CN106520757A - Preparation method of listeria monocytogenes nucleic acid standard substance - Google Patents
Preparation method of listeria monocytogenes nucleic acid standard substance Download PDFInfo
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Abstract
本发明提供一种单增李斯特氏菌核酸标准物质的制备方法,通过高浓度gDNA的提取、gDNA的特征性验证步骤获得标准物质。采用的引物为LIP1:5'‑GAT ACA GAA ACA TCG GTT GGC‑3';LIP2:5'‑GTG TAA CTT GAT GCC ATC AGG‑3'。解决单增李斯特菌检测的标准化问题,以及检测单增李斯特菌的快速有效性,需要一个统一的标准物质,本发明提供的标准物质能够发挥包括鉴定、评价、分析、安全监控等用途,为生物特性标准物质的研制提供参考价值。The invention provides a method for preparing a Listeria monocytogenes nucleic acid standard substance. The standard substance is obtained through the extraction of high-concentration gDNA and the characteristic verification steps of gDNA. The primers used were LIP1: 5'-GAT ACA GAA ACA TCG GTT GGC-3'; LIP2: 5'-GTG TAA CTT GAT GCC ATC AGG-3'. To solve the problem of standardization of Listeria monocytogenes detection and the rapid effectiveness of detection of Listeria monocytogenes, a unified reference material is needed. The reference material provided by the present invention can be used for identification, evaluation, analysis, safety monitoring, etc. Provide reference value for the development of biological characteristic reference materials.
Description
技术领域technical field
本发明属于生物技术领域,具体涉及一种单增李斯特氏菌核酸标准物质的制备方法。The invention belongs to the field of biotechnology, and in particular relates to a method for preparing a Listeria monocytogenes nucleic acid standard substance.
背景技术Background technique
20世纪90年代以来,以核酸扩增为基础的基因诊断技术发展迅速,在食品领域已应用到微生物学、遗传学等多个学科,动植物检疫也得到广泛的应用。并逐渐成为出入境口岸检验检疫快速检测方法之一。而单核细胞增生李斯特氏菌(单增李斯特菌)是一种人和动物共患病的病原菌。人畜感染后主要表现为单核细胞增多、败血症和脑膜炎。国内使用最普遍的是目的基因片段PCR技术,而且以实时荧光定量PCR检测技术为主。但由于国内现在没有统一的标准,各试剂盒采用的标准并不一致,同一工作标准也无法将提取效率等因素考虑周全,这样就造成同一份样品不同试剂不同人员操作结果相差很大,给进出口产品检验检疫带来很大的误差。要解决单增李斯特菌检测的标准化问题,以及检测单增李斯特菌的快速有效性,需要一个统一的标准物质,故研制单增李斯特菌基因组DNA(gDNA)标准物质势在必行。本发明提供的标准物质能够发挥包括鉴定、评价、分析、安全监控等用途,为生物特性标准物质的研制提供参考价值。Since the 1990s, genetic diagnosis technology based on nucleic acid amplification has developed rapidly, and has been applied to many disciplines such as microbiology and genetics in the food field, and animal and plant quarantine has also been widely used. And it has gradually become one of the rapid detection methods for inspection and quarantine at entry-exit ports. Listeria monocytogenes (Listeria monocytogenes) is a comorbid pathogen of humans and animals. The main manifestations of human and animal infection are mononucleosis, sepsis and meningitis. The most commonly used in China is the target gene fragment PCR technology, and the real-time fluorescent quantitative PCR detection technology is the main one. However, since there is no unified standard in China, the standards adopted by each kit are not consistent, and the same working standard cannot fully consider factors such as extraction efficiency, which leads to great differences in the operation results of different reagents and different personnel for the same sample, which is difficult for import and export. Product inspection and quarantine brings a lot of error. To solve the problem of standardization of L. monocytogenes detection and the rapid effectiveness of detection of L. monocytogenes, a unified reference material is needed. Therefore, it is imperative to develop L. monocytogenes genomic DNA (gDNA) reference material. The standard substance provided by the invention can be used for identification, evaluation, analysis, safety monitoring and the like, and provides reference value for the development of biological characteristic standard substance.
发明内容Contents of the invention
本发明的目的在于提供一种单增李斯特氏菌核酸标准物质的制备方法,解决单增李斯特菌检测的标准化问题,以及检测单增李斯特菌的快速有效性。The object of the present invention is to provide a preparation method of Listeria monocytogenes nucleic acid standard substance, solve the standardization problem of Listeria monocytogenes detection, and detect the rapid effectiveness of Listeria monocytogenes.
为实现上述目的,本发明采用如下技术方案:To achieve the above object, the present invention adopts the following technical solutions:
一种单增李斯特氏菌核酸标准物质的制备方法,通过高浓度gDNA的提取、gDNA的特征性验证步骤获得标准物质。A method for preparing Listeria monocytogenes nucleic acid standard substance, the standard substance is obtained through the extraction of high-concentration gDNA and the characteristic verification steps of gDNA.
