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Forensics Research Unit/Systems Biology Research Laboratory, Faculty of Health and Life Sciences, De Montfort University,
Hawthorn Building, The Gateway, Leicester, LE1 9BH, UK
Received 22 January 2006; received in revised form 9 July 2006; accepted 16 July 2006
Abstract
Accurate quantitative assays are required for enforcing food labelling procedures and preventing food ingredient contamination,
misdescription and fraud. Simplex and duplex TaqMan real-time PCR systems have been tested for the identication and quantication
of DNA in meat, milk and cheese. DNA was isolated from meat and cheese using a standard CTAB protocol and from milk using a
Promega Wizard Magnetic kit and puried by Qiagen silicon spin columns. High quality DNA isolated from beef mince was used
for standard curve construction in the TaqMan real-time PCR assay using a bovine-specic primer pair for the mitochondrial cytb gene
and a FAM-labelled mammalian-specic cytb probe. The real-time PCR assay can quantitatively detect as little as 35 pg bovine DNA
and showed no cross-reaction with ovine, caprine or porcine DNA. The system has been successfully used to measure bovine DNA in
fresh and processed meat, milk and cheese, and will prove useful for bovine species identication and quantitative authentication of
animal-derived products.
2006 Elsevier Ltd. All rights reserved.
Keywords: Real-time PCR; Bovine DNA; Quantitative detection; Meat; Milk; Cheese
1. Introduction
Food safety, quality and composition have become the
subjects of increasing public concern. Consumers have
been given more choices with regard to food composition
and dietary requirements via food labels. A number of people are allergic to specic molecules in meats, milks or
cheeses. Healthy diet followers tend to prefer chicken
instead of beef, pork or lamb, due to its low dietary fat content. Various religious groups avoid specic meats such as
beef or pork; whilst vegetarians choose not to consume any
meat. Each constituency has an interest in ensuring the
authenticity of the foods that they consume.
*
Corresponding authors.
E-mail addresses: clzhang@dmu.ac.uk (C.-L. Zhang), ads@dmu.ac.uk
(A. Slater).
0956-7135/$ - see front matter 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.foodcont.2006.07.018
The fraudulent misdescription of food contents on product labels is a widespread problem, particularly with high
added-value products commanding a premium price
(Woolfe & Primrose, 2004). There can be intentional or
unintentional contamination in the production chain or
during processing. Proving conclusively that adulteration
or contamination has occurred requires the detection and
quantication of food constituents. This can be dicult
because the materials replaced are often biochemically very
similar and food matrices are extremely complex and
variable.
Lipid, protein and DNA based methods have been
established for food identication. Lipid analysis is only
applicable for gross measurement of animal-derived fats
(Lumley, 1996; Saeed, Ali, Abdul Rahman, & Sawaya,
1989). Protein-based methods such as high performance liquid chromatography (HPLC) (Espinoza, Kirms,
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Table 1
Commercial food products used in general and real-time PCR assays
Products
Descriptions
Beef mince
Lamb mince
Pork mince
Chicken portions
Turkey mince
Corned beef
Steak pie
Tinned oxtail soup
Fresh whole cows milk
Fresh whole cows milk
Fresh goats milk
Cheddar cheese
Cheese onion and chive quiche
Somerset goats cheese
Welsh goats cheese
Italian mozzarella cheese ball
Italian mozzarella cheese
E
B
A
A
B
B
B
C/F
B
C
B/D
B
A
B
A
B
A
A and 4 ll of RNaseA. This step avoided further processing of the cream and skimmed milk fractions which contain
lower concentrations of DNA than the sediment (Poms,
Glossl, & Foissy, 2001). Further DNA extraction procedures followed the manufactures instructions. The isolated
DNA was eluted from the magnetic beads with 50 ll of
MQ water.
