CLAS RESEARCH RESOURCE February 2021
A YEAR INTO COVID, AND CLAS RESEARCH REMAINS STRONG I always find February a little hard, and I don’t just mean spelling it. The parties, presents, and travel associated with the holiday season (sadly attenuated in 2020) are over. The welcome slower pace of winter break and the subsequent excitement of a fresh new semester (again, dampened by COVID anxiety this time) have also passed. As I write this, another blizzard just blew through, Punxsutawney Phil predicted 6 more weeks of winter, and ice dams are causing water to drip into my house. But hey, Valentine’s Day is just around the corner, right? Right. This February also marks the one-year anniversary of the novel coronavirus fully entering our consciousness, with the first news reports of its arrival in the United States. Even though the subsequent months brought, as they always do, the arrival of spring, it sometimes felt like a never-ending snow day (without the fun sledding or snowball fights): cooped up inside, normal work suspended or difficult to do, worries about travel being treacherous. Summer brought little relief, with widespread civil unrest following the murder of George Floyd and other instances of police brutality, increasing political polarization, and—wait for it—a kind of inland hurricane known as a derecho (a name coined and first written about in 1888 by a pre-CLAS UI faculty member in Chemistry and Natural Philosophy named Gustavus Hinrichs). And yet I am struck by the degree to which our college’s researchers stuck to their mission and made the best of the situation in which they found themselves. Many grant applications went in during the research shutdown, and an impressive number of them were successful in garnering external funding. Several humanities faculty received prestigious fellowships that will help them advance their scholarship. The art studios at our new Oakdale Studio Facility are humming, and our performing artists have found inventive ways to pursue their scholarship even in the absence of traditional in-
person audiences. Some of our faculty even received rapid grants to support their efforts to understand the impact of COVID-19 itself, which will help inform our responses to the pandemic going forward. Research laboratories in CLAS’s science departments have also been providing a model for safe work and experiential learning environments that should increase confidence in our ability to return largely to in-person instruction next fall: since laboratories reopened in June, there have been no outbreaks. Just as we look for green shoots peeking up as a sign of spring, we can find reasons for hope all around us. Biomedical researchers around the world have developed multiple highly-effective vaccines with a rapidity unimaginable just a short time ago. We would all like to see these vaccines rolled out faster than they have been, but they are coming, and with several new ones that are easier to work with on the way, supplies should increase. Even the sources of our latest worries—new COVID variants that are more easily transmitted—are understandable thanks to decades of virological research and advances in sequencing and molecular analysis. As academic researchers, we believe that current and future problems can best be identified, understood, and solved through free scholarly inquiry and practice driven by a thirst for knowledge and truth. Our college has embodied this since 1900 and with your help, we’ll continue to do so. The news and stories in this issue provide some examples of CLAS research and scholarship that I hope you’ll enjoy. Keep your eyes on this space for a special issue in April focused on the research of CLAS graduate and undergraduate students; if you have stories about their work that you’d like us to know about, feel free to reach out to me and to our Director of Strategic Communications, Nic Arp. I’m confident that by then, at least, my ice dams will have thawed and the flowers will be here again. Joshua Weiner Associate Dean for Research Professor of Biology College of Liberal Arts and Sciences joshua-weiner@uiowa.edu
CLAS RESEARCH AND INFRASTRUCTURE UNITS: Associate Dean for Research CLAS Technology Services Space, Facilities, and Equipment Grant Support Office Office of Sustainability and the Environment
UPCOMING GRANT AND FELLOWSHIP DEADLINES: FEBRUARY – MARCH This is a list of selected grant and fellowship programs that have deadlines in January and February. For a more comprehensive list of active grant programs, please visit the UI Grant Bulletin.
