| Dr. Eran Agmon
Center for Cell Analysis and Modeling |
For this summer project, the student will work on a computational model of bacterial interactions in the human gut microbiome. The student will write code to add new mechanistic details to the model, will simulate it, visualize the results, and evaluate the results by comparing with experimental data. The final model and results will be presented in a Python notebook and shared online for others to learn from. |
HRP SU25-1 |
| Dr. Srdjan Antic
Department of Neuroscience |
This is a basic science research project aimed at understanding cellular determinants of Alzheimer’s disease (AD). We use an animal model of AD -- mice carrying specific genes, which trigger development of amyloid plaques in the cerebral cortex. By the means of brain slice technology, electrophysiology (synaptic stimulation), and optical imaging (calcium and voltage imaging) we seek to determine if synaptic transmission in disease-free animals (Control) is any different from that occurring in the AD model animals developing amyloid plaques. The student will learn software for analysis of the optical imaging records (physiological), organization and presentation of measurements, some basic histology techniques for detecting plaques in saved brain sections, and if interested, the student may perform optical imaging of synaptically evoked depolarizations in brain slices working together with a postdoc. |
HRP SU25-2 |
| Dr. Michael Blinov
Center for Cell Analysis and Modeling |
I have a variety of computational projects described at https://health.uconn.edu/blinov-lab/projects/, and can accommodate students with an interest in applications of computers and mathematics to biology in many directions: reading publications and coding biological mechanisms, using software to model, web development, algorithms coding, visualization using graphical tools, etc. |
HRP SU25-3 |
| Dr. Manuel Castro-Alamancos
Department of Neuroscience |
The project is for students in the fields of data science, engineering, computer science, applied math, statistics, biology, psychology, or neuroscience who have programming skills in Python, R, and/or Labview (or others) and who are interested in helping develop tools for automated analyses of complex data pipelines originating from neuroscientific experiments addressing the neural basis of behavior in mice. The student would be involved in developing the software tools used to control the experiments (actuators and computer vision) and/or analyze the data (data models), which includes recordings from hundreds of neurons in behaving mice. Opportunities to participate in the research by conducting experiments are also available. |
HRP SU25-4 |
| Dr. Steven Chou
Department of Molecular Biology and Biophysics |
Biochemical Characterization of the NPR1 Transmembrane Signaling Complex
Natriuretic peptide receptor 1 (NPR1) is a single-transmembrane guanylyl cyclase that plays a critical role in regulating blood pressure. The binding of atrial natriuretic peptide (ANP) to the extracellular domain (ECD) of NPR1 induces conformational changes in the transmembrane helices, propagating the signal to the intracellular domain (ICD) and its binding partners. However, the structural and biochemical characterization of NPR1 has been challenging due to its extensive post-translational modifications (PTMs) and high conformational flexibility, which hinder analysis using overexpression systems.
To overcome these challenges, we propose an alternative approach to isolate the NPR1 signaling complex directly from natural sources. We aim to purify the intact complex and identify its components using mass spectrometry. |
HRP SU25-5 |
| Caroline Dealy
Orthopedic Surgery, Orthodontics, Biomedical Engineering and Cell Biology |
The meniscus is a C-shaped fibrocartilage cushion that stabilizes and protects the knee joint. Tears to the meniscus are common and often heal poorly, even when surgically repaired. This project is a collaboration with Orthopedic surgeons who are providing tissue from patients with meniscal tears. The project will compare the transcriptome of meniscal tears that heal poorly to those that heal well. The long-term goal is to identify genes that correlate with better healing outcomes, which might offer potential for clinical use as meniscal pro-healing factors. Experiments this summer will include preparation of meniscal cell isolates and analysis of RNA transcriptomal data using bioinformatics software. Additionally, there is opportunity to carry out validation studies in meniscal tissue sections. All IRB approvals for this project are already in place; as are University-approved safety protocols for handing human tissue. |
