2009 Summer Researchers Participants-HHMI Undergraduate Program - Carnegie Mellon University

2009 HHMI Summer Researchers Participants

Karen Akasaka

Karen Akasaka
Mentor: Dr. Justin Crowley

Development of Visual Cortex

Tiffany Barth

Tiffany Barth
Mentor: Dr. Newell Washburn

Emulsion Polymerization of Hyaluronic Acid

Hyaluronic acid (HA) is a naturally occurring linear polysaccharide that is one of the chief components of the extracellular matrix and connective tissues. A substantial amount of research has been done on modifying HA in order to crosslink the material and produce biocompatible gels. By using a technique called emulsion polymerization, methacrylated hyaluronic acid is polymerized into small microgels that can be used in various applications. The main goal of this project is to create microgels containing moieties capable of deactivating the signaling proteins that cause scarring. Because protein communication is produced by a positive feedback system, a large surface area is required to absorb and deactivate the signals to avoid amplification and scarring. The mechanical properties of the microgels can be tuned depending on the method of purification of the microgels.

Santosh Bhavani

Santosh Bhavani
Mentor: Dr. Robert Murphy

Automated Learning of Generative Models for Protein Subcellular Locations

The overarching goal of proteomics is the comprehensive study of protein subcellular locations. Although there exist methods for identifying protein subcellular location groups, there is no effective model that conveys how these location patterns interact within the cell. We will develop a generative model for 3-dimensional images of protein subcellular location patterns. This model is expected to not only represent the subcellular protein localizations, but also generate "virtual" images that exhibit statistically similar location patterns as the actual data. The data is carefully classified 3-dimensional image stacks (a set of 2D images representing cross sections along the z-axis) of both HeLa and NIH 3T3 cells. A good model must be able to capture cell to cell variation of similar protein location patterns. This poses a very important issue: The variation must be reflected in the image preprocessing stage in order to have a feasible data set for the generative model. For this summer's work, we want to determine and execute the necessary preprocessing methods for the generative model. The preprocessing stage is needed to reduce possible bias introduced by imaging hardware. Unlike 2D image analysis, in 3D image analysis we are not choosing the best planar cross section but rather constructing the best 3D image stack. Hence, in addition to 2D image processing techniques, the images must first be improved to account for the variation in light intensity and texture along the stack. Then, by choosing proper intermediate forms from the deformation path in the stack we can interpolate along the z-axis. Deconvolution and level set method have been used for these purposes. Other preprocessing techniques include denoising, intensity equalization, thresholding and active contour techniques.

Katherine Chen

Katherine Chen
Mentor: Dr. Peter Berget

Site Directed Cysteine Mutagenesis in Single Chain Variable Fragment K7-DIR

Alyssa Chinen

Alyssa Chinen
Mentor: Dr. Bruce Armitage

Selection of a Human Single-Chain Variable Fragment Antibody to Bind to and Activate the Fluorogenic Dye TO1-2p-Cy5

One method of fluorescent biomolecule detection is based on the development of fluorophores. In this approach, fluorogenic dyes that do not fluoresce when free in solution bind to a human single-chain variable fragment antibody (scFv) and become fluorescent. Currently, most fluoromodules utilize dyes with one chromophore and emit light at a wavelength similar to their maximum excitation wavelength. While these systems have found many uses in biological imaging, they are not always optimal choices because auto-fluorescent cells increase the ratio of background noise to signal. The bichromophoric dye TO1-2p-Cy5 utilizes Fluorescence Resonance Energy Transfer (FRET) to shift the emission wavelength more than 100 nm from the excitation wavelength. Selection of an scFv that binds to and activates TO1-2p-Cy5 is necessary to complete the fluoromodule for use in fluorescent imaging. Starting with a library of yeast cells expressing scFvs known to bind to the TO1 component of the dye, Fluorescence Activated Cell Sorting (FACS) was used to select only cells that emitted strong TO1-2p-Cy5 signal for growth. Following five rounds of FACS sorting, the population of cells expressing scFvs that bound and activated TO1-2p-Cy5 was greatly enriched.  Individual cells were sorted onto an induction plate for growth and each clone was picked and added to a solution containing TO1-2p-Cy5.  The six individual clones that emitted the brightest TO1-2p-Cy5 signal were chosen to be analyzed using Flow Cytometry. From this, five of the six clones were selected for sequencing. These clones will be analyzed further, but hopefully they may be used in a fluoromodule containing TO1-2p-Cy5.

