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PHY3323 / Spr10

PHY7097 / Fall10

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Office:
2362 New Physics Bldg.

Lab:
1012 New Physics Bldg.

Contact:
University of Florida
P.O. Box 118440
Gainesville FL 32611-8440

tel. 352-392-4716
fax 352-392-7709
email:

Office hours
Spring 2011: (sabbatical)
Fall 2011: TBA

Hagen Laboratory Research

In our laboratory we study the dynamics of biological systems. Areas of interest include protein conformational dynamics and folding, which we have studied using time-resolved laser fluorescence and absorption spectroscopy. More recently we have been studying dynamics of gene regulatory systems. We are particularly interested in the dynamics of bacterial quorum sensing. Quorum sensing is a mechanism by which bacteria communicate with each other and detect their own population density through the exchange of chemical signals. We are using microfluidic devices to control and manipulate bacterial environments so that we can study the ways that bacteria use quorum sensing to probe and respond to their local environment. The diagram at upper left is a rough schematic of the quorum sensing gene regulatory network of Vibrio fischeri, a bioluminescent (light-emitting) marine bacterium that lives in symbiosis with several fish and squid species. This network controls the luminescence output of the bacterium, in response to levels of chemical signals (red symbols) received from other bacteria. The microscopy images show individual V.fischeri cells as illuminated by an external light source (Dark Field, left) and by their own natural luminescent emission (Luminescence,right).

Graduate Students | Undergraduates | Equipment | Contact

Graduate Students

• Minjun Son | PhD in progress | Microfluidic devices for studying genetic competence in Streptococcus mutans| Publications

• Gabriel Dilanji | PhD in progress | Autoinducer signalling and diffusion in Sinorhizobia | Publications

• Jessica Langebrake | PhD 2013 (Mathematics and Physics) | Reaction Diffusion Equations in Biological Systems: Marine Protected Areas and Quorum Sensing | Publications

• Pablo Delfino Pérez | PhD 2011 | Stochasticity in Quorum Sensing: lux Expression in Vibrio fischeri at the Single Cell Level | Publications



• Ranjani Narayanan | PhD 2009 | Title: Time-Resolved Laser Spectroscopic Studies of Rate-Limiting Events in Protein Folding and Binding | Publications

• Omjoy K. Ganesh | PhD 2008 | Title: Intrinsic Disorder In Proteins: Folding of the Yeast Proteinase Inhibitor IA3 | Publications

• Dana E. Doucet | MS 2006 | Loop formation in unfolded polypeptides | Publications

• Suzette A. Pabit | PhD 2004 | Title: Fast Dynamics in Protein Folding: Time-Resolved Fluorescence and Absorbance Studies of Polypeptide Reconfigurations | Publications

• Linlin Qiu | PhD 2003| Title: Laser Induced Temperature Jump Investigations of Fast Protein Folding Dynamics| Publications

• Priiyank Shukla | MS 2005 | Laser temperature-jump studies of peptide folding

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• Lab Alumni: Lauren McLeod⁹ | Dylan Billiodeaux | Joel T. Weiss⁸ (BS 2011) | Jonathan H. Young⁷ (BS 2009) | Leslie Pelakh (BS expected 2011) | Juan Jaspe (BS 2006) | Elaine L. Johnson²(BS 2009) | Christian Pecora (REU) | Adam Hunnell⁴ (REU) | Geoff Gordon | Ki Park¹ | Michelle (Planicka) Neeley³ (REU) | Kimberly Ferraro | James E. Crooks| Lawrence Dunn⁵ (REU) | Rachel West¹⁰ (REU) | Caleb Carswell | Erik Sjolander | Melissa R. Sarantos⁶ | Rupika Madhavan² (REU) (BS 2013) | (incomplete listing)
• Notes: 1. MD University of Florida, Fellow in Cardiology; 2. Teach for America; 3. MS 2009, Medical Physics, University of Tennessee; 4. PhD Physics, Case Western Reserve; 5. PhD Physics, University of Texas - Austin; 6. PhD 2006, Biomedical Engineering, UC Davis; 7. Graduate student in applied mathematics, University of Texas - Austin; 8. Currently a PhD student in physics, Cornell University; 9. 2012 Barry M. Goldwater Scholar and currently a PhD student in physics at Cornell University; 10. Economist, Volpe National Transportation Systems Center.

• Nikon TE2000U Inverted Fluorescence Microscope with Coolsnap HQ2 camera - This microscope is enclosed in a temperature- and atmosphere- controlled chamber, which was expertly constructed by the UF Physics Machine Shop.
• Laser Temperature Jump Fluorescence Spectrometer - This instrument allows us to collect complete fluorescence spectra (with UV laser excitation) of a protein following an IR laser temperature jump. Time resolution extends from ~20 ns to ~ 0.1 ms.
• Aviv 202 Circular Dichroism Spectrometer - We do make this machine available to other UF researchers. However we do not have resources to provide extensive user training. If you are already experienced in the use of CD spectrometers and you would like to use this machine, please contact Dr. Hagen directly.
• Optical trap (laser tweezer)