Biomolecular condensates are a class of important biomaterials inside the cell that have unique sequence-defined mechanical properties. This project will examine mitochondrial nucleoid biomolecular condensates, which are formed from mitochondrial DNA (mtDNA) and packaging protein TFAM. Very little is known about how the mechanical properties of the mitochondrial nucleoids are encoded by the TFAM and mtDNA sequences, though this new knowledge could shed light on how mitochondria biophysically regulate (...)
Life Sciences Alliance SURF
Engn - Chemical & Biochemical Engineering
Biochemistry, Biomedical Engineering, Chemical Engineering, (...)
"The organization of the cell's genome in three dimensions is fundamental to different cellular functions. The nucleus is divided into distinct chromosomal territories and each chromsome is segregated into active or repressed regions. While the utility of organizing the chormsome remains under investigation, it is known that multiple mechanisms orchestrate DNA organization. Crucially, Topologically Associating Domains (TADs) serve as key structural units, forming DNA loops that physically segregate (...)
Life Sciences Alliance SURF
SAS - DLS - Cell Biology and Neuroscience
Cell & Molecular Biology, Genomics , Life Sciences
"Here, we aim to develop surrogate deep learning models to replace finite element (FE) modeling and optimization for characterizing the mechanical response of soft tissues such as brain white matter. The forward problem of predicting the evolution of stress for a given tissue geometry—typically performed using FE modeling—is replaced by a recurrent neural network (RNN) that learns the structure–property relationship between tissue microstructure, material properties and stress-strain behavior. The (...)
Life Sciences Alliance SURF
Engn - Mechanical & Aerospace Engineering
Artificial Intelligence, Data Science, Life Sciences
This research project introduces a Unified Computational Framework to integrate cell morphology with single-cell transcriptomics. The proposal employs deep learning to perform morphometrics, extracting fine-grained, structural features (shape, size, morphology) of individual cochlear cells from immunofluorescent images. This structural information is then unified with corresponding single-cell genomics data, to reveal the molecular identity of the same cell types through their gene expression profiles. (...)
Life Sciences Alliance SURF
SAS - DLS - Cell Biology and Neuroscience
Artificial Intelligence, Data Science, Life Sciences
"Evolutionary biology has traditionally been a retrospective discipline, focusing on the history of life on Earth. However, the rapid evolution of many extant organisms, such as microbial pathogens in response to drugs or ecosystems in response to climate change, has motivated the need to make evolution a predictive, quantitative science. Can we predict the future evolution of these organisms?
Before making evolutionary predictions, we first must understand how predictable evolution even is. (...)
Life Sciences Alliance SURF
SAS - DLS - Molecular Biology & Biochemistry
Biochemistry, Cell & Molecular Biology, Artificial (...)
"Diet is one of the most well-established lifestyle factors influencing longevity and health, as demonstrated by laboratory studies, clinical trials, and large-scale biomedical analyses. However, diet effects on aging are highly context dependent, shaped by multiple environmental and genetic factors. We currently lack both the knowledge and a robust framework to predict the outcomes of dietary interventions at the individual level. To capture this biological complexity and guide public health strategies, (...)
Life Sciences Alliance SURF
SAS - DLS - Molecular Biology & Biochemistry
Genetics, Artificial Intelligence, Data Science, Life (...)
"Ribosomal proteins are essential components of the ribosome, working with ribosomal RNA (rRNA) to form the core machinery that translates mRNA into proteins. While rRNA carries out most catalytic steps, ribosomal proteins stabilize rRNA structure, guide ribosome assembly, and help correctly position mRNA and tRNA during translation. Because many ribosomal proteins are evolutionarily conserved, their structures provide useful models for understanding general mechanisms of RNA recognition.
In (...)
Life Sciences Alliance SURF
SAS - Chemistry & Chemical Biology
Biochemistry, Artificial Intelligence, Data Science, (...)
Self-limiting electrospray deposition (SLED) has been developed by our group for the conformal coating of macromolecules onto complex 2D and 3D surfaces. We have recently demonstrated two capabilities that have opened up a new potential application area: (1) SLED from 99.8% water solutions and (2) multilayer SLED with controlled layer thickness. We propose to use these capabilities to deposit bilayer coatings of protein + excipient coated by a biocompatible polymer shell. Based on the thickness (...)