UI Internal Programs 02/15/21 – Environmental Health Sciences Research Center Pilot Grant Program (College of Public Health) 02/15/21 – Innovation in Teaching with Technology Awards (Information Technology Services) 02/16/21 - Book Ends – Obermann/ OVPR Book Completion Workshop (The Obermann Center) 02/28/21 – International Travel Awards (International Programs)
03/29/21 – Summer Policy Research Grants – Building Undergraduate Research Experiences (Public Policy Center) 03/31/21 – International Travel Awards (International Programs) Rolling - Special Projects Awards (International Programs) UI Limited Submission Programs 02/17/21 – Reeve Foundation: Quality of Life Grants Program 02/28/21 – NIH Prize for Enhancing Faculty Gender Diversity
03/02/21 – Arts & Humanities Initiative (Office of the Vice President for Research) 03/08/21 – Arts Midwest GIG (Grow, Invest, Gather) Fund 03/26/21 – PPC Summer Scholar-inResidence Request for Proposals (Public Policy Center)
03/08/21 – USDA: Food and Agriculture Service Learning Program (FASLP) 03/16/21 – National Endowment for the Humanities: Infrastructure and Capacity Building Challenge Grants 03/29/21 – Mellon Foundation Sawyer Seminar Program 2021-2022 03/29/21 – Whiting Public Engagement Programs 2022-2023 03/30/21 – NIH: Collaborative Program Grant for Multidisciplinary Teams (RM-1 – Clinical Trial Optional) National Endowment for the Arts 03/29/21 – Research Grants in the Arts
National Endowment for the Humanities – All Grant Program Opportunities 02/11/21 – Summer Seminars and Institutes for Higher Education Faculty
03/01/21 – Vision and Change in Undergraduate Biology Education
03/15/21 – OPE: Fulbright-Hays Group Projects Abroad – Short Term Project
03/16/21 – Integrative Research in Biology
03/15/21 – OPE: Fulbright-Hays Group Projects Abroad – Long Term Project
03/02/21 – Institutes for Advanced Topics in the Digital Humanities
03/23/21 - Future of Work at the HumanTechnology Frontier: Core Research
03/09/21 – Institutes for Higher Education Faculty
03/26/21 – Dimensions of Biodiversity
National Institutes of Health – Complete list of standard due dates 02/16/21 – Other Research Grants (R03, R21, R33, R21/33, R34, R36 – new only) 02/25/21 – Academic Research Enhancement Award (R15 – all) 03/05/21 – Research Grants (R01-renewal, resubmission, revision)
US Department of Energy 02/17/21 – Connected Communities (Letter of Intent) US Department of Justice – Upcoming Grant Programs 02/25/21 - Research & Evaluation on Promising Reentry Initiatives 03/22/21 – Research on Juvenile Reoffending
03/05/21 – Research Grants – Cooperative 03/22/21 – Supporting Effective Agreements (U01-renewal, resubmission, Interventions for Adolescent Sex Offenders revision) and Children with Sexual Behavior 03/12/21 – Research Career Development Problems (K Series-renewal, resubmission, revision) 03/22/21 – Research and Evaluation of Trafficking in Persons 03/16/21 - Other Research Grants (R03, R21, R33, R21/33, R34, R36 – renewal, 03/22/21 – Research and Evaluation on resubmission, revision) School Safety National Science Foundation – Active 03/25/21 – Research on Juvenile Justice Funding Opportunities (several deadlines Topics each month; selected programs below) 02/16/21 – Integrative Strategies for US Department of Housing and Urban Understanding Neural and Cognitive Development Systems (NCS) Rolling – Office of Policy Development and Research Unsolicited Research Proposals 02/17/21 – Algorithms for Threat Detection US Department of Education – Upcoming Grant Programs 02/22/21 – Ethical and Responsible 02/25/21 – IES: Education Research: Research Research Networks Focused on Critical Problems of Education Policy and Practice 02/23/21 – Understanding the Rules of Life: Microbiome Interactions and 03/01/21 – OPE: Graduate Assistance in Mechanisms Areas of National Need 02/24/21 – Smart and Connected Communities
National Historical Publications & Records Commission 02/25/21 – Access to Historical Records: Major Initiatives (Preliminary) Society for Research in Child Development 02/24/21 – Towards 2044: Horowitz Early Career Scholar Program for Graduate Students American Lung Association 02/18/2021 - COVID-19 and Respiratory Virus Research (Letter of Intent) American Philosophical Society 03/01/21 – Native American Research – Philips Fund Evolving Earth Foundation 03/01/21 – Research Grant Program for Students International OCD Foundation 03/01/21 – Research on Obsessive Compulsive Disorders Telligen Community Initiative 03/01/21 – Grant Program (Health Innovation, Social Determinants of Health, Health Equity, Workforce Development) Robert Wood Johnson Foundation Rolling – Evidence for Action: InvestigatorInitiated Research to Build a Culture of Health Rolling - Pioneering Ideas: Exploring the Future to Build a Culture of Health
GEARING UP TO PROVIDE ALL CLAS UNITS WITH PRE- AND POST-AWARD GRANT SUPPORT In 2019, the Grant Support Office (GSO) was tasked with developing a vision for how it could best support the College of Liberal Arts and Sciences’ research mission across all departments, while also being mindful of our limited resources. As the centralization of grant support in the college is still a new initiative, the extent of grant support capacity remains uneven across departments, generally in line with their past submission activity.
