The Perkin-elmer Corporation

Genomyx, Inc.

Thermo Separation Products, Inc.

Douglas H Smith

Deborah E Dodge

Timothy M Woudenberg

John S Shigeura

Samuel Ascher Marquiss

Leslie A Miller

Thomas E Davis

Thomas J McCall, Jr

Dean S Burgi

Nicole M Ellis

Richard F Johnson

Charels R Connell

Steven M VanHuystee

Brian J Mifsud

The invention relates the discovery that the polymorphisms in 16S rRNA genes may be used to identify unknown bacterial isolates at the level of species, subspecies and strain identification. The invention also relates to the discovery that the sequences of individual are required. The invention involves the generation of composite polynucleotide sequence of the 16S rRNA genes of a microorganism of interest. The invention is to provide methods for identifying microorganisms. The methods comprise the steps of generating a composite 16S rRNA region sequence from a microorganism of interest. The composite 16S rRNA region sequence reveals polymorphisms within the 16S ribosomal RNA gene of the microorganism. The composite 16S rRNA region sequence may then be compared with a list of previously obtained composite 16S rRNA region sequences from reference microorganisms so as to determine the species, subspecies, or strain of the microorganism of interest. Another aspect of the invention is to provide computer based methods of identifying a microorganism.

Ribosomal RNA gene polymorphism based microorganism identification

The present invention relates to improved methods of generating polynucleotide sequencing reaction products from cycle sequencing and relates to various instruments and reagents for use in the subject methods. The use of 'step-down' thermal profiles in conjunction with cycle sequencing is described. Step-down thermal profiles are formed by combining several thermal cycle sets such that the annealing temperature of each thermal cycle set is less than the annealing temperature of the preceding thermal cycle set. One embodiment of the invention is a method of generating a plurality of polynucleotide sequencing reaction products in parallel by subjecting a plurality of sequencing solution preparations to a step-down thermal profile, i.e., exposure to repeated thermal cycle sets, each thermal cycle set having an annealing temperature that is lower than the annealing temperature of the annealing phases of the preceding thermal cycle set. Other embodiments of the invention include systems for generating a plurality of polynucleotide sequencing reaction products in parallel. The systems comprise (i) a programmable thermal cycler programmed to perform a step-down thermal profile and (ii) a plurality of polynucleotide sequencing preparations. Additional embodiments of the invention include sets of polynucleotide sequencing reaction preparations that may be used in the methods of the invention. Another aspect of the invention is a device for generating a plurality of polynucleotide sequencing reaction products. The devices of the invention include (i) a plurality of polynucleotide sequencing reaction preparation chambers, each chamber containing a sequencing primer, (ii) a common fluid entry port, and (iii) a fluid dispensing channel, the channel connecting each of the sequencing reaction preparation chambers to the common fluid entry port. At least two of the sequencing primers in the device have Tms different from one another by at least 2.degree. C.

Cycle sequencing thermal profiles

Apparatus are disclosed that thermally cycles samples between at least two temperatures. These apparatus operate by impinging fluid jets onto the outer walls of a sample containing region. Because the impinging fluid jets provide a high heat transfer coefficient between the jet and the sample containing region, the sample containing regions are uniformly cycled between the two temperatures. The heat exchange rate between the jets and the sample regions are substantially uniform.

Apparatus for a fluid impingement thermal cycler

A gel electrophoresis separation apparatus comprising, in combination, a gaseous heat-exchange medium, a gaseous heat-exchange medium driving means, and an impingement means, whereby the gaseous heat-exchange medium is driven by the gaseous heat-exchange medium driving means across the impingement means to provide a flow of the gaseous heat-exchange medium on the surface of the gel plates, whereby the flow induced by passage of the gaseous heat-exchange medium through the impingement means thereby minimizes temperature gradients within the gel by forced convection.

Control of temperature gradients during gel electrophoresis using

A vial transport apparatus which is capable of storing and retrieving samples and then transporting them from one location in a sampling system to another without the complexity and expense of robotic arms or gripper elements is provided. A passive hook arrangement is utilized to engage the vials for transport and can be operated using a standard three motor system for transport in the X, Y, and Z directions. The hook supports the vial from beneath and at least partially surrounds the vial to entrap it during transport thereof.

Transport apparatus

A rotary scanning apparatus for scanning a plurality of separation lanes where the separation lanes are disposed in a nonplanar array. The scanning apparatus includes an optical detection system for detecting radiation emanating from the separation lanes, the optical detection system including collection optics for collecting and focusing the radiation, a detector for measuring the intensity of the radiation, and a rotary scanner for providing relative movement between the collection optics and the separation lanes.

Growing community of inventors

Los Altos, CA, United States of America

Douglas H Smith