Stephen J Hagen

Stephen J Hagen,

Professor

Department: LS-PHYSICS-GENERAL
Business Phone: (352) 392-4716
Business Email: sjhagen@ufl.edu

Teaching Profile

Courses Taught
2020-2021
PHY3101 Introduction to Modern Physics
2019-2020
PHY2048 Physics with Calculus 1
2011-2013,2017-2019
PHY3513 Thermal Physics 1
2018,2022
PHY4911 Undergraduate Research in Physics
2007-2012,2018
PHY6905 Individual Work
2010-2012,2018
PHY6910 Supervised Research
2010,2018
PHY7979 Advanced Research
2009-2013,2018
PHY7980 Research for Doctoral Dissertation
2017-2018
GMS6070 Sensory and Motor Systems
2012-2018
PHZ4710 Introduction to Biological Physics
2016
IDH3931 Interdisciplinary Junior Honors
2014-2016
PHY3221 Mechanics 1
2009,2012
PHY4905 Individual Work
2010-2012
PHY5905 Individual Work
2010
PHY7097 Advanced Topics in Theoretical Physics
2008-2010
PHY3323 Electromagnetism 1
2008-2009
PHY2064L Accelerated Physics with Calculus Laboratory
2009
IDH4905 Individual Work
2007,2009
PHY3400 Light, Color and Holography
2006-2007
PHY4523 Statistical Physics

Research Profile

Open Researcher and Contributor ID (ORCID)

