The Effects of Differential Extraction Conditions on the Premature Lysis of Spermatozoa,

The purpose of this study was to determine the effect Proteinase K, sodium dodecyl sulfate (SDS), incubation times, and temperatures had on differential extraction efficiencies and the premature lysis of spermatozoa. The effect was measured using Quantifiler^® Duo and Identifiler? PCR Amplification kits, where the resultant male and female DNA concentrations and their ratios within the nonsperm‐ and sperm fractions (SFs) were determined. Comparisons between expected and observed ratios illustrate the quantity of female DNA in the SF increased when Proteinase K was absent during the initial incubation. Additionally, there is no indication of simultaneous sperm and epithelial cell lysis in the absence of DTT at Proteinase K concentrations ranging from 10 to 300 μg/mL. All other conditions exhibited minimal variation in DNA concentration. Therefore, despite the various protocols used for the differential lysis of cell mixtures encountered in casework, the method is robust and successful at most conditions.     

Proteinase K challenged by a novel protease

Proteinase K is used in forensic DNA extraction methods for cell lysis and degradation of proteins. Here we compare Proteinase K with a novel protease. We conclude that there is no need to exchange Proteinase K in our methods.     

Extraction of high quality DNA from biological materials and calcified tissues

Calcified tissues, such as bone and tooth, and some other sample types, such as those containing adhesive, present a challenge to standard extraction protocols. We have developed a lysis reagent, BTA™ lysis buffer, which is designed for use with PrepFiler™ Kit reagents. The BTA™ lysis buffer disrupts calcified tissue matrices and achieves effective extraction of DNA from pulverized bone and tooth samples. In addition, the BTA™ lysis buffer mildly but efficiently extracts DNA from challenging substrates like tape, chewing gum, and cigarette butts and, as with bone and tooth, DNA from these lysates is purified using established PrepFiler™ reagent extraction protocols.We successfully extracted DNA from powdered human bone samples, chewed gum and smoked cigarettes using BTA™ lysis buffer. Extraction yields for bone, gum and cigarette samples tested were consistent and reproducible. This extraction method efficiently removed potential PCR inhibitors from all samples tested, and C_T values for the internal PCR control of Quantifiler^® Human DNA Quantification Kit were consistent and within the normal range. The DNA extracted from these samples also provided conclusive profiles that were free of PCR artifacts when amplified using the AmpF?STR^® Identifiler^® PCR Amplification Kit. The protocol is easily adapted for automation.     

The modified method of two-step differential extraction of sperm and vaginal epithelial cell DNA from vaginal fluid mixed with semen

This investigation was undertaken as an efficient method for isolating sperm DNA from a mixed fluid sample which contains vaginal epithelial cells in a greater amount. The modified method of the two-step differential extraction procedure was found to be suitable for separating sperm DNA and vaginal epithelial cell DNA from the mixed stains. As the first step of digestion, vaginal epithelial cells in the mixed stains were lysed with Proteinase K and SDS, and sperm heads remaining in the lysed solution were collected by centrifugation. As the second step digestion, the sperm heads were lysed with the buffer containing Proteinase K, SDS and DTT as reducing agent. DNA fractions extracted from the two lysed solutions were enriched, one with sperm DNA and the other with vaginal epithelial cell DNA. MCT118(D1S80), ApoB VNTR and HLADQα types of sperm DNA were detected and were confirmed by matching with corresponding male blood DNA. In the case of vaginal secretion mixed with semen of two males, the mixture of MCT118 types of the two males was detected in sperm DNA fraction.     

