Preparing biological samples for analysis

Abstract

Methods and devices for preparing a biological sample for analysis are described. The biological sample from an organism has at least macromolecule having a primary structure that naturally degrades after the sample is removed from the organism. The method includes causing the biological sample to adopt a shape to permit rapid and uniform heating. The shaped sample is then rapidly and uniformly heated, thereby altering a secondary structure of the macromolecule while preserving its primary structure.

What is claimed is: 
     
         1 . A method for preparing a biological sample for analysis, the sample comprising at least one macromolecule having a primary structure and a secondary structure, the method comprising:
 causing a volume of the sample to adopt a shape wherein the shape permits uniform and rapid heating, thereby forming a shaped sample; and heating the shaped sample so that the secondary structure of the macromolecule is disrupted, but the primary structure is not.   
     
     
         2 . The method of  claim 1 , wherein the method further comprises:
 extracting the biological sample from an organism.   
     
     
         3 . The method of  claim 1 , wherein the causing takes place at a first period of time after extracting the biological sample from an organism, wherein the first period of time is sufficiently short to prevent degradation of the primary structure of the macromolecule. 
     
     
         4 . The method of  claim 3 , wherein the first period of time is 3 minutes. 
     
     
         5 . The method of  claim 3 , wherein the first period of time is 2 minutes. 
     
     
         6 . The method of  claim 1 , wherein the heating is carried out for a second period of time, wherein the second period of time is from about 10 seconds to about 2 minutes. 
     
     
         7 . The method of  claim 1 , wherein the second period of time is up to about 10 seconds. 
     
     
         8 . The method of  claim 1 , wherein the heating includes heating the shaped sample to at least 70° C. 
     
     
         9 . The method of  claim 2 , wherein the organism is a human. 
     
     
         10 . The method of  claim 2 , wherein the organism is an animal. 
     
     
         11 . The method of  claim 1 , wherein the sample is a tissue predominantly in solid phase. 
     
     
         12 . The method of  claim 1 , wherein the sample is predominantly in liquid phase. 
     
     
         13 . The method of  claim 1 , wherein the causing comprises pressing the biological sample into a thin film. 
     
     
         14 . The method of  claim 1 , wherein the shaped sample is a slice that is between about 1 and about 1,000 microns thick. 
     
     
         15 . The method of  claim 1 , wherein the shaped sample is such that no part of it is greater than a threshold distance from a source of heating, and wherein the threshold distance is between 1 mm and 1 cm. 
     
     
         16 . The method of  claim 1 , wherein during the heating, the sample is substantially free of aldehydes or fixative material. 
     
     
         17 . The method of  claim 1 , wherein the causing comprises adding a filler to the biological sample. 
     
     
         18 . The method of  claim 17 , wherein the filler has a similar dielectric constant to a dielectric constant of the biological sample. 
     
     
         19 . The method of  claim 1 , wherein the heating includes irradiating the biological sample with microwave radiation. 
     
     
         20 . The method of  claim 1 , further comprising freezing the sample prior to the heating. 
     
     
         21 . The method of  claim 20 , wherein the freezing comprises reducing the sample to a temperature below −20° C. immediately after extraction from an organism. 
     
     
         22 . The method of  claim 20 , wherein the heating is initiated while the shaped sample is below −20° C. 
     
     
         23 . The method of  claim 20 , wherein the heating is initiated when the shaped sample is above −20° C. for a sufficiently short time to prevent degradation of the primary structure of the macromolecule. 
     
     
         24 . The method of  claim 1 , wherein the causing includes placing the biological sample in a container, reducing the pressure within the container, and sealing the container after reducing the pressure. 
     
     
         25 . A method for preparing a biological sample for analysis, the sample comprising at least one macromolecule having a primary structure and a secondary structure, the method comprising:
 causing a volume of the sample to adopt a shape wherein the shape permits uniform and rapid heating, thereby forming a shaped sample; and heating the shaped sample so that the secondary structure of the macromolecule is disrupted, but the primary structure is not, wherein the heating reduces proteolytic activity by at least 70%.   
     