0000-0002-3373-5033

Publications

2022
Amyloid Aggregates Are Localized to the Nonadherent Detached Fraction of Aging Streptococcus mutans Biofilms
Microbiology Spectrum. 10(4) [DOI] 10.1128/spectrum.01661-22. [PMID] 35950854.
2021
Dimension-reduction simplifies the analysis of signal crosstalk in a bacterial quorum sensing pathway.
Scientific reports. 11(1) [DOI] 10.1038/s41598-021-99169-0. [PMID] 34611201.
2021
Wavelike propagation of quorum activation through a spatially distributed bacterial population under natural regulation
Physical Biology. 18(4) [DOI] 10.1088/1478-3975/ac02ac.
2020
Enhanced purification coupled with biophysical analyses shows cross-β structure as a core building block for Streptococcus mutans functional amyloids.
Scientific reports. 10(1) [DOI] 10.1038/s41598-020-62115-7. [PMID] 32198417.
2020
Environmental Triggers of lrgA Expression in Streptococcus mutans.
Frontiers in microbiology. 11 [DOI] 10.3389/fmicb.2020.00018. [PMID] 32047487.
2020
Spatial Correlations and Distribution of Competence Gene Expression in Biofilms of Streptococcus mutans.
Frontiers in microbiology. 11 [DOI] 10.3389/fmicb.2020.627992. [PMID] 33510740.
2020
Spatially propagating activation of quorum sensing in Vibrio fischeri and the transition to low population density
Physical Review E. 101(6) [DOI] 10.1103/physreve.101.062421.
2020
Spatially propagating activation of quorum sensing in Vibrio fischeri and the transition to low population density
Physical Review E. 101(6) [DOI] 10.1103/physreve.101.062421.
2019
Carbohydrate and PepO control bimodality in competence development by Streptococcus mutans
Molecular Microbiology. 112(5):1388-1402 [DOI] 10.1111/mmi.14367. [PMID] 31403729.
2019
Characterization of LrgAB as a stationary phase-specific pyruvate uptake system in Streptococcus mutans.
BMC microbiology. 19(1) [DOI] 10.1186/s12866-019-1600-x. [PMID] 31606034.
2019
Erratum for Underhill et al., “Intracellular Signaling by the comRS System in Streptococcus mutans Genetic Competence”
mSphere. 4(1) [DOI] 10.1128/msphere.00042-19.
2019
Erratum for Underhill et al., “Intracellular Signaling by the comRS System in Streptococcus mutans Genetic Competence”
mSphere. 4(1) [DOI] 10.1128/msphere.00042-19.
2018
Genome-Wide Screens Reveal New Gene Products That Influence Genetic Competence in Streptococcus mutans
Journal of Bacteriology. 200(2) [DOI] 10.1128/jb.00508-17.
2018
Intracellular Signaling by the comRS System in Streptococcus mutans Genetic Competence
mSphere. 3(5) [DOI] 10.1128/msphere.00444-18.
2018
Intracellular Signaling by thecomRSSystem inStreptococcus mutansGenetic Competence
mSphere. 3(5) [DOI] 10.1128/msphere.00444-18.
2018
The quantitative measure and statistical distribution of fame
PLOS ONE. 13(7) [DOI] 10.1371/journal.pone.0200196. [PMID] 29979792.
2018
Threshold regulation and stochasticity from the MecA/ClpCP proteolytic system inStreptococcus mutanscompetence
Molecular Microbiology. 110(6):914-930 [DOI] 10.1111/mmi.13992. [PMID] 29873131.
2017
Genome-Wide Screens Reveal New Gene Products That Influence Genetic Competence in Streptococcus mutans
Journal of Bacteriology. 200(2) [DOI] 10.1128/jb.00508-17.
2017
Intercellular Communication via the comX -Inducing Peptide (XIP) of Streptococcus mutans
Journal of Bacteriology. 199(21) [DOI] 10.1128/jb.00404-17.
2017
Intercellular Communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans
Journal of Bacteriology. 199(21) [DOI] 10.1128/jb.00404-17.
2017
Origins of Heterogeneity in Streptococcus Mutans Competence: Interpreting An Environment-Sensitive Signaling Pathway
Physical Biology. 14(1) [DOI] 10.1088/1478-3975/aa546c. [PMID] 28129205.
2017
Oxidative Stressors Modify the Response of Streptococcus mutans to Its Competence Signal Peptides
Applied and Environmental Microbiology. 83(22) [DOI] 10.1128/aem.01345-17.
2017
Oxidative Stressors Modify the Response of Streptococcus mutans to Its Competence Signal Peptides
Applied and Environmental Microbiology. 83(22) [DOI] 10.1128/aem.01345-17.
2016
Effects of Carbohydrate Source on Genetic Competence in Streptococcus mutans
Applied and Environmental Microbiology. 82(15):4821-4834 [DOI] 10.1128/aem.01205-16.
2016
Effects of Carbohydrate Source on Genetic Competence in Streptococcus mutans
Applied and Environmental Microbiology. 82(15):4821-4834 [DOI] 10.1128/aem.01205-16.
2015
Bidirectional signaling in the competence regulatory pathway of Streptococcus mutans.
FEMS microbiology letters. 362(19) [DOI] 10.1093/femsle/fnv159. [PMID] 26363019.
2015
Modeling Analysis of Signal Sensitivity and Specificity by Vibrio fischeri LuxR Variants.
PloS one. 10(5) [DOI] 10.1371/journal.pone.0126474. [PMID] 25962099.
2015
Sharply Tuned pH Response of Genetic Competence Regulation in Streptococcus mutans: a Microfluidic Study of the Environmental Sensitivity of comX
Applied and Environmental Microbiology. 81(16):5622-5631 [DOI] 10.1128/aem.01421-15.
2015
Sharply Tuned pH Response of Genetic Competence Regulation in Streptococcus mutans: a Microfluidic Study of the Environmental Sensitivity ofcomX
Applied and Environmental Microbiology. 81(16):5622-5631 [DOI] 10.1128/aem.01421-15.
2014
Entropy-driven motility of Sinorhizobium meliloti on a semi-solid surface.
Proceedings. Biological sciences. 281(1784) [DOI] 10.1098/rspb.2013.2575. [PMID] 24741008.
2014
Folding dynamics and pathways of the trp-cage miniproteins.
Biochemistry. 53(38):6011-21 [DOI] 10.1021/bi501021r. [PMID] 25184759.
2014
Predicting pre-Columbian anthropogenic soils in Amazonia.
Proceedings. Biological sciences. 281(1777) [DOI] 10.1098/rspb.2013.2475. [PMID] 24403329.
2014
Traveling waves in response to a diffusing quorum sensing signal in spatially-extended bacterial colonies
