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Current Trainees

Brooke Angell

Grad Program: IBiS
PhD Adviser: Jason Brickner

Doctoral Research Project:  Gene expression leads to precise control of protein abundance and plays critical roles in defining cell identity, responding to environmental cues, and is perturbed in many human diseases. Maintaining a stable equilibrium of transcripts is therefore a critical component of proper gene expression. Transcript buffering is a phenomenon whereby cells are able to maintain a steady‐state level of mRNA by globally decreasing the rate of mRNA degradation when transcription is perturbed. Likewise, when mRNA degradation is perturbed, there is a global decrease in the rate of synthesis. This suggests the existence of a feedback loop that connects mRNA synthesis and decay, however the mechanisms underlying such a feedback loop are unclear. In the Brickner Lab, I am combining my interests of gene expression regulation and next generation sequencing to uncover the mechanisms behind transcript buffering.

Laura Hertz

Grad Program: IBiS
PhD Adviser: Julius Lucks

Doctoral Research Project:  Developing biotechnologies allow for improved ways to address public health concerns, such as high levels of fluoride in drinking water. Previously, the Lucks lab developed a rapid and easy-to-use fluoride biosensor using a cell-free gene expression platform. The platform senses fluoride through a structured non-coding RNA, called a riboswitch, that turns transcription on or off in the respective presence or absence of fluoride. Specific structural features of the fluoride riboswitch are poorly understood, which hinders our ability to optimize its performance. As such, I am studying several of its critical structural features through systematic RNA sequence variation.

Rebecca Keate

Grad Program: BME
PhD Adviser: Jonathan Rivnay & Guillermo Ameer

Doctoral Research Project:  The transmission of electrical signals is critical to a variety of physiological and regenerative processes, yet until recently, the potential benefits of electroactive materials have remained largely unexplored for regenerative applications. Preliminary studies have revealed that electrical stimulation is highly beneficial for diverse types of tissue repair, but the mechanism still remains unclear. Conducting polymers are organic electrically conductive molecules rapidly emerging as promising materials to enhance regenerative outcomes and elucidate the benefits of electrical stimulation. My research aims at understanding the mechanisms by which conductive polymer biomaterials and electrical stimulation are beneficial for regeneration. This will allow us to optimize existing tissue engineering approaches by applying conductive polymers and electrical stimulation in various tissue types. 

Anika Marand

Grad Program: IBiS
PhD Adviser: Keara Lane

Doctoral Research Project:  Salmonella typhimurium (STm) is an invasive intracellular pathogen that can establish systemic infection by proliferating within macrophages. Antibiotics used to treat infectious diseases are becoming less effective due to an increase in antimicrobial resistance, and new treatment methods are urgently needed to combat this problem. STm replication is heterogeneous between infected macrophages, with some bacteria replicating while others remain dormant inside the phagosome and evade host immune responses and antibiotics. However, the factors that regulate this difference in replication among clonal populations of STm remain poorly characterized. My research in the Lane Lab will focus on determining the extent to which pre-existing variation of STm populations, such as in two-component systems, regulates replication within the phagosome. To do this, I will use dynamic, single-cell approaches such as integrating STm cell fate reporters with live-cell microscopy and droplet-based microfluidics to determine how pre-existing variation in STm environmental sensing regulates bacterial replication. 

Roxi Mitrut

Grad Program: ChBE
PhD Adviser: Josh Leonard

Doctoral Research Project:  Extracellular vesicles (EVs) can be engineered to have novel functions, including targeting EVs to specific cell types and directing loading of specific biomolecular cargo molecules, and have broad therapeutic potential. However, they can be costly and challenging to produce on clinically-relevant scales. In order to further expand the potential for these therapies, my research is currently focused on creating an implantable device capable of sustained, local production and delivery of a bioactive engineered EV therapeutic in situ. Isolation of the engineered cells from their environment by embedding them within a hydrogel matrix should also shield the implanted cells from surrounding host cells and the immune system.

