Abstract: A method for separating microorganisms, especially infectious agents, from a mixture by two dimensional centrifugation on the basis of sedimentation rate and isopycnic banding density, for sedimenting such microorganisms through zones of immobilized reagents to which they are resistant, for detecting banded particles by light scatter or fluorescence using nucleic acid specific dyes, and for recovering the banded particles in very small volumes for characterization by mass spectrometry of viral protein subunits and intact viral particles, and by fluorescence flow cytometric determination of both nucleic acid mass and the masses of fragments produced by restriction enzymes. The method is based on the discovery that individual microorganisms, such as bacterial and viral species, are each physically relatively homogeneous, and are distinguishable in their biophysical properties from other biological particles, and from non-biological particles found in nature.

Abstract: The present invention provides an integrated, fully automated, high-throughput system for two-dimensional electrophoresis comprised of gel-making machines, gel processing machines, gel compositions and geometries, gel handling systems, sample preparation systems, software and methods. The system is capable of continuous operation at high-throughput to allow construction of large quantitative data sets.

Abstract: The present invention provides an integrated, fully automated, high-throughput system for two-dimensional electrophoresis comprised of gel-making machines, gel processing machines, gel compositions and geometries, gel handling systems, sample preparation systems, software and methods. The system is capable of continuous operation at high-throughput to allow construction of large quantitative data sets.

Abstract: A computer-implemented method analyzes a scanned image of a 2-D electrophoresis gel producing spot specific data (SSD). The computer creates an object pattern of a suitably processed scanned image and uses the spot information in the object pattern in order to warp a master pattern into alignment with the object pattern (and hence the scanned image). The object pattern is replaced with the warped master pattern, augmented by addition of well-defined spots in the object image not present in the warped master pattern, and optimized to fit a processed version of the scanned image. This new object model thus contains identifying and relative position information from the master pattern and other spot specific data (SSD) from the old object model. The new object pattern thereby forms a basis upon which to compare the scanned image with other scanned images similarly processed.

Abstract: The present invention provides an integrated, fully automated, high-throughput system for two-dimensional electrophoresis comprised of gel-making machines, gel processing machines, gel compositions and geometries, gel handling systems, sample preparation systems, software and methods. The system is capable of continuous operation at high-throughput to allow construction of large quantitative data sets.

Abstract: A float is used for preparing a density gradient in a parallel-walled vessel. The float has an outer peripheral surface that has a diameter smaller than an inner diameter of an inner surface of the vessel. With the float placed inside the vessel a liquid is introduced onto the float such that the liquid flows around the float between the float and the inner wall of the vessel. The shape and configuration of the float slows the velocity of the liquid such that there is only laminar flow as the liquid contacts other liquid below the float. Elimination of turbulent flow prevents mixing of different liquid introduced into the same vessel thereby forming layers of fluid. Preferably, the vessel is a centrifuge tube. In one embodiment, the outer diameter of the float is large enough to cause capillary action between the float and the inner surface of the centrifuge tube to force liquid to remain between the float and the inner surface of the centrifuge tube.

Abstract: An apparatus for expressing and unloading an isoelectric focusing gel from an electrophoresis gel tube includes a first support for supporting the gel tube, a plunger rod and a second support for supporting the plunger rod. The first support is mounted on a movable carriage and is moved toward the second support so that the gel tube slides onto the plunger rod to unload the gel from the gel tube. A plurality of gel tubes can be mounted in a rack and the rack coupled to the first support. The first support preferably includes a plurality of openings oriented with the gel tubes for guiding a respective plunger rod through the axial passage of the gel tubes. In preferred embodiments, the second support supporting the plunger rods is substantially stationary while the first support moves toward the second support so that the gel tubes slide onto the plunger rods.

Abstract: A method for separating microorganisms, especially infectious agents, from a mixture by two dimensional centrifugation on the basis of sedimentation rate and isopycnic banding density, for sedimenting such microorganisms through zones of immobilized reagents to which they are resistant, for detecting banded particles by light scatter or fluorescence using nucleic acid specific dyes, and for recovering the banded particles in very small volumes for characterization by mass spectrometry of viral protein subunits and intact viral particles, and by fluorescence flow cytometric determination of both nucleic acid mass and the masses of fragments produced by restriction enzymes. The method is based on the discovery that individual microorganisms, such as bacterial and viral species, are each physically relatively homogeneous, and are distinguishable in their biophysical properties from other biological particles, and from non-biological particles found in nature.