Pre-award staff assist with the proposal development process by:
Our primary goal is to develop a staffing structure that would allow every department to have dedicated staff to help prepare and submit proposals (preaward), as well as to support grant recipients with managing the funds (post-award). After researching how grant support is organized at other institutions, as well as reviewing best-practice recommendations from professional organizations such as the Society of Research Administrators and the National Organization of Research Development Professionals, it became clear that there is not one “right” way to organize grant services.
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We are excited to move forward with a structure that retains pre- and post-award services under the GSO umbrella, but splits our personnel into two teams. Once our vision has been fully implemented, every department will have one pre-award and one postaward professional person assigned to their unit. As much as possible, pre- and post-award staff members will be paired to support the same group of departments so that they can back each other up and ensure continuity of support in the event that one of them must be out of the office. This will also allow us to cater to the strengths of each staff member’s skillset and allow them to develop deep expertise in their areas of responsibility. This will be critical for our goal of alleviating some of the ever-increasing administrative burden of applying for and managing grants.
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identifying funding opportunities interpreting grant application guidelines and developing checklists and timelines providing institutional information, drafting boilerplate language, and reviewing proposals for compliance and responsiveness developing budgets and budget justifications and documenting cost-sharing proofreading documents managing electronic upload and submission, including UIRIS routing forms and other UI internal processes
Post-award staff assist with the grant management process by: • •
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managing budgets, providing projections, and processing subaward agreements navigating internal compliance requirements by coordinating with the Division of Sponsored Programs, Grant Accounting and other UI units facilitating budget revisions, no-cost extensions, and other sponsor documents providing information for progress reports and managing project closeout
I am pleased to report that we are making progress towards implementing this vision. We just hired two new staff members (one filling a vacant position and one a new, additional position) and are in the process of shifting responsibilities so that we can expand coverage to those departments that have lacked comprehensive support. If you are in one of these departments, you will be hearing from us in the near future! Check this space in the March issue of Research Resource as we will feature the college’s impressive preaward staff and share some tips for how researchers can take full advantage of their skills and expertise. Kristi Fitzpatrick Director, Grant Support Office
FEATURED FUNDING PROGRAMS – OBERMANN CENTER FOR ADVANCED STUDIES The Obermann Center for Advanced Studies, a unit of the Office of the Vice President for Research, provides a uniquely supportive environment where scholars working individually or in collaboration can reflect, write, and interact. The Obermann Center helps nurture and deepen the impact of research and creative projects by offering various programs to support the work of our artists, researchers, and scholars. A few of their programs are highlighted below but please refer to their website for a complete listing.
Deadline: The letter of intent is due by March 1, 2021 at 5:00 p.m. Final proposals are due March 29, 2021 by 5:00 p.m.
Andrew W. Mellon Sawyer Seminar
Overview: This program is designed to assist faculty members turn promising manuscripts into important, field-changing, published books. Book Ends will bring two senior scholars to campus for a candid, constructive three-hour workshop on the faculty member’s book manuscript. The award will cover travel, accommodations, and a $500 honorarium for each visiting scholar. We will also ask two UI senior faculty members to participate. Authors will leave the workshop with concrete suggestions for revision, advice about appropriate presses, and a timeline that will lead to a revised manuscript ready for presses to review within six months.
Overview: The Mellon Foundation’s Sawyer Seminars were established in 1994 to provide support for comparative research on the historical and cultural sources of contemporary developments. The seminars have brought together faculty, foreign visitors, postdoctoral fellows, and graduate students from a variety of fields mainly, but not exclusively, in the arts, humanities, and interpretive social sciences, for intensive study of subjects chosen by the participants. Foundation support aims to engage productive scholars in comparative inquiry that would (in ordinary university circumstances) be difficult to pursue, while at the same time avoiding the institutionalization of such work in new centers, departments, or programs. Sawyer Seminars are, in effect, temporary research centers. The Obermann Center will be supporting the Office of the Vice President for Research and the College of Liberal Arts and Sciences by assisting with nominations for this program. Sawyer Seminar awards provide up to $225,000 for one postdoctoral fellow and for the dissertation research of two graduate students for the period of one year. Eligibility: Program is open to tenure-track faculty
Information Sessions: Tuesday, February 9, 2021, 8:30-9:30 a.m. Friday, February 12, 2021, 8:30-9:30 a.m. Learn more: To see additional details about the program and how to apply, please visit the Obermann Center’s Mellon Sawyer Seminars.
