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By the time, you receive this issue of the JBT, the Executive Board Election 2004 will have been completed and two new members will have been elected to serve a four-year term on the Executive Board (EB). The EB of the ABRF is composed of eight members elected by the ABRF membership. The terms are staggered so that each year only two members rotate off the board. This year, Preston Hensley and Ted Thannhauser are each finishing their term. Both have contributed to the association in numerous ways; their vision and input have had significant impact on the continuous growth and development of our organization. Fortunately, both have agreed to continue to serve the ABRF by participating in several ongoing efforts, such as the Long-Range Planning Committee, the Web committee, and the co-organization and planning for the 2006 ABRF meeting. We would like to thank them for their work, service and dedication to the ABRF.
Based on nominations made by ABRF members and internal discussions, the nominations committee, Mark Lively, Laurey Steinke and Barbara Merrill did an excellent job of assembling a list of nominees from which the EB selected the final four candidates. The result of this year’s election will not be known until after this column goes to press; nonetheless, we would like to thank those four outstanding ABRF members who agreed to stand for election:
Kevin Knudtson Dr. Knudtson is the director of the DNA Facility at the University of Iowa that provides DNA sequencing, DNA microarray, and quantitative RT-PCR services. He obtained his Ph.D. from the Iowa Sate University and was a postdoctoral fellow at the University of Utah School of Medicine. There, his research involved the use of various gene and protein expression and purification systems to examine the host–parasite interactions of Mycoplasma arthritidis. His current research focuses on the immunopathology of type 1 diabetes utilizing DNA microarrays and fragment analysis to examine the natural variation in gene expression. He is currently an executive committee member of the University of Iowa’s Center for Biostatistics and Computational Biology working with investigators to develop and incorporate bioinformatics tools in their research. He has over twenty years of laboratory experience in performing recombinant DNA and protein expression studies. Dr. Knudtson has also been an active member of the ABRF. He has been a past member of the ABRF Nominations Committee and coordinated the ABRF presentation at the 14th annual Genome Sequence and Analysis Conference. He has also participated in the DNA Sequencing Research Group and the Microarray Research Group as a research group member and as the past chair of the MARG.
Nancy Denslow Dr. Denslow is currently an associate professor in the Department of Physiological Sciences at the University of Florida. Previously, she was the director of the Protein Chemistry and Molecular Biomarkers Core Facility at the University of Florida for 15 years. This core facility provides services mainly directed toward protein characterization and identification, including Edman sequencing, amino acid analysis, peptide synthesis, 1- and 2D-gel electrophoresis, BIAcore, and protein identification by MALDI-TOF and ESI-MS, MS/MS. Dr. Denslow has been a member of the ABRF since 1988, serving as member and chair of several research committees including the Survey Committee, the Amino Acid Analysis Committee, and currently the Edman Sequencing Committee. Current research interests include using genomics and proteomics tools to understand molecular changes in animals exposed to environmental contaminants. She has authored over seventy five papers.
Dr. Denslow believes that the ABRF is an excellent forum to further research objectives in biotechnology, especially to champion a “systems biology” approach to science. In her opinion, the ABRF should continue to foster member education, methods development and state-of-the-art symposia in the “omics” and bioinformatics, and stay abreast of new developments in biotechnology.
Michael L. Doyle Dr. Doyle obtained his Ph.D. in biophysical chemistry from the University of Colorado, Boulder and completed post-doctoral training in molecular biophysics at Washington University School of Medicine. In 1991, he joined SmithKline Beecham Pharmaceuticals as the assistant director of Structural Biology. He is currently group leader of the Protein Biochemistry Core Laboratory at Bristol-Myers Squibb Pharmaceutical Research Institute, where he is responsible for expression, purification, and biophysical characterization of recombinant proteins for assays and structural biology. His research interests include quantitative analysis of molecular interactions, and high-throughput methods for protein expression, purification, and crystallization. He has been an active participant in the ABRF since 1996 and has served in multiple roles including speaker at scientific sessions, speaker and chair for the Molecular Interactions Research Group presentations, and roundtable organizer and scientific-session organizer on molecular interactions. He has also served as member and chair of the ABRF MIRG. Additional scientific service includes scientific organizer, Biocalorimetry Conference (Boston, 2003); co-organizer, 10th Annual Gibbs Conference on Biothermodynamics (1996); and symposium organizer, Gibbs (1992), Calorimetry (2002), Protein Society (2004), and ASBMB (2004) conferences. He was the recipient of the Sunner Young Scientist Award for Thermochemistry (1997 Calorimetry Conference). He has published over sixty scientific articles and is co-editor of Biocalorimetry: Applications of Calorimetry in the Biological Sciences II (John Wiley, 2004).
