CN103436610A - PCR-RFLP rapid detection method for common sturgeons - Google Patents
PCR-RFLP rapid detection method for common sturgeons Download PDFInfo
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Abstract
The invention relates to the field of molecular biology and taxonomy and discloses a PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) rapid detection method for common sturgeons as well as a primer and a kit for the rapid detection method. The PCR-RFLP rapid detection method for the common sturgeons comprises the following steps: firstly, extracting a genome DNA (Deoxyribose Nucleic Acid) of a sample to be detected as a template; secondly, carrying out PCR amplification reaction to obtain a PCR product by taking the genome DNA as the template; thirdly, digesting the PCR product by using restriction endonuclease to obtain a digested product; fourthly, carrying out agarose gel electrophoresis detection on the PCR product and the digested product and identifying species according to electrophoretogram. According to the PCR-RFLP rapid detection method disclosed by the invention, the simplicity in operation is realized; a small amount of fin rays or muscle is needed to be sheared on the basis of ensuring the survival of fingerling; the identification of fingerlings of the common sturgeons is quickly and accurately carried out; the accuracy and the reliability of the identification result are improved; the working efficiency is greatly increased.
Description
Technical field
The present invention relates to molecular biology and taxonomy field, particularly the PCR-RFLP method for quick of a kind of common sturgeons.
Background technology
Sturgeon (sturgeon) is under the jurisdiction of Osteichthyes (Osteichthyes), Actinopterygii (Actinopterygii), hard shell catalogue (Ganoidomorpha), Gadiformes (Acipenseriformes), and the whole world has 27 kinds of 2 sections' 6 genus now.China has 2 sections 3 to belong to 8 kinds within the border, be respectively Amur Sturgeon (Acipenser schrenckii), Da Shi huso sturgeon (Huso dauricus), mandarin sturgeon (Acipenser sinensis), Da Shi huso sturgeon (Acipenser dabryanus), paddlefish (Psephurus gladius), siberian sturgeon (Acipenser baerii), sterlet (Acipenser ruthenus), naked abdomen sturgeon (Acipenser nudiventris), sturgeon is the ancient cartilage ganoid of a class, and the title of " living fossil " is arranged.These ancient sturgeons are all in Critical Condition in various degree, the danger that extinction is arranged even had.The sturgeon ovum is nutritious, and the sturgeon caviar of being processed into its ovum is expensive, is internationally recognized luxurious food materials, is compared to " black gold ".
Carry out in the world at present the method that the sturgeon Identification of Species mainly adopts and comprise the methods such as morphology, biological chemistry and genetics.The use AFLP molecule marking methods such as Congiu have carried out the discriminating application of sturgeon and caviar product, and the use RAPD molecule markers such as Chelomina carry out cross-fertilize seed discriminatory analysis in the Amur Sturgeon Natural Population.The research that the plastosome of take is studied the sturgeons evolutionary relationship as material is reported relatively also more.Mainly concentrate on the genes such as plastosome D-loop Sequence, cytochrome B, 12s rRNA, 16s rRNA.To the research discovery of mitochondrion DNA control area, all there is heterogeneous phenomenon in the sturgeon Mitochondrial DNA of a plurality of kinds.Recent domestic mitochondrion DNA control area sequence commonly used and microsatellite DNA mark are carried out the Molecular Identification of sturgeon.Although these technique means can be in various degree, sturgeon and sturgeon product are carried out relatively identifying accurately,, also there are the shortcomings such as technological operation is loaded down with trivial details, qualification time length, apparatus expensive, and higher to operator's technical requirements.
Given this, need develop and can fast, accurately detect the molecular detection technology of mandarin sturgeon and other common sturgeons, for purposes such as market surpervision, Idioplasm identification.
Summary of the invention
One of the object of the invention is to provide the PCR-RFLP method for quick of a kind of common sturgeons.The present invention has used less reagent and convenient and swift maneuverable experimentation, can within a short period of time, on the basis of not putting to death fingerling, only need a small amount of fin ray of clip or muscle, and fast and accurately mandarin sturgeon and other common sturgeon kinds are distinguished.
