METHOD OF SAMPLING
TECHNICAL FIELD
This invention relates to an improved method for the sampling and storage of biological material.
Reference throughout this specification shall now be made to use of the present invention for sampling DNA for the purposes of profiling using a PCR method. However, this should not necessarily be seen as a limitation.
BACKGROUND ART
DNA testing is widely used in many areas of modern society and is expected to become increasingly important.
In medicine, DNA analysis can provide information on predisposition to inherited genetic diseases, or adverse drug reactions. In public and animal health, DNA analysis can determine the presence and type of a bacterial infection or contamination.
In forensic and evidential applications, DNA profiling can establish the identity of a suspect.
In food regulation and marketing, there is considerable consumer concern about the introduction of genetically modified foods and a desire to know where foods originate. DNA tests can be used to assure the species, origin and GMO status of products.
In plant and animal breeding, DNA tests can be used to select organisms with a beneficial genotype.
However, when primary food items are reduced into saleable portions, the exact origin of material is often lost which means specific product information and potential value is also lost.
In all applications of DNA technologies, the basic first step is to remove a sample of DNA from the living organism or the remains of an organism.
Many methods and devices have been developed for sample collection for subsequent DNA extraction and analysis. Some methods of DNA sampling include the use of blood spot or saliva sampling papers. Such products include FTA™ paper (Whatmann) and S&S Isocode™ papers (Schleicher & Schuell). These are used to store a sample of saliva or a single drop of blood from a heel or thumb prick.
Modifications to these products have been described by PCT/AU96/00344 and US Patent No. 5,496,562 which include the incorporation of Tris-HCl, EDTA and SDS. These chemical elements are included to increase the storage time of DNA held in the matrix of the blotting paper.
Other methods and devices include general-purpose blood sampling devices such as Vacutainer™, and single or multi-use biopsy devices, which remove milligrams or micrograms of tissue.
While these existing systems can often provide an effective sample of DNA for analysis and storage, there are drawbacks that make sampling impractical or inefficient in some situations.
Current techniques are invasive in that the skin must be punctured to obtain a blood sample, or an object inserted into the mouth of the patient to obtain a swab or saliva sample. A less invasive technique that gave the same result would be an
advantage.
In testing of animals, an invasive act or momentary pain caused by sampling often means the animal must be restrained, which may lead to aversion behaviour with repeated sampling.
Blotting paper products also require liquid to be absorbed, making dry surfaces or clotted blood difficult if not impossible to sample with this medium.
Blotting paper, blood or biopsy samplers are all designed to obtain a sample of tissue or internal body fluid of a subject. Sampling of surfaces, for example for the purpose of analysing bacterial contamination, cannot easily be conducted using these methods.
Blotting paper can also become oversaturated with sample, which has implications for sample storage in impregnated papers such as FTA™. Blotting paper can also create large variations in the concentration of a DNA sample, making subsequent DNA analysis more difficult.
Many of the current and future applications of DNA testing require sampling from very large numbers of individuals. In high volume applications, adding an extra step of DNA sampling may be a significant issue. It would thus be advantageous to combine DNA sampling within another existing or necessary step or function.
There are systems in common use which replicate labels down a product chain using bar codes, or trace food products by sequence or batch production. While the systems work with large food items that can be separately labelled, the costs of labelling small or low value items are prohibitive. Food hygiene and safety are also a problem with labels.
Recently systems have been developed that take DNA samples from the animal or plant in its entire form, for example a live animal or carcass. For example, the applicant has developed a cost effective method of sampling DNA from a carcass or primary food item and this is described in Patent Application No. PCT/NZ00/00050. This system, while efficient compared to alternative systems, still adds additional processing steps (taking and labelling of the sample) to the process chain.
It is an object of the present invention to address the foregoing problems or at least to provide the public with a useful choice.
Further aspects and advantages of the present invention will become apparent from the ensuing description which is given by way of example only.
DISCLOSURE OF INVENTION
According to one aspect of the present invention there is provided a method for the sampling and storage of biological material,
characterised by the step of
applying to a sample a self adhesive strip, having
an adhesive, and
a backing substrate
whereupon removing the strip, the adhesive layer removes a protein of biological material for analysis.
The term "biological material" should be taken to mean a representative portion of the sample including some or all constituents of the sample, including but not
limited to DNA, RNA, carbohydrates, fats, protein, bacteria, metabolites and chemical residues.
In preferred embodiments, the present invention may be used for taking a sample of genetic material such as DNA from a meat product.
The term "strip" should not be seen as a limitation, for the device could be of any shape, eg rectangular, circular, oval or so forth.