HRP SU25-6 |
| Dr. Abhijit Deb Roy
Department of Cell Biology, Center for Cell Analysis and Modeling |
We are interested in interactions between different cytoskeleton (actin, microtubules and intermediate filaments) in cell motility. We apply molecular cloning, advanced fluorescent live cell imaging modalities and synthetic biology approaches to examine the molecular cross-talk between these cytoskeletal entities. Students working in our lab will learn to perform molecular biology techniques, mammalian cell culture, live cell microscopy and working with synthetic biology molecular tools to address fundamental questions in biological and biomedical context. |
HRP SU25-7 |
| Dr. Alix Deymier
Department of Biomedical Engineering |
The project would focus on the characterization and analysis of data related to bone-like apatite crystals with varying substitutions. The student would learn to fabricate crystals, characterize them using techniques such as Raman, FTIR, XRD, etc... They would then analyze the data using Matlab and GraphPad programs. |
HRP SU25-8 |
| Dr. Ellis Dillon
Center on Aging |
We are conducting short satisfaction surveys with residents and family members from each nursing home in Connecticut. Over the summer we are looking for someone to assist with recruiting family members to complete a brief 3-question survey. You will be based in our office helping email, mail, and call individuals who are the family members of nursing home residents to ask them to complete the survey. You will also accompany research team members to conduct surveys in nursing homes with residents. You will help analyze the data collected with this survey to understand differences across nursing homes. |
HRP SU25-9 |
| Dr. Mallika Ghosh
Department of Cell Biology, Center for Vascular Biology |
Cell-cell fusion is a highly specialized process mediated by fusion regulatory proteins involved in a variety of diverse cellular functions. CD13, a transmembrane protein that we study in my lab, controls many events including adhesion, migration, membrane organization, and endocytosis which are critical in cell-cell fusion. We hypothesize that CD13 is a negative regulator of cell-cell fusion during osteoclastogenesis and macrophage giant cell formation, and thus is a novel target for therapeutic intervention in pathological conditions mediated by defects in cell-cell fusion such as osteoporosis and failure of medical implants such as hernia mesh, glucose sensors, stents, and many medical devices. |
HRP SU25-10 |
| Dr. Andres Grosmark
Department of Neuroscience |
The cognitive maps that we use to navigate the world around serve as a fundamental stage in which we organize our day-to-day memories (what happened where) and the ability to generate and use these maps is one of the first cognitive capacities to decline in a number of psychiatric diseases including Alzheimer's disease (AD). My lab studies the formation and long-term evolution of spatial cognitive maps in mice traversing through 3D virtual reality environments using custom made 3d headsets, while we either track the real-time activity of thousands of neurons with two-photon imaging or manipulate neural activity using optogenetic methods. This combination of modern tools allow us to get a unique view of memory that is both detailed - looking at the activity of thousands individual neurons, and broad - tracking these neurons over many days and relating their activity to behavior in both healthy and AD mice. The insights gained from these studies will help us better understand the foundations of how our memories both define and are defined by the world around us, and how these processes can go awry in psychiatric diseases such as AD. |
HRP SU25-11 |
| Dr. Yuan Gui
Department of Medicine/Nephrology |
The project explores how MFAP2 remodels the kidney fibrotic microenvironment. We will subject CKD models, including ischemia-reperfusion injury (IRI), low-dose cisplatin injection, and Unilateral Ureteral Obstruction (UUO) to WT and MFAP2 knockout mice to evaluate kidney fibrosis after MFAP2 deletion. Besides, global/phosphor-proteomics will performed to explore the underlying mechanism. |
HRP SU25-12 |
| Dr. Xiaoyan Guo
Department of Genetics and Genome Sciences |
The accumulation of dysfunctional mitochondria is closely linked to various diseases, including neurodegenerative disorders. Our lab focuses on uncovering the molecular and cellular mechanisms that maintain mitochondrial health. One key mechanism is mitophagy—the selective degradation of damaged mitochondria.
