Multiplex DNA amplification and barcoding in a single reaction for 454 Roche sequencing: A comprehensive study on the control region of the mitochondrial genome

The analysis of the non-coding region of the mitochondrial genome using Sanger sequencing remains a laborious and time-consuming assay with too low resolution for the identification of low-frequency heteroplasmy or for mixture interpretation. In this study, an experimental design was tested in which the complete hypervariable region of the mitochondrial genome was sequenced using a novel barcoding strategy. The strategy involves a single-step multiplex nested PCR and we demonstrate its effectiveness by sequencing two multiplex reactions of two amplicons each covering the complete hypervariable region of the mitochondrial genome for 58 reference samples, 30 of which were analysed in triplicate, and 10 casework samples, each analysed in triplicate, on a 454 Roche DNA pyrosequencer with GS FLX chemistry using Multiplex Identifier (MID) primers to discriminate between samples. The generated reads for forensic (±3600 reads/MID) and reference samples (±466 reads/MID) allowed us to evaluate the accuracy in SNP calling and the variation in heteroplasmy and sequencing error rates in homopolymeric stretches between replicates.     

甲醛处理后人脊髓中的利多卡因和布比卡因的同时测定

目的建立经甲醛防腐处理后人脊髓中利多卡因和布比卡因同时定量测定的HPLC分析法,以满足法医学鉴定的需要。方法以空白人脊髓经甲醛防腐处理后添加标准利多卡因和布比卡因,对样品的前处理方法及仪器测试条件、方法的线性范围、检测限、精密度、回收率进行系统考察。结果所建方法中两药物的线性范围为0.5～10.0ug.g-1(利多卡因r=0.9999;Bupivacaine r=0.9998),检测限利多卡因为15ng布比卡因为20ng,日内、日间分析的相对标准偏差均在4.3％以内,加样回收率在97.3％～100.3％之间。结论经甲醛防腐处理后的脊髓可同时进行利多卡因和布比卡因定量测定。所建方法准确、实用,适用于法医学鉴定及相关研究。     

Forensic analysis of soil and sediment traces by scanning electron microscopy and energy-dispersive X-ray analysis: an experimental investigation

This paper reports the results of a series of experiments carried out to determine the precision of soil trace comparisons based on elemental peak height ratios determined by energy-dispersive X-ray analysis (EDXRA) in a variable pressure scanning electron microscope (VP-SEM). Experiments were conducted on 'bulk' soil aggregates, ground powders prepared from the <150 microm soil fractions and on smears of both the bulk soil and <150 microm material placed on cotton cloth. X-ray count data were obtained using area scans and spot analyses at different magnifications. The effects on elemental peak height ratios of varying the SEM chamber pressure, beam spot size, emission current and accelerating voltage were also examined. The peak height ratios for oxygen, silicon, aluminium, potassium, calcium and iron were found to show little variation as a function of chamber pressure, spot size and emission current over the ranges examined, but a strong dependency on accelerating voltage was observed. Within-sample variation in results, expressed by the percentage coefficient of variation, was found to be lowest for area scan analyses of the ground <150 microm fractions and greatest for the spot analyses of the bulk soil aggregates and the <150 microm fractions. We conclude that comparison of elemental peak height ratios determined by EDXRA can be a useful tool for rapid screening of soil samples, especially when combined with investigation of other attributes of the soil traces such as colour, fabric and the composition, shapes and surface textures of individual particles or aggregates within the soil traces. If sufficient material is available and can be readily separated without contamination or loss, higher resolution and more precise elemental data should be obtained by methods such as inductively coupled plasma atomic-emission spectrometry (ICP-AES) or mass-spectrometry (ICP-MS).     