For ease of reference throughout the specification the self adhesive strip shall herein be referred to as a label. It should be appreciated however that this is given by way of example only and should not be seen as limiting in any way.
In preferred embodiments the adhesive is a glue which does not interfere with the chemistry of DNA analysis or storage of the sample. It should be appreciated that many glue residues interfere with DNA analysis and sample storage.
In further preferred embodiments the adhesive will comply with food safety regulations such that any residue from the adhesive does not pose a threat to public health and is suitable for direct contact with fatty and aqueous foodstuffs.
The adhesive layer may remove a sample of cellular material by direct adhesion and/or may have absorbent properties to facilitate the absorption of cells into the adhesive.
The absorbent properties of the adhesive will also preferably allow liquids to be sampled.
In other embodiments an absorbent material may be combined with the glue coating to facilitate absorbent of liquid samples.
In some embodiments, one and or both the adhesive layer and the backing substrate may also be impregnated with chemicals, for example to extend the storage time of the DNA or to prevent bacterial growth. In other embodiments, the chemical may be an enzyme or enzymes which act to facilitate the removal of cellular material by solubilising the tissue. These features may also be properties of the adhesive alone.
In preferred embodiments the adhesive will bond to the sample substantially simultaneously upon contact, and may remain bonded for any length of time. There is no maximum time limit for the contact of the label with the sample, which may also provide another function such as labelling or identifying the tissue, to be removed at some later time. The minimum time is dictated only by the need to ensure sufficient sample for analysis is removed. Accordingly, the label may perform no other function than removing a DNA sample and may be removed substantially immediately after application.
The adhesive will also preferably remain bonded in a wide range of conditions and temperatures in which the label may be used. For example between +40 °C and - 30°C, and in humid environments.
In preferred embodiments of the present invention there is provided a backing substrate to which an adhesive has been applied.
In preferred embodiments the backing substrate is a white polypropylene or paper base sheet. However, this should not be seen as limiting and the backing substrate may be any material, for example plastic or metal foil.
In another preferred embodiment the backing substrate is coated on one side with a thermal imaging coating and on the other side with an adhesive.
Preferably the product is supplied with the adhesive covered by a protective backing sheet that is removed just prior to use. This ensures the adhesive is kept sterile and free from contamination.
The thermal coating is preferably protected with an additional environmental protection coating to provide resistance to the thermal coating for example from oil, water and/or light. Having an additional protective coating will allow any information' recorded on the label to be preserved.
In preferred embodiments the thermal coating of the label may be printed with identification barcodes or other indica using a thermal printer, just prior to use of the label.
In other embodiments, information may be printed onto the label with ink, or may be incorporated into the label in the form of an electronic or magnetic strip.
In a further preferred embodiment the label and the backing strip may pass through the printer which automatically removes the backing strip and leaves the printed label protruding and readily available for use.
According to one aspect of the present invention there is provided a self adhesive label for use in DNA sampling of a meat product. However, this should not be seen as limiting and the invention could equally be used to remove a DNA sample from any biological material that is harvested and packaged or processed.
In other embodiments it may also be used for non-invasively removing a sample of DNA from a person or animal, for the purposes of DNA profiling or sample storage.
The collection and storage of a sample from an animal carcass after slaughter may
provide a reference sample that can be used for
• DNA profiling,
• to test for bacterial or other contaminants on the carcass;
• to test the sample for the presence or absence of GMO or genes of commercial significance; or
• to identify any tissue from the carcass which is subsequently marketed or purchased.
In preferred embodiments the label serves the purpose of one and or both the identification of a carcass or portion of a carcass during processing and packaging and the purpose of removing a DNA sample from the carcass.
In other embodiments the label may be placed on the tissue and removed substantially immediately, performing no other function than removing a DNA sample.
In preferred embodiments the label will pass through a thermal printer before being placed on the carcass by hand.
In other embodiments an automated adhesive ticket applicator may be used where one ticket at a time is fed into an application pad before being pressed against the carcass.
In preferred embodiments the ticket is attached at the grading station after the animal has been processed.
In preferred embodiments the label will be stuck to a preferred position on the animal, such as the rump or shoulder areas of the carcass. However, any
accessible area of the carcass may be used.
h preferred embodiments a single carcass label may be attached. However, in other embodiments multiple identification tickets could be attached.
In other embodiments, labels may be used to identify portions of the carcass after it has dismembered. These may have been attached prior to dismemberment, or may be attached at this stage.
The label may remain with the carcass for any length of time. In preferred embodiments, the label may remain with the carcass until just prior to dismemberment.
