Supramolecular Biology Group's Home Page

SUPRAMOLECULAR BIOLOGY GROUP
COMPARATIVE GENOMICS CENTRE

Mail Address: Comparative Genomics Centre,
Molecular Sciences Bldg 21, James Cook University,
Townsville, 4811, Queensland, Australia
Telephone: 61-7-4781 5567 Fax: 61-7-4781 6078

CONTENTS:

Overview of Research in the Medical Genomics Group
Staff
Projects Available in the Medical Genomics Group

RESEARCH OVERVIEW:

The SSBG research interests are broadly based on the study at the molecular level of protein-ligand interactions and in particular protein-DNA interactions. The study and discovery of these interactions is primordial to the understanding of the complex spatio-temporal molecular communication patterns occurring within the cell. The discovery and study of novel interactions can provide new molecular tools with applications in the field of bio- and nanotechnology (e.g. molecular diagnostics, drug discovery, functional genomics and proteomics).
The SSBG is currently developing innovative methods for the discovery, characterization and quantification of such interactions. The SSBG has current collaborations with the research groups of Prof. Dixon (U of Wollongong), Prof. Otting (ANU Canberra), Dr Oakley (CSIRO Mebourne), Dr Sevick (ANU, Canberra) Dr Van Oijen (Harvard Medical School, Boston), Prof. Strazewski (Université Claude-Bernard, Lyons, France) and Prof. Keene (James Cook University). The research undertaken in the SSBG is multidisciplinary and spans across the disciplines of Molecular Biology, Biochemistry and Chemistry.
The SSBG is grateful for the generous support of the National Health and Medical Research Council of Australia.

STAFF:

Group Head:

Patrick M. Schaeffer, DEUG, Licence, Maitrise, DEA, PhD

Undergraduate Students

Dahdah Dahdah
Morgane Moreau

PROJECTS AVAILABLE:

Postgraduate
      A variety of multidisciplinary projects spanning across the disciplines of Molecular Biology, Biochemistry and Chemistry are available in the SSBG. Students with an interest in one or more of these disciplines are encouraged to contact Patrick Schaeffer to obtain information about possible PhD or Masters projects available in the SSBG. Higher degrees students are generally expected to be eligible for a scholarship through the Australian Postgraduate Award (APA) scheme, the James Cook University Postgraduate Research Scholarship (JCUPRS) or an equivalent national or international scholarship (APRS).
      The Australian Postgraduate Award (APA) and James Cook University Postgraduate Research Scholarship (JCUPRS) are open to applicants with, or who expect to hold, a first class honours degree or equivalent by the end of the year and who wish to undertake full-time research Masters or PhD program. APA applicants must be Australian citizens or have been granted permanent resident status and lived in Australia continuously for 12 months prior to 31 October of the year of application. Information and application forms can be obtained from the Research Scholarships Officer, or from the following website: http://www.jcu.edu.au/office/grs/scholarships/index.html (Annual Closing Date: 31 October)

Honours  
      Students who have completed their undergraduate training in a BSc, BBiomedSc, BMedlabSc or equivalent program and are interested in participating in the Biochemistry and Molecular Biology Honours Program are encouraged to contact Patrick Schaeffer for a description of currently available projects. Honours studies require a full-time commitment for one year (two semesters) and can start in either February or August.

Undergraduate  
      There are two main opportunities for undergraduates to participate in the ongoing research of the SSBG.
      Students enrolled in BC3202 (Special Topics in Biochemistry and Molecular Biology - second semester) could ask that they undertake their research project in the Laboratory.
      Students can apply for a Comparative Genomics Centre Vacation Scholar Award. The successful applicants receive instruction in Genomics and Proteomics, receiving a stipend of $200 per week for a full-time commitment of between 6 and 10 weeks over the summer break. Applications for the CGC Vacation Studentships will be announced later in the year and will close in late October. Contact Patrick Schaeffer for further details  

RECENT PUBLICATIONS:

Patents

Dixon, N.E., Schaeffer, P.M., Mulcair, M. Double stranded oligonucleotide and uses thereof. (2006) PCT/AU2006/000136
Dixon, N.E., Schaeffer P.M. Diagnostics in monoplex/multiplex. (2007) PCT/AU2007/000798

Book Sections

Brand, G., Hosseini, M.W., Félix, O., Schaeffer, P., Ruppert, R. Molecular Tectonics: Self-Assembly of Charged Molecular Tectons into One- and Two-Dimensional Solids, (1996) NATO ASI Series: Series C, Ed. O. Kahn, Kluwer, 484, 129-142.
Hädener, A., Ritter, G., Schaeffer, P. M., Stamford N. P. J. Are there enzyme-catalysed Diels-Alder reactions? An investigation into the polyketide-synthase system required for the biosynthesis of cytochalasans. in U. Diederichsen et al. (Eds.) Bioorganic Chemistry. (1999) Wiley-VCH, Weinheim, 89-94.