All DNA preparations were puried through a Qiagen
silicon spin column and dissolved in MQ water. Initial
DNA analysis was carried out using agarose gel electrophoresis (1% SeaKem LE agarose gel containing ethidium
bromide). DNA aliquots (12 ll for meats, 15 ll for milks
and 20 ll for cheeses) were loaded into each well and electrophoresed at 75 V/cm for 1.5 h. Electrophoresis gels were
visualized by UV transillumination, photographed and
processed using GeneSnap software. DNA amount and
quality were determined with a Unicam Hekios spectrophotometer at 260 nm and 280 nm. DNA concentrations
of various samples were calculated and further DNA samples were obtained by dilution with MQ water or mixed
with lamb and pork, or chicken DNA (see Section 3 for
details). For serial dilution, 3 ll of DNA solution was
transferred into 27 ll MQ water and mixed thoroughly.
A water bualo milk DNA sample (40 ng/ll) and a goat
blood DNA sample (350 ng/ll) were provided by Dr. Isabel Gonzalez, Universidad Complutense de Madrid, Spain.
2.2. PCR primers and probes
PCR primers and probes were based on those described
by Dooley et al. (2004). Bovine-specic cytochrome b gene
(cytb) primers were Bovcytbf: CGG AGT AAT CCT TCT
GCT CAC AGT, Bovcytbr: GGA TTG CTG ATA AGA
GGT TGG TG to amplify a 116 bp fragment. Ovinespecic cytb gene primers were Ovicytbf: GAG TAA
TCC TCC TAT TTG CGA CA, Ovicytbr: AGG TTT
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Fig. 1. Alignment of selected animal cytb sequences using the ClustalW programme indicating the position of the mammalcytprobe, and bovine and
ovine-specic cytb primers. Bovcytbf and complementary sequence to Bovcytbr are boxed and shown in red colour. Ovicytbf and complementary sequence
to Ovicytbr are boxed and shown in green colour. The cytb sequences shown are: OvisX56284 for lamb (Ovis aries) X56284, CapraX56289 for goat (Capra
hircus) X56289, BubalusD82894 for water bualo (Bubalus bubalus) D82894, BosD34635 for beef (Bos taurus) D34635, SusX56295 for pork (Sus scrofa)
X56295, GallusL08376 for chicken (Gallus gallus) L08376 and MeleagL08381 for turkey (Meleagris gallopavo) L08381. * indicates identical nucleotide
base. (For interpretation of the references in color in this gure legend, the reader is referred to the web version of this article.)
General Promega Taq DNA polymerase and buersbased PCR mixture included MQ water 12.75 ll, 10 reaction buer 2.5 ll, 25 mM MgCl2 solution 5 ll, 10 mM each
dNTPs 1 ll, 5 u/ll Taq polymerase 0.25 ll, primers
(25 lM) 1 ll each, probe (10 lM) 0.5 ll, DNA solution
1 ll. MQ water (1 ll) instead of DNA was used as a negative control.
2.5. Gel electrophoresis of PCR products
Gel electrophoresis with SeaKem LE agarose (1.7% for
general PCR, 3% for duplex PCR) gel containing ethidium
bromide was used to separate the PCR products.
PCR (13 ll) products was loaded onto each well. Electrophoretic proles reecting dierent molecular sizes of
PCR products were visualized and analysed as described
in Section 2.1.
2.6. Data analysis
Primary real-time PCR data were analysed by the Opticon
Monitor 3 software and the threshold cycle (Ct) was
calculated. Replicate standard curves of Ct value (Y) vs
log10[DNA amount] (X) were analysed using Microsoft Excel software and a linear regression equation of the
Ct value plotted against the log10[DNA amount] was
calculated.
Fig. 2. Gel electrophoresis of total DNA extracted from meats, milks and
cheeses. Lane 1, fresh beef mince DNA; lane 2, fresh lamb mince DNA;
lane 3, corned beef DNA; lane 4, steak pie DNA; lane 5, tinned oxtail soup
DNA; lane 6, C cows milk DNA; lane 7, B cows milk DNA; lane 8,
goats milk DNA; lane 9, Welsh goats cheese DNA; lane 10, B Mozzarella
cheese DNA; lane 11, cheese quiche DNA. Lane M1, HindIII digested k
DNA; lane M2, 1 kb DNA ladder.