The PCR-RFLP rapid detection test kit of a kind of common sturgeons, is characterized in that, comprising: primer pair and
Primer pair
The conventional reagent of PCR: Taq archaeal dna polymerase, 10 * buffer PCR damping fluid, MgCl
2and dNTPs;
And enzyme is cut reagent: 10 * buffer enzyme cutting buffering liquid, 100 * BSA and Taq α 1 restriction enzyme.
Preferably, described primer pair is:
Upstream primer, it is the polynucleotide sequence shown in SEQ ID No.1;
Downstream primer, it is the polynucleotide sequence shown in SEQ ID No.2.
The PCR-RFLP method for quick of a kind of common sturgeons, is characterized in that, right to use requires 2 described test kits to comprise the following steps for the PCR-RFLP method for quick of common sturgeons:
Preferably, the reaction system of described pcr amplification reaction is 15 μ l: be that to add 0.1 μ l concentration in 200 μ l PCR reaction tubess be 2, the Taq archaeal dna polymerase of 500units/mL, 1.5 μ l10 * buffer PCR damping fluid, 1.5 the dNTPs that μ l concentration is 10pm/ μ l, 1.2 μ l25mM MgCl
2, the described genomic dna of 2 μ l, the described upstream primer that 0.5 μ l concentration is 10pm/ μ l, the described downstream primer that 0.5 μ l concentration is 10pm/ μ l and 7.7 μ l sterilized waters.
Preferably, the reaction conditions of described pcr amplification reaction is 94 ℃ of denaturation 5min, then 94 ℃ of pre-thermally denature 30s, 58 ℃ of couplings annealing 30s, 72 ℃ extend 45s, from preheating, be annealed to and extend 35 circulations of coreaction, then 72 ℃ are extended 10min.Preferably, described restriction enzyme is Taq α 1.
Preferably, the reaction system of described endonuclease reaction is 20 μ l: be and add the described PCR product of 1 μ l in 200 μ l PCR reaction tubess, 2 μ l10 * buffer enzyme cutting buffering liquid, 0.2 μ l100 * BSA, 0.5 μ l Taq α 1, add sterilized water to 20 μ l, then by described endonuclease reaction system at 65 ℃ of incubation reaction 1h, 80 ℃ of heat inactivation 20min.
Preferably, described common sturgeon kind is mandarin sturgeon, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and Acipenser gueldenstaedti Brandt.
Preferably, the PCR-RFLP method for quick of described common sturgeons can be used for distinguishing in mandarin sturgeon and Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon or Acipenser gueldenstaedti Brandt any.
Preferably, phosphodiester bond between 586 and 587 bases that described restriction enzyme Taq α 1 restriction enzyme site is polynucleotide sequence 5` in the described PCR product of mandarin sturgeon, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and Acipenser gueldenstaedti Brandt do not have described restriction enzyme site; In the described PCR product of mandarin sturgeon, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and Acipenser gueldenstaedti Brandt, the amplifying polynucleotides sequence is respectively sequence shown in SEQ ID No.3, SEQ ID No.4, SEQ ID No.5, SEQ ID No.6, SEQ ID No.7, SEQ ID No.8, SEQ ID No.9 and SEQ ID No.10.
The invention has the beneficial effects as follows that the inventive method is according to the Site discrepancy existed between mandarin sturgeon and Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon or Acipenser gueldenstaedti Brandt Mitochondrial DNA, the detection method of cutting by pcr amplification technology and enzyme is differentiated mandarin sturgeon and other common sturgeons.The inventive method only need be extracted the genomic dna of sample to be detected, and described primer pair can carry out amplified reaction by specific joint line mitochondrial DNA.The present invention has used less reagent and convenient and swift maneuverable experimentation, can within a short period of time, on the basis of not putting to death fingerling, only need a small amount of fin ray of clip or muscle, and identify fast and accurately fingerling.The present invention is conducive to actual production department, and scientific research department's Rapid identification samples this, has increased accuracy and the confidence level of qualification result, has greatly improved working efficiency.