Peer Reviewed Scientific Papers & Review Articles

Hosseini, M.W., Ruppert, R., Schaeffer, P., De Cian, A., Kyritsakas, N., Fischer, J. (1994) A Molecular Approach to Solid-State Synthesis - Prediction and Synthesis of Self-Assembled Infinite Rods. J. Chem. Soc., Chem. Commun., 2135-2136.
Hosseini, M.W., Brand, G., Schaeffer, P., Ruppert, R., De Cian, A., Fischer, J. (1996) Molecular Tectonics. 2. Synthesis of Molecular Sheets by Self-Assembly of Complementary Molecular Units in the Solid-State. Tetrahedron Lett., 37, 1405-1408.
Loscha, K., Oakley, A.J., Bancia, B., Schaeffer, P.M., Prosselkov, P., Otting, G., Wilce, M.C.J. & Dixon, N.E. (2004) Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase. Protein Expr. Purif., 33, 304–310.
Ozawa, K., Headlam, M.J., Schaeffer, P.M., Henderson, B.R., Dixon, N.E. & Otting, G. (2004) Optimization of an Escherichia coli system for cell-free synthesis of selectively 15N-labelled proteins for rapid analysis by NMR spectroscopy. Eur. J. Biochem., 271, 4084–4093.
Schaeffer, P.M., Headlam, M.J. & Dixon, N.E. (2005) Protein-protein interactions in the eubacterial replisome. IUBMB Life, 57, 5–12
Robinson, A., Wu, P.S.-C., Harrop, S.J., Schaeffer, P.M., Dosztányi, Zs., Gillings, M.R., Holmes, A.J., Nevalainen, K.M.H., Stokes, H.W., Otting, G., Dixon, N.E., Curmi, P.M.G. & Mabbutt, B.C. (2005) Integron-associated mobile gene cassettes code for folded proteins: the structure of Bal32a, a new member of the adaptable α+β barrel family. J. Mol. Biol., 346, 1229–1241.
Oakley, A.J., Loscha, K.V., Schaeffer, P.M., Liepinsh, E., Pintacuda, G., Wilce, M.C.J., Otting, G. & Dixon, N.E. (2005) Crystal and solution structures of the helicase-binding domain of Escherichia coli primase. J. Biol. Chem, 280, 11495–11504.
Graham, S.C., Lilley, P.E., Lee, M., Schaeffer, P.M., Kralicek, A.V., Dixon, N.E. & Guss, J.M. (2006) Kinetic and crystallographic analysis of mutant Escherichia coli aminopeptidase P: Insights into substrate recognition and the mechanism of catalysis. Biochemistry, 45, 964-975.
Beck, J.L., Urathamakul, T., Watt, S.J., Sheil, M.M., Schaeffer, P.M. & Dixon, N.E. (2006) Proteomic dissection of DNA polymerisation. Expert Rev. Proteomics, 3, 197-211.
Mulcair, M., Schaeffer, P.M., Oakley, A.J., Cross, H.F, Neylon, C., Hill. T.M. & Dixon, N.E. (2006) A molecular mousetrap determines polarity of termination of DNA replication. Cell, 125, 1309-1319.
Ioannou, C, Schaeffer, P.M., Dixon, N.E., Soultanas, P. (2006) Helicase-binding to DnaI exposes a cryptic DNA-binding site during helicase loading in Bacillus subtilis. Nucleic Acids Res., 34, 5247-58
Su, X.-C., Schaeffer, P.M., Loscha, K.V. Gan, P.H.P., Dixon, N.E., Otting, O. (2006) Monomeric Solution Structure of the Helicase Binding Domain of the Escherichia coli Primase. FEBS J., 273, 4997-5009
Watt, S.J., Urathamakul, T., Schaeffer, P.M., Williams, N.K., Sheil, M.M., Dixon, N.E. Jennifer L. Beck, J.L. (2007) Multiple oligomeric forms of Escherichia coli DnaB helicase revealed by electrospray ionization mass spectrometry. Rapid Commun. Mass Spectrom., 21, 132-140
Tanner, N.A., Hamdan, S.M., Jergic, S., Schaeffer, P.M., Dixon, N.E., van Oijen, A.M. (2008) Single-Molecule Analysis of Escherichia coli DNA Replication: Helicase-Primase Interactions Compromise Fork Progression. Accepted for publication in Nat. Struct. Mol. Biol.

Non-Peer Reviewed Published Papers

Schaeffer, P.M. and Hädener, A. (1997) Stereoselective Preparation of the N-Acetylcysteamine Thioesters of Doubly 13C-Labelled Crotonic, Tiglic, Sorbic, and 4-Methylsorbic Acid and their Use to Probe the Function of a Eukaryotic Polyketide Synthase. Chimia, 51, 635.
Schaeffer, P., Headlam, M. & Dixon, N. (2004) Protein-protein interactions in the bacterial replisome. Australian Biochemist, 35(1), 9–12.
Mulcair, M.D., Schaeffer, P.M., Oakley, A.J., Dixon, N.E., (2005) Replication termination in Escherichia coli: the end of the story? FEBS J. 272: 346-346 Suppl. 1.
Dixon, N.E., Mulcair, M.D., Schaeffer, P.M., Oakley, A.J., (2006) A molecular mousetrap determines polarity of replication fork arrest at Tus-Ter sites in E-coli. FASEB J. 20 (5): A911-A911 Part 2
Schaeffer, P.M. (2007) Unzipping the secret of the last step in DNA replication. Invited contribution to Australasian Science, March, 28-30.

LINKS:

Molecular biology, biochemistry, biological chemistry, bio-inorganic chemistry, biotechnology, diagnostics, ELISA, biacore, surface plasmon resonance, structure, protein interactions, associations, dissociations, affinity, binding, DNA replication, transcription factor, Tus, DnaB, primase, polymerase, SSB, single molecule, protein stability, unfolding, aggregation, green fluorescent protein, chromatin immuno-precipitation, ImmunoPCR, real-time PCR, Escherichia coli, Bacillus, sortase, artificial nuclease, in vivo localization, proteomics, functional genomics, structural genomics, directed evolution, purification.lar science, biology.