User:Torsten Waldminghaus

Me after being productive

Hi, my name is Torsten Waldminghaus, and I'm PI of the Waldminghaus Lab. I was let to OpenWetWare by google years back, searching for certain protocols. I benefit a lot from people sharing their protocols on the internet and thought it might be a good idea to also let the world participate on my wisdom and experince. If you still want to you can email me through OpenWetWare. Below I'll describe a bit more about myself and the stuff I'm interested in.

CV

• since 2011: Professor for Synthetic Microbiology at SYNMIKRO - Center for Synthetic Microbiology of the Philipps-Universität Marburg (Germany) and PI of the Waldminghaus Lab

• 2007-2011: Postdoc at the Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo (Norway) in the lab of Kirsten Skarstad

• 2004-2007: PhD at the Ruhr-University Bochum (Germany) PhD-thesis: ‘RNA-thermometers in bacteria’ in the lab of Franz Narberhaus

• 2002-2004: Studies in bioinformatics at the University of applied science Berlin (Germany) Master-thesis: ‘In silico analysis and selection of RNA secondary structures’ at the Max Planck Institute for Infection Biology under supervision of Volker Patzel

• 1999-2002: Studies in biology at the Ernst-Moritz-Arndt-University Greifswald (Germany) Diploma-thesis: ‘Investigations on the expression of clpX in Bacillus subtilis’ at the Division for Microbial Physiology and Molecular Biology in the lab of Michael Hecker

• 1996-1999: Basic studies in biology at the University of Potsdam (Germany)

• 1996: Theological studies and volunteer at the International Torchbearer Bibleschool in Holsby Brunn (Sweden)

Grants and Awards

• 2008-2010: Two year postdoc grant of the German Research Council (DFG)
• 2008: Ruth Massenberg Prize of Ruhr-University Bochum (Germany) for outstanding PhD thesis
• 2008: Travel grant of FEMS
• 2006: Travel grant of Ruth und Gert Massenberg Stiftung

Research interests

In general I like bacteria and complex systems.

A bit more detailed I enjoy working on:

• Regulation of replication in bacteria
• Synthetic chromosomes
• Searching funny patterns on chromosomes or in proteins [1]

Publications

1. Johnsen L, Flåtten I, Morigen, Dalhus B, Bjørås M, Waldminghaus T, and Skarstad K. The G157C mutation in the Escherichia coli sliding clamp specifically affects initiation of replication. Mol Microbiol. 2011 Jan;79(2):433-46. DOI:10.1111/j.1365-2958.2010.07453.x |
2. Stokke C, Waldminghaus T, and Skarstad K. Replication patterns and organization of replication forks in Vibrio cholerae. Microbiology (Reading). 2011 Mar;157(Pt 3):695-708. DOI:10.1099/mic.0.045112-0 |
3. Waldminghaus T, Weigel C, and Skarstad K. Replication fork movement and methylation govern SeqA binding to the Escherichia coli chromosome. Nucleic Acids Res. 2012 Jul;40(12):5465-76. DOI:10.1093/nar/gks187 |
4. Gaubig LC, Waldminghaus T, and Narberhaus F. Multiple layers of control govern expression of the Escherichia coli ibpAB heat-shock operon. Microbiology (Reading). 2011 Jan;157(Pt 1):66-76. DOI:10.1099/mic.0.043802-0 |
5. Waldminghaus T and Skarstad K. ChIP on Chip: surprising results are often artifacts. BMC Genomics. 2010 Jul 5;11:414. DOI:10.1186/1471-2164-11-414 |
6. Waldminghaus T, Gaubig LC, Klinkert B, and Narberhaus F. The Escherichia coli ibpA thermometer is comprised of stable and unstable structural elements. RNA Biol. 2009 Sep-Oct;6(4):455-63. DOI:10.4161/rna.6.4.9014 |
7. Waldminghaus T and Skarstad K. The Escherichia coli SeqA protein. Plasmid. 2009 May;61(3):141-50. DOI:10.1016/j.plasmid.2009.02.004 |
8. Waldminghaus T, Kortmann J, Gesing S, and Narberhaus F. Generation of synthetic RNA-based thermosensors. Biol Chem. 2008 Oct;389(10):1319-26. DOI:10.1515/BC.2008.150 |
9. Waldminghaus T, Gaubig LC, and Narberhaus F. Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers. Mol Genet Genomics. 2007 Nov;278(5):555-64. DOI:10.1007/s00438-007-0272-7 |
10. Waldminghaus T, Heidrich N, Brantl S, and Narberhaus F. FourU: a novel type of RNA thermometer in Salmonella. Mol Microbiol. 2007 Jul;65(2):413-24. DOI:10.1111/j.1365-2958.2007.05794.x |
11. Narberhaus F, Waldminghaus T, and Chowdhury S. RNA thermometers. FEMS Microbiol Rev. 2006 Jan;30(1):3-16. DOI:10.1111/j.1574-6976.2005.004.x |
12. Waldminghaus T, Fippinger A, Alfsmann J, and Narberhaus F. RNA thermometers are common in alpha- and gamma-proteobacteria. Biol Chem. 2005 Dec;386(12):1279-86. DOI:10.1515/BC.2005.145 |
13. Gerth U, Kirstein J, Mostertz J, Waldminghaus T, Miethke M, Kock H, and Hecker M. Fine-tuning in regulation of Clp protein content in Bacillus subtilis. J Bacteriol. 2004 Jan;186(1):179-91. DOI:10.1128/JB.186.1.179-191.2004 |

Links to follow

• http://reuter.mit.edu/dfgwiki wiki about german stipendiats abroad (in german)
• http://anabench.bcm.umontreal.ca/anabench/ nice starting point for computational biology stuff
• http://collections.plos.org/ploscompbiol/tensimplerules.php 10 rule collection for stuff important for scientist

Personal Links

• My Notebook
• Flow cytometry notes

• My strain list
• My qPCR-primer list
• My primer list
• My double strand oligo list
• primer concentrations
• blogger profile
• CiteULike library
• Protein gel and Western

OWW

• How to present research well
• Reviews
• OpenWetWare:Ideas
• /sandbox
• Affinity purification of antibodies
• ChIP-Chip E. coli
• Baby cell column
• Sodium azide
• Chromosomal DNA isolation from E. coli
• Temperature mixing formula
• Methylation analysis with qPCR
• Hardcore PubMeding (advanced PubMed searching)
• OriC/ter ratio determination
• Cell cycle analysis
• Berkmen lab
• Mazel lab

Lost and found protocols:

• Overlap Extension PCR
• Methylcellulose
• Bone Marrow Macrophages
• GHV-68 Plaque Assay
• Neutral red