A TaqMan real-time PCR system for the identiﬁcation
and quantiﬁcation of bovine DNA in meats,
milks and cheeses
, Mark R. Fowler, Nigel W. Scott, Graham Lawson, Adrian Slater*
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
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 identiﬁcation and quantiﬁcation 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 puriﬁed 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-speciﬁc primer pair for the mitochondrial cytb gene and a FAM-labelled mammalian-speciﬁc 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 identiﬁcation and quantitative authentication of animal-derived products.
2006 Elsevier Ltd. All rights reserved.
Keywords: Real-time PCR; Bovine DNA; Quantitative detection; Meat; Milk; Cheese
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 peo-ple are allergic to speciﬁc 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 con-tent. Various religious groups avoid speciﬁc 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.
The fraudulent misdescription of food contents on prod-uct 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 quantiﬁcation of food constituents. This can be diﬃcult 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 identiﬁcation. 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 perfor-mance liquid chromatography (HPLC) (Espinoza, Kirms,
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& Filipek, 1996), enzyme-linked immunosorbent assays (ELISA) (Chen & Hsieh, 2000) or isoelectric focusing pro-tein proﬁles (Skarpeid, Kvaal, & Hildrum, 1998) are eﬀec-tive mainly for unprocessed food and are unable to diﬀerentiate species such as lamb and goat or chicken and turkey. Both require complicated procedures and it has proved diﬃcult to accurately quantify the analytes in a short time (Mayer, 2005). A variety of DNA-based meth-ods including polymerase chain reaction (PCR) ampliﬁca-tion, RFLP mapping and microarray gene chip assay have now been successfully adapted for the detection of food substitution (Peter, Bru¨nen-Nieweler, Cammann, & Bo¨rchers, 2004; Woolfe & Primrose, 2004). DNA based methods have been well received because of the relative sta-bility of the DNA molecule under extreme conditions and its eﬃcient ampliﬁcation by PCR (Lanzilao, Burgalassi, Fancelli, Settimelli, & Fani, 2005; Matsunaga et al., 1999; Mayer, Hoﬄein, Luthy, & Candrian, 1995; Sun & Lin, 2003; Zhang, Zheng, Zhou, Ouyang, & Li, 1999). The lim-itations of standard PCR assays include the insensitivity and lack of quantitation of end-point analysis, and the dependence on a low throughput technique (agarose gel electrophoresis) for analysis of the products. Real-time PCR assay has provided sensitive and safe solutions by monitoring PCR products continuously using ﬂuorescent markers (Heid, Stevens, Livak, & Williams, 1996; Holland, Abramson, Watson, & Gelfand, 1991). Several real-time PCR methodologies have been developed for meat species identiﬁcation and quantiﬁcation using low copy nuclear genes (Laube et al., 2003), high copy genomic short inter-spersed elements (Walker et al., 2003) or mitochondrial genes (Dooley, Paine, Garrett, & Brown, 2004; Hird et al., 2004; Lo´pez-Andreo, Lugo, Garrido-Pertierra, Pri-eto, & Puyet, 2005). The real-time system is applicable to processed or mixed meats as well (Lo´pez-Andreo et al., 2005).