Sruthi Reddy Chintakunta

Sruthi Reddy Chintakunta
Mentor: Dr. Justin Crowley

Computational Neuroscience

Danica Chiu

Danica Chiu
Mentor: Dr. Talal El-Hefnawy

Endocrine Disruptors in the Envirnonment and the Effects on Cancer

No Picture Available

Jason Cho
Mentor: Dr. Jeffrey Hollinger

Bone Morphogenesis Protein 2

Suhl A Choi

Suhl A Choi
Mentor: Dr. Mark Bier

Atmospheric Thermal Dissociation of Protein

William Chow

William Chow
Mentor: Dr. Frank Jenkins

Hormonal Regulation of Viral Gene Transcription

Ju Ah Chung

Ju Ah Chung
Mentor: Dr. Linda Peteanu

The Fluorescence Properties of Dye-DNA

Phillip Cynn

Phillip Cynn
Mentor: Dr. Rongchao Jin

Reversible Switching of Magnetism in Thiolate-Protected Au25 Superatoms

Jeffrey Dahlen

Jeffrey Dahlen

Morphological Analysis of Activity Reduced Adult Born Neurons in the Mouse Main Olfactory Bulb

Neurogenesis is the process through which new neurons (adult-born neurons) originate in the subventricular zone and migrate along the rostral migratory stream until they reach their final destination in the main olfactory bulb (MOB). These Adult-Born Neurons (ABNs) in the MOB mature morphologically and physiologically within four weeks after arriving at their target layer. Previous work from our lab has shown that activity modulates the survival of ABNs in the MOB through a competitive process. We hypothesize that a reduction in activity during the critical period of development for these ABNs will adversely affect their ability to integrate into mature circuits. To test this, we have injected mice with control GFP-encoding lentivirus, or a lentivirus encoding GFP-siRNA construct that reduces expression of sodium channels. Utilizing this injected siRNA construct as well as unilateral nares occlusion provides for both intrinsic (siRNA knockdown) and circuit level (unilateral nares occlusion) reduction in activity. We are now measuring the ability of these ABNs to integrate into mature circuits by creating three dimensional reconstructions of the dendritic trees of the virus-labeled ABNs. Using these reconstructions we will compare various aspects of neuron size, spine densities and localization within the MOB in both the control and activity reduced neurons. Through these analyses, we hope to obtain a working knowledge of the mechanisms affecting how adult born neurons integrate into mature circuits; where by understanding these mechanisms, we will come closer to future applications of neural stem cells in therapeutic procedures.

Nicole Dangelo

Nicole Dangelo
Mentor: Dr. Newell Washburn

Cytokine – Neutralizing Gels for Local Control of Inflammation

There are three stages of wound healing: inflammation, proliferation, and remodeling which the body must go through when trying to heal breaks in the skin. The longer a wound stays in the inflammation phase the more scar tissue is formed. The severity and length of inflammation is controlled through various factors that are produced when a wound is detected by the body. One of the important factors produced are cytokines, some of which promote inflammation and others that inhibit it. Tumor necrosis factor-alpha (TNFA) is a cytokine that promotes inflammation. Several peptides have been found which bind to TNFA and prevent the expression which in turn reduces inflammation. However, by adding a photocaging group to one of the amino acids, the binding of the peptide to the cytokine can be prevented, allowing inflammation to proceed. But with the addition of UV light, the photocaging group is removed from the peptide. Without the photocaging group to prevent binding, the peptide will readily bind to the cytokine, inhibiting inflammation and allowing the healing process to proceed. The addition of the photocaging group will allow careful control of the inflammatory factor TNFA which will reduce the formation of scar tissue and promote the healing process.

Aimee DeLuca

Aimee DeLuca
Mentor: Dr. Stefan Zappe

Isolation of Cardiac Stem Cells

Avanti Deshpande

Avanti Deshpande
Mentor: Dr. Catalina Achim

Biomimetic Approach for Directional Charge Transfer via Inorganic Hybrid Peptide Nucleic Acid Molecules

Lynley Doonan

Lynley Doonan
Mentor: Dr. John Woolford

Using Synthetic Lethal Screens to Determine the Function of Yeast Ribosome Assembly Factor Drs1

