We are excited to announce our 2025 summer Research Experience for Undergraduates (REU)

The NSF ATP-Bio REU is a 10-week research internship targeting STEM students nationwide, including community college students, who have not participated in prior research. Students will spend their summer doing exciting, cutting-edge research to help “stop biological time” and radically extend the ability to bank and transport cells, aquatic embryos, tissue, skin, whole organs, microphysiological systems (“organs-on-a-chip”), and even whole organisms through a team approach to build advanced biopreservation technologies.

ATP-Bio REU students will work at the University of Minnesota, Massachusetts General Hospital, the University of California-Riverside, or Texas A&M University. Lodging and travel are provided, along with a stipend.

Project descriptions for this summer’s program can be found below.

Metabolic Rewiring of Monocytes to Modulate Immune Activity

Host Lab: Dr. Martin Yarmush
Lead Mentor: Saeed Nazemidashtarjandi 

Immunometabolism studies highlight the critical role of macrophages in orchestrating pro- and anti-inflammatory responses, driven by metabolic reprogramming. Pro-inflammatory monocytes predominantly rely on glycolysis to fuel the production of inflammatory mediators. In contrast, anti-inflammatory monocytes depend on oxidative phosphorylation (OXPHOS) and β-fatty acid oxidation (FAO) to sustain their anti-inflammatory functions. Aligned with ATP-Bio’s mission to extend the preservation of biological samples, this project also seeks to develop protocols for assessing the metabolic maturity of monocytes following mitochondrial transplantation. Additionally, we aim to optimize cryopreservation cocktails to enhance post-thaw viability of monocytes. This project aims to establish pro-resolving monocytes capable of mitigating inflammation through mitochondrial transplantation into circulating monocytes, resulting in reprogramming monocyte metabolism to OXPHOS. Mitochondrial transplantation facilitates a shift in monocyte metabolism toward oxidative phosphorylation (OXPHOS), enhancing the production of anti-inflammatory cytokines like IL-10.

Testing Storage Solutions on Mammalian Cell Populations

Host Lab: O. Berk Usta, Ph.D
Lead Mentors: Luke E. Boudreau
Mathilda F. Holtz

Supercooling is a novel procedure for storing biological material below its freezing point, but without ice formation. Supercooling slows the cell’s metabolism and does not require the addition of toxic cryoprotectants, allowing users to quickly transfer cells directly from storage into culture without additional processing. Creation of optimized storage solutions may allow for longer storage time of cells in suspension and improved quality of samples during/after storage.

In this project, a REU student will test a series of storage solutions on a mammalian cell population with differing concentrations and compositions of potential supplements, including antioxidants and membrane-stabilizing molecules through targeted screening.

The TREAT LAB

Host Lab: Dr. Jin Nam

The Tissue Regenerative Engineering and mechanoTransduction (TREAT) Laboratory at UCR explores how physical environmental factors, such as stiffness, forces, and electric fields, influence cellular behaviors. In this REU opportunity, the student will investigate how cryopreservation of neural cells and tissues is affected by the physical environment, specifically as modulated by hydrogels.

Development of Magnetic Nanostructures for Rapid and Self-Regulated Rewarming

Host Lab: Dr. Yadong Yin

Rapid rewarming is essential in cryopreservation technology to reduce damage caused by the formation and growth of ice crystals in vitrified biological systems. This project aims to develop effective methods for the chemical synthesis of magnetic nanostructures with optimal size, composition, morphology, and spatial arrangement for the rapid rewarming of cryopreserved samples. The candidate will collaborate with a graduate student to study the chemical synthesis and structural characterization of these nanostructures, as well as evaluate their heating performance.

Development of Hybrid Nanostructures for Rapid Rewarming

Host Lab: Dr. Yadong Yin

This project aims to develop innovative hybrid nanostructures that combine both magnetic and plasmonic components with carefully controlled size and shape. These hybrid nanostructures will utilize two heating mechanisms: radio-frequency heating from the magnetic component and photothermal heating from the plasmonic component. This dual approach will facilitate the rapid warming of cryopreserved samples, preventing the formation and growth of ice crystals. The candidate will work in collaboration with a graduate student to synthesize and characterize these hybrid nanostructures and assess their heating performance under both light and radio-frequency fields.

