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Colby Lab Staff

Photo of David Colby

David Wesley Colby - CV

Assistant Professor

Engineered Antibody Therapeutics for the Treatment of Prion and Other Neurodegenerative Diseases

Cellular and protein engineering techniques provide a unique opportunity to investigate a mechanistic understanding of biological processes. Prion disease infectivity is one of the most unique biological processes in that it originates from a protein only pathogen in the absence of viral or cellular pathogens. In our work we seek to identify cellular and protein parameters which block the interaction of the pathogenic form of the prion protein (PrPSc) with the natively expressed prion protein (PrPC). Previous researchers have developed antibodies that bind PrPC and slow the conversion to PrPSc in cell culture and animal models, though few attempts have been made to engineer existing antibodies for greater therapeutic effect. Construction and evaluation of engineered antibodies to more effectively navigate the biological milieu and disrupt the PrPC- PrPSc protein-protein interaction will tie antibody parameters (eg. affinity and thermal stability) to biological function. This work will also enable the development of a quantitative mechanistic model of the kinetic and thermodynamic aspects of antibody based therapies. The model and methods developed here will likely apply more generally to other antibody therapies for more common neurological diseases such as Alzheimer’s and Parkinson’s disease.



Creating a Library of Transcription Factors to Explore Mechanisms of Cellular Reprogramming

The human nervous system is composed of a multitude of different cell types that engage in a complicated network of inter-cellular signaling. Additionally, with recent advances in cellular reprogramming, ectopically expressed transcription factors may be used to induce terminally differentiated somatic cells to revert to a state of pluripotency similar to that of embryonic stem cells or trans-differentiate directly into another distinct cell type. Unfortunately, compared to the diversity of neural sub-types found in the brain, the knowledge of reprogramming cells into specific types of neurons is still somewhat limited. By generating a library of inducible transcription factors spanning a large range of tissue specificity and expression level, the phase space of reprogramming possibilities may be more thoroughly investigated, providing much new insight into the genetic regulatory mechanisms that determine cell type.

Photo of Kyle McHugh

Kyle McHugh - CV

Graduate Student



Photo of Olga Morozova

Olga Morozova - CV

Graduate Student

Detection and structural analysis of misfolded tau protein in neurodegenerative diseases

Tau is a microtubule-associated protein that is localized in axons and is involved in neurite extension and maintenance. Tau misfolded into paired helical filaments (PHFs) is a pathological hallmark of more than 20 sporadic and familial neurodegenerative disorders including Alzheimer’s disease (AD) and frontotemporal dementia. Previous research shows that tau may be induced to misfold into distinct conformations with seeding. Here we explore how tau adopts multiple distinct fibril conformations maintained from nucleation to propagation. Preliminary work for this project includes the development of an assay for the sensitive detection and structural amplification of pathological tau in the brain and cerebrospinal fluid (CSF) of individuals with AD. We then characterized the fibril structure with multiple structural analysis techniques to understand the specific conformational changes in tau protein associated with this disease. With the initial evidence for some structural differences and a possibility of the propagation of seed structure in vitro, characterization of misfolded tau fibrils from other types of tauopathies will be implemented to gain better insight into the differences between the distinct disease pathologies that might lead to possible diagnostic techniques.



Massively parallel flow cytometry and cell sorting using fluorescent barcodes

Flow cytometry and Fluorescence Activated Cell Sorting (FACS) are broadly applied for both analysis and engineering of biomolecular and cellular systems. We are developing a simple yet powerful platform for carrying out the analysis and sorting of biomolecular and cellular libraries in a massively parallel fashion. Individual members of cellular and biomolecular libraries may be genetically tagged and identified in mixtures containing hundreds to thousands of library members. When coupled with one or more fluorescent readouts of interest, such as redox sensitive fluorescent proteins, dyes for membrane potential, or expression of GFP fusion proteins, the response of each member within a library may be analyzed in a single experimental sample. This new platform facilitates the generation of proteomic datasets for systems biology which are both rich and robust, as measurements previously requiring thousands of individual samples may be combined into a single sample, enabling the evaluation of more experimental conditions, higher numbers of replicates, and the dynamic response of such libraries to perturbations.

Photo of Stefanie Berges

Stefanie Berges - CV

Graduate Student



Photo of Elisa Ovadia

Elisa Ovadia - CV

Graduate Student

Tunable Hydrogels for a Cell Culture Model of Huntington's Disease

Huntington's disease (HD) is a hereditary neurodegenerative disease caused by a polytglutamine expansion on the Huntingtin gene. This genetic mutation causes a loss of medium spiny neurons in the brain, disrupts cellular processes, and is ultimately fatal. Currently, there are no therapies or treatments to impede disease progression. Therefore, A cell culture model that can recapture the most affected neuron by HD can aid as a resource to develop drug therapies and study disease pathology. Using induced Pluripotent Stem Cells or iPSCs we are examining different pathways to differentiate stem cells into medium spiny neurons. Additionally, we are utilizing PEG biomaterials to mimic the extracellular matrix (ECM) of the brain and study how an in vivo-like microenvironment can affect MSN differentiation.


Undergraduate Researchers

Photo of Quentin Dubroff

Quentin Dubroff - CV



Photo of Isha Purang

Isha Purang - CV



Former Lab Members

Graduate Students

Kyle Doolan, '15

Abhinav Jain, MChe, '13

Post Docs, Research Support, and Visitors

Ming Dong, PhD, '14

Maria Stoessel, Fraunhofer Exchange Student, '13

Shy'Ann Jie, Lab Manager, '13

Michael Page, visiting, '12

Sharad Gupta, PhD, '12

Priyen Patel, visiting, '12

Brittany Earnest, REU student, '11

Colin Heberling, '11

Natalie Barnes, '10


Seth Ritter, '14

Zachary March, '14

Erin Aho, '12

Sabrina Casas, '12

Ryan O'Boyle, '12

Benjamin Werth, '11