Research Highlights 2013

Welcome to the RIT College of Science Research Highlights page. The goal of this page is to highlight some of the college's faculty-student research projects.

 Thomas H. Gosnell School of Life Sciences

 

Discovery of novel compounds that possess antibiotic properties

Faculty Advisor: André O. Hudson, Thomas H. Gosnell of Life Sciences

Student Researchers: Alexander Triassi, Biotechnology and Molecular Bioscience,

Matthew Wheatley, Biotechnology and Molecular Bioscience

Links: Faculty Website: http://people.rit.edu/aohsbi/

Manuscript Link: http://www.sciencedirect.com/science/article/pii/S0968089613009292

The identification of novel targets for the discovery and or development of new antibiotics is a bottleneck in the scientific community. Here we identified a novel target by showing the identification of 5 compounds that inhibit the enzyme diaminopimelate aminotransferase (DapL) involved in the synthesis of bacterial cell wall and the proteogenic amino acid lysine. The work was facilitated through a high throughput inhibition screen using a compound library.  Each inhibitor is derived from one of four classes with different central structural moieties:  a hydrazide, a rhodanine, a barbiturate, or a thiobarbiturate. This study provides important information to expand our current understanding of the structure/activity relationship of DapL and putative inhibitors that are potentially useful for the design and or discovery of novel biocides. The study was collaboration between the Hudson lab at RIT, the Vederas lab at the University of Alberta, Canada, and The Dobson lab at the University of Canterbury, New Zealand. The work was funded by an NSF and a COS DRIG award to the Hudson Lab.

Submission Date: November 15, 2013

 

School of Chemistry and Materials Science

 

 Fluoride Ions at the Cu-Fluoropolymer Interface

 

 A. Naujokas*, D. G. Abreu*, G. A. Takacs#, T. Debies, M. Mehan and A. Entenberg#
*RIT Students; #Faculty Advisors

The desire to achieve faster circuit speeds and reduced signal interconnect delay times in the packaging of microelectronic devices has led to the examination of low-dielectric constant Teflon® substrates such as poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP)and poly(tetrafluoroethylene-co-perfluoropropyl vinyl ether) (PFA).

In the present investigation, X-ray photoelectron spectroscopy (XPS) was used to analyze the interface of Teflon® samples deposited with Cu produced from evaporation and two different sputtering instruments. While XPS studies are usually with a fixed take-off angle between the sample and the analyzer, by varying the take-off angle, angle-resolved XPS provides a non-destructive in-depth profile of the fluoride ion within the top 2–10 nm of the thin Cu film deposited on the fluoropolymers. In-situ argon ion etching was then used to expose the fluoride ions and ex-situ evaporated Cu was deposited on the exposed fluoride surface to test for adhesion improvement.

For the Cu-treated FEP and PFA samples, the F 1s spectra, e.g., see the above Figure, show two definite peaks at binding energies of about 688.5 and 684 eV arising from the fluoropolymer and fluoride ion bonded to copper, respectively, while the cleaned, untreated  samples have only the fluoropolymer peak. The sputtered Cu atoms arrive at the FEP and PFA surfaces with sufficient energy to cause surface reactions to produce fluoride ions in contrast to Cu evaporation experiments where the F 1s spectra are nearly identical to the cleaned fluoropolymer samples.

Surface and Interface Analysis 45(6), 1056-1062 (2013).

Submission Date: September 30, 2013

School of Chemistry and Materials Science

  

Targeted Molecular Imaging Agents for Detection of Cancer

 Targeted Molecular Imaging Agents for Detection of Cancer

Faculty Advisor: Hans Schmitthenner, Chemistry and Imaging Research Scientist, CIS and SCMS, College of Science.

Student Researchers: Taylor Barrett, Stephanie Beach, Chelsea Wiedman, Lauren Heese, Kevin Kirk, Michael Regan (SCMS), Sean Aronow, Sarah Wang, Dylan Weil (SOLS).