Psychedelic fungus (Psilocybe sp.) authentication in a case of illegal drug traffic: sporological,molecular analysis and identification of the psychoactive substance

In nature, there are >200 species of fungi with hallucinogenic properties. These fungi are classified as Psilocybe, Gymnopilus, and Panaeolus which contain active principles with hallucinogenic properties such as ibotenic acid, psilocybin, psilocin, or baeocystin. In Chile, fungi seizures are mainly of mature specimens or spores. However, clandestine laboratories have been found that process fungus samples at the mycelium stage. In this transient stage of growth (mycelium), traditional taxonomic identification is not feasible, making it necessary to develop a new method of study.Currently, DNA analysis is the only reliable method that can be used as an identification tool for the purposes of supporting evidence, due to the high variability of DNA between species. One way to identify the species of a distinctive DNA fragment is to study PCR products analyzed by real time PCR and sequencing. One of the most popular sequencing methods of forensic interest at the generic and intra-generic levels in plants is internal transcribed spacer (ITS). With real time PCR it is possible to distinguish PCR products by differential analysis of their melting temperature (Tm) curves.This paper describes morphological, chemical, and genetic analysis of mycelia of psychedelic fungi collected from a clandestine laboratory. The fungus species were identified using scanning electron microscopy (SEM), mass spectrometry, HRM analysis, and ITS sequencing. The sporological studies showed a generally smooth surface and oval shape, with maximum length 10.1?μm and width 6.4?μm. The alkaloid Psilocyn was identified by mass spectrometry, while HRM analysis and ITS sequencing identified the species as Psilocybe cubensis. A genetic match was confirmed between the HRM curves obtained from the mycelia (evidence) and biological tissue extracted from the fruiting bodies. Mycelia recovered from the evidence and fruiting bodies (control) were genetically indistinguishable.     

Classification and individualization of black ballpoint pen inks using principal component analysis of UV-vis absorption spectra

The technique of principal component analysis has been applied to the UV-vis spectra of inks obtained from a wide range of black ballpoint pens available in the UK market. Both the pen ink and material extracted from the ink line on paper have been examined. Here, principal component analysis characterised each spectrum within a group through the numerical loadings attached to the first few principal components. Analysis of the spectra from multiple measurements on the same brand of pen showed excellent reproducibility and clear discrimination between inks that was supported by statistical analysis. Indeed it was possible to discriminate between the pen ink and the ink line from all brands examined in this way, suggesting that the solvent extraction process may have an influence on these results. For the complete set of 25 pens, interpretation of the loadings for the first few principal components showed that both the pen inks and the extracted ink lines may be classified in an objective manner and in agreement with the results of parallel thin layer chromatography studies. Within each class almost all inks could be individualised. Further work has shown that principal component analysis may be used to identify a particular ink from a database of reference UV-vis spectra and a strategy for developing this approach is suggested.     

An analysis of single and multi-copy methods for DNA quantitation by real-time polymerase chain reaction

The goal of this paper was to examine and compare two different commercially available approaches to the determination of the relative quantities of autosomal and Y chromosomal DNA using real-time PCR. One, Quantifiler^® Duo, utilizes a TaqMan^® assay with single copy probes for both autosomal human and Y quantification. The other method, Plexor HY^® utilizes a primer quenching assay with multi-copy probes for its quantification of autosomal human and Y chromosomal DNA. To test these approaches we have utilized the NIST Human DNA Quantitation Standard Reference Material 2372, a set of three different NIST human DNA quantification standards, to examine the precision, accuracy and sensitivity of the real-time PCR assays. We also examined data from both systems utilizing casework samples. The results show that both systems produced linear estimates for DNA quantity over a broad range of input DNA. However we did observe some apparent copy number effects when comparing the three different NIST standards which we attributed to issues with sequence variations in the different standards. Overall, the single copy approach provided better accuracy while the multi-copy approach produced better sensitivity. Thus the choice of which system to use should depend upon the goals of the user.     