Journal of Theoretical Biology. 363:53-61 [DOI] 10.1016/j.jtbi.2014.07.033.
2013
Integrating Biological Physics Into the Undergraduate Advanced Laboratory
. 246
2012
Analysis of gene expression levels in individual bacterial cells without image segmentation.
Biochemical and biophysical research communications. 421(3):425-30 [DOI] 10.1016/j.bbrc.2012.03.117. [PMID] 22487793.
2012
Laser temperature-jump spectroscopy of intrinsically disordered proteins.
Methods in molecular biology (Clifton, N.J.). 896:267-81 [DOI] 10.1007/978-1-4614-3704-8_18. [PMID] 22821531.
2012
Microfluidic study of competence regulation in Streptococcus mutans: environmental inputs modulate bimodal and unimodal expression of comX.
Molecular microbiology. 86(2):258-72 [DOI] 10.1111/j.1365-2958.2012.08187.x. [PMID] 22845615.
2012
Quorum activation at a distance: spatiotemporal patterns of gene regulation from diffusion of an autoinducer signal.
Journal of the American Chemical Society. 134(12):5618-26 [DOI] 10.1021/ja211593q. [PMID] 22372494.
2011
Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme.
PLoS computational biology. 7(4) [DOI] 10.1371/journal.pcbi.1001118. [PMID] 21490720.
2011
Noise and crosstalk in two quorum-sensing inputs of Vibrio fischeri.
BMC systems biology. 5 [DOI] 10.1186/1752-0509-5-153. [PMID] 21959018.
2010
Bacterium in a box: sensing of quorum and environment by the LuxI/LuxR gene regulatory circuit.
Journal of biological physics. 36(3):317-27 [DOI] 10.1007/s10867-010-9186-4. [PMID] 21629592.
2010
Exponential Growth of Bacteria: Constant Multiplication Through Division
American Journal of Physics. 78(12):1290-1296 [DOI] 10.1119/1.3483278.
2010
Heterogeneous response to a quorum-sensing signal in the luminescence of individual Vibrio fischeri.
PloS one. 5(11) [DOI] 10.1371/journal.pone.0015473. [PMID] 21103327.
2010
Solvent viscosity and friction in protein folding dynamics.
Current protein & peptide science. 11(5):385-95 [PMID] 20426733.
2009
Solvent friction changes the folding pathway of the tryptophan zipper TZ2.
Journal of molecular biology. 390(3):538-46 [DOI] 10.1016/j.jmb.2009.05.021. [PMID] 19450609.
2008
Kinetics of folding and binding of an intrinsically disordered protein: the inhibitor of yeast aspartic proteinase YPrA.
Journal of the American Chemical Society. 130(34):11477-85 [DOI] 10.1021/ja803221c. [PMID] 18681437.
2007
Kinetics of internal-loop formation in polypeptide chains: a simulation study.
Biophysical journal. 92(7):2281-9 [PMID] 17208979.
2007
Probe-dependent and nonexponential relaxation kinetics: unreliable signatures of downhill protein folding.
Proteins. 68(1):205-17 [PMID] 17387735.
2006
Characterizing the residue level folding of the intrinsically unstructured IA3.
Biochemistry. 45(45):13585-96 [PMID] 17087512.
2006
Do protein molecules unfold in a simple shear flow?
Biophysical journal. 91(9):3415-24 [PMID] 16891374.
2005
Protein folding: defining a “standard” set of experimental conditions and a preliminary kinetic data set of two-state proteins.
Protein science : a publication of the Protein Society. 14(3):602-16 [PMID] 15689503.
2004
A limiting speed for protein folding at low solvent viscosity.
Journal of the American Chemical Society. 126(11):3398-9 [PMID] 15025447.
2004
IA3, an aspartic proteinase inhibitor from Saccharomyces cerevisiae, is intrinsically unstructured in solution.
Biochemistry. 43(14):4071-81 [PMID] 15065849.
2004
Internal friction controls the speed of protein folding from a compact configuration.
Biochemistry. 43(39):12532-8 [PMID] 15449942.
2004
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy.
Proceedings of the National Academy of Sciences of the United States of America. 101(12):4077-82 [PMID] 15020773.
2003
Exponential decay kinetics in “downhill” protein folding.
Proteins. 50(1):1-4 [PMID] 12471594.
2003
Fast chain contraction during protein folding: “foldability” and collapse dynamics.
Physical review letters. 90(16) [PMID] 12732017.
2002
IA3, A Yeast Proteinase A Inhibitor, Is Intrinsically Unstructured in Solution.
TheScientificWorldJournal. 2:99-101 [DOI] 10.1100/tsw.2002.47. [PMID] 29973821.
2002
Laminar-flow fluid mixer for fast fluorescence kinetics studies.
Biophysical journal. 83(5):2872-8 [PMID] 12414719.
2002
Rapid intrachain binding of histidine-26 and histidine-33 to heme in unfolded ferrocytochrome C.
Biochemistry. 41(4):1372-80 [PMID] 11802740.
2002
Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros.
Journal of the American Chemical Society. 124(44):12952-3 [PMID] 12405814.
2001
Rate of intrachain contact formation in an unfolded protein: temperature and denaturant effects.
Journal of molecular biology. 305(5):1161-71 [PMID] 11162121.
2000
Fast kinetics and mechanisms in protein folding.
Annual review of biophysics and biomolecular structure. 29:327-59 [PMID] 10940252.
2000
Two-state expansion and collapse of a polypeptide.
Journal of molecular biology. 301(4):1019-27 [PMID] 10966803.
2000
Two-state expansion and collapse of a polypeptide.
Journal of molecular biology. 297(3):781-9 [PMID] 10731428.
1996
Diffusion-limited contact formation in unfolded cytochrome c: estimating the maximum rate of protein folding.
Proceedings of the National Academy of Sciences of the United States of America. 93(21):11615-7 [PMID] 8876184.
1995
Protein reaction kinetics in a room-temperature glass.
Science (New York, N.Y.). 269(5226):959-62 [PMID] 7638618.
Environmental Triggers oflrgAExpression inStreptococcus mutans
. [DOI] 10.1101/668731.
Spatial correlations and distribution of competence gene expression in biofilms of Streptococcus mutans
. [DOI] 10.1101/2020.11.23.394429.
Threshold regulation and stochasticity from the MecA/ClpCP proteolytic system inStreptococcus mutanscompetence
. [DOI] 10.1101/263210.

