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
                               Office: Donahue 513
                               Lab: Archer 631 

Research Interests

• Investigating the molecular components of the bacterial mating pore apparatus using a combination of biochemistry, bioinformatics, 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 of Biochemistry

2008-(summers), Massachusetts Institute of Technology, Cambridge, MA, Visiting Scientist in the laboratory of Alan Grossman

2002-2007, Massachusetts Institute of Technology, Cambridge, MA, Postdoctoral Fellow in the laboratory of Alan Grossman

Fellowships and Awards

2007-2008   Suffolk University Summer Stipend Award
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

Vrentas CE, Gaal T, Berkmen MB, Rutherford ST, Haugen SP, Ross W, Gourse RL. (2008) Still looking for the magic spot: the crystallographically defined binding sire for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J Mol Biol, 277(2):551-64.

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

2008     Sabanci University, Istanbul, Turkey
2008     Suffolk University, Boston, MA
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-   Member of the American Society For Microbiology
2004-5 Co-chair of the organizing committee of the Boston Bacterial Meeting

Courses Taught

CHEM 331 - Biohemistry I (Fall 2007)
CHEM L333 - Advanced Biochemical Techniques and Research (Spring 2008)
CHEM 428 - Research and Seminar I (Fall 2007)
CHEM 429 - Research and Seminar II (Spring 2008)
Advanced Seminar in Microbial Cellular and Molecular Biology (Fall, 2005, MIT)