The term definition arrived involved in the present invention
Unless otherwise defined, otherwise all technology used herein and scientific terminology all have with those skilled in the art and usually understand identical implication.Although can use any method, device and the material similar or equivalent with person described herein in practice of the present invention or test, describe now preferred method, device and material.
Term " polynucleotide " means deoxyribonucleotide (DNA), dezyribonucleoside, ribonucleoside or ribonucleotide (RNA) and the polymkeric substance thereof of sub-thread or bifilar form.Unless specific limited, otherwise the nucleic acid of the known analogue that contains natural nucleotide contained in described term, described analogue has the binding characteristic that is similar to reference nucleic acid and carries out metabolism in the mode of the Nucleotide that is similar to natural generation.Unless other specific limited, otherwise described term also means oligonucleotide analogs, it comprises PNA (peptide nucleic acid(PNA)), DNA analogue (thiophosphatephosphorothioate, phosphamide acid esters etc.) used in antisense technology.Unless otherwise, otherwise specific nucleic acid sequence is also impliedly contained its conservative varient of modifying (including, but is not limited to degenerate codon replaces) and complementary sequence and the clear and definite sequence of appointment.
Term " PCR " means polymerase chain reaction (Polymerase Chain Reaction), is called for short PCR.Polymerase chain reaction (PCR) is a kind of method of the synthetic specific DNA fragment of external enzymatic, by a few step reaction composition one-period such as high-temperature denatured, low-temperature annealing (renaturation) and thermophilic extensions, loop, make target DNA be able to rapid amplification, there is high specificity, highly sensitive, easy and simple to handle, the characteristics such as save time.It not only can be used for the fundamental researchs such as gene isolation, clone and nucleic acid sequence analysis, also can be used for the diagnosis of disease or the place of any DNA of having, RNA. polymerase chain reaction (Polymerase Chain Reaction is called for short PCR) claims again cell-free molecular cloning or the directed enzymatic amplification technique of the external primer of specific DNA sequences.
Term " PCR-RFLP detection method " means polymerase chain reaction-restriction fragment length polymorphism detection method, it is a kind of employing polymerase chain reaction (PCR) amplification target DNA fragment, then by DNA fragmentation digestion with restriction enzyme to be detected, special sequence is identified and cut to restriction enzyme, then the product after enzyme being cut carries out electrophoresis, analyzed again the special restriction enzyme site of this section sequence by restriction endonuclease map (restriction map), compare the otherness of different sources gene order by the diversity of fragment.
Term " primer " means a bit of single stranded DNA or RNA, starting point as DNA replication dna, unless specific limited, otherwise the primer (being generally DNA primer) of synthetic in DNA replication dna biological in nature and polymerase chain reaction (PCR) contained in described term.Archaeal dna polymerase why need primer to be because only can be added to new Nucleotide on existing DNA chain in DNA is synthetic.Unless specific limited, upstream primer is when DNA replication dna, the primer of the replication origin of holding as DNA profiling 3`, downstream primer is when DNA replication dna, the primer of the replication origin of holding as DNA profiling 5`.
Term " agarose gel electrophoresis " means a kind of electrophoresis method of making supporting dielectric with agar or agarose.By the molecular sieve effect of sepharose, polynucleotide passage is because of its molecular weight or shape of molecule difference, and the electrophoresis translational speed is variant and separate, and is important method commonly used in genetic manipulation.
Term " restriction enzyme " means the enzyme that a class has in vivo; they can cut off external DNA; can limit the intrusion of allogeneic dna sequence DNA and make it to lose vigor, but to oneself the harmless effect of DNA, like this can the original genetic information of Cell protection.Restriction enzyme described in the present invention is Taq α 1.