Abstract: An automated assembly for carrying out a first dimension electrophoresis separation of proteins and other macromolecules includes a supply magazine, an automated transferring device and an electrophoresis tank. The tank includes a rack supporting a plurality of gel tubes and includes a chamber for containing a buffer solution in contact with one end of the gel tubes. The assembly includes a planar cover member overlying the tank. The cover member has a plurality of apertures with a guide surface for guiding the pipette through the chamber to the top end of the gel tubes. The supply magazine includes a carousel for storing sample containers, a bar code reader, a holding device and an arm for transferring the sample container from the carousel to the bar code reader and the holding device. The transferring device includes a robotic assembly that is movable in three dimensions for removing a sample from a sample container and delivering the sample to a selected gel tube in the electrophoresis tank.

Abstract: A method for separating microorganisms, especially infectious agents, from a mixture by two dimensional centrifugation on the basis of sedimentation rate and isopycnic banding density, for sedimenting such microorganisms through zones of immobilized reagents to which they are resistant, for detecting banded particles by light scatter or fluorescence using nucleic acid specific dyes, and for recovering the banded particles in very small volumes for characterization by mass spectrometry of viral protein subunits and intact viral particles, and by fluorescence flow cytometric determination of both nucleic acid mass and the masses of fragments produced by restriction enzymes. The method is based on the discovery that individual microorganisms, such as bacterial and viral species, are each physically relatively homogeneous, and are distinguishable in their biophysical properties from other biological particles, and from non-biological particles found in nature.

Abstract: The present invention provides an integrated, fully automated, high-throughput system for two-dimensional electrophoresis comprised of gel-making machines, gel processing machines, gel compositions and geometries, gel handling systems, sample preparation systems, software and methods. The system is capable of continuous operation at high-throughput to allow construction of large quantitative data sets.

Abstract: A method and device for transferring an electrophoresis gel from a cassette to a carrier includes a tray having a dimension to receive a cassette and a carrier device. The tray has a bottom wall with a surface with channels or recesses formed by projections to reduce contact of an electrophoresis gel with the bottom wall of the tray. The projections are typically pyramid-shaped members extending to a peak having a small surface area to prevent the electrophoresis gel from adhering to the bottom wall. The bottom wall also includes a recessed area to receive the carrier so that the gel can slide easily from the cassette to open jaws of the carrier. A retaining arm extends from a side wall of the tray to hold the jaws of the carrier in an open position while the gel is being positioned between the clamping surfaces of the jaws.

Abstract: A computer-implemented image processing method and apparatus for warping a plurality of gel electrophoresis images is provided. The method includes the steps of assigning tiepoints in a reference image and in one or more object images. The tiepoints in the object image are evaluated one-by-one by comparison to regions about a corresponding tiepoint in the reference image, and the location of the tiepoint in the object image is adjusted by slight movement to a location with respect to recognizable features in both the reference and object image thereby defining a tiepoint pair linking a location in the reference image with a location in the object image. outlier tiepoint pairs may be rejected if that pair does not meet predetermined conditions. Warping functions are generated and then globally optimized. The plurality of images are tied together using the tiepoint pairs such that all of the images may be subsequently warped into registration to a single base image selected from the plurality of images.

Abstract: A slab gel processing tank is provided according to the invention. The slab gel processing tank comprises a bottom, two substantially parallel end panels, and two substantially parallel side panels having substantially vertical lower portions and outwardly angled upper portions, with the upper portions being textured to minimize contact with a gel slab, wherein the tank is adapted to be filled with a gel processing working fluid.

Abstract: A method for separating microorganisms, especially infectious agents, from a mixture by two dimensional centrifugation on the basis of sedimentation rate and isopycnic banding density, for sedimenting such microorganisms through zones of immobilized reagents to which they are resistant, for detecting banded particles by light scatter or fluorescence using nucleic acid specific dyes, and for recovering the banded particles in very small volumes for characterization by mass spectrometry of viral protein subunits and intact viral particles, and by fluorescence flow cytometric determination of both nucleic acid mass and the masses of fragments produced by restriction enzymes. The method is based on the discovery that individual microorganisms, such as bacterial and viral species, are each physically relatively homogeneous, and are distinguishable in their biophysical properties from other biological particles, and from non-biological particles found in nature.