Abstract
A method has been devised in which a set of oligonucleotides are created and linearly amplified from template structures pre-exiting in genomic DNA without the use pre-synthesized probes or primers. The molecular signatures are composed of oligonucleotides that are 6 to 16 n n    nucleotides in length that can be used to trigger their own exponential amplification. By utilizing adjacent, close, nicking enzyme recognition sites alone or in combination with Type II and TypeIIs restriction endonucleases, which occur in genomic DNA, amplification-templates are generated by coupling a nicking enzyme (N.BstNBI) and a polymerase in an isothermal reaction at 60 C. The "triggers" from the linear amplification can then be coupled to an isothermal method for exponentially amplifying the triggering sequences in true chain reactions. The triggering and amplification reaction can be made a homogenous assay in which 10⁶- 10⁹ -fold amplification can be achieved in as little as 3 minutes. A useful example is taken from E. coli K12 in which 54 unique oligonucleotides can be generated from genomic DNA using two nicking enzymes (N.BstNBI and Alw I). The read-out is accomplished by mass spectrometry (LC-TOF or MALDI) but can also be accomplished using real-time fluorimetry or "self-amplifying arrays". Foreknowledge of the sequence of the individual or organism is not necessary as it is possible to generate the fragments de novo from genomic DNA. This method for creating molecular signatures does not require the denaturation of the genomic DNA thus dramatically reducing the complexity of single strand DNA that has to be surveyed during the assay. The methods described here permit the creation an assay panel of diagnostic oligonucleotides that can identify any organism or individual, measure gene expression, map a haplotype or, in general, create useful biological patterns.

Background
Jeff Van Ness has been working in the biotech area for 20 years, starting with MicroProbe in the mid-80s.  Jeff received two degrees from the University of Colorado, one in Molecular, Cellular and Developmental Biology and one in Chemical Engineering.  He developed the first dipstick diagnostic using tethered oligonucleotides to capture 16s rRNA from different type of pathogens.  He moved to Darwin Molecular in 1994 as a founding Scientist and led a major project that positionally cloned a gene that causes a massive increase in bone mineral density when mutated in humans.  At Darwin he was a founder of a spinout company that developed a new tagging system for mass spectrometry readout.  He moved to the Keck Graduate Institute three years ago with David Galas where they founded Ionian Technologies.  Jeff is the holder of 20 issued US patents, numerous patent applications and publications.
 

Meeting details

Date:	Wednesday	July 23, 2003
Time:	6:00 pm	Social hour, registration (no-host cocktails)
	7:00 pm	Dinner
	8:00 pm	Lecture
Dinner:	Choice of:	Buffet style featuring Roast Turkey, Crab and Shrimp Canneloni and four salads
	includes	(various side dishes & dessert)
Cost:	$25.00	BAMS members.  Reservations required by noon on Friday July 18, 2003
	$35.00	Non-members.  Reservations required by noon on Friday July 18, 2003
	$15.00	Students only.  Reservations required by noon on Friday July 18, 2003

Note: 2003 dues need to be paid to obtain member price.  Dues ($20) may be paid while registering for dinner.

Maps & directions
Michaels at Shoreline
2960 Shoreline Blvd.
Mountain View,  CA  94043
(650) 962-1014
(directions)

As a service to our members, we post Employment postings.

As a trial service to our members, we are now posting Situations Wanted.  (Note: BAMS isn't a career center and will only post brief positions wanted for BAMS members only).

The San Francisco Bay Area Mass Spectrometry discussion group was formed in 1980 to provide a regular gathering for people interested in mass spectrometry and allied topics. BAMS currently has a membership of about 280 individual and 20 corporate members, and meets 8-10 times per year for a midweek dinner and lecture.  Meetings attract between 30 and 90 people, and are held at a restaurant or hotel in the bay area convenient for our speaker.  We usually convene at 6:00 pm for cocktails, dinner at 7:00 pm, and lecture at 8:15 pm.

If you have suggestions for a meeting topic, or know of a prominent mass spectroscopist who will be visiting the bay area, please contact our program chair.

To become a member, please fill out and mail in a membership form.
BAMS has been fortunate to have had many excellent speakers in our short history.
If you have suggestions for a meeting topic please contact our program chair.
If you have questions or comments about BAMS, please contact one of the BAMS officers.
Please thank our corporate sponsors who help keep BAMS membership and dinner costs low.
Here are some internet links that may be of interest to BAMS members.
 

If you have comments or suggestions for this web site, please email me at hugh-gregg@llnl.gov

Last update: 7/11/2003