Book Ends
Eligibility: University of Iowa tenure-track assistant and associate professors with mature drafts of monographs on track for publication are eligible. Application deadline: February 16, 2021 (5:00 p.m.) Information Session: Tuesday, February 12, 2021, 8:30-9:30 a.m. Learn more: To see additional details about the program and how to apply, please visit The Obermann Center’s Book EndsObermann/OVPR Book Completion Workshop.
Obermann Working Groups Overview: Obermann Center Working Groups provide space, structure, and discretionary funding for groups led by faculty that may include advanced graduate students, staff members, and community members with a shared intellectual interest. Groups have used this opportunity to explore new work and to share their own research, to organize a symposium, and to develop grant proposals. This program allows participants from across the campus and beyond to explore complex issues at a moment when crossdisciplinary collaboration is crucial to address shifting domains of knowledge and a rapidly changing world. Eligibility: May have one or two co-directors; one must be a UI faculty member.
Whiting Public Engagement Fellowship and Whiting Public Engagement Seed Grant Overview: The University of Iowa is invited to nominate one humanities professor for each of the following two programs: Whiting Public Engagement Fellowship and Whiting Public Engagement Seed Grant. These programs celebrate and empower early-career faculty who embrace public engagement as part of their scholarly vocation by funding ambitious, often collaborative projects to infuse into public life the richness and nuance that give the humanities their lasting value. Nominees’ public-facing projects and professional expertise should be squarely in the humanities. In this cycle, Whiting is focusing on the following disciplines: history; the study of literature, visual art, music, and other arts; philosophy; and area studies combining these fields, like classics and African-American studies. Whiting Public Engagement Fellowship of $50,000 is for projects far enough into development or execution to present specific, compelling evidence that they will successfully engage the intended public.
Deadline: April 13, 2020 (5:00 pm) Learn More: To see additional details about the program and how to apply, please visit The Obermann Center’s Working Groups Program.
Interdisciplinary Research Grants
Overview: The Obermann Interdisciplinary Research Grants (IDRG) foster collaborative scholarship and creative work by offering recipients time and space to exchange new ideas leading to invention, creation, and publication. IDRG groups work together for two or four weeks and will likely be in a virtual format for summer 2021. Applicants propose work on a project with colleagues from across the University, across disciplines within their own department, or with colleagues from other parts of the country or the world. Projects are intended to result in an important scholarly or creative work. Eligibility: We welcome IDRG applications from artists, researchers, and scholars in any discipline and on any topic. In addition, funds from Laura SpelmanRockefeller grant are available to support one or two groups that are working specifically on projects focused on children’s learning and development, child welfare, and/or maternal education. Deadline: Fall 2021 Learn More: To see additional details about the program and how to apply, please visit The Obermann Center’s Interdisciplinary Research Grants.
Whiting Public Engagement Seed Grant of up to $10,000 supports projects at a somewhat earlier stage of development, where more modest resources are needed to test or pilot a project or to collaborate with partners to finalize the planning for a larger project and begin work. Eligibility: To be eligible for either program, nominees must be full- or parttime humanities faculty in both the 2020-21 and 2021-22 academic years. Faculty need not be on a tenure track to be eligible. Nominees should have received their doctorate between January 1, 2008 and December 31, 2020. Deadline: The university’s internal deadline is March 29, 2021. If selected, full proposals due to the sponsor on June 14, 2021. Information Sessions: Wednesday, March 3, 2021 2:00 PM Wednesday, April 7, 2021 2:00 PM Wednesday, May 5, 2021 2:00 PM Wednesday, June 2, 2021 2:00 PM Learn more: To see additional details about the program and how to apply, please visit the Office of the Vice President for Research’s Whiting Public Engagement Programs 2022-23.