高浓度gDNA的提取方法具体为:The extraction method of high-concentration gDNA is as follows:
(1)吸取20 mL细胞培养物至50mL置冰上的离心管;13000-16000g离心5s沉淀细胞,离心1-2次;用移液枪小心弃去上清液;(1) Pipette 20 mL of cell culture into a 50 mL centrifuge tube placed on ice; centrifuge at 13,000-16,000 g for 5 s to pellet the cells, and centrifuge 1-2 times; carefully discard the supernatant with a pipette;
(2)吸取10 mL TE与沉淀混合均匀后,13000-16000g离心5s沉淀细胞,重复离心1-2次;用移液枪小心弃去上清液;(2) After absorbing 10 mL TE and mixing with the pellet evenly, centrifuge at 13000-16000g for 5s to pellet the cells, and repeat the centrifugation 1-2 times; carefully discard the supernatant with a pipette;
(3)加入20 mL 细胞悬浮液,上下吹吸;再加入100 μL 酶裂解溶液,并上下颠倒25下;37℃孵育40min;13000-16000g离心1min沉淀细胞;移弃上清液;(3) Add 20 mL of cell suspension, pipette up and down; add 100 μL of enzyme lysis solution, and invert up and down 25 times; incubate at 37°C for 40 minutes; centrifuge at 13000-16000g for 1 minute to pellet the cells; discard the supernatant;
(4)加入20 mL 细胞溶解液,并用移液枪上下吹吸,80℃孵育5min溶解细胞;(4) Add 20 mL of cell lysate, blow up and down with a pipette gun, and incubate at 80°C for 5 minutes to dissolve the cells;
(5)加入100μL RNase A液,上下颠倒25次混合;36℃孵育60min;在冰上冷却孵育1min;加入8mL 蛋白沉淀剂,高速充分的涡旋20s;13000-16000g离心3min,沉淀的蛋白质必须形成一个紧密的颗粒,如无将样本放置冰上孵育5min并重新离心;(5) Add 100 μL RNase A solution, mix upside down 25 times; incubate at 36°C for 60 min; cool and incubate on ice for 1 min; add 8 mL protein precipitation agent, vortex at high speed for 20 s; centrifuge at 13000-16000 g for 3 min, the precipitated protein must Form a compact pellet. If not, incubate the sample on ice for 5 minutes and re-centrifuge;
(6)吸取20mL异丙醇至一个干净的50mL的离心管中,并小心吸取上步的上清液混合;轻轻的颠倒混合50次,异丙醇保存于-20℃,取出直接使用;13000-16000g离心1min,管底见白色的颗粒沉淀,弃去上清液,轻轻倒置离心管后用无菌吸水纸将吸干剩余液体,获得白色的颗粒即为gDNA。(6) Pipette 20 mL of isopropanol into a clean 50 mL centrifuge tube, and carefully pipette the supernatant from the previous step to mix; gently invert and mix 50 times, store the isopropanol at -20°C, take it out and use it directly; Centrifuge at 13,000-16,000 g for 1 min. White particles precipitate at the bottom of the tube. Discard the supernatant, invert the centrifuge tube gently, and blot the remaining liquid with sterile absorbent paper to obtain white particles that are gDNA.
gDNA的特征性验证方法为:对gDNA中的prfA基因片段进行扩增、测序、比对,根据特征标志确定获得gDNA标准物质。The characteristic verification method of gDNA is as follows: amplify, sequence, and compare the prfA gene fragment in gDNA, and determine the gDNA standard substance according to the characteristic marker.
所述的gDNA的特征性验证方法中采用的引物如下:The primers adopted in the characteristic verification method of the gDNA are as follows:
鉴定单核细胞增李氏特氏菌是通过prfA基因的序列分析。Listeria monocytogenes was identified by sequence analysis of the prfA gene.
LIP1 5'-GAT ACA GAA ACA TCG GTT GGC-3';LIP1 5'-GAT ACA GAA ACA TCG GTT GGC-3';
LIP2 5'-GTG TAA CTT GAT GCC ATC AGG-3'。LIP2 5'-GTG TAA CTT GAT GCC ATC AGG-3'.
引物是由上海生工生物工程技术服务有限公司合成。Primers were synthesized by Shanghai Sangon Bioengineering Technology Service Co., Ltd.
本发明的优点在于:The advantages of the present invention are:
研制单核细胞增生李斯特氏菌gDNA标准物质每瓶含有约1μg的gDNA干粉样。prfA基因序列在线Blast结果:Score =507 bits (274), Expect = 2e-140,Identities = 274/274(100%),Gaps = 0/274 (0%),Strand=Plus/Minus。gDNA标准物质的A280/A260=1.86。gDNA标准物质在8个月的周期内-20℃、4℃、25℃ 3个温度均能保存较好的稳定性,浓度仍然保持在1μg/瓶,gDNA标准物质的0.8%琼脂糖凝胶电泳和prfA基因扩增均有清晰的目标条带。不确定度评估结果,当检验结果以3次测量值的平均值表示时,其值区间分布于±0.735 μg/mL之间。Each bottle of Listeria monocytogenes gDNA standard material contains about 1 μg of gDNA dry powder sample. Online Blast results of prfA gene sequence: Score =507 bits (274), Expect = 2e-140, Identities = 274/274 (100%), Gaps = 0/274 (0%), Strand = Plus/Minus. A280/A260=1.86 of gDNA standard material. The gDNA standard substance can be stored at three temperatures of -20°C, 4°C, and 25°C within an 8-month period with good stability, and the concentration is still maintained at 1 μg/bottle. 0.8% agarose gel electrophoresis of the gDNA standard substance and prfA gene amplification have clear target bands. Uncertainty evaluation results, when the test results are expressed as the average value of three measurements, the value range is distributed between ±0.735 μg/mL.