Cows’ milk is more widely available and cheaper than that of goat and water buﬀalo. Cows’ milk is also processed in large quantities to produce a range of dairy produce including a wide variety of cheeses. On the other hand, spe-cialist cheeses such as Greek Feta cheese made from goats’ and sheep’s milk and Italian mozzarella di bufala campana cheese made from water buﬀalo milk, both registered by European law with the Protected Designation of Origin (PDO), have become widely accepted throughout the EU and command a premium price because of their production from more costly milks than cows’ milk. It is also more dif-ﬁcult to stretch out mozzarella cheese prepared from buf-falo milk and to spin it mechanically due to the diﬀerent rheologic characteristics of buﬀalo milk casein compared to cows’ milk casein. Adulteration of goat and water buf-falo milk and their products by cows’ milk is therefore eco-nomically attractive. Their products are traditionally tested for adulteration by immunological and/or electrophoretic methods (Amigo, Ramos, Calhau, & Barbosa, 1992; Cerquaglia & Avellini, 2004; Hurley, Ireland, Coleman, & Williams, 2004; Levieux & Venien, 1994; Mayer, 2005;
Mimmo & Pagani, 1998). Identiﬁcation of milk by PCR ampliﬁcation of DNA is based on the presence of mamma-lian somatic cells in the milk (Herman, 2001). Several sim-plex PCR procedures have been developed for species identiﬁcation in milk, cheese and yogurt based on primers designed to amplify a number of mitochondrial genes: cytochrome b (cytb) (Bania, Ugorski, Polanowsk, & Adamczyk, 2001; Di Pinto, Conversano, Forte, Novello, & Tantillo, 2004; Herman, 2001), D-loop region (Maudet & Taberlet, 2001), 12S ribosomal RNA gene ( Lo´pez-Calleja et al., 2004; Lo´pez-Lo´pez-Calleja et al., 2005), cytochrome oxidase II (Mayer, 2005), cytochrome oxidase I (Feligini et al., 2005), and nuclear encoded genes e.g. coat colour MC1R (Maudet & Taberlet, 2002). Procedures have also been developed for duplex PCR based on cow and buﬀalo-speciﬁc cytb primers (Bottero, Civera, Anastasio, Turi, & Rosati, 2002; Rea et al., 2001), bovine and ovine 12S and 16S rRNA genes (Mafra, Ferreira, Faria, & Oliveira, 2004), and multiplex PCR based on bovine, ovine and caprine 12S and 16S rRNA genes (Bottero et al., 2003). Procedures based on polymerase chain reaction-restriction fragment length polymorphism have also been developed using cytb primers to diﬀerentiate mozzarella cheese made from water buﬀalo milk and from less expensive bovine milk and also Feta cheeses made from bovine, ovine, and caprine milk (Branciari, Nijman, Plas, Di Antonio, & Lenstra, 2000) and ovine yogurt (Stefos et al., 2004). However, most of these procedures are not applicable for accurate quantitative measurement and have the disadvan-tages of conventional PCR discussed above. This study showed that TaqMan real-time PCR is applicable to the authentication of milk and cheese.
2. Materials and methods 2.1. Sample preparation
Fresh and processed meats, milks and cheeses were pur-chased from several national food retailers and/or produc-ers (randomly coded as A–F) in Leicester, UK (Table 1).
Meats and cheeses were cut into small pieces with a hand knife. DNA was isolated using a standard cetyltrim-ethylammonium bromide (CTAB) method (Murray & Thompson, 1980; Zhang et al., 2001). Brieﬂy, about 1.8 g of chopped tissues were mixed with 5 ml of extraction buf-fer and incubated at 65C for 2 h. The above mixture was extracted twice with an equal volume of chloroform and an equal volume of isopropanol was added to the aqueous fraction. After centrifugation the precipitate was washed with ethanol. The dried pellet was dissolved in 0.5 ml ster-ilised Millipore MQ water.
DNA from milks was isolated by the Promega Wizard Magnetic kit following the manufacturer’s instructions as only a small amount of DNA was extracted from fresh whole milk using the CTAB method. Firstly, 3 ml of milk was centrifuged at 13,000 rpm for 10 min. The sediment portions were collected and mixed with 0.4 ml lysis buﬀer
A and 4 ll of RNaseA. This step avoided further process-ing of the cream and skimmed milk fractions which contain lower concentrations of DNA than the sediment (Poms, Glossl, & Foissy, 2001). Further DNA extraction proce-dures followed the manufacture’s instructions. The isolated DNA was eluted from the magnetic beads with 50 ll of MQ water.
All DNA preparations were puriﬁed through a Qiagen silicon spin column and dissolved in MQ water. Initial DNA analysis was carried out using agarose gel electro-phoresis (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 elec-trophoresed 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 spectro-photometer at 260 nm and 280 nm. DNA concentrations of various samples were calculated and further DNA sam-ples 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 buﬀalo milk DNA sample (40 ng/ll) and a goat blood DNA sample (350 ng/ll) were provided by Dr. Isa-bel Gonza´lez, Universidad Complutense de Madrid, Spain.
