelve doctoral rotation students in my laboratory to provide training to the students in their first year. I have so far mentored four MSBS-MD students for their major research projects. The MSBS-MD is a bridge course to the UT-COMLS MD program. All of my previous MSBS-MD students have been accepted into the MD program at UT-COMLS. I have also mentored six MD students for the medical student’s research program (MSRP) so far. Many of my MD students have been benefited from co-authored publications of research and/or review articles. I pay particular attention that all of my research mentees benefit from their research projects in my laboratory with publications or conference abstracts. In addition, both of my recent graduate students (MS and PhD) completed their graduation in a timely manner and have been placed in their next career stages. My students have been awarded numerous academic awards and honors both at UToledo, regionally, and nationally. My graduate student (Gayatri Subramanian) has been an Outstanding Graduate Student in 2020 and was selected for the Commencement Speech. My graduate students (Gayatri Subramanian - PhD and Anna Glanz - MS) also participated in the 3MT (3-minute thesis) competition and were placed either as a winner (Gayatri, 2019) or runner-up (Anna, 2020). Gayatri also represented the UToledo at the national level of 3-MT competition in 2019.

I was also involved in teaching, both in the classroom and laboratory settings, during my graduate studies at the Indian Institute of Technology Delhi. As a teaching assistant, I was involved in teaching undergraduate (B.Tech) and post-graduate (M.Tech) students for biotechnology, bioengineering, and microbiology courses. I have also been engaged in private tutoring the high school and undergraduate students for chemistry lessons since during undergraduate and graduate studies.

Overall, my teaching career has so far been productive and satisfying, with excellent student evaluations (both at clinical and graduate teaching levels) and student success. I was recently nominated for an Outstanding Advisor Award for the UToledo (2021). I plan to continue to deliver the teaching expectations of my department, college, and the university and ensure that my mentees are successful in their research and professional careers.

Professional Service Narrative: Since joining the University of Toledo, I am deeply involved in various professional services at the university, college, local, regional, national, and international levels. At the university level, currently, I serve as a member of the University Graduate Council (2019 - to date), a body that is critical for all matters related to the graduate students and faculty members. This committee meets every two weeks to discuss various aspects of graduate studies. I also serve as a member of the Institutional Biosafety Committee (IBC) since 2017. IBC is a reasonably busy committee that meets once a month and reviews protocols from various investigators. In addition, I served on the University Faculty Senate as a member from 2017-2019. All of these committees are very important for the university functions and research activities. At the college level, I serve as a member of the UT College of Medicine and Life Sciences (UT-COMLS) Academic Progress Committee (APC, 2020 – till date), which critically evaluates the progress of the MD students at various levels. I also serve as an interviewer for the applicants of the UT-COMLS (2016 – till date). In this role, I serve as an interviewer to assist the admission committee in selecting the most suitable MD students for the college. At the graduate college level, I serve as a judge for the oral and poster presentation for the annual Graduate Research Forum, organized by the UT-COMLS graduate students (2016 – till date). I have also served as a panel member for the COVID-19 town halls at the college level, organized by the Dean of UT-COMLS. As a panel member, my role was to represent the university in the mission of educating the local community with our ongoing endeavors on COVID-19 research. At the department level, I serve on various departmental committees, e.g., research forum committee, faculty search committee, BSL3 committee, shared equipment committee, ethics committee, graduate students promotion committee, etc.

At the local and community level, I have engaged in various activities in the last several years. I have participated as an assistant coach for the soccer program of the Sylvania Recreation District. I have also participated in various roles for the Sylvania School Science Olympiad events. I have participated as a coach for the Microbe Mission event in the Sylvania McCord Junior High School Science Olympiad. I also served as a volunteer for various events (e.g., elastic gliders) at the annual state competition of the Science Olympiad, organized by the Ohio State University, Columbus. At the district level, I have participated as a judge for various Science Olympiad events, e.g., Thermodynamics, Experimental Design, Optics, etc., organized by Sylvania Southview School district. In addition to the Science Olympiad events, I have served as a judge for the High School Speech and Debate events organized by the Sylvania Northview High School. I found these activities very exciting and a great way to return to the community. These are listed under the 'Community Service' section in my activities. 