附图说明Description of drawings
图1 20瓶gDNA标准物质的0.8%琼脂糖凝胶电泳结果。M:DNA Ladder Marker;图上方为抽取样本的编号。Figure 1 0.8% agarose gel electrophoresis results of 20 bottles of gDNA standard substances. M: DNA Ladder Marker; above the picture is the number of the sample taken.
图2 20瓶gDNA标准物质prfA基因扩增1.5%琼脂糖凝胶电结果。M:100 bp DNA LadderMarker;图上方为抽取样本的编号。Fig. 2 1.5% agarose gel electrophoresis results of 20 bottles of gDNA standard substance prfA gene amplification. M: 100 bp DNA LadderMarker; the number of the sample is drawn above the figure.
具体实施方式detailed description
实施例1Example 1
1.1 菌液培养物制备1.1 Preparation of bacterial culture
单核细胞增生李斯特氏菌(ATCC33090)冻干菌株复水后,吸取10μL于20mL胰酪胨大豆酵母浸膏肉汤(TSB-YE)中进行复苏,36±1℃,220r/min摇床培养18-24h。挑取一环新鲜菌液划线于血平板 36±1℃ 培养18-24h ,从血平板上挑取单菌落分别接种到100mL TSB-YE中,36±1℃,培养18-24h。After rehydration of Listeria monocytogenes (ATCC33090) lyophilized strain, pipette 10 μL into 20 mL tryptone soybean yeast extract broth (TSB-YE) for recovery, 36±1°C, 220r/min shaker Cultivate for 18-24h. Pick a ring of fresh bacterial liquid and streak it on the blood plate for 18-24 hours at 36±1°C. Pick single colonies from the blood plate and inoculate them into 100mL TSB-YE respectively, and incubate for 18-24 hours at 36±1°C.
1.2 高浓度大量gDNA提取1.2 Extraction of high concentration and large amount of gDNA
利用液体培养基TSB-YE培养新鲜菌液至浓度达到2.0×1011cells,利用PuregeneYeast/Bact.Kit B for Purification of Archive-quality DNA from Gram-PositiveBacteria Culture Medium提取gDNA,根据gDNA纯度对提取步骤进行改进:Use the liquid medium TSB-YE to cultivate the fresh bacterial liquid to a concentration of 2.0×10 11 cells, use PuregeneYeast/Bact.Kit B for Purification of Archive-quality DNA from Gram-PositiveBacteria Culture Medium to extract gDNA, and perform the extraction steps according to the purity of gDNA Improve:
(1)吸取20 mL细胞培养物(约含有2.0×1011 cells)至50mL置冰上的离心管(平行2个离心管)。(2)13000-16000g离心5s沉淀细胞,观察沉淀是否紧密,否则重复离心一次。(3)用移液枪小心弃去上清液。(4)吸取10 mL TE 与沉淀混合后,13000-16000g离心5s沉淀细胞,观察沉淀是否紧密,否则重复离心一次。用移液枪小心弃去上清液。(5)加入20 mL 细胞悬浮液,上下吹吸。(6)加入100 μL酶裂解溶液,并上下颠倒25下。37℃孵育40min。(1) Pipette 20 mL of cell culture (approximately containing 2.0×10 11 cells) into a 50 mL centrifuge tube placed on ice (two centrifuge tubes in parallel). (2) Centrifuge at 13000-16000g for 5s to pellet the cells, observe whether the pellet is compact, otherwise repeat the centrifugation once. (3) Carefully discard the supernatant with a pipette gun. (4) After aspirating 10 mL TE and mixing with the pellet, centrifuge at 13000-16000g for 5s to pellet the cells, observe whether the pellet is tight, otherwise repeat the centrifugation once. Carefully discard the supernatant with a pipette. (5) Add 20 mL of cell suspension and pipette up and down. (6) Add 100 μL enzyme lysis solution and invert up and down 25 times. Incubate at 37°C for 40min.
(7)13000-16000g离心1min沉淀细胞。移弃上清液。(8)加入20 mL 细胞溶解液,并用移液枪上下吹吸,溶解细胞。80℃孵育5min才能溶解细胞。(9)加入100μL RNase A 液,上下颠倒25次混合。36℃孵育60min。(10)在冰上冷却孵育1min。(11)加入8mL蛋白沉淀剂,高速充分的涡旋20s。(7) Centrifuge at 13000-16000g for 1min to pellet the cells. Discard the supernatant. (8) Add 20 mL of cell lysate, and blow up and down with a pipette gun to dissolve the cells. Incubate at 80°C for 5 minutes to lyse the cells. (9) Add 100 μL RNase A solution and mix by inverting up and down 25 times. Incubate at 36°C for 60min. (10) Cool and incubate on ice for 1 min. (11) Add 8mL of protein precipitation agent, and vortex at high speed for 20s.
(12)13000-16000g离心3min沉淀,沉淀的蛋白质必须形成一个紧密的颗粒,假如蛋白质颗粒不够紧的话,将样本放置冰上孵育5min并重新离心。(12) Centrifuge at 13000-16000g for 3 minutes to precipitate. The precipitated protein must form a compact particle. If the protein particle is not tight enough, place the sample on ice and incubate for 5 minutes and centrifuge again.
(13)吸取20mL 异丙醇至一个干净的50mL的离心管中,并小心吸取上步的上清液混合。轻轻的颠倒混合50次。异丙醇保存于-20℃,取出直接使用。(13) Pipette 20mL of isopropanol into a clean 50mL centrifuge tube, and carefully pipette the supernatant from the previous step to mix. Mix by gentle inversion 50 times. Isopropanol was stored at -20°C and used directly.
