Created: 1st December 1999, last updated: 21st February 2000, © 1999 ABRF
Published Article
The Nucleic Acids Research Group (NARG) recently published the results of a study on primer design for DNA sequencing in the September issue of BioTechniques (1999;27(3):528-536) entitled "Design Strategies and Performance of Custom DNA Sequencing Primers." The study surveyed primer design protocols used by DNA sequencing facilities and evaluated the effectiveness of those primer design criteria. The results indicated that for clean templates, the majority of primers produced good sequence data despite the presence of sequence characteristics that are commonly believed to have a negative impact on the quality of DNA sequencing.
Other Studies
The NARG recently completed a Web-based survey of DNA synthesis core facilities. The results of the survey were presented at ABRF '99 and have been submitted for publication in JBT.
The next study to be presented at ABRF2000 is an internal study by group members focusing on the synthesis and analysis of "boutique oligos," or oligonucleotides containing modified phosphoramidites such as biotin and fluorescent labels.
Membership
As of September 1999, Martha Gunthorpe replaced Karl Hager as chair of NARG. Currently, the NARG is seeking new members. If interested, please send your curriculum vitae to marthag@itsa.ucsf.edu.
Research Activities
The DNA Sequencing Research Group (DSRG) reported the latest results of its 1999 study on the effects of different methodologies on sequencing performance at the 11th International Genome Sequencing and Analysis Conference (GSAC) in Miami in September 1999. Susan Hardin and Ted Thannhauser presented the results of the study at the meeting in an well-attended ABRF DSRG-sponsored roundtable discussion on current technology and methodology in DNA sequencing laboratories. The DSRG also presented the results of the study in a poster presentation at the meeting. A poster summarizing the results of the 1999 study is now available on the ABRF Web Site (http://www.abrf.org/ABRF/ResearchCommittees/dsrg_members.html#Electronic). Other members of the DSRG (Scottie Adams, Duane Bartley, George Grills, and Dina Leviten) gave presentations and participated in the ABRF roundtable discussion at the GSAC meeting. Results of the study were also presented at the Cornell Biotechnology Program Symposium in October 1999.
The DSRG is currently planning its year 2000 study. The study will focus on strategies for sequencing large-scale templates such as BACs. In addition, as part of its year 2000 study, the DSRG will conduct its biannual survey of DNA sequencing core laboratories. The aim of the survey will be to provide a current and detailed portrait of the average sequencing laboratory. Information on how to participate in the year 2000 study can be found on the Web (http://brcweb.bio.cornell.edu/dsrg2000). A preliminary report on the results of this study will be presented at ABRF2000.
New and Departing Members
We are delighted to announce that Dina Leviten of ICOS Corporation and James Van Ee of Cornell University joined the DSRG as a member and ad hoc member, respectively. Unfortunately, Mary Kay Dolejsi and Scottie Adams have retired from active participation in the DSRG. All the members of the DSRG would like to take this opportunity to thank Scottie and Mary Kay for their many years of dedicated service. The departure of these two long-time members means there is a need for new members. Anyone interested in becoming a member of the DSRG should contact Ted Thannhauser at tt34@cornell.edu
Over the past year the Fragment Analysis Research Group (FARG) has been trying to assess the needs of facilities that perform fragment analysis. The first endeavor was to survey the ABRF membership on how, with what, where, and when they are perfoming fragment analysis. The results of this survey were presented at ABRF'99 and are now available on the ABRF Web Site (http://abrf.org/ABRF/ResearchCommittees/FARG/FARG.html). Members of the group would like to express their appreciation to everyone who participated in the survey.
It was decided that enough members were involved with fragment analysis in their facilities to make feasible a study involving analysis of an actual sample. This year the FARG will be conducting a multicenter study for facilities or individual researchers currently involved in fragment analysis. The study will consist of analyzing two test samples that have been amplified and are labeled. No polymerase chain reaction or purification will be required. The FARG is interested in comparing the allele-size calling characteristics related to different equipment, gel types, standards, and other operating parameters. Results from the study will be presented at ABRF2000. For those who are interested in participating, test samples are now available and can be requested by contacting dbartley@jhmi.edu
The Peptide Synthesis Research Group (PSRG) of ABRF is conducting a study on the synthesis of cyclic peptides using an amide bond formation between the free N-terminus of the peptide with a free C-terminus. A variety of biological studies have suggested that a cyclic peptide may exhibit improved metabolic stability, increased potency, better receptor selectivity and more controlled bioavailability. To prepare for this study, the PSRG synthesized and characterized the following cyclic peptide:
cyclo(Tyr-Glu-Ala-Ala-Arg-D-Phe-Pro-Glu-Asp-Asn)
The method used by the PSRG in the synthesis of this peptide and some useful references are provided in the study letter. Member laboratories are asked to synthesize this peptide using the method of their choice and submit the crude product without purification. The PSRG will evaluate the peptides by RP-HPLC, capillary electrophoresis, amino acid analysis, MALDI-TOF/MS, and ESI/MS. The results of this study will be reported at ABRF2000. If you would like to participate in this study, please contact Ashok Khatri (khatria@helix.mgh.harvard.edu).
The Survey Committee of ABRF would like to encourage you to participate in their 1999 survey on Biotechnology Salary and Compensation. Please contact Deb McMillen, Chair of the Survey Committee (mcmillen@molbio.uoregon.edu) for information or to obtain a copy of the survey. This 1999 survey will encompass all members of the ABRF around the world and will address compensation, job description and job satisfaction. The last comprehensive survey, entitled Compensation and Employment Profiles in North American Biotechnology Core Facilities, was published by the ABRF Survey Committee in the December 1996 issue of ABRF News (http://www.abrf.org/ABRFNews/1996/December1996/Compensation.html).