Term " archaeal dna polymerase " means the enzyme that a class plays an important role in the process of cellular replication DNA, with DNA for copying template, from DNA is started to copy to the enzyme of 3 ' end by 5 ' end points.The main activity of archaeal dna polymerase is the synthetic and mutually auxiliary activity of catalytic dna.The polysaccharase of TaqDNA described in the present invention can be used long-chain Taq archaeal dna polymerase, better effects if in long-chain DNA synthetic.
Term " damping fluid " means a class when in some solution, adding a certain amount of bronsted lowry acids and bases bronsted lowry, and the solution that hinders pH value of solution variation effect is arranged.
The accompanying drawing explanation
The agarose gel electrophoresis figure that the described PCR product that Fig. 1 is mandarin sturgeon of the present invention, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and Acipenser gueldenstaedti Brandt and described enzyme are cut product.
Embodiment
Below in conjunction with accompanying drawing, the present invention is described in further detail, to make those skilled in the art, with reference to the specification sheets word, can implement according to this.
Embodiment 1:
Extract the genomic dna of detected sample, recommend adoption DNA extraction test kit extracts genomic dna:
A) the known mandarin sturgeon of difference clip, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and each tail fin sub-fraction of Acipenser gueldenstaedti Brandt, the about 0.5g fin ray of clip, shred, and puts into respectively the 1.5mL centrifuge tube and be numbered 1~8;
B) add 0.45mL Pehanorm base ethyl sulfonic acid (TES) to mix, add the sodium laurylsulfonate (SDS) that 50 μ l mass concentrations are 10%, 5.0 μ l concentration are the 20mg/mL Proteinase K, after fully mixing again, in 56 ℃ of insulation 4-6h, every 2h shakes 1 time.
C) after insulation 4-6h, by step b) in be placed into room temperature containing the 1.5mL centrifuge tube of mixed solution, add the saturated phenol of equal-volume (500 μ l), put upside down and mix, 12000rpm, centrifugal 10min, water phase separated and organic phase, the careful water of upper strata containing nucleic acid of drawing, in a new 1.5mL centrifuge tube.
D) by step c) add equal-volume phenol in the 1.5mL centrifuge tube of isolated water: chloroform: primary isoamyl alcohol (25: 24: 1), put upside down and mix, 12000rpm, centrifugal 10min, get supernatant liquid and transfer in new 1.5mL centrifuge tube.
E) by steps d) in add the equal-volume chloroform in the 1.5mL centrifuge tube of the supernatant liquor that finally obtains: primary isoamyl alcohol (24: 1), put upside down and mix, 12000rpm, centrifugal 10min, get in supernatant liquid to a new 1.5mL centrifuge tube.
F) by step e) in add the dehydrated alcohol precipitation genomic dna of-20 ℃ of precoolings of 2.5 times of volumes in the 1.5mL centrifuge tube of the supernatant liquor that finally obtains, observe supernatant liquor in the 1.5mL centrifuge tube and produce gradually muddiness.
G) 12000rpm, centrifugal 10min, genomic dna is separated out, and is attached to the centrifuge tube bottom, removes ethanol.
75% washing with alcohol of h)-20 ℃ of preservations, 12000rpm, centrifugal 5min, remove ethanol, 55 ℃ of dry genomic dnas.
I) add 20 μ l sterilized waters to dissolve genomic dna ,-20 ℃ save backup.
Embodiment 2:
The rapid detection of common sturgeon kind
Use the inventive method and described test kit to carry out the rapid detection of common sturgeon kind, comprise following concrete steps:
Above-mentioned PCR system is loaded in 200 μ l PCR pipes, the PCR pipe that the PCR system is housed is put into to the pcr amplification instrument and carry out pcr amplification, described pcr amplification reaction reaction conditions is 94 ℃ of denaturation 5min, then 94 ℃ of sex change 30s, 58 ℃ of annealing 30s, 72 ℃ extend 45s, from preheating, be annealed to and extend 35 circulations of coreaction, 72 ℃ are extended 10min, after having reacted, the PCR product are put into to 4 ℃ and save backup;
Although embodiment of the present invention are open as above, but it is not restricted to listed utilization in specification sheets and embodiment, it can be applied to various applicable the field of the invention fully, for those skilled in the art, can easily realize other modification, therefore do not deviating under the universal that claim and equivalency range limit, the present invention is not limited to specific details and illustrates here and the legend of describing.
