User:Dstoebel

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==Contact Information==
==Contact Information==
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'''Dan Stoebel'''<br>
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===[http://www.hmc.edu/academicsclinicresearch/academicdepartments/biology/facultystaff1/biofaculty1/stoebel.html Dan Stoebel]===
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Department of Microbiology<br>
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Department of Biology<br>
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Moyne Institute of Preventive Medicine<br>
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Harvey Mudd College<br>
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Trinity College, Dublin<br>
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Claremont, CA 91711<br>
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Dublin 2<br>
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Ireland<br>
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==About me==
==About me==
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I am interested in the evolution of regulatory networks in bacteria, and how horizontally acquired genes are integrated into those networks.  I am currently a post-doctoral fellow with Charles Dorman at Trinity College, Dublin.  I did my Ph.D. with Dan Dykhuizen in the Department of Ecology and Evolution at Stony Brook University, graduating in December, 2006.  My undergraduat degree is from Pomona College.
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I am interested in the evolution of regulatory networks in bacteria, and how horizontally acquired genes are integrated into those networks. Research in my lab in the [http://www.hmc.edu/academicsclinicresearch/academicdepartments/biology1.html Biology Department] of Harvey Mudd College focues on the evolution of the RpoS regulon in ''E. coli'' and its close relativesBefore moving to Harvey Mudd, I held post-doctoral research positions with [http://web.mac.com/tim_f_cooper/Cooper_lab/Cooper_lab.html Tim Cooper] at the University of Houston and with [http://www.tcd.ie/Microbiology/research/cj_dorman.php Charles Dorman] at Trinity College, Dublin.  I did my Ph.D. with [http://life.bio.sunysb.edu/ee/people.htm Dan Dykhuizen] at Stony Brook University.  My undergraduate degree is from Pomona College.
==Publications==
==Publications==
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A. D. S. Cameron, '''D. M. Stoebel''', and C. J. Dorman. 2011. DNA supercoiling is differentially regulated by environmental factors and FIS in ''Escherichia coli'' and ''Salmonella enterica''. ''Molecular Microbiology'',''' 80''':85-101 [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2011.07560.x/abstract Abstract]
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'''D. M. Stoebel''', and C. J. Dorman. 2010. The effect of mobile element IS''10'' on experimental regulatory evolution in ''Escherichia coli''. ''Molecular Biology and Evolution'', '''27''':2105-2112.  [http://mbe.oxfordjournals.org/cgi/content/full/27/9/2105 Full Text]
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'''D. M. Stoebel''', and D. E. Dykhuizen. 2010. Waste and yet want not. ''Molecular Cell'', '''38''':625-626. [http://www.cell.com/molecular-cell/fulltext/S1097-2765%2810%2900414-4 Full Text]
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'''D. M. Stoebel''', K. Hokamp, M. S. Last, and C. J. Dorman. 2009. Compensatory evolution of gene regulation in response to stress by ''E. coli'' lacking RpoS. ''PLoS Genetics'', '''5''': e1000671
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[http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000671 Full Text]
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'''D. M. Stoebel''', A. Free, and C. J. Dorman. 2008. Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. ''Microbiology'', '''154''': 2533-2545. [http://mic.sgmjournals.org/cgi/content/full/154/9/2533 Full Text]
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'''D. M. Stoebel''', A. M. Dean, and D. E. Dykhuizen. 2008. The cost of expression of ''Escherichia coli lac'' operon proteins is in the process, not in the products.  ''Genetics'', '''178''':1653-1660. [http://www.genetics.org/cgi/content/full/178/3/1653 Full Text]
'''D. M. Stoebel.''' 2005. Lack of evidence for horizontal transfer of the ''lac'' operon into ''Escherichia coli''. ''Molecular Biology and Evolution''. '''22''':683-690.  [http://mbe.oxfordjournals.org/cgi/content/full/22/3/683 Full Text]
'''D. M. Stoebel.''' 2005. Lack of evidence for horizontal transfer of the ''lac'' operon into ''Escherichia coli''. ''Molecular Biology and Evolution''. '''22''':683-690.  [http://mbe.oxfordjournals.org/cgi/content/full/22/3/683 Full Text]
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M. Feldgarden, '''D. M. Stoebel''', D. Brisson, and D.E. Dykhuizen. 2003. Size doesn't matter: microbial selection experiments address ecological questions. ''Ecology'' '''84''':1679-1687.
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M. Feldgarden, '''D. M. Stoebel''', D. Brisson, and D.E. Dykhuizen. 2003. Size doesn't matter: microbial selection experiments address ecological questions. ''Ecology'' '''84''':1679-1687. [http://micropopbio.org/cooper/files/2008/03/feldgarden-selection-experiments.pdf Full Text]
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==Protocols that I use==
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[[Dorman:Lambda_Red_mediated_Recombination|λ-red mediated recombination]]
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[[Dorman:Chloroquine_gel_analysis|Chloroquine gels]]
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[[Sauer:P1vir_phage_transduction|P1 transduction]]
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[[Dorman:P22_transduction|P22 transduction]]
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[[Dorman:Preparing_electrocompetent_cells|Quick and dirty electrocompotent cells]]
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[[Dorman:Intracellular_Salts_Medium|Making Intracellular Salts Medium]]

Current revision

Contents

Contact Information

Dan Stoebel

Department of Biology
Harvey Mudd College
Claremont, CA 91711

About me

I am interested in the evolution of regulatory networks in bacteria, and how horizontally acquired genes are integrated into those networks. Research in my lab in the Biology Department of Harvey Mudd College focues on the evolution of the RpoS regulon in E. coli and its close relatives. Before moving to Harvey Mudd, I held post-doctoral research positions with Tim Cooper at the University of Houston and with Charles Dorman at Trinity College, Dublin. I did my Ph.D. with Dan Dykhuizen at Stony Brook University. My undergraduate degree is from Pomona College.

Publications

A. D. S. Cameron, D. M. Stoebel, and C. J. Dorman. 2011. DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica. Molecular Microbiology, 80:85-101 Abstract

D. M. Stoebel, and C. J. Dorman. 2010. The effect of mobile element IS10 on experimental regulatory evolution in Escherichia coli. Molecular Biology and Evolution, 27:2105-2112. Full Text

D. M. Stoebel, and D. E. Dykhuizen. 2010. Waste and yet want not. Molecular Cell, 38:625-626. Full Text

D. M. Stoebel, K. Hokamp, M. S. Last, and C. J. Dorman. 2009. Compensatory evolution of gene regulation in response to stress by E. coli lacking RpoS. PLoS Genetics, 5: e1000671 Full Text

D. M. Stoebel, A. Free, and C. J. Dorman. 2008. Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology, 154: 2533-2545. Full Text

D. M. Stoebel, A. M. Dean, and D. E. Dykhuizen. 2008. The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics, 178:1653-1660. Full Text

D. M. Stoebel. 2005. Lack of evidence for horizontal transfer of the lac operon into Escherichia coli. Molecular Biology and Evolution. 22:683-690. Full Text

M. Feldgarden, D. M. Stoebel, D. Brisson, and D.E. Dykhuizen. 2003. Size doesn't matter: microbial selection experiments address ecological questions. Ecology 84:1679-1687. Full Text

Protocols that I use

λ-red mediated recombination

Chloroquine gels

P1 transduction

P22 transduction

Quick and dirty electrocompotent cells

Making Intracellular Salts Medium

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