Evaluation of the Differex™ System

Differential extraction is an efficient method to separate sperm cells from epithelial cells. A manual Chelex^®-100 based method is used at the Swedish National Laboratory of Forensic Science, SKL. The Differex™ System (Promega) uses a Proteinase K digestion of epithelial cells followed by centrifugation and phase separation. The sperm- and epithelial fractions are further purified with DNA IQ™ System (Promega) or with phenol/chloroform. The Differex™ System in combination with DNA IQ™ System were evaluated and compared to the Chelex^®-100 method used routinely. After modifications, the Differex™ System gave comparable results to the Chelex^®-100 method. The modifications included additional Proteinase K and DTT, longer incubation time and additional steps when removing the solid support from the Digestion Solution. In the Chelex^®-100 based method microscopic examination is done on the sperm pellet in a total volume of 50 μl. It was not possible to do a microscopic examination in less than 100 μl using the Differex™ System. Additionally the sperms were in clusters of epithelial cell debris. Microscopic examination is an important part of the differential extraction at SKL. Therefore, the Differex™ System will not be implemented at our laboratory.     

Alternative direct-to-amplification cell lysis techniques for forensically relevant non-sperm cells

While efforts have been made to reduce the pervasive backlog of sexual assault evidence collection kits, the actual laboratory process remains very time-consuming due to the requirement of a differential lysis step before DNA purification, as well as intricate mixture analysis towards the end of the DNA workflow. Recently, an alternative, direct-to-amplification sperm lysis method (using 1 M NaOH) was identified. However, a direct cell lysis method for non-sperm cells has not been identified yet. Thus, the primary objective of this work was to find an alternative method that is quick, inexpensive, and does not require multiple purification steps for the lysis of non-sperm cells in sexual assault samples. In this study, vaginal swab samples were lysed with the control method, prepGEM™, as well as six alternative reagents: alkaline buffer with 25–200 mM NaOH, high-salt stain extraction buffer, modified radioimmunoprecipitation assay (RIPA) buffer, mammalian protein extraction reagent (M-PER™), digitonin buffer, and urea/thiourea buffer. Quantification using Quantifiler® Trio of vaginal and semen lysates revealed that the alkaline (25 mM NaOH) and M-PER™ methods were efficient for the lysis of vaginal epithelial cells without substantial sperm cell lysis. Following quantification, analysis of STR profiles from vaginal lysates revealed that the M-PER™ method showed promising results across all metrics examined, including the percentage of detected STR alleles, mean peak heights, peak height ratio, and interlocus balance. Thus, this method was recommended as an alternative to the traditional differential lysis method for non-sperm cells given its ability to produce amplification-ready lysates without any DNA purification step.     

蛋白酶K-Chelex100法提取肋软骨DNA技术的优化

目的优化蛋白酶K的用量和消化时间,用于提取肋软骨DNA。方法 30份肋软骨样本各取大小为0.2cm×0.3cm×0.4cm的软骨块5份,分别编为A～E组。采用不同蛋白酶K用量和消化时间的Chelex100方法,提取5组各30份软骨块DNA,进行DNA定量、采用Sinofiler试剂盒扩增后进行电泳检测,采用非参数检验法比较检验成功率。结果 A～E组样本中采用加入2μL蛋白酶K并消化30min的D组方法成功率最高(96.7%),组间差异具有统计学意义。结论采用蛋白酶K-Chelex100方法,选择加入2μL蛋白酶K,消化30min可有效提高肋软骨DNA分型检验成功率。     

AutoMate Express™ forensic DNA extraction system for the extraction of genomic DNA from biological samples

Abstract: The AutoMate Express? Forensic DNA Extraction System was developed for automatic isolation of DNA from a variety of forensic biological samples. The performance of the system was investigated using a wide range of biological samples. Depending on the sample type, either PrepFiler? lysis buffer or PrepFiler BTA? lysis buffer was used to lyse the samples. After lysis and removal of the substrate using LySep? column, the lysate in the sample tubes were loaded onto AutoMate Express? instrument and DNA was extracted using one of the two instrument extraction protocols. Our study showed that DNA was recovered from as little as 0.025 μL of blood. DNA extracted from casework‐type samples was free of detectable PCR inhibitors and the short tandem repeat profiles were complete, conclusive, and devoid of any PCR artifacts. The system also showed consistent performance from day‐to‐day operation.     

