Melanie Berkmen
Dr. Melanie Barker Berkmen
Assistant Professor, Department of Chemistry and Biochemistry
Contact Information
Phone: 617-973-5321
Email: mberkmen@suffolk.edu
Website: http://openwetware.org/wiki/Berkmen
Office Hours: TBA
Donahue 513
Research Interests
• Defining and characterizing the molecular components of the Gram-positive bacterial mating pore apparatus using a combination of bioinformatics, biochemistry, and molecular and cellular biology
• Understanding how proteins and DNA are targeted to the correct subcellular addresses in bacteria
Education
University of Wisconsin-Madison, Ph.D., Molecular and Cellular Biology (2001)
University of Dayton, B.S., Biochemistry, summa cum laude (1995)
Employment
2007-, Suffolk University, Boston, MA, Assistant Professor
2002-2007, Massachusetts Institute of Technology, Cambridge, MA, Postdoctoral Fellow in the laboratory of Alan Grossman
Fellowships and Awards
2002-2005 Jane Coffin Childs Postdoctoral Fellowship
2001 UW-Madison Bacteriol. Dept. Award for outstanding graduate research
1998-2001 Pfizer Inc. Graduate Fellowship in Microbial Physiology
1995-1998 Molecular Biosciences NIH Graduate Fellowship
Publications
Wang JD, Berkmen MB, Grossman AD. (2007) Genome-wide co-orientation of replication and
transcription reduces adverse effects on replication in Bacillus subtilis, PNAS, 104(13): 5608-5613.
Berkmen MB and Grossman AD. (2007) Subcellular positioning of the origin region of the Bacillus subtilis chromosome is independent of sequences within oriC, the site of replication initiation, and the replication initiator DnaA. Mol Microbiol, 63(1): 150-165.
Berkmen MB, Grossman AD. (2006) Spatial and temporal organization of the Bacillus subtilis replication cycle. Mol. Microbiol, 62(1): 57-71.
Haugen SP, Berkmen MB, Ross W, Gaal T, Ward C, Gourse RL. (2006) rRNA promoter regulation by nonoptimal binding of σ region 1.2: An additional recognition element for RNA polymerase. Cell, 125(6): 1069-1082.
Paul BJ, Berkmen MB, Gourse RL (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. PNAS, 102(22):7823-8.
Paul BJ, Barker MM, Ross W, Schneider DA, Webb C, Foster JW, Gourse RL (2004) DksA: A critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell, 118(3): 311-322.
Wang JD, Rokop ME, Barker MM, Hanson NR, Grossman AD (2004) Multi-copy plasmids affect replisome positioning in Bacillus subtilis. J Bact, 186(21):7084-90.
Barker MM, Gourse RL (2002) Control of stable RNA synthesis. In Translation Mechanisms. (Lapointe J, Brakier-Gingras L. ed.). Landes Biosciences, Austin, TX.
Barker MM, Gourse RL (2001) Regulation of rRNA transcription correlates with nucleoside triphosphate sensing. J Bact, 183, 6315-6323.
Barker MM, Gaal T, Josaitis CA, Gourse RL. (2001) Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 305(4): 673-688.
Barker MM, Gaal T, Gourse RL (2001) Mechanism of regulation of transcription initiation by ppGpp II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol 305(4): 689-702.
Gourse RL, Gaal T, Aiyar SE, Barker MM, Estrem ST, Hirvonen CA, Ross W. (1998) Strength and regulation without transcription factors: Lessons from bacterial rRNA promoters. Cold Spring Harb Sym 63: 131-139.
Presentations
2007 Functional Gemonics of Gram-positive Microorganisms, Tirrenia, Italy
2006 Boston Bacterial Meeting, Boston, MA
2005 ASM Conference on Prokaryotic Development, Vancouver, Canada
2004 Molecular Genetics of Bacteria and Phages, Cold Spring Harbor, NY
Professional Activities
2004-5 Co-chair of the organizing committee of the Boston Bacterial Meeting
Courses Taught
CHEM 331 - Biohemistry I (Fall 2007)
CHEM428 - Research and Seminar I (Fall 2007)
Advanced Seminar in Microbial Cellular and Molecular Biology (Fall, 2005, MIT)