However, label may remain in contact with the carcass for any length of time. Experiments by the applicant have shown labels removed immediately, after two hours or after 24 hours remove sufficient DNA for analysis.
In preferred embodiments the label is removed and placed onto a storage roll. The roll may be formed so the labels from at least one shift or day's production are stored on a single roll.
In preferred embodiments the storage roll may consist of a roll of adhesive with a backing strip separating each layer. However, this should not be seen as limiting and in other embodiments the storage roll may simply be a matrix to which the self-adhesive label adheres and may not have any additional binding properties.
In preferred embodiments the backing strip may be removed and a section of the storage roll exposed. The labels may then be removed from the organism and applied to the storage roll, and the roll reformed with a backing strip to separate successive layers.
In some embodiments, the surface of the storage roll to which the samples are placed may be impregnated with chemicals, to preserve DNA or to identify the presence of bacteria.
In other embodiments the label may simply be folded back on itself, sandwiching the sample between the two sides of the label.
In preferred embodiments an automated dated time stamp may be placed on the roll as the samples are collected.
In other embodiments, the roll when completed may be placed in a storage box and labelled with the date and time, or any other information required to properly identify the sample.
According to another aspect of the present invention there is provided a method substantially as described above for examining the DNA profile from a sample.
In preferred embodiments, labels on a roll can be identified by barcode or time of sample, sequence number or other indica for the purposes of DNA analysis.
To remove a DNA sample from a label, the outer surface of the label, which may potentially contain contamination from handlers or from touching other carcasses may be cleaned with ethanol or briefly irradiated with UV light to cross link any contaminating DNA.
In preferred embodiments, a hole is punched through the label, including the top sheet, backing (storage sheet) and sample sandwiched between. The DNA can then be extracted from the punch and analysed using standard DNA procedures.
The present invention solves many of the problems associated with previous DNA sampling systems, namely: invasiveness; the requirement for fluid transfer and the
potential for overloading.
The present invention also enables DNA sampling to be easily incorporated into systems as part of existing process of device, as it does not add a separate step.
DETAILED DESCRIPTION OF THE INVENTION
As defined above, the present invention is directed to a method of biological sampling and storage using a self adhesive strip.
The invention is based upon the inventors' investigation into the use of an adhesive strip to non-invasively remove a biological sample, without interfering with the chemistry of molecular analysis or storage of the sample.
Non-limiting examples of the invention will now be provided.
Example 1
Laboratory methods
A leg of lamb was purchased from a retail outlet. The lamb was un-wrapped and three 5cm2 patches of a polypropylene label coated with acrylic adhesive (Avery Denison) were placed onto the leg of lamb. One was removed immediately, one was removed after 2 hours and one was removed after 24 hours,
Immediately after removal, the patches were folded into two so that the two adhesive surfaces stuck together sandwiching sample bonded to the adhesive between the backing sheet.
The samples were stored at room temperature until extraction that took place 3 days after original placement of the samples.
To extract DNA a 2mm diameter punch was taken from the folded sampling strip and placed in a 1.5ml microtube
lOOμl of 200mM NaOH was added to the tube containing the strip and the tube placed in a boiling water bath for 15 minutes. After boiling the tube was removed lOOμl of the following neutralizing solution added:
Neutralizing solution recipe (lOOmM Tris-HCl, pH 8.5 with an extra 200mM HCl)
Add 10 ml 1 M Tris-HCL, pH 8.5
Add 1.67 ml cone. HCl
Make up to 100 ml with distilled water.
PCR
1.5 μl of the crude DNA extract from the punch tube was transferred into a well of a 96 well PCR plate. The plate location of each sample was recorded on a laboratory database. lOμl of PCR Cocktail (below) was added, mixed well, overlaid with mineral oil and centrifuged briefly to remove air bubbles. The tray was then placed on a thermocycler and the heated and cooled in the sequence outlined below.