Grants

Jul 2018 ACTIVE
Gene Regulation and Physiology of Streptococcus mutans
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDCR
Jun 2018 – May 2021
OR-DRPD-ROF2018: Probing the Electrical Nature of Bacterial Communication
Role: Co-Investigator
Funding: UF RESEARCH
Aug 2017 – Jul 2022
Collaborative Research: Evolution of information processing in the Vibrio fischeri pheromone-signaling network
Role: Principal Investigator
Funding: NATL SCIENCE FOU
Mar 2017 ACTIVE
Functional amyloid formation in streptococcus mutans
Role: Co-Investigator
Funding: NATL INST OF HLTH NIDCR
Apr 2016 – Mar 2022
Streptococcus mutans adaptation to oxidative stress by the Cid/Lrg system
Role: Project Manager
Funding: NATL INST OF HLTH NIDCR
Dec 2013 – Aug 2020
Environmental regulation of gene expression dissected by microfluidics
Role: Principal Investigator
Funding: NATL INST OF HLTH NIDCR

Contact Details

Phones:
Business:
(352) 392-4716
Emails:
Business:
sjhagen@ufl.edu
Addresses:
Business Mailing:
PO BOX 118440
PHYSICS DEPARTMENT
GAINESVILLE FL 326118440
Business Street:
#92 NPB ROOM 2362
PHYSICS
GAINESVILLE FL 326118440