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URMC / Labs / Benjamin Miller Lab / Lab Members

 

Lab Members

 

Principal Investigator

Benjamin Miller
Benjamin L. Miller, Ph.D.
MC 6-6820
Phone: (585) 275-9805
Email Benjamin

Research Staff

Alanna Klose

Alanna M. Klose
Technical Associate
MC 5-8527
Phone: (585) 273-2149

Research Interest: My research focuses on new applications of the arrayed imaging reflectometry (AIR) platform. One recent project focused on the design and development of a self-assembling biological thin film enabling new approaches to microarray fabrication. This includes the growth, characterization, and stabilization of the surface. The film expands the capabilities of the established AIR substrate to include the attachment of novel probes such as aptamers and biotinylated proteins. I am using this surface to generate mixed antibody-aptamer arrays that address clinical needs for multiplex biosensing devices.

Ethan Luta
Ethan Luta
Laboratory Technician
 

Graduate Students

Viktoriya  Anokhina
Viktoriya Anokhina, M.S.
BMB Biochemistry & Molecular Biology Ph.D. Program

Research Interest: Despite the progress in treatment with combination antiretroviral therapy (cART), HIV/AIDS remains one of the world's most significant public health challenges, since there is no complete recovery from the disease. More research is needed to explore new viral targets and develop other therapies. Targeting functionally important RNA elements can potentially provide a new avenue for therapeutic development. In addition, principles learned from the development of molecules targeting HIV-1 RNA elements can be applied to other pathological RNAs. One of the potential targets in HIV-1 is the Frameshifting Stimulatory Signal (FSS), a highly stable RNA hairpin that is essential for precisely regulating the ratio of translation for “structural” and “enzymatic” polyproteins. Misregulation leads to formation of non-infectious viral particles. Thus, it has been hypothesized that targeting HIV-1 FSS could be of therapeutic value.
 
In the Miller lab, we developed compounds that bind to HIV-1 FSS RNAs with affinities 16-100 nM. Compounds ablate virus production and infectivity in human MT-2T cells infected with laboratory HIVIIIB and with a drug-resistant patient isolate. Several pieces of evidence altogether demonstrate that the antiviral effectivity of compounds is due to compound-mediated interference with ribosomal frameshifting via binding to the HIV-1 FSS. While the binding affinities of these molecules to the HIV-1 FSS lie in the nM range, biological activity in cellular assays is observed at μM range. We hypothesized that this discrepancy is associated with low cellular permeability of the compounds. My efforts are focused on testing methods of improving compounds efficacy by developing new delivery strategies, while maintaining compound selectivity and affinity toward the target. These methods should have general utility for RNA-targeted drugs.
Diego Arévalo
Diego Arévalo
Chem Chemistry Ph.D. Program

Research Interest: Expanding the chemical toolbox for RNA recognition: My research is devoted to developing a synthetic scaffold that will expand the known chemical space for RNA recognition efforts. This scaffold will be used to generate a Resin-Bound Dynamic Combinatorial Library to identify high affinity compounds for the C-C Chemokine Receptor type 5 (CCR5) mRNA, a coreceptor for HIV-1 for entry into CD4 T cells.
Jeffrey Beard
Jeffrey Beard
BME Biomedical Engineering Ph.D. Program

Research Interest: New diagnostics for HIV in resource-limited environments: There are approximately 37.9 million people living with the human immunodeficiency virus (HIV) world-wide, each of whom require regular monitoring of their HIV viral loads. Currently, nucleic acid amplification tests are the only tests available for obtaining HIV viral load, but these tests are expensive, labor-intensive, and require the use of a laboratory. The goal of my project is to develop a decentralized point-of-care HIV viral load test that is cost-effective, robust, and user friendly. This goal will be accomplished by passively isolating serum from whole blood through a capillary driven device and optically detecting isolated HIV RNA that has been amplified using DNA nanotechnology.
Michael Bryan
Michael Bryan, M.S.
BSCB Biophysics, Structural & Computational Biology Ph.D. Program

Research Interest: Integration of Silicon Nitride Photonic Microring Resonators for Sensing and Spectrometry to Detect Biologically Relevant Protein Targets
John Cognetti
John Cognetti
BME Biomedical Engineering Ph.D. Program

Research Interest: I am developing new photonic sensor-integrated organ-on-a-chip systems to study disease and injury. Organ-on-a-chip devices are an emerging method to study human physiology and disease, and to test responses to therapeutics. By incorporating sensitive, specific, real-time photonic biosensors, we can determine the mechanism of various diseases and therapies in a way that is more detailed and much cheaper than in extremely heterogeneous in vivo or clinical studies.
Gabrielle Kosoy
Gabrielle Kosoy
BSCB Biophysics, Structural & Computational Biology Ph.D. Program

Research Interest: Using sensor arrays to understand the immune response to flu: The human immune system response to influenza virus is complex and thus not well understood. I am using Arrayed Imaging Reflectometry (AIR) technology to create arrays of flu surface proteins as well as arrays of whole virus to understand the antibody response to antigen presented in a three-dimensional context.
Daniel Steiner
Daniel J Steiner, M.S.
BSCB Biophysics, Structural & Computational Biology Ph.D. Program

Research Interest: Photonic sensors at the Point-of-Care: Diagnostics at the Point-of-Care are of considerable interest to modern healthcare. Taking a multidisciplinary approach using photonic integrated circuits, (microchips that guide light instead of electrons) in a disposable format, I’m working to create an inexpensive sensing platform that quantitatively measures biological targets on disposable substrates.
Elinore Vangraafeiland
Elinore Vangraafeiland
BMB Biochemistry & Molecular Biology Ph.D. Program

Research Interest: Developing methods of targeting programmed ribosomal frameshifting in HIV and SARS-CoV-1
Pengyi Wang
Pengyi Wang
BME Biomedical Engineering Ph.D. Program

Research Interest: Detection of biomolecules and other molecules such as therapeutics, drugs of abuse, and environmental pollutants is important to understanding our health. Devices which are easy to operate yet can provide reliable results for such detection are in huge demand. Current detection methods are either too expensive or complicated, or limited to a small category of molecules. To bridge this gap, my research is focused on platforms for the point-of-care (POC) for multiplexed detection of small molecules and biomarkers (e.g. inflammatory biomarkers).
 
The first platform is expanding applications of Arrayed Imaging Reflectometry (AIR) developed in the Miller lab. AIR has been able to detect small-molecules and larger-molecule protein biomarkers separately in slightly different approaches. By combining the two approaches together, AIR can perform small-molecule drug and protein biomarker detection at once. The second platform is sorbent polymer-coated Waveguide-Enhanced Raman Spectroscopy (WERS) on a reusable integrated photonic chip. Raman spectroscopy can identify analyte molecules by their unique spectral features and has been studied as a potential diagnostic tool, using the evanescent field to excite and collect the Raman signal of the molecule selectively absorbed by the coated polymer of the waveguide. The tiny size and low power requirement makes WERS ideal for POC, and selective signal enhancement increases its sensitivity.