Using CRISPR-based genetic screening, we have identified candidate genes involved in this process. This summer project offers students an exciting opportunity to investigate these genes and explore their roles in regulating mitochondrial health. |
HRP SU25-13 |
| Dr. Baihai Jiao
Department of Medicine |
This summer research opportunity focuses on investigating the molecular mechanisms underlying chronic kidney disease (CKD), specifically the role of macrophages in inflammation and fibrosis. The project will involve studying the activation and polarization of macrophages and their impact on kidney tissue damage, with an emphasis on the PU.1 transcription factor and the NLRP3 inflammasome pathway. Students will gain hands-on experience in cell culture, gene expression analysis, cell differentiation, PCR, real time RT-PCR, Western blot, immunohistochemistry, immunofluorescence and histology to uncover key regulatory pathways. This research aims to identify novel therapeutic targets for CKD, providing students with valuable insights into biomedical research and translational science. |
HRP SU25-14 |
| Dr. Brian Kelley
Department of Neurosurgery |
This project focuses on blood-meningeal barrier responses to traumatic brain injury. Using an animal model of concussive injury, the student would investigate cellular and molecular changes in neurovascular composition within the meninges following injury. The student would be responsible for tissue processing, immunohistochemistry, microscopic image acquisition, and quantitative analyses of meningeal blood vessels and fibroblasts in control and experimental groups. |
HRP SU25-15 |
| Dr. Kshitiz Kshitiz
Department of Biomedical Engineering |
We have pioneered the field of Evolutionary Medicine to understand and develop therapies for human pathologies by understanding how the same physiology works "normally" in other mammals. The project will entail quantification of cancer metastasis in animal models, bioinformatics, imaging, microscopy, and specialized techniques.
Please check our lab website for more details. www.kshitizlab.org |
HRP SU25-16 |
| Dr. Guangfu Li
Department of Surgery |
A high fat and high sugar diet (HFS), a typical Western-type diet (WD), is now recognized as a major risk factor for the development of nonalcoholic fatty liver disease (NAFLD). Mounting evidence indicates that the interaction between HFS and gut microbiota generates a spectrum of dietary and microbial components and outcome metabolites that can induce inappropriate hepatic immune activation, suggesting a key role of the diet/gut/liver/immune axis in NASH. However, the mechanisms underlying HFS-induced hepatic pathologic reactions are poorly understood. Furthermore, very little is known about the specific microbes and metabolites that regulate intrahepatic immunity. We propose to address these major knowledge gaps by identifying NASH-associated microbes and metabolites and dissecting the underlying cellular and molecular mechanisms. |
HRP SU25-17 |
| Dr. Changchun Liu
Department of Biomedical Engineering |
Rapid, sensitive and affordable molecular detection plays a critical role in disease early diagnostics and health monitoring. In this summer project, we will develop a portable point of care diagnostic system to detect the molecular biomarkers of diseases in microfluidic chip. We will use microfluidic chip to detect the biomarkers. We will build a point of care diagnostic system to read the chip signal and operate microfluidic chip. Please find more detail on our current research through the website: https://smds.engr.uconn.edu/. |
HRP SU25-18 |
| Dr. Xin-Ming Ma
Department of Neuroscience |
Understanding the mechanisms underlying depression and anxiety using a novel COP1 genetic mouse model.
Depression is often comorbid with anxiety. The Currently available antidepressants produce unsatisfactory results due to the limited understanding of the mechanisms underlying depression and anxiety. COP1 is a known risk factor for both conditions, and its protein is present in the brain areas associated with depression and anxiety. This study aims to determine whether COP1 deficiency or excess in the brain contributes to the development of depression and/or anxiety in a COP1 genetic mouse model. The findings will enhance our understanding of the mechanisms that underlie depression and anxiety. |
HRP SU25-19 |
| Dr. Pedro Mendes
Center for Cell Analysis and Modeling |
The project consists of an assessment of two different methods for modeling multicellular biological systems: full differential equation models and hybrid agent-based / differential equation models. A couple of representative models of multicellular systems (e.g. microbial communities, epithelial tissues, or connected spiking neurons) will be chosen from the literature, and models will be set up in the software COPASI for the full differential equations approach, and also in a combination of COPASI and Vivarium for the hybrid agent-based/differential equations approach. An assessment of the error introduced by the hybrid approach will be estimated by comparison with the full differential equation approach. |