The fate of the chemical warfare agent during DNA extraction

Forensic laboratories do not have the infrastructure to process or store contaminated DNA samples that have been recovered from a crime scene contaminated with chemical or biological warfare agents. Previous research has shown that DNA profiles can be recovered from blood exposed to several chemical warfare agents after the agent has been removed. The fate of four toxic agents, sulfur mustard, sodium 2-fluoroacetate, sarin, and diazinon, in a lysis buffer used in Promega DNA IQ extraction protocol was studied to determine if extraction would render the samples safe. Two independent analytical methods were used per agent, selected from GC-MS, 1H NMR, 19F NMR, (31)P NMR, or LC-ES MS. The methods were validated before use. Determinations were carried out in a semi-quantitative way, by direct comparison to standards. Agent levels in the elution buffer were found to be below the detectable limits for mustard, sarin, sodium 2-fluoroacetate or low (<0.02 mg/mL) for diazinon. Therefore, once extracted these DNA samples could be safely processed in a forensic laboratory.     

Optimization of recovery of human DNA from envelope flaps using DNA IQ™ System for STR genotyping

An optimized protocol based on the DNA IQ™ System has been tested for the extraction of DNA from envelope flaps. DNA is extracted directly without the need for opening and swabbing the flaps. The method is repeatable with <10% R.S.D. (relative standard deviation). The results of a systematic study show that it is an equilibrium extraction, and a small sample volume as well as high lysis buffer content in sample contribute to high extraction efficiency. The extracted DNA requires no further purification steps following its extraction with the DNA IQ™ System. Complete but skewed 15-locus short tandem repeat (STR) profiles, which is typical of degraded of DNA, have been generated from the DNA extracted from 6 to 9 years old casework envelope samples.     

人体接触检材前处理方式对磁珠法提取DNA效果的影响

目的比较3种常见的接触检材前处理方式对磁珠法提取DNA效果的影响。方法收集烟蒂、牙刷、纱线手套各10份;分别采用95℃、70℃直接裂解和TNE、SDS、PK预消化方式进行前处理,再用磁珠法提取纯化DNA,并进行DNA定量,统计提取的接触DNA量和IPC CT值;同时用Sinofiler复合扩增系统进行STR分型检测。结果 3种方法前处理后用磁珠提取的DNA纯度均较高I,PC CT值在26.63～27.19之间。用预消化法获得的DNA量高于裂解法,而95℃裂解与70℃裂解方法提取的DNA量无显著性差异。STR扩增检测结果亦表明,采用预消化法处理的样品STR分型成功率高于裂解法9,5℃与70℃裂解方法处理的样品STR分型成功率无显著性差异。结论人体接触检材采用预消化磁珠法提取DNA,有助于提高STR检验成功率。     

烧骨DNA检验技术的研究

目的解决陈旧性骨骼和烧骨DNA检验难题。方法研究建立了CTAB法裂解提取DNA,再用磁珠纯化得到的DNA提取液进行STR复合扩增检验。结果实验结果及实际检案显示研究所建立的骨DNA提取方法能较好地去除DNA扩增抑制物,得到高质量的DNA模板。结论本研究所建立的烧骨DNA检验方法其识别率为10×10-12,达到个人同一认定的目的,在解决实际工作中杀人焚尸案、火灾、爆炸等恶性案件和事故中有重要的作用。     

Touch DNA collection from improvised explosive devices: A comprehensive study of swabs and moistening agents