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soup) and low yield (33322 lg/g fresh weight). DNA isolated from cheeses and cooked dairy products (quiche) was
also degraded with a yield of 34349.6 lg/g fresh weight
(Table 3). Using the Wizard Magnetic kit (a mini-prep system) small amount (2.43 lg/ml) of DNA was extracted
from pasteurised cows milks. This was not degraded
(Fig. 2) and had A260/A280 ratios of 1.442.0. The DNA
yields of various products were calculated from the A260 values and are included in Tables 2 and 3 for reference though
these values obtained for highly degraded DNA or samples
with a low A260/A280 ratio may not be reliable.
3.2. Specicity of bovine-specic and ovine-specic cytb
primers
In conventional PCR analysis, the pair of bovine-specic cytb primers amplied bovine DNA isolated from beef
meat and produced a 116 bp fragment using 1 mM MgCl2
(lane 1 in Fig. 3a). No PCR product was obtained using the
bovine-specic primers with DNA extracted from lamb,
pork, goat, turkey and chicken tissue and water bualo
milk. The pork, turkey and chicken DNA were all PCR
positive with corresponding species-specic primers, indicating that the negative reaction was not the result of poor
quality DNA or PCR inhibitory contaminants (data not
shown). The ovine-specic cytb primers amplied the lamb
mince DNA and produced a 133 bp fragment (lane 10 in
Fig. 3a), but did not amplify DNA from beef, pork turkey
and water bualo samples. The ovine cytb primers did,
however, amplify a 133 bp fragment from goat DNA samples at a low eciency.
Bottero et al. (2003) reported that ovine-specic cytb
gene primer amplied caprine DNAs from a few breeds.
Table 2
Ct values and their derived target DNA amount for DNA extracted from fresh or frozen and processed meats and mixed DNA samples measured by realtime PCR with bovine-specic cytb primers and a FAM-labelled mammalian-specic cytb probe
DNA samples
DNA yield
(lg/g fresh tissue)
A260/A280
Input DNA
amount (ng)
Ct valuea
Target DNA
amount (ng) derived
from Ct value
Eciency
(target DNA/input
DNA 100)%
Beef DNA
Beef DNA
Beef DNA
Beef DNA
Beef DNA
Beef DNA
Beef DNA
Lamb DNA
Pork DNA
Chicken DNA
Turkey DNA
Beef DNA mixed with
lamb and pork DNA
Beef DNA mixed with
lamb and pork DNA
Corned beef
Steak pie
Tinned oxtail soup
357.8
357.8
357.8
357.8
357.8
357.8
357.8
498.2
673.0
1104.4
2157.2
N/A
1.73 0.17
1.73 0.17
1.73 0.17
1.73 0.17
1.73 0.17
1.73 0.17
1.73 0.17
1.81 0.14
2.12 0.05
1.90 0.25
2.11 0.01
N/A
18.73 1.90
21.12 1.07
24.71 2.42
27.77 0.95
32.1 0.83
37.03 3.35
55
54.87
44.23
50.4
51.99
25.81 1.11
350
35
3.5
0.35
0.035
0.0035
N/D
N/D
N/D
N/D
N/D
1.93
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
275.71
N/A
N/A
350
35
3.5
0.35
0.035
0.0035
0.00035
37.5
32.5
70
80
0.7 + 37.5
(lamb) + 32.5 (pork)
0.07 + 37.5
(lamb) + 32.5 (pork)
500
200
60
30.67 1.08
0.088
125.71
17.94 2.46
19.30 1.17
35.21 7.01
287.45
121.12
0.0049
57.49
60.56
0.0082
32.7
189.2
322.0
1.69 0.08
1.56 0.22
1.35 0.15
Data (average SE) represent three repeats. N/D, not detectable. N/A, not applicable.