(15)13000-16000×g离心1min沉淀。管底可见白色的颗粒沉淀(即为DNA)。(15) Centrifuge at 13000-16000×g for 1 min to precipitate. White pellets (that is, DNA) can be seen at the bottom of the tube.
(16)弃去上清液,轻轻倒置离心管后用无菌吸水纸将吸干剩余液体,并确保白色的颗粒仍在管底。(16) Discard the supernatant, gently invert the centrifuge tube and blot the remaining liquid with sterile absorbent paper, and ensure that the white particles are still at the bottom of the tube.
(17)加入30mL 70%乙醇并颠倒数次清洗DNA颗粒。70%乙醇保存于-20℃,取出直接使用。(18)13000-16000g离心1min沉淀。(19)操作同步骤(16)。(17) Add 30mL of 70% ethanol and invert several times to wash the DNA particles. 70% ethanol was stored at -20°C and used directly. (18) Centrifuge at 13000-16000g for 1min to precipitate. (19) The operation is the same as step (16).
(20)在生物安全柜中静置,干燥5min左右,并避免过度干燥而导致DNA将难以溶解。(20) Let it stand in a biological safety cabinet and dry for about 5 minutes, and avoid over-drying, which will cause DNA to be difficult to dissolve.
(21)加入8mL DNA溶解液并用中速涡旋5s。65℃孵育1h以溶解DNA。在室温下孵育,轻轻摇动过夜。确保管帽紧闭,以避免泄漏。(21) Add 8mL DNA solution and vortex at medium speed for 5s. Incubate at 65°C for 1 h to dissolve the DNA. Incubate overnight at room temperature with gentle shaking. Make sure the tube caps are tightly closed to avoid leaks.
1.3 gDNA浓度及纯度测定1.3 gDNA concentration and purity determination
应用The Picofluor™便携式荧光仪结合Picogreen染料对提取的DNA进行浓度检测。选用48502 bp,2 μg/mL的λDNA作为标准曲线校准的外标准物。The concentration of extracted DNA was detected by using The Picofluor™ portable fluorometer combined with Picogreen dye. 48502 bp, 2 μg/mL λDNA was selected as the external standard for calibration of the standard curve.
利用TE buffer 稀释样品,使其浓度为100μg /mL。利用超微量核苷酸测定仪对稀释的gDNA进行纯度的检测。Dilute the sample with TE buffer to make the concentration 100μg/mL. The purity of the diluted gDNA was tested using an ultra-trace nucleotide analyzer.
1.4 gDNA标准物质的制备1.4 Preparation of gDNA standard substance
单增李斯特菌gDNA标准物质的制备工艺主要是采用浓度均匀的gDNA液进行等量的分装、预冻、冻干、包装、特征性基因片段验证、均匀性测定、短效稳定性试验、长效稳定性试验等环节。具体步骤如下:The preparation process of Listeria monocytogenes gDNA reference material is mainly to use uniform concentration of gDNA liquid for equal volume subpackaging, pre-freezing, freeze-drying, packaging, verification of characteristic gene fragments, uniformity determination, short-term stability test, Long-term stability test and other links. Specific steps are as follows:
(1)将储存在-20℃的gDNA(浓度:100μg /mL,合计40mL )化冻,置于冰上。(1) Thaw the gDNA stored at -20°C (concentration: 100μg/mL, 40mL in total) and place it on ice.
(2)同1.3 步骤方法检测保存的gDNA液浓度及纯度。(2) Check the concentration and purity of the preserved gDNA solution with the method in step 1.3.
(3)利用6×loading buffer,0.8%琼脂糖凝胶电泳检测gDNA的完整性。10×loading buffer,1.5%琼脂糖凝胶电泳验证特性基因prfA基因片段。(3) Use 6×loading buffer, 0.8% agarose gel electrophoresis to check the integrity of gDNA. 10×loading buffer, 1.5% agarose gel electrophoresis to verify the characteristic gene prfA gene fragment.
(4)将检测完的gDNA溶液分装于无菌的0.5mL聚丙烯瓶,10μL/瓶,即1μg/瓶。(4) Dispense the tested gDNA solution into sterile 0.5mL polypropylene bottles, 10μL/bottle, that is, 1μg/bottle.
(5)将步骤(4)的样品于-70℃冰箱中预冻4h,取出后迅速放进冷冻干燥机中进行冻干;(5) Pre-freeze the sample in step (4) in a -70°C refrigerator for 4 hours, take it out and quickly put it into a freeze dryer for freeze-drying;
(6)冻干程序结束后,将氮气瓶的接口与冻干机的吸气口相连接。充进氮气,使聚丙烯瓶也充有氮气。(6) After the freeze-drying process is over, connect the interface of the nitrogen bottle to the suction port of the freeze-dryer. Nitrogen was filled so that the polypropylene bottle was also filled with nitrogen.
1.5单增李斯特菌gDNA特征性片段验证1.5 Verification of characteristic fragments of Listeria monocytogenes gDNA
prfA基因是编码单核细胞增生李斯特氏菌主要毒力因子李氏杆菌溶血素的转录调控蛋白。对gDNA中的prfA基因片段进行扩增、测序、比对等步骤。本实验是用高保真HotStarHiFidelity Polymerase扩增prfA基因,送至基因公司测序。The prfA gene is a transcriptional regulatory protein encoding the major virulence factor listeria hemolysin of Listeria monocytogenes. Steps such as amplification, sequencing, and alignment are performed on the prfA gene fragment in the gDNA. In this experiment, the high-fidelity HotStarHiFidelity Polymerase was used to amplify the prfA gene and sent it to a gene company for sequencing.