The goal of our research program is to provide versatile, easy-to-use methodology to synthesize single and multi-modal imaging agents for the early detection and diagnosis of cancer.   We have discovered a new means of introducing gadolinium, a contrast agent for molecular resonance imaging (MRI), and for bonding near infrared dyes (NIR) for use in confocal fluorescent microscopy (CFM) and photoacoustic imaging (PAI) onto a peptide template.  These pre-formed single or dual MR and NIR agents are conjugated to targeting agents enabling selective illumination of diseased tissues. In the example shown below students cultured, stained and imaged human cancer cells in-vitro by CFM.  Targeted dual modal agents for PA-MR are currently being synthesized to target other types of cancer.   

Submission Date: September 30, 2013

Chester F. Carlson Center for Imaging Science

 

Remote Sensing Phenomenology of Glacial Scenes

Faculty Advisor: John Kerekes, Professor of Imaging Science
Student Researcher: Kimberly Horan, Imaging Science M.S. Student
Link: http://dirs.cis.rit.edu

The monitoring of polar ice sheets has become a critical component in assessing climate change. Remote sensing satellites and aircraft using a variety of technologies are routinely gathering data over these areas. While tools exist to analyze these data to a reasonable accuracy, there is increasing demand for more accurate monitoring of glacier extent and ice elevation. The best way to achieve these high accuracies is to combine data from the multiple sources available. This project explored the combined use of Landsat optical imagery and Radarsat-2 synthetic aperture radar (SAR) imagery, together with airborne photon-counting lidar data. The image above shows a Radarsat SAR image of the Jakobshavn glacier in Greenland with the various tones indicating the proportion of backscattered radar energy. This research explored the relationships between data measured by the different sensors and the type of snow and ice surfaces sensed to advance our scientific understanding of remote sensing of glaciers. This work will support the interpretation of lidar data to be collected by the upcoming NASA ICESat-2 mission, together with other data sources available.

Submission Date: September 12, 2013

  

 Thomas H. Gosnell School of Life Sciences

 

Amino acid metabolism as a putative target for antibiotic development


Verrucomicrobium spinosum
magnified 25,000 times using scanning electron microscopy

André O. Hudson and Michael A. Savka, Thomas H. Gosnell School of Life Sciences
Sean McGroty (Undergraduate Student-Bioinformatics)
Dhivya Pattaniyil (Undergraduate -Biochemistry)

Hudson Lab Webpage
Link to manuscript

In most bacteria, the proteogenic amino acid lysine (lys) is synthesized using the intermediate diaminopimelate (DAP). Lysine and DAP are cross-linking amino acids in the cell wall of Gram-positive and Gram-negative bacteria respectively. The incorporation of lys and DAP is facilitated by the enzyme MurE (DAP-ligase). Using the bacterium Verrucomicrobium spinosum as a model system, we show that the bacterium utilizes DAP as the intermediate for both cell wall and protein synthesis. As such, the enzymes involved in these pathways are attractive targets for the development and or discovery of novel antibiotics.

Submission Date: June 18, 2013

School of Physics & Astronomy

New proposal for realizing torsional optomechanics

 Shi

Faculty Advisor: Mishkat Bhattacharya, School of Physics & Astronomy

Student Researcher: Hao Shi, Physics

Link to paper

Description: Optomechanics is a rapidly growing field that deals with the interaction between optics and mechanical motion, and is aimed at realizing next generation sensing technologies. We proposed a new design for a nanomechanical rotation sensor: an optically trapped windmill-shaped dielectric interacting with Laguerre–Gaussian cavity modes containing both angular and radial nodes. As an improvement on existing schemes, our proposal can couple the dielectric to the, in principle, unlimited photon angular momentum, allowing for better rotation sensitivity.

H. Shi and M. Bhattacharya, “Coupling a small torsional oscillator to large optical angular momentum”, Journal of Modern Optics, 60, 5 (2013).