WINDOWS UPDATES: REAL WINDOWS, WE MEAN
Buildings are a lot like computer operating systems. Leave a computer running its original operating system without performing any updates and eventually it gets compromised with malware, virus attacks, or other assorted invasions from the outside world. Soon the computer cannot do what it was designed to do. Buildings with deferred maintenance issues are like a computer running an operating system that hasn’t been updated: things start to break down; systems run inefficiently; outside elements start damaging the facility; and many costs are incurred with trying to patch things up. As the largest college on campus, the College of Liberal Arts and Sciences has its share of older buildings that are in need of updates. The good news is that the University of Iowa and Facilities Management (FM) are prioritizing deferred maintenance needs across campus. Beginning this summer, for example, FM is kicking off a capital improvement project that will replace every window in the English-Philosophy Building (EPB). Built in 1966, EPB is one of the most heavily used facilities for academic classes and typically sees 10,000 students using the building on a weekly basis. It houses 38 university classrooms as well as the CLAS departments of English, Philosophy, and
Rhetoric. Most of the occupant complaints in this building have been related to temperature and humidity control. The main contributing causes are the leaky, single-pane windows and inadequate insulation on the exterior walls. The two-year, $2.15 million EPB project will replace all 270 windows with insulated double-pane glass. To further improve the building’s energy efficiency, additional insulation will be installed around each new window and sealants in exterior wall panels will be replaced. The project will be phased to minimize impact to occupants; construction will occur primarily during the summer months in 2021 and 2022 and will follow a sequence that focuses on specific parts and floors of the building before moving on to the next area. This summer, have a look at the progress on EPB as you walk around campus! Additional upcoming deferred maintenance projects that will impact CLAS include a $1.75 million project to replace chilled water coils in Chemistry Building air handling units, and a $400,000 project to replace sections of the Theatre Building roof that are past life expectancy, as well as to address leaking issues in the atrium curtain wall. Nearly every day, our CLAS research team meets with FM representatives to discuss our college’s facilities issues, advocate for solutions, and work with our partners as these positive changes take place. Eugene Buck CLAS Director of Facilities
THE ASHTON RESEARCH PRAIRIE: A LIVING CLASSROOM AND LAB The Ashton Research Prairie (ARP) is located at the site of the Ashton Cross Country Course on the University of Iowa campus. While ARP is the result of a collaborative effort between the Office of Sustainability and the Environment (OSE), Iowa Athletics, environmental sciences units, and several faculty from across the College of Liberal Arts and Sciences and the College of Engineering, the idea began with the vision of a determined Environmental Science major, Megan Lenss. Megan approached OSE, Professor of Biology Andrew Forbes, and former Earth and Environmental Sciences instructor Mike Fallon in 2018, and asked how the UI could restore a prairie on campus. After many conversations, the Athletics groundskeeper, Tony Senio, championed the idea in his department. Athletics provided the space for a future prairie, and the idea took root. This cross-campus effort is part of a broader vision detailed in the 2030 sustainability goals for the university to create living laboratories across campus in order to increase opportunities for students and researchers to use the UI campus as an educational and research laboratory for the simultaneous improvement of campus sustainability and ecosystems. Several courses at the university currently use the prairie to teach or have plans to conduct research or applied coursework at the prairie in the spring semester. As the Prairie Restoration Project continues to grow, we encourage faculty, staff and students who may want to engage with ARP in their courses, conduct research, visit the prairie, or volunteer to reach out to the Office of Sustainability and the Environment. It is our hope that this project, along with other planned living laboratories across campus, will enrich the opportunities of our campus community by offering applied opportunities for research and discovery. Background: Until the early 1840’s, the entirety of Iowa was blanketed in grasses and wildflowers, a landscape known as the Tallgrass Prairie. This vast expanse of wildflowers and grasses up to twelve feet tall was home to indigenous peoples and astonishingly diverse wildlife.
As a public institution serving the greater good, the UI is beginning to face the task of reversing the centuries-long degradation of our vital natural resources. The Prairie Reconstruction Project at Ashton Cross Country Course is essential to this effort, providing hands-on educational experiences for our students, while preserving a rare native Iowa landscape. Reconstruction to Date: Phase I of the Prairie Reconstruction Project involves the conversion of a one-acre plot of unused fallow pasture land to a native prairie. Prairie plant seed used in the reconstruction is biogeographically referenced, assuring that it is native to Johnson County, Iowa. Planned Prairie Reconstruction for 2021: During the current academic year, the UI will expand the current prairie by six acres, using $7,500 in financial support from an EPA Farmer-to-Farmer Cooperative Agreement grant, whose PI is Professor Craig Just of the College of Engineering, who teaches in the Environmental Science Program in CLAS. Dr. Just’s grant is focused on improvements in water quality, habitat, and environmental education. Our partners: We owe special thanks to the UI Department of Athletics for permission to reconstruct ARP at the Ashton Cross Country Course. UI Student Government provided a $1,500 grant, used to purchase native plant seed for this reconstruction, for which we are deeply grateful. Finally, we wish to thank the Iowa Native Plant Society for awarding us $500 to help design and manufacture educational signage.