PCR扩增反应热力学循环参数为:The thermodynamic cycle parameters of PCR amplification reaction are:
PCR反应体系如表1所示。 The PCR reaction system is shown in Table 1.
表1 高保真PCR扩增反应体系组成Table 1 Composition of high-fidelity PCR amplification reaction system
LIP1 5'-GAT ACA GAA ACA TCG GTT GGC-3';LIP1 5'-GAT ACA GAA ACA TCG GTT GGC-3';
LIP2 5'-GTG TAA CTT GAT GCC ATC AGG-3'。LIP2 5'-GTG TAA CTT GAT GCC ATC AGG-3'.
PCR扩增结束后,将两个PCR反应管PCR产物混合,取全部PCR产物约100μL和10μL10×loading buffer混合电泳。将PCR产物盖口封膜后送至上海生工进行测序。将测序获得的prfA基因序列进行在线BLAST。分析比对结果是否存在差异。以此作为该gDNA标准物质的特征标志。After PCR amplification, mix the PCR products of the two PCR reaction tubes, and take about 100 μL of all PCR products and 10 μL of 10×loading buffer for electrophoresis. The PCR product was sealed and sent to Shanghai Sangong for sequencing. Online BLAST was performed on the prfA gene sequence obtained by sequencing. Analyze the comparison results for differences. Take this as the characteristic mark of the gDNA standard substance.
1.6 均匀性试验:从完成制备的标准物质中随机抽取20个样本进行检测,每个样本测试三次。结果采用F检验统计分析。1.6 Homogeneity test: 20 samples were randomly selected from the prepared standard substance for testing, and each sample was tested three times. The results were statistically analyzed using the F test.
1.7 稳定性试验1.7 Stability test
短期稳定性则是模拟不同温度条件下运输该标准物质时是否能够保持足够的稳定。温度设定为-20℃、4℃、25℃、60℃ 4个温度梯度。测定的时间为开始(t=0)、一周后(t=1)、2周后(t=2)、3周后(t=3)、4周后(t=4)、8周后(t=8)。每个温度梯度每次抽3个样本,每个样本每次进行三次测量求平均值。The short-term stability is to simulate whether the standard substance can maintain sufficient stability when transported under different temperature conditions. The temperature was set to 4 temperature gradients of -20°C, 4°C, 25°C, and 60°C. The time of measurement is the beginning (t=0), one week later (t=1), 2 weeks later (t=2), 3 weeks later (t=3), 4 weeks later (t=4), 8 weeks later ( t=8). Three samples were drawn for each temperature gradient, and three measurements were taken for each sample to obtain the average value.
长期稳定性是为了观察该标准物质在-20℃、4℃、25℃、60℃保存条件下是否稳定。测定的时间为开始(T=0)、1月后(T=1)、4月后(T=2)、8月后(T=3)。每个温度梯度每次抽3个样本,每个样本每次进行三次测量求平均值。Long-term stability is to observe whether the standard substance is stable under storage conditions of -20°C, 4°C, 25°C, and 60°C. The measurement time was the beginning (T=0), 1 month later (T=1), 4 months later (T=2), and 8 months later (T=3). Three samples were drawn for each temperature gradient, and three measurements were taken for each sample to obtain the average value.
1.8 测量不确定度评估1.8 Evaluation of measurement uncertainty
本部分gDNA标准物质的测量不确定度主要是由于PicofluorTM荧光计测量样品的荧光值所带来,因此本部分主要考查荧光法测量dsDNA带来的不确定度。这属于A类不确定度。The measurement uncertainty of the gDNA standard substance in this part is mainly due to the fluorescence value of the sample measured by the PicofluorTM fluorometer, so this part mainly examines the uncertainty caused by the measurement of dsDNA by the fluorescence method. This is a Type A uncertainty.
A类不确定度的评估是对观测列进行的统计分析所作评估。.Type A uncertainty is assessed by statistical analysis of the series of observations. .
首先对输入量xI进行n次独立的相同等精度测量,得到的测量结果为:Firstly, n independent measurements of the same precision are performed on the input quantity xI, and the obtained measurement results are:
x1、x2……xn x 1 , x 2 ... x n
为其算术平均值,即为:; Its arithmetic mean is: ;
单次测量结果实验的标准差即为:;The standard deviation of a single measurement result experiment is: ;
观测列的平均值即估计值标准的不确定度为;The mean value of the observed column, that is, the standard uncertainty of the estimated value is ;
2实施结果:单增李斯特氏菌核酸标准物质的制备2 Implementation Results: Preparation of Listeria Monocytogenes Nucleic Acid Standard Substance
2.1 高浓度的gDNA提取2.1 High-concentration gDNA extraction
利用液体培养基TSB-YE培养新鲜菌液至浓度达到2.0×1011cells,利用PuregeneYeast/Bact.Kit B for Purification of Archive-quality DNA from Gram-PositiveBacteria Culture Medium提取gDNA。测定浓度为284μg/mL,A260/280=1.86。将该gDNA按比例用pH8.0 TE buffer稀释至100μg/mL,保存至-20℃待用。基因组完整性通过电泳,确定无杂带。Use the liquid medium TSB-YE to cultivate the fresh bacterial liquid to a concentration of 2.0×10 11 cells, and use PuregeneYeast/Bact.Kit B for Purification of Archive-quality DNA from Gram-PositiveBacteria Culture Medium to extract gDNA. The measured concentration was 284 μg/mL, A260/280=1.86. The gDNA was diluted to 100 μg/mL with pH8.0 TE buffer in proportion, and stored at -20°C until use. The integrity of the genome was confirmed by electrophoresis without any bands.