Claims (9)
1. the PCR-RFLP rapid detection test kit of a common sturgeons, is characterized in that, comprising:
Primer pair
The conventional reagent of PCR: Taq archaeal dna polymerase, 10 * buffer PCR damping fluid, MgCl
2and dNTPs;
And enzyme is cut reagent: 10 * buffer enzyme cutting buffering liquid, 100 * BSA and restriction enzyme Taq α 1.
2. the PCR-RFLP rapid detection test kit of common sturgeons as claimed in claim 1, is characterized in that, described primer pair is:
Upstream primer, it is the polynucleotide sequence shown in SEQ ID No.1;
Downstream primer, it is the polynucleotide sequence shown in SEQ ID No.2.
3. the PCR-RFLP method for quick of a common sturgeons, is characterized in that, right to use requires the PCR-RFLP method for quick of 2 described test kits for common sturgeons, comprises the following steps:
Step 1, extract the genomic dna of detected sample as template;
Step 2, the reagent and the primer pair that use described test kit to comprise described genomic dna are mixed with the PCR system, and the PCR system be mixed with is put into the pcr amplification instrument will carry out pcr amplification, after having reacted, the PCR product be put into to 4 ℃ and save backup;
Step 3, with the described PCR product of digestion with restriction enzyme, obtain enzyme and cut product;
Step 4, cut product race agarose gel electrophoresis by described PCR product and described enzyme, according to electrophorogram, carries out the species evaluation.
4. the PCR-RFLP method for quick of common sturgeons as claimed in claim 3, it is characterized in that, the reaction system of described pcr amplification reaction is 15 μ l: be that to add 0.1 μ l concentration in 200 μ l PCR reaction tubess be 2, the Taq archaeal dna polymerase of 500units/mL, 1.5 μ l10 * buffer PCR damping fluid, 1.5 μ l25mM MgCl
2, the dNTPs that 1.2 μ l concentration are 10pm/ μ l, the described genomic dna of 2 μ l, the described upstream primer that 0.5 μ l concentration is 10pm/ μ l, the described downstream primer that 0.5 μ l concentration is 10pm/ μ l and 7.7 μ l sterilized waters.
5. the PCR-RFLP method for quick of common sturgeons as claimed in claim 3, it is characterized in that, the reaction conditions of described pcr amplification reaction is 94 ℃ of denaturation 5min, then 94 ℃ of sex change 30s, 58 ℃ of annealing 30s, 72 ℃ extend 45s, from preheating, be annealed to and extend 35 circulations of coreaction, then 72 ℃ are extended 10min.
6. the PCR-RFLP method for quick of common sturgeons as claimed in claim 3, it is characterized in that, the reaction system of described endonuclease reaction is 20 μ l: be and add the described PCR product of 1 μ g in 200 μ l PCR reaction tubess, 2 μ l10 * buffer enzyme cutting buffering liquid, 0.2 μ l100 * BSA, 0.5 μ l Taq α 1 and add sterilized water to 20 μ l, then by described endonuclease reaction system at 65 ℃ of incubation reaction 1h, 80 ℃ of heat inactivation 20min.
7. the PCR-RFLP method for quick of common sturgeons as claimed in claim 3, is characterized in that, described common sturgeon kind is mandarin sturgeon, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and Acipenser gueldenstaedti Brandt.
8. the PCR-RFLP method for quick of common sturgeons as claimed in claim 7, it is characterized in that, the PCR-RFLP method for quick of described common sturgeons can be used for distinguishing in mandarin sturgeon and Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon or Acipenser gueldenstaedti Brandt any.