Alexander Edelman

Alexander Edelman
Mentor: Dr. Tomek Kowalewski

Novel Techniques for Printed Electronics: Organic and Inorganic Components

Conducting polymers offer a promising path to the development of inexpensive electrical devices for a variety of applications including printed electronics and biochemical sensors. The majority of conducting polymer-based sensors have been based on the measurement of change in resistance in response to a stimulus. More recent results indicate that the response of a conducting polymer to a stimulus can be measured with greater accuracy in field-effect transistor (FET) devices, where conductivity of the active polymer is modulated by the electric field produced by an insulated gate. Traditional organic-FET (OFET) devices rely on silicon wafer photolithography and low-throughput polymer deposition techniques. This project was focused on the development of a novel procedure for constructing micro-scale OFETs entirely by solution deposition of BOTH metal electrodes and conducting polymers using a computer-controlled micropositioning system and micropipettes used in the patch-clamp technique. Metal electrodes were drawn using novel non-nanoparticle-based precursor “inks”, currently under development by the McCullough Group at Carnegie Mellon. Resistance measurements of such deposited films as a function of temperature revealed they can be metalized at relatively low temperatures (~120ºC), which is essential for integration with conducting polymers. Tapping mode atomic force microscopy (AFM) confirmed that such fabricated metallic electrodes are smooth and uniform. This deposition system was also used to deposit the semiconducting regioregular-poly(3-hexylthiophene) (rr-P3HT) between the electrodes, yielding films which, based on AFM imaging, were free of nanofibrillar structures observed in rr-P3HTs deposited using conventional methods. Importantly, charge mobilities measured for OFETS with conventional metal electrodes and active layers deposited with this technique approached those measured for conventional devices. Also investigated was the sealing of freshly fabricated OFETs against oxidation using water-based correction fluid to prevent degradation of the polymer, allowing the devices to remain functional outside of vacuum. The efficacy of the micropipette-based deposition technique developed in this study suggests the feasibility of fully printable organic electronic devices.

Rachel Ehrlich

Rachel Ehrlich
Mentor: Dr. A. Javier Lopez

Biological Function of Recursive Splicing in the Frizzled-1 Wnt Receptor of Drosophila

No Picture Available

Xochina El Hilali
Mentor: Dr. Subha Das

Chemo-genetic Analysis of the Hepatitis Delta Virus Ribozyme

Adam Foote

Adam Foote
Mentor: Dr. Adam Linstedt

Crystallization of the Active Site of the GRASP55 protein

Zachary Frenchek

Zachary Frenchek

In vivo Protein Phosphatase Activity in Association with Biodirectional Synaptic  Plasticity in the Hippocampus

No Picture Available

Katherine Fu
Mentor: Dr. Kausik Chakrabarti

Characterization of Telomerase RNA Template Sequence in Human Pathogen Plasmodium falciparum

Mark Holfelder

Mark Holfelder
Mentor: Dr. David Yaron

Semiempirical, Subsystem-based Methods for High-accuracy Electronic Structure Calculations

No Picture Available

Paul Jasinto
Mentor: Dr. Subha Das

Analysis of the Photolytic Deprotection of Caged Nucleic Acids

Natalya Khanina

Natalya Khanina
Mentor: Dr. Terrence Collins

Degradation of Sertraline Using Fe-TAML and Hydrogen Peroxide

Cyrus Larijani

Cyrus Larijani

Proteomics of Eye-specific Channels in the Developing Visual System

Shih-dun Liu

Shih-dun Liu
Mentor: Dr. Justin Crowley

Dendritic Spine Plasticity

Evan Lloyd

Evan Lloyd
Mentor: Dr. Terrence Collins

A Green Chemistry Approach to the Selective Oxidation of Sulfides

Donald Mignogna

Donald Mignogna
Mentor: Dr. Mark Macbeth

dADAR Activity

Bassem Mikhael

Bassem Mikhael
Mentor: Dr. John Kirkwood

Phase III Randomized Study of Four Weeks High Dose IFN-alpha2b in Stage T2bN0, T3a-bN0, T4a-bN0 and T1-4, N1a, 2a (microscopic) Melanoma