Improvised explosive devices (IEDs) are used in devastating terrorist attacks worldwide and daily in Thailand. Touch DNA deposited during IED assembly are subjected to intense heat and pressure, resulting in rare events of usable DNA profiles obtained from real casework. No study has simultaneously evaluated both swab brands and moistening agents for touch DNA collection from substrates encountered in IED evidence. In this study, we investigated the effects of swab brands and moistening agents on DNA collection from adhesive tape, a common IED substrate. A full factorial design using four cotton swab brands (two forensic and two medical cotton swabs) and six moistening agents (DNA-free water, phosphate-buffered saline, ethanol, sodium dodecyl sulfate, isopropanol, and lysis buffer) was employed (24 total combinations). Using buffy coats, we found that DNA recovery depended on both swab brands and moistening agents (p < 0.05). The optimal method recovered significantly higher DNA amount from real IED cases compared to the standard Royal Thai Police method. Percentages of high partial profiles also increased. Our results changed the standard operating protocol of the Thai police. Other commonly found substrates from IED cases are being investigated to maximize the evidential value obtained from touch DNA.     

Expedited, chemically enhanced sperm cell recovery from cotton swabs for rape kit analysis

This report focuses on the development of a method for chemically induced enhancement of cell elution and recovery from cotton swabs. The method exploits the exclusive use of detergents for intact cell removal, and can be utilized in conjunction with, or to circumvent, conventional differential extraction (DE). Samples treated with Sarkosyl (54.4 +/- 1.8%) and sodium dodecyl sulfate (SDS) (78.5 +/- 0.7%) yielded higher sperm cell recoveries than a conventional DE buffer (39.4 +/- 2.1%). The results indicated that the choice of detergent affected sperm cell yield, with anionic detergents having the greatest effect. Storage time of samples affected the concentration of detergent required for optimal sperm cell recovery, longer times requiring increased detergent concentrations. In addition, the extent of sperm cell lysis by proteinase K digestion was evaluated. The results indicate that the exclusive use of SDS enhances the release of sperm and epithelial cells from a cotton swab as compared with DE buffer, providing for a more effective DNA analysis.     

精子富集柱分离技术的研究

目的在传统差异裂解法基础上,研究建立新的混合斑检材中精子分离技术。方法根据精细胞的结构特点,研制精子富集柱。取混合斑检材经第一步消化后的混合液,加入精子富集柱中离心,使DNA等小分子物质透过,而精细胞被特异性黏附和拦截在富集层中。采用本文技术和常规裂解方法对12份混合斑检材中精子进行分离,分离后精子DNA采用Identifiler试剂盒进行PCR扩增和电泳检测。结果混合斑检材经精子富集柱分离后均获得单一男性精子的STR分型结果,而12份检材用常规裂解方法分离,其中有6份检材女性成分去除不完全或未能检出精子STR基因型。结论本研究建立的精子富集柱分离技术适用于常见混合斑检材中精子的分离,特别适合对含有大量女性混合物而精子量较少检材的分离提取。     

A study into the rate of incorporation of eight benzodiazepines into rat hair

The incorporation of eight benzodiazepines (chlordiazepoxide, diazepam, estazolam, flunitrazepam, flurazepam, medazepam, oxazepam and triazolam) into rat hair was investigated by HPLC and GC-MS. Each of the benzodiazepines was injected daily into three Dark Agouti (DA) rats for 10 days at 10mg/kg. The back hair of the rats was removed by shaving prior to the first injection and again on the 28th day after the initial administration.To investigate optimum extraction conditions, 10mg aliquots of rat hair incorporated with diazepam, flurazepam or medazepam were extracted by seven different methods (Proteinase K, methanol-ammonia, methanol-trifluoroacetic acid, Soerensens buffer, 1M NaOH, beta-glucuronidase/arylsulfatase, Biopurase). The method found to yield the highest recoveries, for all three drugs, was the acidic methanol extraction. Using this extraction procedure, the incorporation rates (ICR: the ratio of the hair concentration to the plasma AUC) of eight benzodiazepines into rat hair were investigated. The ICRs ranged from 0.002 (flunitrazepam) to 0.049 (flurazepam).The major metabolites of flurazepam were investigated in rat hair. The mean hair concentrations of desalkylflurazepam and 2-hydroxyethylflurazepam were 3.31 and 0.05 ng/mg, respectively, which are 24 and 0.36% of the parent compound in hair.     