PCR Multiplex Cocktail (final concentrations)
Primers:
McM214A (aag cga etc agg age age ag): 0.5μM
McM214B (FAM aat get tgc att tat caa aag cc): 0.5μM
Magnesium Chloride (GibcoBRL®): 3.0mM
dNTPs: 200μM
PCR Buffer (GibcoBRL®): 20mM Tris-HCl (pH 8.4) 50mM KCl
Taq DNA Polymerase (GibcoBRL®): 0.5U per 20μl
Example cocktail: per 20μl reaction
McM214A(20μM) 0.05μl
McM214B(20μM) 0.05μl
dH2O 13.82μl
PCR Buffer 2.0μl
dNTPs 2.0μl
MgCl2 1.2μl
Taq Polymerase O.lμl
Thermocycler Protocol (MJ Research PTC200)
1 cycle 93.0°C 2 min
35 cycles 93.0°C 30sec
56.0°C 1 min
72.0°C 1 min
1 cycle 72.0°C 5 min
PostPCR Procedure
20μl water was added to PCR product and 2.0μl diluted PCR product transferred to a second 96 well PCR plate. To this, 4.0μl of loading dye (below) was added and the samples were heated to 95.0°C on a heating block or PCR machine for 2 min. 4.0μl of the resulting sample was loaded onto an ABI 377 gel (36cm plate), Run module GS 36C/2400 (Applied Biosystems, Perkin Elmer)
Loading dye
50μl TAMRA genescan-350 (Perkin Elmer)
60μl loading dye (Perkin Elmer)
300μl Formamide
The results of the amplification were compared with amplification of 5ng pure sheep DNA and are shown below. Amplification above 300 units usually provides an acceptable DNA genotype. The range 500-2000 is optimal.
Amplification greater than 2000 may overload the analysis gel, requiring further dilution of the amplicon in the post PCR procedure.
Example 2
The aim of the experiment was to test three different adhesive papers for their suitability for use with the present invention.
The three adhesive papers had different adhesives each produced by Avery Dennison:
A: WLK 202, a water-based acrylic adhesive containing rosin ester tackifiers and surfactants;
B: S2059, a hot melt rubber based adhesive (double coat), including a foil layer between the top sheet and the adhesive and containing a mixture of styrene, butadiene rubbers, hydrocarbon resins, liquid polyterpene resins, antioxidants and waxes.
C: DDX, a hot melt rubber based adhesive containing a mixture of styrene, butadiene rubbers, hydrocarbon resins, liquid polyterpene resins, antioxidants and waxes
There were difference in adhesive coat weight between the 3 adhesive papers:
WLK202 adhesive coat weight range is 20-28 gsm
S2059 adhesive coat weight range is 30-50 gsm
DDX adhesive coat weight range is 30-37 gsm
"gsm" is a term which relates to the weight of adhesive applied in grams per square metre. In these applications it refers to how "thickly" the adhesive has been applied to the paper.
A higher adhesive coat weight increases the ability of the adhesive to attach to difficult surfaces, but may also increase the interference of the glue residues on DNA extraction and analysis.
Experiment:
The adhesive papers were stuck onto a leg of lamb/hogget in two different places, with the papers left in contact with the meat for 3 different time periods.
The experiment was conducted in duplicate under two different temperature conditions.
After sampling the adhesive papers were folded in half onto themselves and stored at 4°C overnight before sub-samples were taken using a 2.5mm punch. Each paper was sampled twice and extracted using two different DNA extraction methods.
The 144 samples were then plated out alongside two positive controls and two negative controls.
Results:
"amplified" means DNA amplified in the PCR reaction from the punch taken.
"consistent" means that both duplicate samples amplified.
"amplified well" means that the amplification detected was at a medium to high level.
Individual Label Performance
LABEL A B C amplified 65% 0% 19% consistently 42% 0% 8% amplified well 19% 0% 10%
Label A (WLK202 adhesive) worked reasonably well with 65% amplification across all the variations in the experiment.
Label B (S2059 adhesive) contains a component which inhibits either the PCR reaction or the DNA extraction as no amplification was observed for label B samples.
Label C (DDX adhesive) may also contain something which inhibits the PCR reaction or the DNA extraction to some extent as only 19% amplification was observed for Label C samples which is too low for practical use.
There did not appear to be a significant difference induced by temperature.
For both the WLK202 and DDX adhesives the sampling from the outside of the cut of meat gave the best result. However contamination from DNA other than the meat being used was found in 7/144 samples and 6/7 of these were sampled from the outside of the meat. This has been observed in previous experiments and may be due to cuts of meat from different animals being in contact with each other. For this reason sampling from a fresh cut may give more reliable results.
For WLK202 and DDX adhesives the one extraction method (DNA extraction at 75°C rather than 100°C) was slightly better than the other.
Discussion
Chemical compounds which are not water soluble cannot be easily removed during the DNA extraction procedure and thus remain in the DNA solution. As such, glue residues must be kept remote from the DNA sampling area or alternatively must not interfere with the PCR process.
A number of the chemical components of the S2059 and DDX adhesives are not water soluble and thus are expected to remain in the DNA solution. The lack of consistent PCR amplification from these samples demonstrates that the S2059 and DDX adhesives contain at least one component which inhibits either the PCR reaction or DNA extraction.
