DNA Analysis of Natural Fiber Rope*

Abstract: When rope is found at a crime scene, the type of fiber is currently identified through its microscopic characteristics. However, these characteristics may not always unambiguously distinguish some types of rope from others. If rope samples contain cells from the plants of origin, then DNA analysis may prove to be a better way to identify the type of rope obtained from a crime scene. The objective of this project was to develop techniques of DNA analysis that can be used to differentiate between ropes made from Cannabis sativa L. (hemp), Agave sisalana Perrine (sisal), Musa textilis Née (abaca, “Manila hemp”), Linum usitatissimum L. (flax), and Corchorus olitorus L. (jute). The procedures included extracting the DNA from the rope, performing polymerase chain reaction (PCR) using the extracted DNA as a template, and analyzing the DNA products. A primer pair for PCR, chosen from within a chloroplast gene for the large subunit of ribulose bisphosphate carboxylase/oxygenase, was designed to be specific for plant DNA and complementary to the genes from all five plants. The resulting PCR fragments were approximately 771 base pairs long. The PCR fragments, distinguished through base sequence analysis or restriction enzyme analysis, could be used to identify the five different rope types. The procedure provides a useful addition to visual methods of comparing rope samples.     

衣物载体上人体脱落细胞的负压吸附采集法

目的建立脱落细胞负压吸附方法,用于DNA检验中衣物等载体上人体脱落细胞的采集。方法检材包括由志愿者佩带1、5、10、20m in纱线手套,穿着5、10、20m in的内衣以及外套、鞋、帽子、头套、袜子、水杯、矿泉水瓶等。在吸尘器的进风口处连接特制的吸筒,一端覆盖具有拦截和静电吸附细胞能力的特制吸附膜,选择适当负压对各检材相应部位进行吸扫。收集吸附膜上的脱落细胞,采用Chelex-100法提取DNA,AmpFLSTR Identifiler复合扩增试剂盒扩增检测。结果上述检材用本文负压吸附法采集人体脱落细胞,经检验均获得清晰、完整的STR分型图谱,并与检材提供者的基因型一致。结论本文建立的脱落细胞负压吸附技术可有效吸附载体上的脱落细胞,适用于DNA检案实践。     

Haplotype diversity in human mitochondrial DNA hypervariable regions I–III in the city of Caracas (Venezuela)

In order to expand the database of variable DNA for forensic identification purposes in Venezuela, we analyzed the sequence polymorphisms of mitochondrial DNA (mtDNA) hypervariable regions (HVR) I–III from 100 unrelated individuals from the city of Caracas, using PCR amplification and fluorescent-based capillary electrophoresis sequencing method. Dominant haplogroups corresponded to Native Americans followed by African ones. The inclusion of HVR III although useful for sub-haplogroup assignation, added little to the discrimination capacity of our database.     

Forensic DNA evidence and the death penalty in the Philippines

The death penalty remains a contentious issue even though it has been abolished in countries such as Australia, New Zealand, Canada, European Union member nations and some Asian countries such as Cambodia, East Timor and Nepal. Many argue that the irrevocability of the death penalty, in the face of potential erroneous convictions, can never justify its imposition. The Philippines, the first Asian country that abolished the death penalty in 1987, held the record for the most number of mandatory death offenses (30 offenses) and death eligible offenses (22 offenses) after it was re-imposed in 1994. Majority of death penalty convictions were decided based on testimonial evidence. While such cases undergo automatic review by the Supreme Court, the appellate process in the Philippines is not structured to accept post-conviction evidence, including DNA evidence.Because of the compelling nature of post-conviction DNA evidence in overturning death penalty convictions in the United States, different groups advocated its use in the Philippines. In one such case, People v Reynaldo de Villa, the defendant was charged with raping his 13-year-old niece that supposedly led to birth of a female child, a situation commonly known as ‘criminal paternity’. This paper reports the results of the first post-conviction DNA test using 16 Short Tandem Repeat (STR) DNA markers in a criminal paternity case (People v Reynaldo de Villa) and discusses the implications of these results in the Philippine criminal justice system.     

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.     

Molecular study of time dependent changes in DNA stability in soil buried skeletal residues

In the past years, many publications about identification and sex-determination of dry human bones by means of DNA analysis have been published. However, few studies exist that investigate the potential use of DNA technique to determine the postmortem interval (PMI). In the present study we analyzed the rate of increasingly smaller fragments of chromosomal DNA and PMI.     