Case report: Identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur

Applying two extraction protocols to isolate DNA from a charred femur recovered after a major forest fire, a range of established and recently developed forensic marker sets that included mini-STRs and SNPs were used to type the sample and confirm identity by comparison to a claimed daughter of the deceased. Identification of the remains suggested that the individual had been dead for 10 years and the DNA was therefore likely to be severely degraded from the combined effects of decomposition and exposure to very high temperatures. We used new marker sets specifically developed to analyze degraded DNA comprising both reduced-length amplicon STR sets and autosomal SNP multiplexes, giving an opportunity to assess the ability of each approach to successfully type highly degraded material from a challenging case. The results also suggest a modified ancient DNA extraction procedure offers improved typing success from degraded skeletal material.     

Inference structures for crime analysis and intelligence: the example of burglary using forensic science data

There has been much work dedicated to crime analysis and intelligence in recent times. Independently, physical evidence has shown great potential for linking crimes and bringing solid informative data through the increased use of multiple databases. However, their informative potential is still often underestimated and has been poorly integrated into police information systems. We propose a framework that fully introduces this data into an intelligence based system. This framework is built on the study of inference structures extracted from investigators’ every day implicit reasoning processes. Five specific inferences are studied with the particular problem of serial burglary investigation across independent police and legal structures. On the basis of such an analytical approach, a computer prototype has been designed; it has shown great promise and has resulted in several operational successes.     

Identification of mongoose (Genus: Herpestes) species from hair through band pattern studies using discriminate functional analysis (DFA) and microscopic examination

India is home to seven species of mongoose (Herpestes sp). Mongooses are being poached primarily for their hair, which is used in the production of painting and shaving brushes. Prior to September 2002, mongooses were listed under Schedule-IV of the Wildlife (Protection) Act 1972 (India). Indiscriminate poaching of the mongoose created an immediate threat to their survival and hence mongooses have now been placed under Schedule-II of the Wildlife (Protection) Act-1972 (India). In order to convict a person under this legislation, species identification of case related samples is necessary. Four species of mongoose i.e. H. edwardsii, H. smithii, H. palustris and H. urva were characterised by performing discriminate functional analysis (DFA) on measurements of their dorsal guard hair banding pattern and by microscopic hair characteristics (Cuticular, medullar and cross section). It was possible to distinguish between the four species studied, based on both these methods.     

单细胞凝胶电泳检测大鼠死后肝细胞核DNA降解

目的应用单细胞凝胶电泳技术(SCGE)检测大鼠死后肝细胞核DNA降解规律,分析与死亡时间的关系,为早期死亡时间的推断提供新的方法。方法在大鼠死后30h内,每隔3h取肝组织样本进行单细胞凝胶电泳,用共聚焦显微镜摄取彗星图像,应用彗星图像分析软件(IM I1.0)进行图像分析,并作统计学分析。结果死后大鼠的肝细胞在电泳图像上出现明显的彗星形拖尾,其尾长(TL)、尾矩(TM)在一定的时间范围内(0~18h)随死亡时间的延长而逐渐增大,二者均与死亡时间(PM I)呈现一定的相关回归关系。结论单细胞凝胶电泳技术可应用于早期死亡时间的推断。     

Interrogation of short tandem repeats using fluorescent probes and melting curve analysis: A step towards rapid DNA identity screening

Current forensic DNA profiling methods rely on the analysis of samples at specialised laboratories with an average turnaround time of several days. The ability to rapidly determine a partial profile of short tandem repeats at the point-of-arrest would be of great benefit to police forces around the world, for example enabling a suspect to be rapidly included or excluded from an investigation. We have developed a homogeneous PCR method for the interrogation of STR loci utilising fluorescent oligonucleotide probes and melting curve analysis. Alleles of the D18S51, TH01 and D8S1179 loci were differentiated and identified on the basis of target length and probe melting temperature. Assay performance was evaluated by comparing melting peak data with the AmpFlSTR^® SGM Plus^® system. The method is compatible with direct analysis of unpurified buccal swab samples, enabling a partial STR profile to be generated within 1 h.