     
         26 . The method of  claim 25 , wherein the heating reduces proteolytic activity by at least 80%. 
     
     
         27 . A method for preparing a biological sample for analysis, the sample comprising a proteolytic molecule and a polypeptide, wherein the polypeptide have a primary structure and secondary structure, the method comprising:
 heating the biological sample to cause the sample to uniformly attain a temperature at which the activity of the proteolytic molecule is disrupted enough so that the proteolytic molecule are unable to degrade the primary structure of the polypeptide.   
     
     
         28 . The method of  claim 27 , wherein the heating occurs before the proteolytic molecule has reduced the concentration of the polypeptide by 50% relative to a similar sample in a living organism. 
     
     
         29 . A method for preparing a biological sample from an organism for analysis, the sample comprising at least one macromolecule of interest, wherein the macromolecule of interest has a primary structure and a secondary structure, the method comprising:
 causing a volume of the sample to adopt a shape wherein the shape permits rapid and uniform heating, thereby creating a shaped sample; and heating the shaped sample to cause the shaped sample to attain a temperature wherein the temperature causes a secondary structure of a digestive molecule to degrade, wherein the digestive molecule naturally digests the macromolecule of interest when its secondary structure is intact, and wherein the temperature does not cause the primary structure of the macromolecule of interest to degrade.   
     
     
         30 . A system for preparing a biological sample, the system comprising:
 a heat source;   a retaining member in communication with the heat source, and configured to contact the biological sample, and wherein the retaining member conducts heat from the heat source into the biological sample;   a zone in which the biological sample can be held at a controlled temperature; and a transfer element configured to move the biological sample out from the zone and onto the retaining member.   
     
     
         31 . The system of  claim 30 , wherein the temperature of the zone is less than −20° C. 
     
     
         32 . The system of  claim 30 , further comprising a sealing element configured to create a seal around the retaining member when the biological sample is heated. 
     
     
         33 . The system of  claim 32 , further comprising a vacuum pump, wherein the retaining member and the sealing element together form a cavity that is in communication with the pump. 
     
     
         34 . A heating device, comprising:
 a chamber configured to receive a shaped biological sample, wherein the chamber has one or more internal surfaces that are in contact with the biological sample, and wherein the sample is totally contained within the chamber; one or more heating elements in communication with the one or more internal surfaces;   a heat sensor in communication with the one or more internal surfaces; an inlet adapted to permit the sample to be directed into the chamber; and wherein the chamber has a shape so that no part of the sample is greater than 10 mm from a point on any one of the one or more internal surfaces.   
     
     
         35 . A treated biological sample, comprising:
 a sample of biological material that has been extracted from an organism and that has a macromolecule which is not degraded, at least 60% of which has been denatured, per unit volume, as compared to the same macromolecule in the biological material in vivo.   
     
     
         36 . The treated biological sample of  claim 35 , wherein the sample has at least 80% of the macromolecule which has been denatured, per unit volume, as compared to the biological material in vivo. 
     
     
         37 . The treated biological sample of  claim 35 , wherein the sample has at least 99% of the macromolecule which has been denatured, per unit volume, as compared to the biological material in vivo. 
     
     
         38 . The treated biological sample of  claim 35 , wherein the organism is a human. 
     
     
         39 . The treated biological sample of  claim 35 , wherein the sample has a stathmin level that is less than 40% than a stathmin level found in the biological material in vivo. 
     
     
         40 . The treated biological sample of  claim 35 , wherein the sample contains ATP, present in at least 10% of the in vivo ATP level. 
     
     
         41 . The treated biological sample of  claim 35 , wherein the biological sample is free of fixation agents. 
     
     
         42 . The treated biological sample of  claim 40 , wherein the biological sample is free of aldehydes. 
     
     
         43 . A biological sample, prepared according to the method of  claim 1 .