2.2 gDNA的分装与冷冻干燥2.2 Aliquoting and freeze-drying of gDNA
将提取的gDNA液用TE稀释至100μg/mL,10μL分装于聚丙烯小管中,每瓶标准物质含有gDNA的量为1μg左右。-70℃预冻4h后进行冷冻干燥及填充氮气。The extracted gDNA solution was diluted with TE to 100 μg/mL, and 10 μL was dispensed into polypropylene small tubes. The amount of gDNA contained in each bottle of standard substance was about 1 μg. Freeze-dry and fill with nitrogen after pre-freezing at -70°C for 4 hours.
2.3 gDNA标准物质的特征性片段验证2.3 Verification of characteristic fragments of gDNA reference materials
对标准物质样品进行gDNA完整性检验(0.8%琼脂糖凝胶电泳)及prfA基因片段进行扩增。反应产物100μL和10μL 10×loading buffer混合电泳。结果如图1和2所示。The standard substance samples were tested for gDNA integrity (0.8% agarose gel electrophoresis) and the prfA gene fragment was amplified. Mix 100 μL of the reaction product with 10 μL 10×loading buffer for electrophoresis. The results are shown in Figures 1 and 2.
2.4 prfA基因的测序峰图2.4 Sequencing Peak Map of prfA Gene
选择上述能扩增出约274bp条带的PCR产物送至基因公司进行测序,测序结果用Chromas打开,测序峰图信号强,没有干扰的结果,清晰可见。Select the above-mentioned PCR product that can amplify a band of about 274bp and send it to the gene company for sequencing. The sequencing result is opened with Chromas. The sequencing peak signal is strong, and there is no interference, which is clearly visible.
用所设计的引物将该基因的274个碱基从测序的序列中找出,用FASTA格式表示如下:Use the designed primers to find out the 274 bases of the gene from the sequenced sequence, and express it in FASTA format as follows:
>Listeria monocytogenes strain ATCC 7644 positive regulatory factor Agene> Listeria monocytogenes strain ATCC 7644 positive regulatory factor Age
TGTAATCTTGATGCCATCAGGAGTTTCTTTACCATACACATAGGTCAGGATTAAAAGTTGACTGCAAATAGAGCCAAGCTTCCCGTTAATCGAAAAATCATTAAATTTAGCTAGGCTGTATGAAACTTGTTTTTGTAGGGTTTGGAAAACATAGAAAAAGTGCGTAAGATTTTTGCTCAGTAGTTCTTTTAGTTCGTTTATTTTGATAACGTATGCGGTAGCCTGCTCGCTAATGACTTCTAAATTATAATAGCCAACCGATGTTTCTGTATCA。TGTAATCTTGATGCCATCAGGAGTTTCTTTACCATACACATAGGTCAGGATTAAAAGTTGACTGCAAATAGAGCCAAGCTTCCCGTTAATCGAAAAATCATTAAATTTAGCTAGGCTGTATGAAACTTGTTTTTGTAGGGTTTGGAAAACATAGAAAAAGTGCGTAAGATTTTTGCTCAGTAGTTCTTTTAGTTCGTTTATTTTGATAACGTATGCGGTAGCCTGCTCGCTAATGTTCATGTAG
2.5 prfA基因的比对实验结果2.5 Comparison experiment results of prfA gene
将测序的结果以FASTA的格式上传至http://blast.ncbi.nlm.nih.gov/进行nucleotide blast,数据库选择nucleotide collection(nr/nt)。其与已知单核细胞增生李斯特氏菌ATCC 19113的prfA进行比对。经过比对分析发现,该274bp与在线单核细胞增生李斯特氏菌ATCC19113 prfA基因的相似度达到100%,274bp全部一样。Score =507, Expect= 2e-140。由此可以推断,该gDNA标准物质的具备单核细胞增生李斯特氏菌特征。符合基因组标准物质的要求。Upload the sequencing results to http://blast.ncbi.nlm.nih.gov/ in FASTA format for nucleotide blast, and select nucleotide collection (nr/nt) as the database. This was compared to the known prfA of L. monocytogenes ATCC 19113. After comparative analysis, it was found that the similarity between the 274bp and the online Listeria monocytogenes ATCC19113 prfA gene reached 100%, and all 274bp were the same. Score=507, Expect=2e-140. It can be inferred that the gDNA standard substance has the characteristics of Listeria monocytogenes. Meet the requirements of genomic reference materials.
2.6均匀性试验2.6 Uniformity test
均匀性试验采用方差分析评价样品的均匀性。方法参照CNAS-GL03:2006《能力验证样品均匀性和稳定性评价指南》要求,利用荧光值法对同一个样品测定3次,并进行方差分析。Homogeneity test ANOVA was used to evaluate the homogeneity of the samples. Methods According to the requirements of CNAS-GL03:2006 "Guidelines for Evaluation of Sample Homogeneity and Stability of Proficiency Testing", the same sample was measured three times by fluorescence value method, and variance analysis was carried out.
