University Of Nebraska Lincoln

NIH Research Projects · FY 2025 · 2016-08

PROJECT SUMMARY/ABSTRACT Regulation of biomolecular communication pathways is critical to maintaining physiological function. Unraveling these pathways and filling in critical knowledge gaps will provide novel opportunities to understand, diagnose, and treat human diseases. During Phase 1, the Nebraska Center for Integrated Biomolecular Communication (CIBC) supported 15 early stage investigators (ESIs), helped recruit four new faculty members to the University of Nebraska-Lincoln (UNL), and established two research cores. CIBC’s ESIs secured $16.7 million in external research funds and authored 82 peer-reviewed publications. Building on Phase 1, the goal of the CIBC in Phase 2 is to continue building a critical mass of biomedical investigators and supporting research infrastructure in the area of biomolecular communication pathways at UNL that will position CIBC for a successful transition to long- term sustainability in Phase 3. CIBC will continue to develop multidisciplinary teams to interrogate complex disease pathways, especially by connecting researchers developing new molecular probes and analytical techniques with those unravelling molecular mechanisms of human diseases. CIBC’s Phase 2 specific aims are to: 1) strengthen UNL’s biomedical research infrastructure by supporting the research efforts and career development of biomedical investigators whose research is broadly focused on understanding the regulation of biomedically relevant communication pathways; 2) enhance research capabilities by maintaining and expanding the Systems Biology Core (SBC) to facilitate acquisition of essential bioanalytical data and the Data and Life Sciences Core (DLSC) to provide critical bioinformatics support and data management, storage, and sharing to Center members; and 3) advance interdisciplinary research collaborations with broad disciplinary representation to pursue high-impact research into complex disease from diverse perspectives. The initial Phase 2 Project Leaders will pursue projects interrelated by their fundamental focus on different aspects of the biomolecular basis of disease-associated communication pathways. These projects, which signify CIBC’s interdisciplinary nature, are directed toward: 1) developing novel chemical probes and targeted mass spectrometry approaches to study the cocaine and amphetamine-regulated transcript peptide and receptor(s), 2) understanding how the 7SK RNP regulates transcription and its implications in human diseases, 3) conducting near real-time detection of methicillin-resistant S. aureus by developing a generalizable electrochemical peptide-based biosensing platform, and 4) developing a novel Unnatural Amino Acid-based Chromatin Isolation Method (UChIMe) with improved accuracy and sensitivity. CIBC will further expand SBC and DLSC to enable Nebraska’s biomedical researchers to pursue high-impact biomedical research. CIBC’s innovation is in integrating the research activities of chemists, biochemists, engineers, and bioinformaticians to understand how cells communicate and integrate metabolic and regulatory pathways relevant to disease development and progression.

NIH Research Projects · FY 2025 · 2016-05

Project Summary/Abstract Testing high volumes of clinical specimens for infectious diseases requires the use of efficient testing approaches. One approach used by laboratories is a procedure known as group testing (also known as pooled testing). In its most basic application, portions of specimens from different people are combined together into “groups” so that each corresponding individual is represented within one group. These groups are tested as if they were only single specimens. Members of negative groups are declared negative. Members of positive groups are retested separately in a second stage of testing to determine who is positive and who is negative. When group sizes are chosen in a statistically appropriate manner, the number of people represented by negative groups is much larger than those in positive groups. This leads to significant reductions in the overall number of tests required when compared to testing each specimen separately. These reductions subsequently result in significant increases for laboratory testing capacity by applying the resources saved to test more specimens. Current applications of group testing include: 1) testing blood donations for viruses, including hepatitis B and West Nile; 2) screening for bacteria that lead to chlamydia and gonorrhea; 3) checking for antiretroviral treatment failure among HIV-positive individuals; and 4) testing for viruses during a pandemic, including SARS-CoV-2. There are different algorithmic approaches to group testing. Members of positive testing groups can be successively split into smaller groups over two or more stages of testing. Alternatively, individual specimens can be allocated to multiple groups during the initial stage of testing in an effort to reduce the number of subsequent stages of testing. The first goal of this research to develop new group testing strategies that require few stages. This will enable laboratories to more easily implement group testing and to report test results quicker. The second goal is to develop new statistical learning methods for data arising through group testing. These methods will result in better predictions for the probability of positivity and can be used to develop more efficient approaches to implement group testing. The third goal is to create tools for laboratories so that they can apply this research. These tools will include a web-based application that allows laboratories to choose the most efficient group testing strategy for their particular situation.