2.2. PCR primers and probes
PCR primers and probes were based on those described byDooley et al. (2004). Bovine-speciﬁc 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. Ovine-speciﬁc cytb gene primers were Ovicytbf: GAG TAA TCC TCC TAT TTG CGA CA, Ovicytbr: AGG TTT
GTG CCA ATA TAT GGA ATT to amplify a 133 bp fragment. The universal mammalian-speciﬁc cytb gene probe (mammalcytprobe) was TGA GGA CAA ATA TCA TCA TTC TGA GGA GCW ARG TYA. A ﬂuores-cent dye, 6-carboxyﬂuorescein (FAM) was attached to the 50 end of the probe. The quencher moiety,
6-carboxy-tetramethylrhodamine (TAMRA), was added to the 30
end of the probe. The pair of chicken-speciﬁc cytb primers was: Chicytbf: AGC AAT TCC CTA CAT TGG ACA CA, Chicytbr: GAT GAT AGT AAT ACC TGC GAT TGC A to amplify a 133 bp fragment. A universal poul-try-speciﬁc cytb gene probe was ACA ACC CAA CCC TTA CCC GAT TCT TC. TET, 6-carboxy-4,7,20,70
-tetra-chloroﬂuorescein, a ﬂuorescent dye, was attached to the 50 end of the probe. The quencher moiety TAMRA was
added to the 30end of the probe. Turkey and pork-speciﬁc
cytb primer pairs were the same as those described by Doo-ley et al. (2004). The PCR primers were synthesized by Invitrogen and the TaqMan probes were synthesized by Applied Biosystems. The alignment of selected animal cytb sequences was performed using the ClustalW programme (Chenna et al., 2003) and shown inFig. 1.
2.3. Conventional PCR protocol
MJ Research PTC-200 or Techne A thermal cyclers were used in this study. Simple PCR reaction mixtures (50 ll) comprised MQ water 38 ll, 10· buﬀer 5 ll, 25 mM MgCl2
solution 2 ll, 10 mM each dNTPs 0.5 ll, 5 unit/ll Promega Taq polymerase 0.5 ll, primers (25 lM) 1.5 ll each and DNA (32.5–37.5 ng/ll) 1 ll. MQ water (1 ll) instead of DNA was used as a negative control. PCR cycling parame-ters were 95C 4 min, followed by 35 cycles of 94 C 30 s, 60C 1 min, 72 C 1 min, and ﬁnal extension at 72 C 10 min. Duplex PCR reaction mixtures were performed using the same PCR conditions, except that 0.5–2 ll of each primer (25 lM) was used per 50 ll reaction (see Section3.4).
Commercial food products used in general and real-time PCR assays
Products Retailers and/or producers Descriptions
Beef mince E Fresh minced beef
Lamb mince B Fresh minced lamb
Pork mince A Fresh minced pork
Chicken portions A Frozen chicken portion meat
Turkey mince B Fresh minced turkey
Corned beef B Processed beef meat
Steak pie B Cooked beef in pie
Tinned oxtail soup C/F Prepared soup with vegetables and oxtail
Fresh whole cows’ milk B Standardized pasteurised homogenised cows’ milk
Fresh whole cows’ milk C Standardized pasteurised homogenised cows’ milk
Fresh goats’ milk B/D Fresh pasteurised homogenised goats’ milk
Cheddar cheese B Contains milk
Cheese onion and chive quiche A Processed quiche, containing milk, cheese and egg
Somerset goats cheese B Contains milk
Welsh goats cheese A Contains goats’ milk
Italian mozzarella cheese ball B Made in Italy, contains milk
2.4. Real-time PCR protocol
A MJ Research real-time PCR system, Chromo4 Con-tinuous Fluorescence Detector, was used for these experi-ments. Real-time PCR cycling parameters were optimized based on the Chromo4 Fluorescence Detector operation manual as: 50C 2 min, 95 C 10 min, followed by 55 cycles of 95C 15 s, 60 C 45 s, reading products, 72C 1 min, then 72 C 10 min and ﬁnally, melting point analysis. This programme is controlled by Opticon Moni-tor 3 software. Experiments were repeated three to ﬁve times.