Jacob Mohin

Jacob Mohin
Mentor: Dr. Tomasz Kowalewski

Novel Techniques for Printed Electronics: Organic and Inorganic Components

Conducting polymers offer a promising path to the development of inexpensive electrical devices for a variety of applications including printed electronics and biochemical sensors. The majority of conducting polymer-based sensors have been based on the measurement of change in resistance in response to a stimulus. More recent results indicate that the response of a conducting polymer to a stimulus can be measured with greater accuracy in field-effect transistor (FET) devices, where conductivity of the active polymer is modulated by the electric field produced by an insulated gate. Traditional organic-FET (OFET) devices rely on silicon wafer photolithography and low-throughput polymer deposition techniques. This project was focused on the development of a novel procedure for constructing micro-scale OFETs entirely by solution deposition of BOTH metal electrodes and conducting polymers using a computer-controlled micropositioning system and micropipettes used in the patch-clamp technique. Metal electrodes were drawn using novel non-nanoparticle-based precursor “inks”, currently under development by the McCullough Group at Carnegie Mellon. Resistance measurements of such deposited films as a function of temperature revealed they can be metalized at relatively low temperatures (~120ºC), which is essential for integration with conducting polymers. Tapping mode atomic force microscopy (AFM) confirmed that such fabricated metallic electrodes are smooth and uniform. This deposition system was also used to deposit the semiconducting regioregular-poly(3-hexylthiophene) (rr-P3HT) between the electrodes, yielding films which, based on AFM imaging, were free of nanofibrillar structures observed in rr-P3HTs deposited using conventional methods. Importantly, charge mobilities measured for OFETS with conventional metal electrodes and active layers deposited with this technique approached those measured for conventional devices. Also investigated was the sealing of freshly fabricated OFETs against oxidation using water-based correction fluid to prevent degradation of the polymer, allowing the devices to remain functional outside of vacuum. The efficacy of the micropipette-based deposition technique developed in this study suggests the feasibility of fully printable organic electronic devices.

No Picture Available

Young Hyun Noh
Mentor: Dr. Catalina Achim

Study of the Effect of Metal Ion Incorporation on Ligand-Containing Peptide Nucleic Acid

Frank Olechnowicz

Frank Olechnowicz
Mentor: Dr. Catalina Achim

Thermodynamics of Peptide Nucleic Acid Bonding

Anna Park

Anna Park
Mentor: Dr. John Woolford

The Assembly Pathway of Protein Drs1

Joshua Patent

Joshua Patent
Mentor: Dr. Terry Collins

TAML Catalyst Breakdown Analysis

Mina Pi

Mina Pi
Mentor: Dr. Nader Shaikh

Cochrane Review: Decongestants, Antihistamines, and Nasal Irrigation for Acute Sinusitis in Children

David Plotkin

David Plotkin
Mentor: Dr. John Rawlins

Description of a New Taxa of the Genus Nedra

Sang Ah Roh

Sang Ah Roh
Mentor: Dr. A. Javier Lopez

Alternative Splicing Mechanism in Dopamine D3 Receptor (DRD3) Pre-mRNA

Riddhi Roy

Riddhi Roy
Mentor: Dr. Terry Collins

Heterogenization of TAMLs

Orr Rozov

Orr Rozov
Mentor: Dr. Brooke McCartney

Microtubule Dynamics at the Cortex of Syncytial Drosophila Embryos

No Picture Available

Judith Savitskaya

Alternative Splicing of DRD3

Howard Soh

Howard Soh
Mentor: Dr. Preet Chaudhary

Characterization of K13-NEMO Interaction

Akanksha Vaidya

Akanksha Vaidya
Mentor: Dr. Alison Barth

Investigation of a Novel Splice Variant of the BKβ4 Protein

Swati Varshney

Swati Varshney

Emitting Polyfluorenes with Peptide and Nucleic Acid Linkages for Application in Polymer Light-Emitting Diodes

Shriya Venkatesh

Shriya Venkatesh
Mentor: Dr. Brooke McCartney

The Effect of Anti-Cancer Therapies on the Metastatic Index of Ductal Breast Cancer Cells

Yuriy Zubovski

Yuriy Zubovski
Mentor: Dr. Stephanie Tristram-Nagle

Effects of the Bioflavonoids Genistein and Daidzein on Interactions and Properties of Lipid Membranes

Phospholipids form lipid bilayers which are the underlying structure of every plant and animal cell membrane. In this work we studied two phosphatidylcholine lipids, DOPC (diC18:1PC) and diC22:1PC, which differ in bilayer thickness by 7Å. Both lipids were x-rayed using synchrotron radiation at CHESS (Cornell) with varying concentrations of bioflavonoids. In addition to a specific interaction with estrogen receptors, it was shown that genistein, but not daidzein, dramatically increases ion channel lifetimes and rates of formation (Biochemistry 42:13646 (2003)) especially when there is a hydrophobic mismatch between the membrane and the channel. In that work it was suggested that genistein alters the bending modulus of lipid membranes. By using liquid-crystal theory analysis in the Nagle Lab, I determined the bending modulus, Kc, and the compressibility modulus, B, for both lipids as a function of concentration of bioflavonoid. Although there was little change in Kc with genistein for DOPC, there was a factor of ~2 decrease in Kc for diC22:1PC. Daidzein on the other hand had almost no effect on Kc for either lipid. We interpret these results to support the idea that genistein affects ion channels by softening a stiffer bilayer, thus overcoming a hydrophobic mismatch.