To learn more about how you can incorporate ARP in your research and teaching, please contact: With the arrival of Euro-American settlers, the once rich and nutrient-dense soil became over-exploited, through a combination of poor farming methods and industrialized agricultural practices. Stratis Giannakouros Today, less than 0.01% of native Tallgrass Prairie remains in Iowa. Director, Office of Sustainability and the Environment
MEET THE RESEARCHER: CESARE TINELLI What is the focus of your work? I mostly work on automated reasoning and constraint solving. A variety of problems in computer science and beyond can be recast as constraint solving problems. This includes analyzing the functional correctness of computer hardware or software components, identifying security vulnerabilities in software, and optimizing program execution, among many others. The constraint solving problems generated in these applications are often computationally challenging because they require the exploration of an exponentially large space of solutions. In my group, we focus on the theoretical foundations and tool development for a groundbreaking and successful form of constraint solving called Satisfiability Modulo Theories, or SMT.
Tell us about the broad impact it has/could have. In the last 10-15 years, SMT has become an enabling technology for several areas of computer science, often revolutionizing research there thanks to the reasoning power of SMT solvers. In collaboration to Professor Clark Barrett’s group at Stanford University, we have been developing a leading SMT solver, called CVC4, which is used widely in academia and industry. Most recently, Amazon Web Services has started to use it to verify that its customers set up correct control access policies for their data on the Amazon cloud. Such policies can be quite difficult for customers to specify correctly, potentially resulting in unauthorized data access. AWS relies on CVC4 to discover errors in them or certify their correctness. The same technology is also used to improve the quality of other software services at AWS, resulting overall in millions of calls per day to our tool.
What excites you about the environment in CLAS? I would say the large number of disciplines represented by the many departments and programs in the college, and the opportunities that this offers for interdisciplinary research and education. In the Computer Science department, we have exciting and fruitful collaborations with colleagues from several other departments in the college.
What are your hobbies and pursuits outside of work? I am an avid reader of non-fiction. I am generally curious about how things work, which makes me interested in many topics: technology, of course, but also engineering, physics, economics, sustainable agriculture, linguistics, history, cinema, and more. I do not seek any kind of expertise in these areas. I simply enjoy learning about them to satisfy my curiosity. In the age of search engines, Wikipedia, and online publications of any sort, this activity easily ends up taking most of my free time.
Favorite things to do in Iowa City? It must be urban hiking. My wife and I like walking and love the city’s extensive trail system. In addition, sometimes we will drive to some random neighborhood and just walk around to discover the surroundings. We also enjoy more traditional hiking in the Coralville Lake area and love that it is just a short drive from home.
Professor Cesare Tinelli joined the Department of Computer Science in 1999. His work has focused on software verification and on automated reasoning, in particular in Satisfiability Modulo Theory (SMT), a field he helped establish through his research and service activities. He is a founder and coordinator of the SMT-LIB initiative, an international effort aimed at standardizing benchmarks and I/O formats for SMT solvers. He led the development of the award winning Darwin theorem prover and leads the development of the Kind model checker. Together with Prof. Clark Barrett of Stanford University he also leads the development of the award winning and widely used CVC4 SMT solver. He also is involved in the development of StarExec, a cross community web-based service for the comparative evaluation of logic solvers.
BIOLOGISTS UNRAVEL FULL SEQUENCE OF DNA REPAIR MECHANISM By: Richard C. Lewis Every living organism has DNA, and every living organism engages in DNA replication, the process by which DNA makes an exact copy of itself during cell division. While it’s a tried-and-true process, problems can arise. Break-induced replication (BIR) is a way to solve those problems. In humans, it is employed chiefly to repair breaks in DNA that cannot be fixed otherwise. Yet BIR itself, through its repairs to DNA and how it conducts those repairs, can introduce or cause genomic rearrangements and mutations contributing to cancer development. “It’s kind of a double-edged sword,” says Anna Malkova, professor in the Department of Biology at the University of Iowa, who has studied BIR since 1995. “The basic ability to repair is a good thing, and some DNA breaks can’t be repaired by other methods. So, the idea is very good. But the outcomes can be bad.” A new study led by Malkova, published Jan. 20 in the journal Nature, seeks to tease out BIR’s high riskreward arrangement by describing for the first time the beginning-to-end sequence in BIR. The biologists developed a new technique that enabled them to study in a yeast model how BIR operates throughout its repair cycle. Until now, scientists had only been able to study BIR’s operations at the beginning and end stages. The researchers then introduced obstructions with DNA replication, such as transcription—the process of copying DNA to produce proteins—that are believed to be aided by BIR. “Our study shows that when BIR comes to the rescue at these collisions, its arrival comes at a very high price,” says Malkova, the study’s corresponding author. “When BIR meets transcription, it can introduce even more instability, which can lead to even higher mutations. As a result, we think that instabilities that mainly were found at collisions between transcription and replication that have been suggested to lead to cancer might be caused by BIR that came to
the rescue. It comes, it rescues, but it’s kind of questionable how helpful it really is.” Scientists have known how BIR works at some stages. For example, they know the DNA repair apparatus forms a bubble of sorts around the damaged DNA, then moves forward, unzipping the DNA, copying intact segments, and finally transferring those copied segments to a new DNA strand.