表2 方差分析结果Table 2 Results of variance analysis
通过上述的方差分析计算结果,F值为1.522,F临界值F0.05(19,40)=1.853 计算的,该值< F 临界值,这表明在0.05 显著性水平时,样品中的gDNA含量是均匀的。Calculated by the above analysis of variance, the F value is 1.522, and the F critical value F 0.05 (19, 40) =1.853 is calculated, and this value is < F critical value, which indicates that at the 0.05 significance level, the gDNA content in the sample is average.
2.7 稳定性试验2.7 Stability test
2.7.1 短期稳定性2.7.1 Short-term stability
实验室模拟不同的温度运输环境下该gDNA标准物质的稳定性,主要考察4℃、25℃、60℃ 3个温度梯度。测定的时间为开始(t=0)、一周后(t=1)、2周后(t=2)、3周后(t=3)、4周后(t=4)、8周后(t=8),共持续8周。每个温度梯度每次抽3个样本,每个样本每次进行三次测量求平均值。而标准物质的完整性及特征基因扩增则是将每个时间点的全部温度下的gDNA一起验证。将上述测定的gDNA标准物质浓度绘制成曲线,从曲线上可以直观的看出标准物质在-20℃条件下保存条件下8周之内均能稳定在1.00μg//瓶的水平。The laboratory simulates the stability of the gDNA standard substance under different temperature transportation environments, mainly investigating three temperature gradients of 4°C, 25°C, and 60°C. The time of measurement is the beginning (t=0), one week later (t=1), 2 weeks later (t=2), 3 weeks later (t=3), 4 weeks later (t=4), 8 weeks later ( t=8), for a total of 8 weeks. Three samples were drawn for each temperature gradient, and three measurements were taken for each sample to obtain the average value. The integrity of the reference material and the amplification of the characteristic gene are verified together with the gDNA at all temperatures at each time point. The concentration of the gDNA standard substance determined above was plotted into a curve, and it can be seen intuitively from the curve that the standard substance can be stable at the level of 1.00 μg/bottle within 8 weeks under storage conditions at -20°C.
通过数理统计分析gDNA标准物质的稳定性和琼脂糖凝胶电泳分析该标准物质的完整性,可知,t检验分析该标准物质在-20℃、4℃、25℃ 3个温度梯度下保存8周均能保持稳定性,每瓶标准物质gDNA含量在1.00μg左右。0.8%琼脂糖凝胶电泳结果显示,该标准物质在-20℃、4℃、25℃ 3个温度梯度下保存8周能保持基因组的完整性。单核细胞增生李斯特氏菌gDNA特征基因prfA扩增结果显示,保存在-20℃、4℃、25℃ 3个温度梯度下8周能完整扩增出prfA基因。而在60℃高温下保存该标准物质,经过荧光法测定结果表明该标准物质在60℃高温下保存1周后只剩0.1μg左右的dsDNA,0.8%琼脂糖凝胶电泳结果显示,该温度下gDNA基本上已经降解成小片段,但是prfA特征基因仍然能够扩增出来,条带清晰,说明gDNA在60℃保存条件下断裂的片段大于274bp,还能保证特征基因的存在。Through statistical analysis of the stability of the gDNA standard substance and the integrity of the standard substance by agarose gel electrophoresis, it can be seen that the standard substance can be stored for 8 weeks under three temperature gradients of -20°C, 4°C, and 25°C through the t test. To maintain stability, the content of gDNA in each bottle of standard substance is about 1.00 μg. The results of 0.8% agarose gel electrophoresis showed that the standard substance could maintain the integrity of the genome when stored at three temperature gradients of -20°C, 4°C, and 25°C for 8 weeks. The amplification results of gDNA characteristic gene prfA of Listeria monocytogenes showed that the prfA gene could be completely amplified after being stored at three temperature gradients of -20°C, 4°C, and 25°C for 8 weeks. However, when the standard substance was stored at a high temperature of 60°C, the results of fluorescence measurement showed that only about 0.1 μg of dsDNA remained after the standard substance was stored at a high temperature of 60°C for one week. The results of 0.8% agarose gel electrophoresis showed that at this temperature The gDNA has basically been degraded into small fragments, but the prfA characteristic gene can still be amplified with clear bands, indicating that the fragments broken by gDNA at 60°C are larger than 274bp, and the existence of the characteristic gene can also be guaranteed.
2.8 长期稳定性:2.8 Long-term stability:
长期稳定性是为了观察该标准物质在-20℃、4℃、25℃、60℃保存条件下是否稳定,保存时间一般持续2年,但是由于实验开始至今约9个月,所以长期稳定性实验先做前8月的数据。测定的时间点为开始(T=0)、1月后(T=1)、4月后(T=4)、8月后(T=8)。每个温度梯度每次随机抽3个样本,记下抽取的编号,对每个样本每次进行三次测量求平均值,然后进行t检验。检验的结果。和短期稳定性一样,标准物质的完整性及特征基因扩增则是将每个时间点的全部温度下的gDNA一起验证。The long-term stability is to observe whether the standard substance is stable under the storage conditions of -20°C, 4°C, 25°C, and 60°C. The storage time generally lasts for 2 years, but since the experiment has been started for about 9 months, the long-term stability test First do the data for the previous August. The time points of measurement were the beginning (T=0), 1 month later (T=1), 4 months later (T=4), and 8 months later (T=8). Three samples are randomly selected for each temperature gradient, and the number drawn is recorded, and the average value of each sample is measured three times, and then the t test is performed. The result of the inspection. Like the short-term stability, the integrity of the reference material and the amplification of the characteristic gene are verified together with the gDNA at all temperatures at each time point.