Reanimation of Large Mammalian Organs

Host Lab: Dr. Paul Iaizzo
Lead Mentor: Ryan Nadybal

Imperative to the success of ATP-Bio’s research mission is the ability to effectively retain organ function post rewarming. To aid in that effort, this project will focus on developing tools to assess the function and health of large mammalian organs (such as lungs and hearts). The goal of the project is to better understand what types of measurements are effective in describing isolated organ health and viability. This project would be particularly well suited for students that have an interest or experience in coding, computer-aided drawing (CAD), or manufacturing and fabrication. Students should expect to further develop these skills during the course of the project as well as get a well rounded exposure to experimental design, data collection, and analysis.

Optimizing Cryoprotective Agent Formulations for Lung Vitrification

Host Lab: Dr. John Bischof
Lead Mentor: Zonghu Han

We have successfully cryopreserved rat kidneys and aim to expand this capability to other organ systems, such as lungs, which remain largely unexplored. Achieving lung vitrification requires the delivery of cryoprotective agents (CPAs) into the organ via perfusion. Optimizing the CPA formulation is critical to reducing toxicity while maintaining its vitrification performance. In this project, the student will gain hands-on experience in CPA toxicity screening using rat lung slices to assess tissue viability after CPA exposure. The project involves the following steps:

1. Training and Familiarization: The student will shadow Zonghu to learn essential techniques, including lung slice preparation with the Stadie-Riggs tissue slicer, stepwise CPA loading, tissue incubation, and viability assays. This phase ensures proficiency with the system and methods.

2. Baseline Toxicity Assessment: The student will start by assessing the toxicity of the gold standard CPA, VMP, on lung slices, establishing a benchmark for comparison.

3. CPA Optimization: With Zonghu’s guidance, the student will design and test new CPA formulations to minimize toxicity while maintaining vitrifiability. Each candidate formulation will undergo iterative toxicity testing on lung slices.

4. Candidate Evaluation: The student will identify the CPA formulation with the lowest toxicity based on repeated experiments, contributing to advancements in lung cryopreservation.

This project offers an opportunity to develop expertise in lung cryopreservation, CPA optimization, and tissue viability assessment while addressing critical challenges in the field.

Ranking Cryoprotective Agents by Ice-Prevention Ability 

Host Lab: Dr. John Bischof
Lead Mentor: Casey Kraft

Cryogenic storage (-150 C) would extend preservation time indefinitely. Loading samples with CPA(s) prior to cooling is a critical component to cryopreservation success in samples ranging from cells to, recently in our group, whole kidneys. To date, there is no universal CPA solution, and researchers often undergo an iterative process involving serial CPA toxicity testing to arrive at a suitable CPA solution for their system. Increased knowledge would aid this process. The goal of this project is to use a simple strategy (visual inspection upon cryogenic cooling) to rank CPAs by their ice avoidance properties, which are dependent on cooling/rewarming rate. In this project, the student will learn experimental techniques such as thermometry as well as statistical techniques such as factorial analysis and model fitting in R.