Nicolas Moya

Grad Program: IBiS
PhD Adviser: Erik Andersen

Doctoral Research Project:  Human genetics is focused on the identification of genetic variants that underlie complex disease. Short-read sequencing has been crucial for furthering our understanding of genetics. However, due to the fragmented nature of these data, most large-scale structural variation remains hidden. Recent advances in long-read sequencing technologies allow us to generate high-quality reference genomes and build full-length RNA transcripts. My research in the Andersen Lab is focused on characterizing gene and genome structure in individual genomes of Caenorhabditis species with the aim to uncover hidden genetic variation. I will develop methodologies for accurate and sensitive gene prediction to study genetic differences that underlie complex traits.

Reyvin Reyes

Grad Program: IBiS
PhD Adviser: Amy Rosenzweig

Doctoral Research Project:  Metals play a vital role in many biological processes, especially in bacteria such as methanotrophs. In these organisms, copper is used to regulate and produce an enzyme called methane monooxygenase which catalyzes the oxidation of methane as the first step in their metabolic pathway. In copper-starved conditions, methanotrophs release and uptake methanobactin, a ribosomally-synthesized and post-translationally modified peptide (RiPP), that have high affinity for copper. Currently, the identity of certain enzymes and mechanisms involved in its biosynthesis are unknown. My studies will further elucidate the biosynthesis of methanobactin through enzymatic studies using structural and biochemical techniques like X-ray crystallography and mutagenesis. In addition, I am designing heterologous methods of expressing methanobactin such as in vivo expression in E.coli and cell-free expression as the mature RiPP has not been successfully synthesized outside of the native organism. These studies can aid in large scale production and engineering efforts of this peptide, which have promising applications as treatment for disorders involving copper metabolism such as Wilson's disease.

Reese Richardson

Grad Program: IBiS
PhD Adviser: Luis Amaral

Doctoral Research Project:  RNA sequencing (RNA-seq) has been the premier transcriptomic technology of the last decade and has arguably revolutionized biomedical research. However, research from our laboratory and others has demonstrated that the analytical results of RNA-seq studies are highly sensitive to a user’s choice of tools and parameters in the analysis pipeline. This inconsistency has been identified as a major obstacle for the adoption of RNA-seq in diagnostic tests. In my research, I am working towards better characterization of the limits of computational reproducibility in bioinformatics and biases inherent to RNA-seq analysis pipelines. I hope to better elucidate the effects of experimental choices on reproducibility, as well as develop methods for processing RNA-seq data for counteracting these limits.

Erica Rosario

Grad Program: IBiS
PhD Adviser: Laura Lackner

Doctoral Research Project:  Cell compartmentalization allows organelles to efficiently perform distinct functions. Interestingly, studies have shown that sites of contact between organelles contribute to organelle function and are important for cell survival. These sites, known as membrane contact sites (MCSs), facilitate interorganelle communication and coordinated function. A common characteristic of many contacts is the use of proteins to bridge the membranes of different organelles. The influence of membrane mechanics on the association and insertion of membrane proteins at contact sites and, consequently, the formation and function of the contact site is poorly understood.The goal of my project is to use synthetic biology approaches both in-vitro and in in-vivo to investigate the relationship between membrane mechanics and the proper association and insertion of membrane proteins vital for MCS formation and function.One in-vitro approach will be the development of a minimal system to examine MCS protein-membrane interactions.An in-vivo approach will be the isolation of MCSs from cells and examining the properties of contact site lipids. The work proposed will help to better understand MCS biogenesis,which will improve our ability to efficiently manipulate and control biological systems.

Stephanie Zelenetz

Grad Program: BME
PhD Adviser: Evan Scott

Doctoral Research Project:  Cancer surgery is the standard of care for patients with solid tumors in the clinic. While surgeons often remove excess tissue to ensure that as much of the tumor is removed as possible, this can cause complications for the patient. Additionally, despite these large margins, minimal residual disease and postoperative immune suppression, remain a challenge and provide an ample opportunity for recurrence. There is no standard of care to treat this period of immunosuppression, largely due to concerns about surgical wound healing. My research entails the development of a novel injectable delivery system to address these limitations of cancer surgery.

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