Real-time PCR reaction mixtures (25 ll) using the Taq-Man master mix kit (Applied Biosystems) were: MQ water 10 ll, 2· TaqMan master mix 12.5 ll, primers (25 lM) 0.5 ll each, probe (10 lM) 0.5 ll, DNA (minute amount up to 625 ng/ll) 1 ll. The 2· TaqMan master mix is opti-mized for 50 nuclease assay using TaqMan probes and
contains ROX as a passive reference dye, 2 units of Amp-liTaq Gold DNA Polymerase, 0.4 units of AmpErase uracil DNA glycosylase (UNG), 400 lM dATP, dCTP, dGTP with 800 lM dUTP and 6 mM MgCl2. Duplex
PCR reaction mixtures were the same as above with the inclusion of additional primers (0.5 ll each of bovine-spe-ciﬁc cytb primers and 1 ll each of chicken-spebovine-spe-ciﬁc cytb primers) and probes (0.5 ll each of mammalian and poul-try-speciﬁc cytb probe).
General Promega Taq DNA polymerase and buﬀers-based PCR mixture included MQ water 12.75 ll, 10· reac-tion buﬀer 2.5 ll, 25 mM MgCl2solution 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 nega-tive 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. Electro-phoretic proﬁles reﬂecting diﬀerent molecular sizes of PCR products were visualized and analysed as described in Section2.1.
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
Micro-soft Excel Micro-software and a linear regression equation of the Ct value plotted against the log10[DNA amount] was
Fig. 1. Alignment of selected animal cytb sequences using the ClustalW programme indicating the position of the mammalcytprobe, and bovine and ovine-speciﬁc 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 buﬀalo (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 ﬁgure legend, the reader is referred to the web version of this article.)
3. Results and discussion
3.1. Extraction of DNA from fresh and processed foods DNA was isolated from fresh meats, processed meats and cheeses using the standard CTAB method, which was very eﬀective for solid products, and analysed by agarose gel elec-trophoresis (Fig. 2). DNA extracted from fresh beef mince was of relatively good quality, as determined by an A260/
A280 ratio of 1.73 (Table 2) and lack of degradation (Fig 2), and high yield (357.8 lg/g fresh tissue), whilst DNA obtained from cooked, processed cows’ meats was of lower quality (A260/A280ratio of 1.35–1.69), highly degraded (very
little high molecular weight DNA was observed in oxtail
soup) and low yield (33–322 lg/g fresh weight). DNA iso-lated from cheeses and cooked dairy products (quiche) was also degraded with a yield of 34–349.6 lg/g fresh weight (Table 3). Using the Wizard Magnetic kit (a mini-prep sys-tem) small amount (2.4–3 lg/ml) of DNA was extracted from pasteurised cows’ milks. This was not degraded (Fig. 2) and had A260/A280 ratios of 1.44–2.0. The DNA
yields of various products were calculated from the A260
val-ues and are included inTables 2 and 3for reference though these values obtained for highly degraded DNA or samples with a low A260/A280ratio may not be reliable.
3.2. Speciﬁcity of bovine-speciﬁc and ovine-speciﬁc cytb primers
In conventional PCR analysis, the pair of bovine-spe-ciﬁc cytb primers ampliﬁed bovine DNA isolated from beef meat and produced a 116 bp fragment using 1 mM MgCl2
(lane 1 inFig. 3a). No PCR product was obtained using the bovine-speciﬁc primers with DNA extracted from lamb, pork, goat, turkey and chicken tissue and water buﬀalo milk. The pork, turkey and chicken DNA were all PCR positive with corresponding species-speciﬁc primers, indi-cating that the negative reaction was not the result of poor quality DNA or PCR inhibitory contaminants (data not shown). The ovine-speciﬁc cytb primers ampliﬁed 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 buﬀalo samples. The ovine cytb primers did, however, amplify a 133 bp fragment from goat DNA sam-ples at a low eﬃciency.
Bottero et al. (2003) reported that ovine-speciﬁc cytb gene primer ampliﬁed caprine DNAs from a few breeds.
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.