9. the PCR-RFLP method for quick of common sturgeons as claimed in claim 8, it is characterized in that, phosphodiester bond between the 586th and 587 bases that described restriction enzyme Taq α 1 restriction enzyme site is polynucleotide sequence 5` in the described PCR product of mandarin sturgeon, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and Acipenser gueldenstaedti Brandt do not have described restriction enzyme site; In the described PCR product of mandarin sturgeon, Amur Sturgeon, siberian sturgeon, sterlet, Da Shi huso sturgeon, Ou Huang, flash of light sturgeon and Acipenser gueldenstaedti Brandt, the amplifying polynucleotides sequence is respectively sequence shown in SEQ ID No.3, SEQ ID No.4, SEQ ID No.5, SEQID No.6, SEQ ID No.7, SEQ ID No.8, SEQ ID No.9 and SEQ ID No.10.
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CN105002170A (en) * | 2015-07-31 | 2015-10-28 | 中国长江三峡集团公司 | Amur sturgeon germplasm molecular marker identification kit and application thereof |
CN105525020A (en) * | 2016-02-01 | 2016-04-27 | 辽宁省海洋水产科学研究院 | Kit for rapidly identifying flathead fish and callionymus koreanus and identification method |
CN108531620A (en) * | 2018-06-29 | 2018-09-14 | 四川农业大学 | Identify the primer and method of Amur Sturgeon, siberia platform and its filial generation |
CN108660224A (en) * | 2018-06-29 | 2018-10-16 | 四川农业大学 | Identify the primer and method of siberia platform, Amur Sturgeon and its filial generation |
CN108660223A (en) * | 2018-06-29 | 2018-10-16 | 四川农业大学 | Siberia platform and to the west of miscellaneous identification method |
CN109337962A (en) * | 2018-08-24 | 2019-02-15 | 暨南大学 | Primer and probe and its kit and method based on fluorescence quantitative PCR detection sturgeon |
CN110846419A (en) * | 2019-11-25 | 2020-02-28 | 中国水产科学研究院长江水产研究所 | SSR primer pair group, kit, identification method and application for species identification of huso and acipenser ruthenus |
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CN116904610A (en) * | 2023-08-01 | 2023-10-20 | 西南大学 | Yangtze sturgeon primer, probe and detection method based on environmental DNA |
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CN105002170A (en) * | 2015-07-31 | 2015-10-28 | 中国长江三峡集团公司 | Amur sturgeon germplasm molecular marker identification kit and application thereof |
CN105002170B (en) * | 2015-07-31 | 2017-08-01 | 中国长江三峡集团公司 | Amur Sturgeon germplasm molecular markers for identification kit and its application |
CN105525020A (en) * | 2016-02-01 | 2016-04-27 | 辽宁省海洋水产科学研究院 | Kit for rapidly identifying flathead fish and callionymus koreanus and identification method |
CN108660223B (en) * | 2018-06-29 | 2021-10-29 | 四川农业大学 | Siberian sturgeon and identification method of Siberian sturgeon |
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CN108660223A (en) * | 2018-06-29 | 2018-10-16 | 四川农业大学 | Siberia platform and to the west of miscellaneous identification method |
CN108531620A (en) * | 2018-06-29 | 2018-09-14 | 四川农业大学 | Identify the primer and method of Amur Sturgeon, siberia platform and its filial generation |
CN108531620B (en) * | 2018-06-29 | 2021-10-29 | 四川农业大学 | Primer and method for identifying acipenser schrencki, acipenser sibiricus and filial generation thereof |
CN109337962A (en) * | 2018-08-24 | 2019-02-15 | 暨南大学 | Primer and probe and its kit and method based on fluorescence quantitative PCR detection sturgeon |
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CN110846419B (en) * | 2019-11-25 | 2023-05-26 | 中国水产科学研究院长江水产研究所 | SSR primer pair group, kit, identification method and application for identifying huso and flash sturgeon species |
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Application publication date: 20131211 |