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Table 3
Ct values and their derived target DNA amount for DNA isolated from milks and cheeses measured by real-time PCR with bovine-specic cytb primers
and a FAM-labelled mammalian-specic cytb probe
DNA samples
DNA yield
(lg/g tissue)
A260/A280
Input DNA
amount (ng)
Ct valuea
Target DNA
amount (ng) derived
from Ct value
Eciency
(target DNA/input
DNA 100)%
B cows milkb
C cows milkb
Cheddar cheese
Cheese quiche
B Italian mozzarella cheese ball
A Italian mozzarella cheese
Fresh goats milkb
Somerset goats cheese
Welsh goats cheese
3.0
2.4
180.0
258.8
34.0
35.0
0.75
349.6
162.7
1.44 0.23
2.0
1.66
1.27
1.48 0.18
1.63 0.37
2.00
1.86 0.09
1.73 0.06
25
20
5
50
15
150
15.6
200
625
25.50 0.49
26.05 0.70
28.13 1.76
29.68 1.02
31.86 2.44
24.12 2.39
55
55
55
2.36
1.66
0.443
0.17
0.041
5.66
N/D
N/D
N/D
9.44
8.30
8.86
0.34
0.27
3.77
N/A
N/A
N/A
a
b
Fig. 3. PCR amplication of DNA isolated from meats, milks and cheeses. (a) PCR amplication of DNA with bovine and ovine-specic cytb primers.
Lanes 17, PCR amplication of bovine cytb gene with DNA from fresh beef mince, water bualo milk, lamb mince, goat blood, pork mince, chicken meat
and turkey mince respectively; lanes 811, PCR amplication using ovine cytb gene primers with DNA from fresh beef mince, water bualo milk, lamb
mince and goat blood, respectively. (b) PCR amplication of DNA using bovine-specic cytb primers. Lane 1, beef mince DNA; lane 2, B cows milk
DNA; lane 3, Cheddar cheese DNA; lane 4, B Italian mozzarella cheese DNA; lane 5, Somerset goats cheese DNA. Arrows indicate the molecular size of
expected PCR products: unlled arrow for the 116 bp bovine sequence and lled arrow for a 133 bp sequence.
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Fig. 4. Duplex PCR amplication of mixed meats DNA with bovine and
ovine or chicken-specic cytb primers. (a) Duplex PCR amplication using
primers for bovine and ovine cytb genes with fresh beef/lamb mince DNA
(15 ng/15 ng). Lane 1, 1 ll ovine primers; lane 2, 0.5 ll bovine primers/1 ll
ovine primers; lane 3, 1 ll bovine primers/1 ll ovine primers; lane 4, 1 ll
bovine primers. The unlled and lled arrows indicate the expected 116 bp
bovine/133 bp ovine PCR products, respectively. (b) Duplex PCR
amplication using primers for bovine and chicken cytb genes with beef/
chicken mince DNA (30 ng/35 ng). Lane 1, 1 ll chicken primers; lane 2,
0.3 ll bovine primers/1 ll chicken primers; lane 3, 0.5 ll bovine primers/
1 ll chicken primers; lane 4, 1 ll each of bovine/chicken primers. The
unlled and lled arrows indicate the expected 116 bp bovine/133 bp
chicken PCR products, respectively. Lane M, 100 bp ladder molecular
marker.
Fig. 5. Real-time PCR graph obtained with bovine DNA using bovine-specic cytb primers and a mammalian-specic cytb probe. (a) Quantitation graphs
of DNA isolated from fresh beef mince. The amount of DNA from 350 ng to 0.035 ng was used and was shown in red, green, blue, yellow and pink colour,
respectively (from left to right). Data from one typical experiment were shown here. (b) A generalised standard curve for real-time quantitation of bovine
DNA. Ct values of fresh beef mince DNA (3500.035 ng) in three repeated experiments were used for the construction of standard curve. (For
interpretation of the references in color in this gure legend, the reader is referred to the web version of this article.)
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