Richard T. Pon Dr. Pon is adjunct professor in the Department of Biochemistry and Molecular Biology, Faculty of Medicine, at the University of Calgary, Calgary, Alberta, Canada, and the director of the University Core DNA Services facility (www.med.ucalgary.ca/dnaservices). The core services facility performs DNA/RNA synthesis and DNA sequencing for researchers across Canada using a staff of six technicians. Research is conducted in nucleic acid chemistry, especially solid-phase oligonucleotide synthesis. Research topics involving solid-phase supports and technologies, such as the “Q-Linker” linker arm for fast cleavage, reusable supports for large-scale synthesis, tandem synthesis of multiple oligonucleotides and optimized RNA synthesis, have been investigated. This has resulted in over ninety scientific publications and book chapters, several patents, and numerous conference presentations.
Prior to joining the University of Calgary in 1985, Richard Pon was a graduate student in the Department of Chemistry, McGill University, working with Professor Kelvin K. Ogilvie in the area of RNA synthesis. A modified DNA synthesizer built by BioLogicals (Ottawa, Ontario) was adapted for use as the first automated solid-phase RNA synthesizer. Dr. Pon graduated with a Ph.D. in 1984 and his thesis received the Carl A. Winkler award for excellence in the Department of Chemistry.
Dr. Pon has been a member of the ABRF since 1991. He helped the ABRF establish their first nucleic acid-related activities as a member and chair of the Nucleic Acid Research Group. He has also served on the ABRF Travel Awards committee.
The preparations for the annual ABRF meeting in Savannah, GA, February 5–8, 2005, are nearing completion. Ruth Angeletti and her co-organizers George Orr and Andras Fiser have worked very hard to organize our tenth international meeting. Highlights of the program include plenary lectures by Andrej Sali, University of California, San Francisco, Pamela Stanley, Albert Einstein College of Medicine, New York, and Nat Heintz, Rockefeller University, New York. There will be a number of scientific sessions on a wide variety of topics such as next generation DNA sequencing technologies, protein biomarkers, single-molecule analysis, developments in phosphorylation and O-glycosylation analysis, quantitative proteomics, and siRNA to name only a few.
We are very pleased to offer again a one-day satellite meeting that will be held on February 5, 2005: “Protein and Peptide Identification Using Mass Spectrometry Database Search Engines.” This meeting is organized by David Landsman, NCBI, NLM, NIH Computational Biology Branch, Bethesda, MD, in collaboration with the Education committee. Please register early since space is limited to sixty attendees.
Full registration information for the annual meeting and the satellite meeting can be found on the ABRF and FASEB websites.
ABRF 2005 also marks the ten-year anniversary of the annual ABRF award. We are grateful to Agilent Technologies for their continuous support providing sponsorship over the past decade for this important award. This year, the recipient of the ABRF Award is Stephen Fodor, Affymetrix. Stephen Fodor was the primary individual responsible for pioneering the development and applications of high-density DNA arrays. He and his colleagues at Affymax and Affymetrix have brought the powerful and well-established photolithographic fabrication methods employed for integrated circuit manufacture into the biological realm—a landmark in interdisciplinary technology development. The nucleic acid arrays that they originally developed have evolved over the last decade into tools of unparalleled power for the comprehensive analysis of gene expression. The ability to simultaneously analyze the expression of tens of thousands of genes has provided a perfect complement to the genome sequences generated by the Human Genome Project. This work now serves as a model for the current efforts to develop comparable technologies for the parallel analysis of proteins (proteomics) and small molecules (metabolomics). High-density nucleic acid arrays have also proven to be very powerful platforms to re-sequence complex genomes, and were recently introduced into the clinical diagnostic market for the analysis of genetic variations involved in drug metabolism.
With the introduction of the technologies (wet methods) and informatics (in silico methods) that compose systems biology, the manner in which we interrogate and understand cellular structure and function is beginning to change. For the past year and half, the ABRF has been working to understand how our society should best evolve to accommodate these changes.
At the EB fall meeting this year in Washington, DC, the Long-Range Planning Committee and the EB heard the following presentations from four speakers covering the areas of proteomics, expression profiling, drug discovery, computational biology, and the trends in national research funding that are being considered to support research in systems biology:
Steve Carr The Broad Institute, Proteomics & Biomarker Discovery
Tim Zacharewsky Michigan State University, Systems Biology & Drug Development
Rajeev Aurora St. Louis University, Systems Biology: Data Integration & Hypothesis Generation
Judith Vaitukaitis National Center for Research Resources, Impact of Biocomplexity on Infrastructure
The speakers were asked to provide us with their perspective on integrating systems biology into the ABRF.