HRP SU25-20 |
| Dr. Megan O'Grady
Department of Public Health Sciences |
Drug overdoses are at an all-time high, contributing to over 100,000 deaths per year. Opioids have been a major contributor to these mortality rates. The research assistant will have the opportunity to work at the Center for Prevention Evaluation and Statistics (CPES) at UConn Health on projects that are evaluating opioid prevention and overdose initiatives across Connecticut. The research assistant will work with the CPES team to collect and examine data, conduct research interviews, and create presentations and reports from evaluation activities. |
HRP SU25-21 |
| Dr. Hideyuki Oguro
Department of Cell Biology |
The Oguro laboratory investigates the molecular and cellular mechanisms that regulate the development, self-renewal, mobilization, and malignant transformation of blood-forming hematopoietic stem cells (HSCs) using mutant mouse models, patient samples, and human induced pluripotent stem cells (iPSCs). Potential projects involve studying gene expression modifications in mouse HSCs or human iPSCs to explore the roles of candidate genes in HSC biology. This includes tasks such as plasmid constructions, lentiviral and/or transposon gene delivery, CRISPR-activation/interference of gene expression, and flow cytometric analysis of cultured mouse HSCs or human iPSCs. |
HRP SU25-22 |
| Dr. Carla Rash
Departments of Medicine & Psychiatry |
Addictions lab. Multiple studies ongoing: 1) app-based treatment for cocaine use disorder; 2) assessing use of responsible gaming tools among Connecticut residents; and 3) promoting employment in persons living with HIV. |
HRP SU25-23 |
| Dr. Danielle Rux
Department of Orthopedic Surgery |
We are interested in understanding mechanisms that drive the development of synovial joints and articular cartilage, the cushion that prevents damage to articulating bones. The selected student will learn to perform PCR, tissue histology, staining and imaging techniques from a novel genetically modified mouse model to test molecular mechanisms that control articular cartilage growth and maturation during embryonic and postnatal development. |
HRP SU25-24 |
| Dr. Sarvenaz Sarabipour
Center for Cell Analysis & Modeling, Cell Biology, Center for Vascular Biology, Biomedical Engineering, Molecular Biology & Biophysics |
Our lab is interested in building mechanistic computational models to study protein interactions (coupling, trafficking, activation, and downstream signaling) in human cells. Our current projects include studying families of cellular receptors in vascular endothelial cells. In these projects, we will use rule based model building to construct computational models of receptor movement across cellular compartment. We will then simulate the system to numerically solve ordinary differential equations that describe receptor interactions. We will implement detailed biophysics and biochemical parameters from experimental findings in the literature to build these state of the art models of receptor interactions to test the effect of therapeutic agents on blood vessels. |
HRP SU25-25 |
| Dr. Benjamin Sinder
Department of Orthopedic Surgery |
Bone is a highly dynamic tissue and your entire skeleton is replaced every ~10 years! Using specialized animal models, we study how bone strength is maintained (including in rare diseases), how it adapts to mechanical loading and heals, and specific signalling pathways that modulate this response. The selected student will get the opportunity to use a variety of cutting-edge histology, fluorescent microscopy, microCT imaging, and/or mechanical testing techniques to address these questions. There may be opportunities to focus on certain techniques/aspects of a project depending on the candidate. |
HRP SU25-26 |
| Dr. Henry Smilowitz
Department of Cell Biology |
Our lab, in collaboration with a biotech company, has shown that a well tolerated, biologically compatible nanoparticle can enhance radiation therapy of tumor cells using a clinical irradiator. We have also shown that the nanoparticle is taken up by tumors growing in mice more than the surrounding tissue. Initial microlocalization studies show a heterogeneous distribution within the tumor. Experiments going forward will be designed to test the efficacy of the nanoparticle as a radiation enhancer of tumors growing in mice, to maximize tumor uptake of the nanoparticles and to understand the basic biology of nanoparticle-tumor interaction. |
HRP SU25-27 |
| Dr. Dongyuan Song
Department of Genetics and Genome Sciences |
For this summer project, the student will work on improving our single-cell omics simulator, scDesign3 (Nature Biotechnology 2024). The student will add new functions for the existing R package and expand the current model to other types of data, such as proteomics or spatial multi-omics. |