Ctvalues and their derived target DNA amount for DNA extracted from fresh or frozen and processed meats and mixed DNA samples measured by real-time PCR with bovine-speciﬁc cytb primers and a FAM-labelled mammalian-speciﬁc cytb probe
DNA samples DNA yield (lg/g fresh tissue)
A260/A280 Input DNA amount (ng)
Ctvaluea Target DNA amount (ng) derived from Ctvalue
Eﬃciency (target DNA/input DNA· 100)%
Beef DNA 357.8 1.73 ± 0.17 350 18.73 ± 1.90 350 N/A
Beef DNA 357.8 1.73 ± 0.17 35 21.12 ± 1.07 35 N/A
Beef DNA 357.8 1.73 ± 0.17 3.5 24.71 ± 2.42 3.5 N/A
Beef DNA 357.8 1.73 ± 0.17 0.35 27.77 ± 0.95 0.35 N/A
Beef DNA 357.8 1.73 ± 0.17 0.035 32.1 ± 0.83 0.035 N/A
Beef DNA 357.8 1.73 ± 0.17 0.0035 37.03 ± 3.35 0.0035 N/A
Beef DNA 357.8 1.73 ± 0.17 0.00035 55 N/D N/A
Lamb DNA 498.2 1.81 ± 0.14 37.5 54.87 N/D N/A
Pork DNA 673.0 2.12 ± 0.05 32.5 44.23 N/D N/A
Chicken DNA 1104.4 1.90 ± 0.25 70 50.4 N/D N/A
Turkey DNA 2157.2 2.11 ± 0.01 80 51.99 N/D N/A
Beef DNA mixed with lamb and pork DNA
N/A N/A 0.7 + 37.5
(lamb) + 32.5 (pork)
25.81 ± 1.11 1.93 275.71
Beef DNA mixed with lamb and pork DNA
N/A N/A 0.07 + 37.5
(lamb) + 32.5 (pork)
30.67 ± 1.08 0.088 125.71
Corned beef 32.7 1.69 ± 0.08 500 17.94 ± 2.46 287.45 57.49
Steak pie 189.2 1.56 ± 0.22 200 19.30 ± 1.17 121.12 60.56
Tinned oxtail soup 322.0 1.35 ± 0.15 60 35.21 ± 7.01 0.0049 0.0082
Here we observed non-speciﬁc ampliﬁcation of goat DNA with ovine cytb primers at a low eﬃciency (lane 11 in
Fig. 3a). Alignment of the ovine primers with the caprine cytb sequence present in the Genbank database (Accession number X56289) shows that there are four base diﬀerences at the 30end of the primers (Fig. 1), indicating that they are
unlikely to amplify caprine DNA eﬃciently. However, a diﬀerent caprine cytb sequence (AB110597), was identiﬁed with greater similarity at 30 end to the ovine cytb primers
(data not shown). Thus, the ovine primers may be able to amplify certain goat varieties, depending upon the cytb DNA sequence. Lo´pez-Calleja et al. (2005)also reported ampliﬁcation of buﬀalo DNA of a few breeds with a bovine-speciﬁc 12S primer. For the development of a robust quantitative animal products detection system it is necessary to check those primers with DNA from many breeds of cow, sheep and goat.
3.3. PCR ampliﬁcation of DNA from milk and cheese samples
The pair of bovine-speciﬁc cytb primers was able to amplify DNA from cows’ milk and Cheddar cheese (lane
2&3 inFig. 3b). Positive PCR results were also obtained with the Italian mozzarella cheese samples indicating the presence of bovine DNA in those cheeses (lane 4 in
Fig. 3b). Positive PCR results were obtained with goats cheeses DNA using ovine cytb primers whilst negative PCR results were obtained using the bovine-speciﬁc prim-ers, indicating that the negative reactions were not the results of poor quality DNA or PCR inhibitory contami-nants (lane 5 inFig. 3b and data not shown). This conﬁrms previous ﬁndings that there are suﬃcient somatic cells pres-ent in mammalian milk to enable the isolation of DNA of suitable quantity and quality for subsequent PCR ampliﬁ-cation (Herman, 2001).