Submission Date: June 10, 2013

 Thomas H. Gosnell School of Life Sciences

Observing fluorescent probes in living cells using a low cost UV LED flashlight retrofitted to a common vintage light microscope

 Babbitt

 Gregory. A. Babbitt 1*, Cheryl. A. Hanzlik 1,2*  and Katelyn. N. Busse 3*.
1. T.H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY
2. Confocal Microscopy Lab, College of Science, Rochester Institute of Technology, Rochester NY
3. Biomedical Engineering, Kate Gleason College of Engineering, Rochester Institute of Technology, Rochester NY

While the application of molecular biological techniques based upon fluorescent probes has rapidly expanded over recent decades, the equipment cost of fluorescent microscopy has largely prevented its adoption in the college and high school classroom. We offer a simple solution to this problem by describing in detail how to build with simple tools, a fluorescent microscope using a common brand of LED flashlight and second-hand components of vintage Nikon microscopes. This extremely low cost solution is qualitatively compared to an expensive modern Leica system.

Submission Date: June 10, 2013

School of Physics and Astronomy

comet Pan-STARRS

 

Photo Data: 17 March, 8:30pm.
4 second exposure, ISO 800,  f/4.5,  100mm lens, Canon 5D II
Photographer:  Grover Swartzlander,
Location: Cobb's Hill Park, Rochester, New York.

 

The comet becomes visible only a short time after sunset.  The sky has to get dark enough, plus the comet is low in the sky and can be lost in the glare of light pollution and atmospheric scattering.  Look about 30-40 minutes after sunset toward the western horizon just a little north of where the sun had set (see guide).  Your eyes may have to dark adapt a little, but you should be able to see it if the sky is clear. Binoculars help.  You may only have about 10-15 minutes of viewing before the comet sets too low in the sky.

Submission Date: March 18, 2013

Chester F. Carlson Center for Imaging Science

Innovative optics for the direct imaging of exoplanets


Faculty Advisor:Grover A. Swartzlander, Jr., Center for Imaging Science and Department of Physics

Student Researcher: Garreth J. Ruane, PhD student, Imaging Science

http://www.rit.edu/cos/optics-rit

An earth-like exoplanet is typically one billion times dimmer than its host star and is separated by a very small angle (similar to the width of mosquito at 36,000 ft!).  Instruments designed to image such exoplanets require extreme high contrast and resolution capability.  The Optical Vortex Coronagraph (OVC) is an elegant solution that blocks starlight without sacrificing light from a nearby exoplanet using a vortex-phase filtering technique.  The Optical Vortex Laboratory in the Center for Imaging Science is working to advance vortex-phase filtering concepts.  An elliptical design of the OVC was recently published in the journal Applied Optics.

Garreth J. Ruane and Grover A. Swartzlander, "Optical vortex coronagraphy with an elliptical aperture," Appl. Opt. 52, 171-176 (2013) 
Link to paper:  http://www.opticsinfobase.org/ao/abstract.cfm?URI=ao-52-2-171

Submission Date: Jan 15, 2013

Chester F. Carlson Center for Imaging Science

Simulation of Individual Human Spectral Sensitivities for Improved Colorimetry

Mark Fairchild

Faculty Advisor: Mark Fairchild, Associate Dean of Research and Graduate Education, Professor of Color and Imaging Sciences

Student Researchers: Rodney Heckaman, Post-Doctoral Fellow, Yuta Asano, Color Science Ph.D. Student, Alex Pagliaro, Color Science M.S. Student

Link:http://www.cis.rit.edu/fairchild/

The average spectral sensitivity to light of the human visual system represents fundamental data required for the practice of colorimetry (the measurement of color) in a wide variety of applications. Unfortunately each observer does not perfectly match these mean data and sometimes it is helpful to understand individual variation in color response. Our aim is to better understand individual variations in color vision through Monte Carlo simulation. Observer variability falls into three major categories: (1) the amount of macular pigmentation which is essentially random, (2) the absorption and scattering of the lens which increases with age, and (3) the spectral absorption characteristics of the cone photoreceptors that can be tied to genetic variations. By modeling these three sources of variation using the demographics and genetics of a typical population, individual observers are simulated. The accompanying figure illustrates the color response for 24 distinct stimuli and 1000 different observers. The fact that the clouds overlap shows that one of the color patches for a given observer might look like a completely different patch for another. This work continues with model refinement and experimental verification.

Submission Date: Jan 9, 2013

 

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