HRP SU25-28 |
| Dr. Timothy Spellman
Department of Neuroscience |
Our lab studies the cortical circuits and cell types supporting executive functioning in the prefrontal cortex, using a wide range of tools including in vivo calcium imaging of neuronal activity in animals actively engaged in complex decision-making tasks, as well as optogenetics, histology, and computational modeling. There are several possible project available for summer students, including examining the effects of Alzheimer's-related mutations on prefrontal coding, studying the effects of chronic stress on cognitive flexibility, and using machine-learning tools to for unbiased classification of animal behavior. The exact project will be tailored to the skills and interests of qualified applicants. |
HRP SU25-29 |
| Dr. Ephraim Trakhtenberg
Department of Neuroscience |
We study how the brain develops and utilize gained knowledge to reverse-engineer regeneration of the brain tissue damaged by an injury or stroke. We employ a multidisciplinary approach spanning cutting edge genetics, epigenetics, bioinformatics, molecular biology, and gene therapy, which will provide a student with an opportunity to explore different approaches and select a project that aligns best with the individual’s career goals and interests. |
HRP SU25-30 |
| Dr. Melanie Tran
Department of Nephrology |
Renal fibrosis is the pathophysiological hallmark of chronic kidney disease, which is characterized by extensive fibroblast activation and extracellular matrix accumulation. The mechanisms implicated in renal fibrosis are not fully understood, and existing therapies are often limited and ineffective. This research project aims to investigate the role of USP22 in the development of renal fibrosis. The student will gain experience in cell culture, immunofluorescence, immunohistochemistry, qPCR, Western blot and mouse models of chronic kidney disease. |
HRP SU25-31 |
| Dr. Sebnem Tuncdemir
Department of Neuroscience |
Discrimination of different contexts composed of distinct constellations of multisensory cues is a hallmark of both episodic memory and spatial navigation, two functions ascribed to the mammalian hippocampus. On the other hand, impairments in contextual discrimination of non-traumatic memories is a hallmark of many stress and trauma disorders, including posttraumatic stress disorder (PTSD); yet, the neural mechanisms by which traumatic contexts are generalized remain unclear. This project will examine whether manipulating the activity of inputs to the hippocampal dentate gyrus can rescue context discrimination deficits in a PTSD model in mice. The student will perform intraperitoneal injections, behavioral induction and testing of contextual fear learning followed by histological examinations and data analysis. |
HRP SU25-32 |
| Dr. Oscar Vargas-Rodriguez
Department of Molecular Biology and Biophysics |
The summer research project aims to decipher the functional role of a superfamily of proteins known as aminoacyl-tRNA synthetases in bacterial pathogenicity. These proteins regulate protein biosynthesis and may enable pathogenic microbes to survive, adapt, and thrive in different environments, particularly within their host during colonization and infection. The student will perform standard molecular biology and biochemistry assays, including molecular cloning, protein, nucleic acid manipulation, enzymatic assays, and cell-based experiments. |
HRP SU25-33 |
| Dr. Rajkumar Verma
Department of Neurosciences |
Following a stroke, a surge of ATP is released from compromised brain cells. This surge, in turn, triggers a cascade of events, including the activation of neurons and microglial purinergic receptor P2X4 (P2X4R). This activation facilitates rapid excitatory neurotransmission through the influx of cations. However, excessive activation of P2X4R can lead to the release of several pro-inflammatory cytokines during the initial stages of ischemic injury. Interestingly, the effects of acute activation stand in contrast to those observed with chronic inhibition or the absence of this receptor. In fact, prolonged inhibition or the lack of P2X4R might hinder the process of stroke recovery. Thus, acknowledging the dual role of P2X4R in different phases of ischemic injury, we are currently engaged in a systematic exploration of its potential as a therapeutic target for enhancing post-stroke recovery. In essence, our research endeavors revolve around deciphering the intricate role of P2X4R, recognizing its potential as a double-edged sword in stroke-induced processes. Through a comprehensive understanding of its temporal dynamics, we aim to pave the way for innovative therapeutic interventions that can tip the balance in favor of improved recovery outcomes. |
HRP SU25-34 |
| Dr. Yanlin Wang
Department of Medicine |