3.4. Duplex PCR
Duplex PCR for bovine and caprine DNA detection was developed using the bovine and ovine-speciﬁc cytb primers (Fig. 4a). For equal ampliﬁcation of bovine and ovine cytb sequences, 1 ll each of forward and reverse bovine or ovine-speciﬁc primers were optimal for the duplex PCR. No preferential DNA ampliﬁcation was observed. A fur-ther duplex PCR using bovine and chicken-speciﬁc cytb
Ctvalues and their derived target DNA amount for DNA isolated from milks and cheeses measured by real-time PCR with bovine-speciﬁc cytb primers and a FAM-labelled mammalian-speciﬁc cytb probe
DNA samples DNA yield
A260/A280 Input DNA amount (ng)
Ctvaluea Target DNA amount (ng) derived from Ctvalue Eﬃciency (target DNA/input DNA· 100)% B cows’ milkb 3.0 1.44 ± 0.23 25 25.50 ± 0.49 2.36 9.44 C cows’ milkb 2.4 2.0 20 26.05 ± 0.70 1.66 8.30 Cheddar cheese 180.0 1.66 5 28.13 ± 1.76 0.443 8.86 Cheese quiche 258.8 1.27 50 29.68 ± 1.02 0.17 0.34
B Italian mozzarella cheese ball 34.0 1.48 ± 0.18 15 31.86 ± 2.44 0.041 0.27
A Italian mozzarella cheese 35.0 1.63 ± 0.37 150 24.12 ± 2.39 5.66 3.77
Fresh goats’ milkb 0.75 2.00 15.6 55 N/D N/A
Somerset goats cheese 349.6 1.86 ± 0.09 200 55 N/D N/A
Welsh goats cheese 162.7 1.73 ± 0.06 625 55 N/D N/A
Data (average ± SE) represent three repeats. b
DNA amount indicted by lg/ml of milk. N/D, not detectable.
Fig. 3. PCR ampliﬁcation of DNA isolated from meats, milks and cheeses. (a) PCR ampliﬁcation of DNA with bovine and ovine-speciﬁc cytb primers. Lanes 1–7, PCR ampliﬁcation of bovine cytb gene with DNA from fresh beef mince, water buﬀalo milk, lamb mince, goat blood, pork mince, chicken meat and turkey mince respectively; lanes 8–11, PCR ampliﬁcation using ovine cytb gene primers with DNA from fresh beef mince, water buﬀalo milk, lamb mince and goat blood, respectively. (b) PCR ampliﬁcation of DNA using bovine-speciﬁc 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: unﬁlled arrow for the 116 bp bovine sequence and ﬁlled arrow for a 133 bp sequence.
primers was optimized for ampliﬁcation of beef and chicken meats DNA (Fig. 4b). 0.5 ll each of bovine cytb primers and 1 ll each of chicken cytb primers were found
optimal for equal ampliﬁcation of beef and chicken DNAs. These parameters were used in the real-time duplex PCR for simultaneous detection of beef and chicken, or of com-plex foods containing eggs and milk.
3.5. Real-time PCR detection of DNA in meat products Serial dilutions of fresh beef mince DNA with sterilised MQ water were tested in real-time PCR assays (Fig. 5a;
Table 2). The lowest Ct value (18.7) was obtained with
350 ng of beef DNA (Table 2). The lowest quantiﬁable level of bovine DNA was found to be 35 pg with Ctvalues
of about 32. The Ctvalues with high DNA concentrations
are in agreement with those reported (Dooley et al., 2004) using the same primers. However, the sensitivity of this assay is lower than 0.5 pg reported by Walker et al. (2003) using primers and probe for a high copy genomic short interspersed element. The mammalian-speciﬁc cytb probe used here was aligned with various cytb genes (Fig. 1). It was observed that the published sequence ( Doo-ley et al., 2004) was not an exact match for the aligned sequences though a reasonable signal was obtained in this study. A modiﬁed universal mammalian-speciﬁc cytb probe, TGA GGA CAA ATA TCA TTY TGA GGR GCW ACR GTY A, is being tested for enhanced sensitivity and wide applications, e.g. for the identiﬁcation of water buﬀalo and goat DNA.
Fig. 4. Duplex PCR ampliﬁcation of mixed meats DNA with bovine and ovine or chicken-speciﬁc cytb primers. (a) Duplex PCR ampliﬁcation 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 unﬁlled and ﬁlled arrows indicate the expected 116 bp bovine/133 bp ovine PCR products, respectively. (b) Duplex PCR ampliﬁcation 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 unﬁlled and ﬁlled 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-speciﬁc cytb primers and a mammalian-speciﬁc 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 (350–0.035 ng) in three repeated experiments were used for the construction of standard curve. (For interpretation of the references in color in this ﬁgure legend, the reader is referred to the web version of this article.)