Recently, at the onset of the COVID-19 pandemic, I found myself deeply involved in a state and regional level project to monitor COVID-19 in wastewater. Because the COVID-19 patients shed viral RNA into their feces and the asymptomatic individuals can also shed the viral RNA, the wastewater can provide a leading indicator of the COVID-19 spread in the community. Since May of 2020, my laboratory began testing for the SARS-CoV-2 gene copies in the wastewater collected from the local wastewater treatment plants (WWTPs) from Toledo and Oregon. This project grew extensively during the summer of 2020 when the Ohio Department of Health (ODH) began a state-wide network of various state university research laboratories to monitor the SARS-CoV-2. My laboratory became the only testing laboratory in the Toledo area, and we have been collaborating with Ohio State University, University of Akron, Kent State University, Bowling Green State University, US EPA, and other commercial units. My laboratory has been testing weekly for the SARS-CoV-2 viral gene copies present in the wastewater collects from the WWTPs of various places in Ohio. We report our data to the ODH, which publishes the data on the state dashboard. In this role, I found myself highly involved and engaged with the community by discussing our results and educating them about our research. I also spoke at the quarterly meetings organized by the Toledo Metropolitan Area Council of Governments (TMACOG) wastewater committee. These are listed under the 'Community Service' section in my activities.

At the national level, my role has been vibrant and stimulating. I have served as a member of the Student and Postdoc Award committee for the American Society for Virology (ASV) from 2017-2020. In this role, I reviewed abstracts submitted for the annual meetings and helped select the Travel awardees. I also serve as an editorial board member for the Journal of Virology (JVI), the leading journal in virology (2018 – till date). I routinely review manuscripts submitted to JVI in my area of expertise to provide my feedback to the editors. During the last couple of years, I have been deeply involved in grant reviews for the National Institutes of Health (NIH) and the American Heart Association (AHA). I have served on four study section panels (related to virology and anti-viral therapeutics) for NIH. I have served as a panel member for four Basic Immunology and Viral Disease fellowship committees for AHA. I have also served as a panel member for the Career Development Award committee for AHA. My editorial roles are listed under the 'Professional Service' and my grant review roles are listed under the 'Other Service' sections in my activities. 

At the international level, I currently serve as an Associate Editor, Editorial Board Member, and a peer-reviewer for several journals. I serve as an associate editor for the Frontiers in Microbiology, Virology section since 2018. I also serve on the editorial board of some newer journals, Frontiers in Cell and Developmental Biology, Frontiers in Chemistry, Immuno, and Annals in Translational Medicine. I have served extensively as a peer reviewer for numerous manuscripts in the last several years (please refer to my Publon record for details). I serve as a guest editor for a special issue, ‘Interferons and Viral Infections’ for the journal Viruses. I have reviewed more than 125 manuscripts in the last five years. I have also served as an Associate Faculty Member (AFM) for the Faculty of 1000, a platform for post-publication peer-review. In this role, I have published more than twenty commentaries on papers published in the area of my expertise. I was also a recipient of the prestigious AFM Travel Award by the Faculty of 1000 for my contribution as a post-publication peer reviewer. In addition to manuscript editing and reviews, I have served as an ad hoc reviewer for grants submitted to Medical Research Council, UK (2019) and the French National Research Agency (Immunologie, Infectiologie et Inflammation Panel, 2020). My editorial roles are listed under the 'Professional Service' and my grant review roles are listed under the 'Other Service' sections in my activities. In addition to serving the scientific communities, I learned tremendously from all of these experiences. 

Overall, I am heavily involved in professional services at various levels, and these experiences help enrich me for my role as a researcher and educator.