ROLE OF GUT-DERIVED METABOLITES FOR ENHANCING LIVER ORGANOID

Host Lab: Dr. Ellie Rabhar
and Dr. Arul Jayaraman
Lead Mentor: Aniruddh Mukunth

Metabolic dysfunction-associated steatohepatitis (MASH) is an emerging global health concern, driven by rising obesity and metabolic disorders. As MASH progresses, severe hepatic dysfunction can lead to end-stage liver failure, often requiring transplantation. However, the limited availability of donor livers and the challenges associated with long-term storage hinder transplantation efforts. The liver, being a highly metabolically active organ, is particularly difficult to cryopreserve due to its susceptibility to ischemia-reperfusion injury (IRI), oxidative stress, and lipid-induced mitochondrial dysfunction. Additionally, hepatic steatosis, a hallmark of MASH, further compromises post-thaw viability and function, increasing susceptibility to ischemic damage. Liver organoids, derived from stem cells, provide a promising 3D model that closely mimics physiological liver function and allows for controlled investigation of metabolic and ischemic stress responses. Recent research highlights the role of gut-derived microbial metabolites in regulating hepatic lipid metabolism, oxidative stress, and inflammation. Among these, tryptophan-derived metabolites, such as indoles and kynurenines, have demonstrated the ability to modulate lipid homeostasis and enhance cellular resilience against metabolic and oxidative stress. This project aims to investigate whether tryptophan metabolites can facilitate defatting, improve mitochondrial function, and protect liver organoids from ischemia-reperfusion injury, particularly in the context of cryopreservation. Using stem cell-derived liver organoids as a model system, this study will assess metabolic and functional adaptations under ischemic conditions through lipidomics, mitochondrial functional assays, and transcriptomic profiling. The findings will contribute to the development of metabolite-based interventions to enhance liver organoid viability, with implications for improving cryopreservation techniques and advancing regenerative medicine strategies for liver transplantation.

INVESTIGATING THE ROLE OF MICROBIAL METABOLITES IN DEFATTING AND REDUCING ISCHEMIA-REPERFUSION INJURY IN THE LIVER

Host Lab: Dr. Arul Jayaraman
Lead Mentor: Aniruddh Mukunth

The liver plays a central role in metabolism, detoxification, and maintaining systemic homeostasis. However, liver transplantation and hepatic surgeries are often complicated by ischemia-reperfusion injury (IRI) a condition characterized by oxidative stress, inflammation, and cellular damage that occurs when blood supply returns to the liver after a period of ischemia (restricted blood flow). Furthermore, hepatic steatosis (fatty liver), prevalent in conditions such as metabolic associated fatty liver disease (MAFLD), exacerbates susceptibility to IRI, impairing liver function and transplant outcomes. Recent studies highlight the gut-liver axis as a critical mediator of liver health, with microbial metabolites playing key roles in modulating hepatic inflammation, oxidative stress, and lipid metabolism. Metabolites such as indoles, flavonoids  and short-chain fatty acids (SCFAs) are known to influence mitochondrial function and lipid metabolism. This project aims to test the hypothesis that tryptophan derived metabolites can defat hepatocytes, improve mitochondrial health, and mitigate ischemia-reperfusion injury in the liver. This project will employ a combination of in vitro liver models, including hepatocyte spheroids to simulate ischemia-reperfusion conditions and assess the effects of microbial metabolites. Advanced techniques such as lipidomics and mitochondrial functional assays will be used to characterize metabolic and signaling changes.

USING ROBOTS TO ENHANCE BIOECONOMY THROUGH INSECT AGRICULTURE

Host Lab: Dr. Minghui Zheng
and Dr. Jeffery Tomberlin
Lead Mentor: Dr. Minghui Zheng

As the human population grows, demands on food production systems increases as well. Furthermore, through increased food production, stress on the environment is compounded. Thus, developing a circular economy where no wastes remain from agriculture is critical. Through this project robotic applications will be investigated to determine efficient methods for recycling wastes with the black soldier fly- an insect whose larvae can be used as bioreactors to recycle waste and produce products of value such as animal feed and fertilizer.

INSECT AGRICULTURE FOR SUSTAINABILITY: FROM EARTH TO MARS!

Host Lab: Dr. Jeffery Tomberlin
Lead Mentor: Dr. Jeffery Tomberlin

Mars-based colonists can sustainably use black soldier flies for food, waste management, and production of rocket fuel, but we need to get them there first. Using cryogenic technologies to put them in a stasis sleep, these little soldiers can boldly go where no fly has flown before. We are looking for an undergraduate to help us in this endeavor. You will aid in colony management and cold temperature experimentation with black soldier fly larvae. Through this opportunity, you will gain experience with entomology, ecology, data management and analyses, and potentially professional presentations and resulting publications.