The real-time PCR data were less aﬀected when beef DNA samples were mixed with lamb and pork DNAs. The cross-reactions with other species, i.e. pork, lamb, goat, chicken and turkey were minimal (Tables 2 and 3). Pork DNA (32.5 ng) had a Ct value of 44 which is well
below the Ctvalue of 37 produced by 3.5 pg bovine DNA.
A standard curve was constructed by plotting Ctvalues
against the log10[calculated DNA amount] (350 ng to
35 pg) (Fig. 5b). The linear regression equation, Y = 3.34X + 26.69, R2= 0.924 (signiﬁcant at P = 0.05) was used to calculate DNA amount from a range of DNA samples isolated from processed meats and mixed foods (Table 2). DNA isolated from a number of processed beef products was tested. Corned beef DNA (500 ng) and steak pie DNA (200 ng) produced Ct values of 17.9 and 19.3,
respectively, corresponding to equivalent amounts of fresh meat DNA of 287 and 121 ng. This indicates that despite the extensive degradation of DNA in these products (Fig. 2), ampliﬁcation occurred at around 60% eﬃciency compared to fresh meat DNA. On the other hand, the oxtail soup sample (60 ng) had a low Ctvalue of 35, at the limits of
sensitivity of the calibration curve, corresponding to about an equivalent of 0.005 ng fresh meat DNA. It is not yet clear whether this reﬂects the extensive degradation of DNA in this sample, the presence of PCR contaminants, or the low proportion of bovine DNA in the product.
The bovine cytb real-time PCR system has been devel-oped as bovine products have been the subject of examina-tion. This TaqMan system could be updated to detect dual or multiple forensic subjects in a duplex or multiplex real-time PCR by using other compatible dyes (e.g. TET, VIC) to label other species-speciﬁc probes, i.e. poultry, water buﬀalo or goat-speciﬁc DNA probes. Duplex real-time PCR using bovine and chicken-speciﬁc cytb primer pairs and FAM-labelled mammalian and TET-labelled poultry-speciﬁc cytb probes was carried out based on the optimized duplex PCR described in Section 3.4. A DNA mixture (fresh beef DNA 30 ng, and chicken DNA 35 ng) produced Ctvalues of 22.22 ± 0.66 and 25.15 ± 1.90 which are
com-parable to data obtained using bovine and chicken single species assays respectively developed in this laboratory. For development of further duplex or multiplex real-time PCR assays, primers and probes could be designed based on those reported: e.g. buﬀalo-speciﬁc mitochondrial cytb genes (Bottero et al., 2002; Rea et al., 2001), ovine and cap-rine mitochondrial 12S and 16S rRNA genes (Bottero et al., 2003; Mafra et al., 2004).
It has been demonstrated that the bovine cytb real-time PCR system is useful for the authentication of fresh and processed meats. It may be valuable in the quality assurance of meat products. The amount of DNA and the size of DNA molecule in a food product are related to the proportion of the meat and the method of prepa-ration (Frezza et al., 2003; Matsunaga et al., 1999; Mayer et al., 1995). The amount and quality of DNA extracted from meat may also be aﬀected by the species, breed, tissue, feeding conditions and processing
proce-dures (Li et al., 2006; Zhao et al., 2005; Zhou et al., 2001). One advantage of real-time PCR is that the ampli-con is typically 100 bp, whereas conventional PCR amplicons are several-fold longer. The application of real-time PCR to the authentication of processed meat products in which the DNA may be highly degraded is therefore promising.
3.6. Real-time PCR detection of DNA in milk and cheese products
The quantitative detection of bovine DNA in milks and cheeses was possible using the real-time PCR assay devel-oped for beef meat. The yield of DNA from milk was low, but the DNA appeared to be high molecular weight. The ampliﬁcation pattern of DNA isolated from cows’ milk monitored by real-time PCR was comparable to those obtained with beef meat DNA (data not shown). However, the target DNA amount derived from Ctvalues for DNA
samples of cows’ milk were only 8–9% of the amount of milk DNA in the assay (Table 3).