Chronic kidney disease (CKD) is characterized by tubular epithelial cell injury and fibrosis of the kidney. The molecular mechanisms underlying the pathogenesis of CKD are not fully understand. The summer research project will examine the role of TRIM28, a transcriptional and epigenetic factor, in tubular epithelial cell injury and regeneration. Molecular, cell, genetic, and pharmacological approaches will be used in this research project. Students can learn a wide range of biological techniques such as cell culture, cell proliferation, apoptosis, cell differentiation, PCR, real time RT-PCR, Western blot, immunohistochemistry, immunofluorescence, histology, animal models of kidney disease. |
HRP SU25-35 |
| Dr. Helen Wu
Department of Psychiatry |
Our project, "Engaging Communities of Color in Lifestyle Changes to Reduce Chronic Disease Risk: Creating Healthy Communities" has focused on reducing systemic racial barriers hindering lifestyle improvement and increasing chronic disease risks in communities of color. Racial and ethnic minorities face higher rates of chronic conditions and mortality due to systemic inequalities, particularly evident in diet-related disparities. The primary barriers to lifestyle changes are a lack of individual and community engagement, exacerbated by health disparities. The activities of the project, includes but is not limited to a) develop and test a community-based lifestyle educational curriculum using experiential learning theory, communication strategies, and S.M.A.R.T. goal settings; b) promote healthier eating norms by reducing structural racism in nutrition insecurity in the communities; and 3) conducting lifestyle interventions to examine individual and community engagement in lifestyle changes and assess their impact on health and dietary behavior improvements in community of color. |
HRP SU25-36 |
| Dr. Ji Yu
Center for Cell Analysis and Modeling |
The summer project requires the student to develop and document test cases for a set of deep-learning models. These models are pre-trained to perform microscopy image analysis and deployed on our high-performance computing (HPC) cluster. The student will work closely with one or several experimental labs to implement image-analysis pipelines for the experimental data, e.g. quantifying the average cell division time of stem cells recorded by time-lapse microscopy, evaluate accuracy of the results, and document the analysis. |
HRP SU25-37 |
| Dr. Kristyn Zajac
Calhoun Cardiology Center, Division of Behavioral Health |
The Collaborative Hub for Emerging Adult Recovery Research (CHEARR) at the UConn Health School of Medicine is recruiting students interested in learning skills to conduct research on recovery support services for emerging adults (ages 18-25) with substance use disorders, with a particular focus on opioid use disorder. CHEARR activities include establishing and collaborating with community boards consisting of emerging adults in recovery and recovery coaches providing services in community settings; developing a range of technical tools to advance the research on recovery support services and communicate these advancements to other researchers, professionals, and the public (e.g., tipsheets, webinars, social media content); develop and validate a measure of recovery capital specifically for emerging adults; and train the next generation of researchers in the field of recovery supports. The student intern would have the opportunity to participate in all of the above activities as well as two ongoing randomized clinical trials led by Dr. Zajac that are relevant to this research area: 1) a clinical trial evaluating the use of recovery coaches to reduce treatment dropout among emerging adults in community-based substance use treatment and 2) a community-based participatory research project that aims to develop a peer-led program to increase retention in medication treatment for opioid use disorder. |
HRP SU25-38 |
| Dr. Yanjiao Zhou
Department of Medicine |
My lab is a computational biology lab. We are interested in understanding the role of the gut microbiome and microbial metabolites in aging and other clinical diseases in mice and humans. The techniques we use include mouse models, anaerobic culture, molecular biology, and multi-OMICS technology. Depending on their interests, students will have the opportunity to learn wet bench techniques and bioinformatics. |
HRP SU25-39 |
| Dr. Dong Zhou
Department of Medicine/Nephrology |
This summer project aims to explore the role of Microfibrillar-associated protein 2 (MFAP2) in the onset and progression of acute kidney injury (AKI). Our preliminary findings indicate that global deletion of MFAP2 exacerbates AKI, but the precise mechanisms remain unclear. The applicant will investigate these mechanisms through in vivo, in vitro, and ex vivo experiments. Additionally, the applicant will acquire bioinformatics skills to analyze proteomics data generated throughout the project, providing a comprehensive understanding of the molecular landscape involved in AKI. |
HRP SU25-40 |