NIH Research Projects · FY 2024 · 2014-08

RESEARCH PLAN: PROJECT SUMMARY GOAL OF THE PARENT AWARD. This administrative supplement is submitted by the Nebraska Center for the Prevention of Obesity Diseases Through Dietary Molecules (NPOD), currently in Phase 2 COBRE funding at the University of Nebraska-Lincoln (UNL). NPOD's mission is to prevent, treat, and cure obesity and co-morbidities by harnessing the power of bioactive food compounds to ameliorate the adverse health effects of obesity. NPOD Phase 2 is guided by four specific aims: 1) Increase NPOD's critical mass of researchers by hiring five early career investigators, recruiting new early stage and senior investigators using pilot and seed grant funding, and continuing to develop strategic alliances with complementary programs; 2) acquire additional equipment for the research core and formalize experimental design services offered through the administrative core; 3) enhance the center's mentoring structure and collaborative, multidisciplinary environment; and 4) implement hiring and recruitment approaches to expand integration of fundamental nutrition and obesity research with clinical, translational, and community research. RESEARCH QUESTION FOR THE SUPPLEMENT AWARD. The proposed research will explore whether the selection of genomic variants in gut bacteria by milk extracellular vesicles (MEVs) alters energy homeostasis in infants. We have pioneered a novel line of discovery by demonstrating that small extracellular vesicles (sEVs) and their regulatory cargo do not originate exclusively in endogenous synthesis but may also be absorbed from milk (milk sEVs, MEVs). Human milk is a rich source of MEVs, and breastfed infants consume approximately 176 trillion MEVs per day. In contrast, formula is essentially free of MEVs and 90% of MEVs are degraded in milk that was frozen in milk banks or at home due to ice crystal formation. The oral bioavailability of MEVs is approximately 50% and the portion of MEVs that escapes absorption interacts with the gut microbiome. MEVs do not only alter bacterial communities, but they also select genomic variants in bacteria where the variants are transcribed into mRNA and clustered in pathways of energy metabolism (purines, glucose). Other studies are consistent with these observations and reveal an up to 120-fold increase in purine metabolites in formula-fed infants and an up to 12.5-fold increase in glucose metabolites in bacteria cultured in media containing a nutritionally relevant concentration of MEVs compared to MEV-free cultures. Motivated by these discoveries, we hypothesize that the dietary intake of MEVs alters energy homeostasis in infants. We will leverage our complementary expertise in bacterial evolution, advanced computational biology, and the development of innovative “energy sensor” mice to complete three specific aims. In Aim 1, we will assess the selection of genomic variants in MEV-defined cultures of infant feces. Specifically, we will assess the selection of genomic variants by MEVs using metagenomics analysis, their transcription using RNA-sequencing analysis, and the effects on pathways implicated in energy homeostasis using metabolomics analysis. In Aim 2, we will assess the effect of MEV selection on a host-adapted infant gut symbiont (Bifidobacterium infantis) in infants. Specifically, we will leverage existing fecal metagenomic data to characterize how MEVs select genetic variants in a host-adapted infant gut symbiont by comparing variants from infants fed frozen pasteurized milk or fresh milk and test the effects of these variants on enteric inflammatory responses. In Aim 3, we will develop NAD(H), NADPH, and ATP sensor mice in collaboration with the University of Arkansas for Medical Sciences' Genetic Models Core and assess if MEV-defined diet consumption alters energy homeostasis in neonate mice. HOW THIS PROJECT BENEFITS FROM A TEAM SCIENCE APPROACH. This research will benefit the IDeA community by supporting three project leaders and four research cores across Nebraska, Nevada, and Arkansas, and two veteran scientist consultants in Kansas and Nevada. A team science approach is essential to project success because the combined expertise required is not currently co-located in one of the participating IDeA states. Only together do we have the necessary expertise and instrumentation to conduct the proposed research. Our team comprises Drs. Qiuming Yao (UNL; NPOD project leader in Phase 2), Steven Frese (University of Nevada, Reno; not supported by NPOD), Jingjie Hao (director of NPOD's Biomedical and Obesity Research Core (BORC)), and leverages the Genomics Core Facility and Mass Spectrometry and Proteomics Core Facilities at the University of Nebraska Medical Center, the Genetic Models Core at the University of Arkansas for Medical Sciences, and UNL's BORC. The parent COBRE grant's principal investigator (PI), Dr. Janos Zempleni, will contribute expertise in milk extracellular vesicles and share archived samples. Ultimately, this project promises to benefit the six million infants annually who consume formula and frozen milk in the United State, e.g., recommending new milk storage protocols that preserve MEVs through economically and technologically feasible approaches that will not raise regulatory agency concerns. This research aligns with NPOD's mission, and we have identified a path to future funding from NIDDK and NCHID (NOT-DK-19-007). NPOD's administrative core will support the team through reciprocal visits by project leaders and an in-person workshop prior to project initiation attended by PI, project leaders and their staff, consultants, and two speakers.