The quantity and quality of DNA in cheese is thought to be low because the processing of cheeses involves high tem-perature, microorganism and chemical treatments. It is known that there are large numbers of microorganisms involved in the cheese fermentation and ripening process (for example, Rademaker, Hoolwerf, Wagendorp, & te Giﬀel, 2006). DNA from Cheddar cheese and Italian moz-zarella cheese samples gave positive reactions, though with Ct values equivalent to considerably lower amounts of
fresh meat DNA (Table 3). A positive identiﬁcation of bovine DNA in the cheese quiche (containing cows’ milk, Cheddar cheese and hens eggs) was also made (Table 3). Using the duplex real-time PCR assay, a further concen-trated cheese quiche DNA sample produced Ctvalues of
28.11 ± 1.11 (bovine results) and 34.87 ± 2.38 (chicken results). No reaction was recorded with goats’ milk and goats’ cheese DNA, using the bovine cytb primers in real-time PCR.
The amount of target DNA estimated by Ctvalue in the
milks and cheeses used in this study was only a small frac-tion of the equivalent amount of fresh meat DNA. This could indicate that the DNA was of low quality, either due to degradation caused by food processing (in the case of cheese) or the presence of PCR inhibitors which were not suﬃciently removed in the puriﬁcation step. Another possible reason is that the mtDNA amount may be lower in somatic cells in milks than cells in meats, and that there is a considerable amount of microbial DNA in cheese sam-ples. Testing those possibilities and optimizing procedures for DNA extraction and puriﬁcation towards a higher accuracy for DNA quantiﬁcation in milks and cheeses are in progress in this laboratory.
Rea et al. (2001) reported that the amount of DNA recoverable from milk and cheese was directly related to the somatic cell content of the raw milk, and also to the strength of the technique used to process the product, as
this can inﬂuence the yield, integrity and extractability of the DNA. Lo´pez-Calleja et al. (2005) analysed pure (100%) bovine milk including raw, pasteurised and steril-ised samples and found heat-treatment halved the number of somatic cells though PCR ampliﬁcation was less aﬀected. It was thought that the detection of low amounts of cows’ milk adulteration in processed cheese will be diﬃ-cult. We did not analyse samples with known percentages of cow component in mixed goat or water buﬀalo milks or cheeses as ﬁnal DNA amount put into each PCR reac-tion determines the real-time PCR result.
Our results indicate that it is possible to detect bovine sequences in meat mixtures by real-time PCR. They also show that bovine DNA can be detected in cows’ milk and cheeses. The negative results obtained with goats’ milk and cheeses using bovine-speciﬁc primers, compared to the positive results obtained in conventional PCR with ovine-speciﬁc primers suggest that it will be possible to use the real-time procedure to detect adulteration of goat milk products with cows’ milk.
It has been reported that more than half of Mozzarella di buﬀalo (POD) cheeses were contaminated or adulterated with cows’ milk (Bottero et al., 2002; Di Pinto et al., 2004). The procedures described here were able to isolate DNA from mozzarella style cheese and obtain a positive reaction with the bovine DNA real-time assay. The same primers were negative against water buﬀalo milk DNA. This real-time assay will be able to detect the adulteration of water buﬀalo mozzarella with cows’ milk.
3.7. Further consideration of real-time PCR system for bovine DNA detection
The uptake of real-time PCR system by the food indus-try depends on its technical advantages and relatively low cost. The most expensive chemicals in the real-time PCR assay are TaqMan probe and the universal PCR master mix. It was found that general PCR reagents were compatible with TaqMan probes (data not shown) but the sensitivity was reduced. This may indicate the impor-tance of UNG in the universal PCR master mix (Longo, Berninger, & Hartley, 1990).
Real-time PCR system based on SYBR Green chemistry can be a cheap alternative to TaqMan system. SYBR Green directly binds to double stranded DNA and facili-tated detection of PCR products. However, this chemical is thought not to be as sensitive as TaqMan chemistry and does not permit the performance of multiple real-time PCR assays.
The TaqMan bovine cytb real-time PCR system for the identiﬁcation of meats, milks and cheeses is sensitive, quick and safe. Its capability to quantify low levels of bovine DNA (35 pg) will meet the standard required by many authentication measurements. A duplex real-time PCR
sys-tem based on bovine and chicken-speciﬁc cytb primers and probes has also been used to measure DNA amounts in meats, milk and egg products.
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