But what remained elusive was following BIR throughout its entire repair cycle. Using a technique involving Droplet Digital PCR and a new DNA purification method developed by biology graduate student Liping Liu, the researchers were able to observe BIR from beginning to end. “If you imagine this as a train, Liping installed a bunch of stations, and she watched how the train proceeded at each station, tracking the increase in DNA at each station, how much increase is occurring at each station, and thus, in aggregate, how the entire process unfolds,” Malkova explains. The team then intentionally introduced obstructions at some stations—transcription and another obstruction called internal telomere sequences—to observe how BIR responded to the obstacles. One finding: when transcription is introduced near the beginning of the
BIR process, the repairs fail to commence, as if they’re being suppressed. Also, the researchers found the orientation of the transcription with respect to BIR can affect the repair cycle and may be an important factor affecting instability that can promote cancer in humans. “Scientists already know there’s a lot of instability in places where high transcription meets normal replication,” Malkova says. “What we did not know until now is where is it coming from and why is it happening.” The first author of the study, “Tracking break-induced replication shows that it stalls at roadblocks,” is Liu, who is a sixth-year graduate student in Malkova’s lab. Co-authors from Iowa include Beth Osia, Jerzy Twarowski, Juraj Kramara, Rosemary Lee, Hanzeng Li, and Rajula Elango (now at Beth Israel Deaconess Medical Center and Harvard Medical School). Co-authors from the Baylor College of Medicine include Zhenxin Yan, Luyang Sun, Sandeep Kumar, Weiwei Dang, and Grzegorz Ira. The National Institutes of Health funded the research.
PROFESSOR OF HISTORY COLIN GORDON AWARDED NEH FELLOWSHIP by realtors, developers, and homeowners in realty transactions and attached as restrictions to titles and deeds in public property records. These covenants prevented African Americans from owning, and often even renting, property in certain neighborhoods, creating neighborhoods for Black residents that were considered less desirable and that received significantly less public investment than their Whites-only counterparts. Though a 1948 U.S. Supreme Court decision banned enforcement of these real estate provisions, their legacy lives on in the residential segregation seen in St. Louis and other northern American cities today.
The prestigious honor will support Gordon’s research into the racerestrictive housing covenants that fueled structural segregation in St. Louis Colin Gordon, the F. Wendell Miller Professor of History at the University of Iowa, has received the nation’s most prestigious award for humanities scholarship, the National Endowment for the Humanities (NEH) Fellowship. Gordon’s fellowship will support research for his upcoming monograph, tentatively titled Dividing the City: Race-Restrictive Covenants and the Architecture of Segregation. The monograph, and a digital companion project, will be the newest publications of his long-running and influential research into policies that created and have sustained residential racial segregation throughout St. Louis, Missouri, and its suburbs. These policies were first seen in explicitly racial zoning laws, and then—after a 1917 U.S. Supreme Court decision banning such public regulations—they took the form of private “deed covenants,” employed
Gordon, who is a senior research consultant for the Iowa Policy Project and a distinguished faculty affiliate at the UI’s Public Policy Center, is a leading expert on public policy as it relates to housing, health, wages and working conditions, and economic development, particularly in urban America. He is the author of Citizen Brown: Race, Democracy, and Inequality in the St. Louis Suburbs (University of Chicago Press, 2019); Growing Apart: A Political History of American Inequality (Institute for Policy Studies, 2013); Mapping Decline: St. Louis and the Fate of the American City (University of Pennsylvania Press, 2008); Dead on Arrival: The Politics of Health in Twentieth Century America (Princeton University Press, 2003), and New Deals: Business, Labor and Politics, 1920-1935 (Cambridge University Press, 1994). His digital projects include Mapping Decline, an interactive mapping project based on his St. Louis research, and Mapping Segregation in Iowa, an ongoing project involving UI undergraduate researchers, documenting the use of race-restrictive deed covenants in Iowa.