The EB felt that while much of the function of core labs will remain the same for the next decade, increasingly ABRF members will see
It was recognized that one of the immediate needs is to significantly improve the aspect of computational biology. The vast amount and the complexity of data that need to be correlated and interpreted in a synergistic fashion are currently considered to be an almost insurmountable roadblock. The EB decided to initiate a Computational Biology Research Group (CBRG) and Rajeev Aurora has agreed to spearhead this group.
Similarly, the EB and the Proteomics Research Group have collaborated on research group expansion to cover key areas of the field. Jeff Kowalak is leading a new Standards PRG (sPRG) and plans are underway to initiate a Quantitative Proteomics RG (qPRG).
In addition, the EB felt that the next steps for the ABRF in a transition to science of this sort would be to insure engagement and feedback from the members and especially the research groups and committees. In order to facilitate such discussion, the EB decided to meet with all research group and committee chairs at the upcoming 2005 ABRF meeting. As a basis for this discussion, a series of questions relating to our long-term planning efforts have been posted and can be viewed on the ABRF web site.
The EB is looking forward to the engagement of all members in this process. This is the beginning of a major transition for the ABRF. However, we appreciate that this change will affect some core labs more than others and that there will remain a need for core labs, as we know them now in many institutions, for a long time to come.
An educational symposium on “Quantitative Analysis of Molecular Interactions with Biophysical Technologies” was jointly sponsored by ABRF and ASBMB (American Society for Biochemistry and Molecular Biology) and held at the ASBMB annual meeting in Boston June 13, 2004. This symposium was the latest in a series of ABRF/ASBMB jointly sponsored educational symposia held nearly every year at annual ASBMB meetings since 1991. The ASBMB membership includes ABRF members, but also includes users of the core facilities and technologies led by ABRF members. The primary goal of the symposium was to educate ASBMB members on biophysical technologies used for the quantitative analysis of biomolecular interactions. The symposium was arranged by ABRF members Ron Niece, who served as the liaison between ABRF and ASBMB, and Mike Doyle, who served as the scientific organizer. The symposium (one of nine parallel sessions) drew a sizable audience of 200 attendees.
The symposium started with introductory comments by Mike Doyle on the role of biophysical technologies in molecular interaction analysis, and a description of the ABRF (its mission, educational outreach programs, web site, and the research groups). The introductory remarks provided an overview of the types of molecular interaction studies that biophysical technologies are used for. Applications were categorized into three areas: (1) basic biochemical science (binding molecular mechanism), (2) drug development (confirm binding of hits from screening, guide structural biology, batch-to-batch quality control of protein therapeutics, drug molecular mechanism of action), and (3) quantitation and validation of regulatory nodes in the interactome (determine accurate binding affinities, effects of post-translational modifications and macromolecular complex formation on affinities).
There were three speakers in the symposium. The first was David Myszka (University of Utah), who introduced the surface plasmon resonance (SPR) technology and described applications of SPR for characterizing both affinity and kinetics for biomolecular interactions. David presented SPR studies characterizing binding of the small molecule ligand 4-carboxybenzenesulfonic acid to the protein carbonic anhydrase [refer to J Biomol Tech (2003) 14 247–269 [PubMed] for some of the data]. David also described some exciting progress on using SPR for characterizing binding reactions of integral membrane proteins. One of the “tricks” for obtaining good quality data was to rely on robotics in order to overcome time-dependent loss of activity on the chip. One of the benefits of the SPR method is that it requires relatively small quantities of biomolecular reagents. Additional information about SPR can be found at David’s web site (http://www.cores.utah.edu/Interaction/).
The next talk was given by Alan Cooper (University of Glasgow), who presented a thorough introduction to biocalorimetry and a wide range of applications. Alan discussed the use of differential scanning calorimetry for characterizing the binding affinity of a protein-DNA interaction. He also discussed several interactions studied by isothermal titration calorimetry that included proteins, carbohydrates, and small molecule drugs. Alan emphasized one of the benefits of ITC is that the reactants can be studied in native, soluble form, and do not require immobilization or labeling. Additional information about calorimetry can be found at Alan’s web site (http://www.chem.gla.ac.uk/staff/alanc/) under the calorimetry services link.
The final talk was given by Mark Labadia (Boehringer-Ingelheim Pharmaceuticals), who presented a talk on the combined use of calorimetry, SPR, fluorescence, and deuterium-hydrogen exchange mass spectrometic technologies to characterize the ternary complex formation between P38 kinase, MAPKAP kinase-2, and clinically important P38 kinase drugs. Mark’s talk described the value of combining these technologies to produce a high resolution analysis of the molecular regulatory mechanisms in this set of interactions, including a quantitative determination of the effect of phosphorylation on affinity.