Whilst the chemical compositions of the S2059 and DDX adhesives are similar, there are significant differences in the amount of glue on the papers (adhesive coat weight). This may explain the observation that whilst a small degree of amplification occurred from DNA extracted from the DDX adhesive, no amplification was observed from S2059, despite seemingly similar chemical compositions.
S2059 also includes a number of mineral fillers such as inert metal salts, for example calcium carbonate. High concentrations of such salts are also likely to interfere with DNA extraction and analysis.
Without long, difficult and expensive testing, it is not possible to determine exactly which components are inhibiting the PCR reaction. A skilled addressee would understand the are a number of chemicals in adhesives which would likely affect PCR reactions, alone or in combination which other chemicals. Further, components of the adhesive may react to chemicals used during the DNA extraction process.
As such, it is more important to identify adhesives which do not interfere with DNA extraction and analysis, rather than concentrating on those that do.
One of the key difficulties that the inventors have overcome is that the chemistry of many types of glue can interfere with the chemistry of the DNA analysis and
the storage of the samples. Typically manufacturers of DNA sampling products have constructed the product so that glues or other chemical binders are remote from the DNA sampling area.
The inventors have demonstrated that products and methods can be developed where adhesive does not interfere appreciably with the PCR process. Alterations to constriction of samplers, glue products, DNA extraction and PCR may well provide systems with the same or better utility.
BRIEF DESCRIPTION OF DRAWINGS
Further aspects of the present invention will become apparent from the following description which is given by way of example only and with reference to the accompanying drawings in which:
Figure 1 is a diagrammatic illustration of the construction of the self- adhesive tissue sampling label; and
Figure 2 illustrates the printing and delivery of self-adhesive label; and
Figure 3 illustrates the removal and storage of the self-adhesive label; and
Figure 4 illustrates the removal of a sample for analysis.
BEST MODES FOR CARRYING OUT THE INVENTION
With respect to the drawings, there is provided a method for DNA sampling and storage, using a self adhesive strip as indicated by arrow 1.
The self adhesive label (1) has an adhesive layer (2). The adhesive is applied to a backing substrate (3), such as a label.
The backing substrate (3) is coated on one side with a thermal imaging coating (4) and on the other side with the adhesive (2).
The thermal coating (4) is protected with an additional environmental protection coating (5) to provide resistance to contamination.
In one preferred embodiment of the present invention with reference to figure 2, the label (1) is constructed and stored in a roll (6) with the adhesive (2) covered by a protective backing sheet (7) that is removed just prior to use. This ensures the adhesive is kept sterile and free from contamination.
The self adhesive label (1) is fed through a thermal printer (8) just prior to the ticket being applied to the sample of interest. The label (1) in the backing strip (6) pass through the printer (8), automatically removing the backing strip (6) leaving the printed label (1) available to be placed onto the sample by hand.
The printer (8) can print the thermal coating (4) of the label with identification barcodes or other information.
The self-adhesive label (1) is then placed onto the carcass (9) requiring identification and DNA sampling as shown in Figure 3. The self-adhesive label (1) may remain in contact with the sample (9) for any length of time. When the label (1) is removed from the carcass (9) a sample of tissue is removed attached to the ticket by adhesion and/or absorption, it is then placed onto a storage roll (10). The roll (10) is formed so the labels (1) from at least one shift or day's production are stored on a single roll.
The storage roll (10) consists of a roll of adhesive with a backing strip (11) separating each layer. The backing strip (11) is removed and a section of the adhesive storage roll is exposed adhesive side out.
The self adhesive labels (1) are applied to the storage roll (10), then the roll reformed with a backing strip (11) to separate successive layers of the roll (12).
An automated date time stamp is placed on the roll as samples are collected.
After the roll is removed it can be accessed to conduct a DNA profile from the sample as shown by Figure 4.
To conduct the required DNA analysis the labels (1) on a roll (10) which are to be analysed are identified by barcode or time of sample, sequence number or other indica.
To sample a label (1), the outer surface of the label which may potentially contain contamination from handlers or from touching other surfaces is cleaned with ethanol, or briefly irradiated with UV light to cross link any contaminating DNA.
A punch (13) removes a 2 millimetre disc (15) that includes the top sheet (3), backing storage sheet (10) and sample sandwiched between, which is then placed into a 1.5 ml tube (14).
The DNA can then be extracted and analysed using standard DNA techniques.
Aspects of the present invention have been described by way of example only and it should be appreciated that modifications and additions may be made as defined in the appended claims.