He writes the biennial State of Working Iowa reports for the Iowa Policy Project, and has written for The Nation, In these Times, Z Magazine, Atlantic Cities, and Dissent (to which he is a regular contributor). In addition, he has provided reports, briefs, and expert testimony in legal cases around the country. His work is featured and archived on his personal website. A member of the Department of History faculty since 1994, Gordon was its chair from 2006-2011. Among other honors, he received the University of Iowa Regents Award for Faculty Excellence in 2016 and the University of Iowa Award for Distinguished Achievement in Publicly Engaged Research in 2015.
In 2014, the College of Liberal Arts and Sciences named him Collegiate Fellow, the college’s highest faculty honor. The College of Liberal Arts and Sciences at the University of Iowa is a comprehensive college offering 73 majors in the humanities; fine, performing and literary arts; natural and mathematical sciences; social and behavioral sciences; and communication disciplines. More than 17,000 undergraduate and 1,900 graduate students study each year in the college’s 37 departments, led by professors at the forefront of teaching and research in their disciplines. The college teaches all UI undergraduates through the General Education Program, and confers about 70 percent of the UI’s bachelor’s degrees each academic year.
NASA EXTENDS JUNO MISSION On-board instrument designed and built at Iowa has yielded numerous discoveries about Jupiter By: Richard C. Lewis | 2021.01.14 | 12:09 pm The University of Iowa will have several more years to study the largest planet in our solar system. The U.S. space agency NASA announced this week it will extend the Juno mission to Jupiter and its moons through September 2025, or until the spacecraft’s end of life. Launched in 2011, the Juno spacecraft arrived at Jupiter on July 4, 2016, with a planned mission completion in July 2021. Along for the ride has been a radio- and plasmawave instrument designed and built at Iowa. Called Waves, the instrument has yielded a trove of impactful discoveries, including the distribution of lightning on Jupiter, insights about the generation of intense auroras on the planet, and the first direct detection of small dust grains between Jupiter’s ring system and its atmosphere near the equatorial plane. Bill Kurth, University of Iowa Department of Physics and Astronomy. “Jupiter is such an extraordinary place. Only superlatives can describe it. So, it is extremely exciting to be able to continue to follow Juno as it orbits in the Jovian system for another four years,” says William “Bill” Kurth, research scientist in Iowa’s Department of Physics and Astronomy and lead investigator for the Waves instrument. With the extension, Juno will make 42 additional orbits, including close passes of Jupiter’s north polar cyclones; flybys of the moons Ganymede, Europa, and Io; and the first extensive exploration of the faint rings encircling the planet.
The data Juno collects will contribute to the goals of the next generation of missions to the Jovian system—NASA’s Europa Clipper and the European Space Agency’s JUpiter ICy moons Explorer (JUICE). Juno’s investigation of Jupiter’s volcanic moon Io addresses many science goals identified by the National Academy of Sciences for a future Io explorer mission.
Kurth is excited for the extended mission, the new realms to be explored, and the promise of potentially more surprises about the gas giant and its cadre of satellites. “Juno to date has raised so many new mysteries and questions,” Kurth says. “The extended mission will allow us to continue to delve deeper into how this planet works and interacts with its moons, rings, and magnetic environment.” The Waves team at Iowa includes George Hospodarsky, co-investigator; Ali Sulaiman, research scientist; Sadie Elliott, postdoctoral scholar; and Donald Gurnett, professor emeritus and collaborator. Doug Menietti, also in physics and astronomy, is a Juno participating scientist closely tied to the Waves team.
“We have a close-knit team at Iowa focused on understanding what Juno is telling us about the Jupiter system,” Kurth says. “In addition to the scientists, there are several current staff at Iowa working to ensure the success of the investigation, not to mention dozens of engineers and technicians who were responsible for the development of the instrument itself. Planetary missions require large teams working together.” JPL, a division of Caltech in Pasadena, California, manages the Juno mission. The mission’s principal investigator is Scott Bolton, of the Southwest Research Institute in San Antonio. Iowa has had instruments on seven of nine American and European missions that have passed through the Jovian system.