Life Sciences Alliance SURF
Engn - Mechanical & Aerospace Engineering
Life Sciences
The Tutwiler laboratory is focused on studying the structure-function relationship of blood clot formation, with a particular focus on the mechanics and enzymatic function. Immune cells and inflammation play a unique role in the activation and regulation of blood clotting and warrant further examination. We are particularly interested in examining the role of inflammation due to its pathophysiolgical relevance to traumatic injury, cancer, spinal cord injury etc. We aim to explore the mechanisms (...)
Life Sciences Alliance SURF
Engn - Biomedical Engineering
Biomedical Engineering, Chemical Engineering, Structural (...)
"The biological carbon pump (BCP) is a natural process where phytoplankton in the surface ocean use carbon dioxide (CO2) from the atmosphere to first build their cells and then transfer this fixed carbon to depth in the form of sinking, aggregated organic particles (commonly referred to as marine snow). This process plays a pivotal role in regulating the Earth's climate by naturally sequestering carbon for long periods in the deep ocean. Broadly, the BCP sequesters carbon if these marine snow particles (...)
Life Sciences Alliance SURF
SEBS - Marine & Coastal Sciences
Computer Science and Engineering, Climate Change, (...)
"Neurodegenerative diseases, including the prevalent Alzheimer’s disease and Parkinson’ disease, virtually always feature inclusion of aggregated proteins within susceptible brain neurons. Propagation of aggregated protein species by cell-to-cell transfer underlies the spread of pathology, the mechanisms that regulate and enact aggregate transfer remain very poorly understood (not unexpectedly, as the mammalian brain is quite a complex and inaccessible tissue). We model neuronal aggregate spreading (...)
Life Sciences Alliance SURF
SAS - DLS - Molecular Biology & Biochemistry
Cell & Molecular Biology, Genetics, Life Sciences
"Age-related decline in auditory processing and memory for speech significantly impacts social well-being, contributing to social avoidance, isolation, depression, and anxiety. Despite these comorbidities, animal models for studying this decline have been limited due to the complex nature of human vocal processing. Songbirds, which learn vocalizations through social interaction (similarly to humans), offer a promising alternative model system.
This study introduces an innovative approach that (...)
Life Sciences Alliance SURF
SAS - Center for Cognitive Sciences
Cognitive Science, Life Sciences
"Humans are exposed to a wide range of drugs over the course of their lives; sometimes decades of exposure of drugs for chronic diseases. While the basic safety and efficacy in treating the target disease have been well-established for all common drugs, we know little about the wider but subtle effects those drugs may have on other aspects of health. Arguably the most important such aspect is lifespan: understanding how drugs affect lifespan could reveal new mechanisms and potential inhibitors of (...)
Life Sciences Alliance SURF
SAS - DLS - Molecular Biology & Biochemistry
Microbiology, Artificial Intelligence, Data Science, (...)
The Lonergan Lab is broadly interested in discovering how opportunistic bacterial pathogens sense and respond to nitric oxide. Nitric oxide is produced as part of the host immune response against invading pathogens. However, certain organisms can overcome host-mediated nitric oxide production and cause disease, which suggests we do not fully understand how nitric oxide limits pathogen survival. Therefore, this summer research experience will utilize molecular biology and genetic techniques to interrogate (...)
Life Sciences Alliance SURF
SAS - DLS - Molecular Biology & Biochemistry
Genetics, Genomics , Life Sciences
Computerized and mobile cognitive tasks have been used to assess psychomotor performance (e.g., slowed response time), but have the disadvantage of high participant burden. In contrast, typing (keystroke dynamics) in daily life provides a low-burden method to infer psychomotor functioning (e.g., fine motor coordination, alertness) that can support remote health monitoring. This project uses the innovative method of keystroke dynamics (e.g., typing speed) to continuously and remotely monitor, with (...)
Life Sciences Alliance SURF
RBHS - RWJMS
Cognitive Science, Artificial Intelligence, Data Science, (...)