PrepFiler Express BTA~(TM)裂解液联合硅珠法快速提取骨骼DNA

目的建立方便、快捷的提取骨骼DNA的方法。方法对15份长骨样本清洗消毒后,采用电钻钻取骨屑,使用PrepFiler Express BTA~(TM)裂解液进行裂解消化后,应用手工硅珠吸附纯化进行DNA提取检验。结果有14份样本获得满意的STR分型,仅1份样本未获得STR分型,检出率为93.33%。结论本研究建立的骨骼DNA快速提取方法操作简单、便捷、有效,适应性强,值得推广应用。     

生物检材DNA碱性裂解提取法的优化与改良

目的通过对DNA碱性裂解提取法进行优化和改进,建立一种操作更简便、检验快速、结果更可靠的生物检材DNA提取方法。方法以抗凝血作为检验样本,通过改变提取试剂的浓度、pH值、保存时间及孵化样本的温度、时间等条件,观测对检验结果峰值的影响,以确定提取试剂最佳条件,DNA提取物最佳保存条件。通过用改良后的碱性裂解法及Chelex100法同时提取不同量的抗凝血样本、各类法医生物检材,用不同厂家的DNA试剂盒扩增,对碱性裂解法的灵敏度、适应性和适用性进行评估。结果改良后的碱性裂解法只需将生物检材用NaOH（0.25mol/L）99℃孵化8min,振荡后加入TrisHCl（0.05mol/L,pH=6.5）中和液,离心后直接扩增检测。DNA提取物于-20℃冰箱可长期保存。对于毛发及精斑类检材优于Chelex100法。DNA提取物适用于现有各种DNA试剂盒扩增检测,其灵敏度与Chelex100法相似。结论改良后的碱性裂解法,操作简便、检验快速、结果可靠,可适合于法庭科学的检案与建库。     

Microchip-based cell lysis and DNA extraction from sperm cells for application to forensic analysis

The current backlog of casework is among the most significant challenges facing crime laboratories at this time. While the development of next-generation microchip-based technology for expedited forensic casework analysis offers one solution to this problem, this will require the adaptation of manual, large-volume, benchtop chemistry to small volume microfluidic devices. Analysis of evidentiary materials from rape kits where semen or sperm cells are commonly found represents a unique set of challenges for on-chip cell lysis and DNA extraction that must be addressed for successful application. The work presented here details the development of a microdevice capable of DNA extraction directly from sperm cells for application to the analysis of sexual assault evidence. A variety of chemical lysing agents are assessed for inclusion in the extraction protocol and a method for DNA purification from sperm cells is described. Suitability of the extracted DNA for short tandem repeat (STR) analysis is assessed and genetic profiles shown. Finally, on-chip cell lysis methods are evaluated, with results from fluorescence visualization of cell rupture and DNA extraction from an integrated cell lysis and purification with subsequent STR amplification presented. A method for on-chip cell lysis and DNA purification is described, with considerations toward inclusion in an integrated microdevice capable of both differential cell sorting and DNA extraction. The results of this work demonstrate the feasibility of incorporating microchip-based cell lysis and DNA extraction into forensic casework analysis.     

Evaluation of an alkaline lysis method for the extraction of DNA from whole blood and forensic stains for STR analysis

A modified alkaline lysis protocol for extracting DNA from forensically relevant specimens is evaluated and compared with the chelex 100 method. For whole blood, bloodstains and sperm stains, both methods yielded comparable results after amplification for a pentameric STR locus (HumCD4). The main advantages of the new method are: only approximately ten minutes and two pipetting steps are necessary and the expenses for the extraction are extremely low as only NaOH, TrisHCl buffer and a single microcentrifuge tube are required. Alkaline lysis also proved to yield DNA suitable for typing longer STRs by using dye-labeled primers and capillary electrophoresis. These advantages should render this protocol especially interesting for high-throughput laboratories in combination with multiplex PCR and fluorescent dye technology, although the storability of the extracts proved to be problematic.