DNA recovery after sequential processing of latent fingerprints on copy paper

Forensic examiners must determine whether both latent fingerprint development and DNA profiling can be performed on the same area of an evidence item and, if only one is possible, which examination offers the best chance for identification. Latent fingerprints can be enhanced by targeting different components of fingerprint residues with sequential chemical treatments. This study investigated the effects of single-reagent and sequential latent fingerprint development processes on downstream DNA analysis to determine the point at which latent fingerprint development should be stopped to allow for DNA recovery. Latent fingerprints deposited on copy paper by one donor were developed using three sequential processes: 1,8-diazafluoren-9-one (DFO) → ninhydrin → physical developer (PD); 1,2-indanedione-zinc (IND-Zn) → ninhydrin → PD; and IND-Zn → ninhydrin → Oil Red O (ORO) → PD. Samples were examined after the addition of each chemical treatment. DNA was collected with cotton swabs, extracted, quantified, and amplified. DNA yields, peak heights, number of alleles obtained, and percentage of DNA profiles eligible for CODIS upload were examined. DNA profiles were obtained with varying degrees of success, depending on the number and type of treatments used for latent fingerprint development. The treatments that were found to be the least harmful to downstream DNA analysis were IND-Zn and IND-Zn/laser, and the most detrimental treatments were DFO, DFO/laser, and PD. In general, as the number of treatments increase, the opportunities for DNA loss or damage also increase, and it is preferable to use fewer treatments when developing latent fingerprints prior to downstream DNA processing.     

Genetic analysis instrumentation innovations built into the SeqStudio ™ Flex Genetic Analyzers

The new Applied Biosystems™ SeqStudio ™ Flex Series Genetic Analyzer have improved the benchmark for research use only for Capillary Electrophoresis (CE) by providing innovative approaches to enhanced hand-free operation, flexibility, ease of use, data quality and connectivity. This newly designed 8 or 24 capillary system supports fragment sizing and DNA sequencing applications providing scientists with medium throughput technology for use in research applications. The steps from system set-up to size or base-called data have been simplified with hardware functionality and user-friendly software enhancements designed into this new CE system.We will discuss innovations related to ease of use including one button start-up, an on-board computer with touchscreen, intuitive software, easier to use capillary arrays, and desktop and cloud-based plate manager software. Innovations related to increased flexibility include continuous plate loading, automated plate linking that be able to maintain traceability from sample to result when using barcoded plates, urgent sample reprioritization, fragment and sequencing samples be run on the same plate, and multi-user support will also be discussed. In addition, gold standard fragment analysis and sequencing data quality has been enhanced through innovative algorithms providing autospectral calibrations, and off-scale recovery of data for fragment analysis. Innovative service and support functionality including remote troubleshooting with instrument system login capability, and on-board instrument help videos are included. Finally, we will touch upon new connectivity, which includes Thermo Fisher connect for remote monitoring, analysis, and data sharing as well as other functionality such as voice commands and Wi-Fi capability that the system will provide. The following summarizes highlights from the developmental validation performed to demonstrate the functionality of SeqStudio ™ Flex Series Genetic Analyzer.     

A Monte Carlo simulation and sensitivity cost benefit analysis for use of nylon 4N6FLOQSwabs®

Forensic genetic laboratories are challenged with implementing innovation even if the benefits to operational performance are well demonstrated often because of internal budget constraints. A prospective cost–benefit analysis (CBA) could support justification for an increased budget by effectively demonstrating in a system-based approach the relatively small cost of increasing a laboratory budget can substantially reduce costs to society (both qualitatively and monetarily). A Monte Carlo simulation and sensitivity CBA was performed using a more expensive swab (i.e., nylon 4N6FLOQSwabs®) compared with a less costly cotton swab. Ranges of input values and tangible and intangible benefits were considered. The outcome is that the relatively small increased cost of using a nylon swab pales compared with the potential tangible and intangible benefits to the overall system. This approach provides a sounder basis for requesting additional funds to support implementation of technologies and better approximates realistic situations while accommodating uncertainty of input values.     

混合样本拆分查询犯罪嫌疑人的应用研究

目的对一起杀人案中的混合样本进行拆分，期望获得嫌疑人的单-分型，以便于DNA数据库检索查询。方法采用专家人工拆分和图挖掘拆分对混合样本进行拆分，结果入“DNA快速协查比对平台”检索。结果2种方法先后比中数据库中同一前科人员。结论对2人份混合样本进行拆分，在DNA数据库中直接查找犯罪嫌疑人，是一种新的办案思路。