gDNA标准物质经过0.8%琼脂糖凝胶电泳结果显示,该标准物质在-20℃、4℃、25℃3个温度梯度下保存8个月能保持基因组的完整性。单核细胞增生李斯特氏菌gDNA特征基因prfA扩增结果显示,保存在-20℃、4℃、25℃ 3个温度梯度下8个月均能能完整扩增出prfA基因。而在60℃高温下保存该标准物质,经过荧光法测定结果表明该标准物质在60℃高温下保存1周后只剩0.1μg左右的dsDNA,0.8%琼脂糖凝胶电泳结果显示,该温度下gDNA基本上已经降解成小片段,但是经过长达8个月的高温保存,prfA特征基因仍然能够扩增出来,条带清晰,说明gDNA在60℃保存条件下8个月后标准物质中的基因片段仍然有大于274bp的片段,还能保证特征基因的存在。The results of 0.8% agarose gel electrophoresis of the gDNA standard substance showed that the standard substance could maintain the integrity of the genome when stored at three temperature gradients of -20°C, 4°C, and 25°C for 8 months. The amplification results of the gDNA characteristic gene prfA of Listeria monocytogenes showed that the prfA gene could be completely amplified after storage at three temperature gradients of -20°C, 4°C, and 25°C for 8 months. However, when the standard substance was stored at a high temperature of 60°C, the results of fluorescence measurement showed that only about 0.1 μg of dsDNA remained after the standard substance was stored at a high temperature of 60°C for one week. The results of 0.8% agarose gel electrophoresis showed that at this temperature The gDNA has basically been degraded into small fragments, but after up to 8 months of high temperature storage, the prfA characteristic gene can still be amplified, and the bands are clear, indicating that the gDNA in the standard material after 8 months of storage at 60°C Fragments still have fragments larger than 274bp, and the existence of characteristic genes can also be guaranteed.
2.9 不确定度评价结果2.9 Uncertainty evaluation results
准备30个含有100μL浓度约为500ng/mL gDNA原液离心管,然后往离心管中加入100μL的水合的PicoGreen工作试剂。充分混合在室温避光孵育2-5min。然后应用The Picofluor™便携式荧光仪经行浓度测定,每次测试读3次数,将其平均值作为分析的结构,现将测定平均值结果列至表3。Prepare 30 centrifuge tubes containing 100 μL of gDNA stock solution with a concentration of approximately 500 ng/mL, and then add 100 μL of hydrated PicoGreen working reagent to the centrifuge tubes. Mix well and incubate at room temperature for 2-5 minutes in the dark. Then use The Picofluor™ portable fluorometer to measure the concentration, read 3 times for each test, and use the average value as the structure of the analysis. The average results of the determination are now listed in Table 3.
表3 The Picofluor™便携式荧光仪读数测定结果Table 3 The Picofluor™ Portable Fluorometer Reading Measurement Results
为其算术平均值,即为:; Its arithmetic mean is: ;
单次测量结果实验的标准差即为:;The standard deviation of a single measurement result experiment is: ;
观测列的平均值即估计值标准的不确定度为;The mean value of the observed column, that is, the standard uncertainty of the estimated value is ;
当检验结果以3次测量值的平均值表示时,其值区间分布于±0.735 ng/mL之间。这个取值区间适合于任何一次测量。When the test results were expressed as the average value of three measurements, the value range was distributed between ±0.735 ng/mL. This range of values is suitable for any measurement.
以上所述仅为本发明的较佳实施例,凡依本发明申请专利范围所做的均等变化与修饰,皆应属本发明的涵盖范围。The above descriptions are only preferred embodiments of the present invention, and all equivalent changes and modifications made according to the scope of the patent application of the present invention shall fall within the scope of the present invention.
SEQUENCE LISTINGSEQUENCE LISTING
<110> 福建出入境检验检疫局检验检疫技术中心<110> Inspection and Quarantine Technical Center of Fujian Entry-Exit Inspection and Quarantine Bureau
<120> 一种单增李斯特氏菌核酸标准物质的制备方法<120> A preparation method of Listeria monocytogenes nucleic acid standard substance
<130> 2<130> 2
<160> 2<160> 2
<170> PatentIn version 3.3<170> PatentIn version 3.3
<210> 1<210> 1
<211> 21<211> 21
<212> DNA<212>DNA
<213> 人工序列<213> Artificial sequence
<400> 1<400> 1
gatacagaaa catcggttgg c 21gatacagaaa catcggttgg c 21
<210> 2<210> 2
<211> 21<211> 21
<212> DNA<212>DNA
<213> 人工序列<213> Artificial sequence
<400> 2<400> 2
gtgtaacttg atgccatcag g 21gtgtaacttg atgccatcag g 21
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CN111621581A (en) * | 2020-06-28 | 2020-09-04 | 河南大学 | Standard plasmid freeze-dried powder for detecting listeria monocytogenes |
CN111719007A (en) * | 2020-08-06 | 2020-09-29 | 南方医科大学 | Plasmid DNA reference sample for nucleic acid detection of Listeria monocytogenes, preparation method and application thereof |
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CN104140994A (en) * | 2014-08-07 | 2014-11-12 | 福建出入境检验检疫局检验检疫技术中心 | Staphylococcus aureus standard substance containing chicken matrix |
CN104450940A (en) * | 2014-12-29 | 2015-03-25 | 南京农业大学 | Nucleotide sequence for detecting listeria monocytogenes and detection method and detection kit |
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