Overall Proportion of Total DNA Consistent with an Individual Briefly Handling a Firearm.

In forensic investigations, DNA profiles are routinely obtained from firearms evidence and alternative hypotheses may be proposed for consideration on the activity level. DNA profiles found to be consistent with the DNA profile of a specific individual could be a result of directly handling the firearm or other modes of transfer of DNA. Sixteen law-enforcement-owned firearms were evaluated with samples collected from the frame and slide area, the trigger and trigger guard area, and the front and rear sights after brief handling by laboratory personnel. Twenty-two out of forty-eight samples resulted in DNA profiles suitable for comparison, of which six resulted in likelihood ratios (LR) that demonstrated support for the hypothesis that included the brief handler as a contributor to the DNA profile obtained from the sample. Five of these samples were obtained from the frame and slide and one was from the trigger and trigger guard area. None of the DNA profiles obtained from the sights supported the inclusion of the brief handler as a contributor to the DNA profile. Gaining knowledge and supporting data on the nature of DNA profiles typically obtained from both owners and brief handlers can be useful for the purposes of evaluative reporting when considering results obtained from firearm evidence.

Stable isotope characterisation of 3,4-methylenedioxyphenyl-2-propanone and 3,4-methylenedioxyamphetamine prepared from piperonal.

RATIONALE: Stable isotopic ratios can provide information for illicit drug profiling. The research presented here investigated the variations in stable isotopic ratios of hydrogen (δ2 H), carbon (δ13 C), nitrogen (δ15 N) and oxygen (δ18 O) during the synthesis of MDP2P (3,4-methylenedioxyphenyl-2-propanone) and MDA (3,4-methylenedioxyamphetamine) prepared via the 'nitrostyrene' route. METHODS: Samples of MDA and MDP2P were synthesised from two isotopically characterised starting materials, piperonal and nitroethane. The isotopic compositions of the nitrostyrene intermediate (3,4-methylenedioxyphenyl-2-nitropropene, MDP2NP) and products MDP2P and MDA were also measured by isotope ratio mass spectrometry. RESULTS: A significantly negative change occurred to δ2 H values during the production of MDP2NP, MDP2P and MDA, indicating a mechanism that favours inclusion or retention of 1 H over 2 H. This suggests that the δ2 H compositions of MDA/MDP2P prepared from piperonal will not provide information on the synthetic history. Minimal changes were observed in δ13 C composition during the synthesis of MDP2NP, MDP2P and MDA, and minimal δ15 N compositional changes occurred in MDP2NP and MDA. Progressing from piperonal to MDP2NP, a minimal change occurred to δ18 O composition. A variable change to δ18 O was observed from MDP2NP with one sample becoming more positive in δ18 O composition and two samples becoming more negative. Progressing from MDP2NP to MDA, a significant negative change occurred to δ18 O composition. CONCLUSIONS: The changes to stable isotopic ratios observed during the preparation of MDA and MDP2P from piperonal may prove useful when attempting to compare batch-to-batch variations between seizures and provide information with tactical intelligence applications.

An assessment of DNA extraction methods from blood-stained soil in forensic science.

In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to the presence of inhibitors which limit the effective extraction and amplification of the deoxyribonucleic acid (DNA) required to produce a reportable DNA profile. There are some extraction methods that have been applied to blood-stained soil in forensic science, but these have produced sporadic results. This research has taken a number of different extraction methods from the fields of ancient DNA and environmental DNA and broken them down into the individual steps of pre-treatment, incubation, separation and purification. These steps were assessed independently then combined into various extraction methods to determine the best technique that can effectively and reliably profile human DNA from blood-stained soil. Testing involved assessment of three extraction buffers, (cetyltrimethylammonium bromide, guanidine thiocyanate, and proteinase K), four pre-treatment methods, (polyvinylpyrrolidone, ethylenediaminetetraacetic acid, hydrochloric acid, and sodium hydroxide), three separation steps, (centrifugation, phenol chloroform, and chloroform) and four purification steps, (size exclusion chromatography, bind elute columns, isopropanol precipitation and silica magnetic beads). The most effective procedure was found to be a polyvinylpyrrolidone pre-treatment with a proteinase K extraction buffer followed by magnetic silica bead purification with or without centrifugation. However, centrifugation separation was found to be equally effective after the pre-treatment step as after the incubation step. Our results shows that most of the current forensic procedures would benefit from the addition of a pre-treatment step prior to processing through the automated DNA profiling pipeline.

65,000-years of continuous grinding stone use at Madjedbebe, Northern Australia.

Grinding stones and ground stone implements are important technological innovations in later human evolution, allowing the exploitation and use of new plant foods, novel tools (e.g., bone points and edge ground axes) and ground pigments. Excavations at the site of Madjedbebe recovered Australia's (if not one of the world's) largest and longest records of Pleistocene grinding stones, which span the past 65 thousand years (ka). Microscopic and chemical analyses show that the Madjedbebe grinding stone assemblage displays the earliest known evidence for seed grinding and intensive plant use, the earliest known production and use of edge-ground stone hatchets (aka axes), and the earliest intensive use of ground ochre pigments in Sahul (the Pleistocene landmass of Australia and New Guinea). The Madjedbebe grinding stone assemblage reveals economic, technological and symbolic innovations exemplary of the phenotypic plasticity of Homo sapiens dispersing out of Africa and into Sahul.

Composition of trace residues from the contents of 11th-12th century sphero-conical vessels from Jerusalem.

The residues from the internal surface of four archaeological ceramic sherds, excavated from the Armenian Gardens, Jerusalem were analysed to characterise the contents of the original vessel. The sherds derive from four small, thick-walled, sphero-conical vessels recovered from a destruction layer, dating between the 11th and 12th century, Jerusalem. The residue has been analysed using light microscopy, biochemical characterisation, gas chromatography mass spectroscopy, inductively coupled plasma atomic emission spectroscopy and cold vapour atomic fluorescence spectrometry. This analysis established the presence of various compounds including fatty acids and notable levels of mercury, sulphur, aluminium, potassium, magnesium, nitrates and phosphorous. The contents and probable functions of the four vessels were characterised from the residues on these sherds as different from each other, reflecting their different decoration, manufacture and ceramic typologies. One of these vessels contains residue that indicate the vessel held oils. The residue of the second vessel is consistent with either scented materials or medicinal contents, while a third probably contained medicinal material. The unique fourth sherd is from a stoneware sphero-conical vessel with very thick walls, no decoration and the residue supports the possibility it was used for the storage of chemicals or may have held the chemical ingredients for an explosive device, consistent with a medieval grenade. This residue analysis of Mamluk sphero-conical vessels provides insight into luxury items, medicines, technology and trade in medieval Jerusalem.

A method validation for the hemoglobin chemical reagent test strip with the addition of ethylenediaminetetraacetic acid to increase the selectivity of this presumptive test for residual blood.

Tetramethylbenzidine based chemical reagent test strips are often used in forensic science as a presumptive test for blood. These tests are designed as urinalysis test strips and include brands such as Combur®, HENSOTest®, Hemastix®, MultiStix® and Chemstrip®. They are used because they are simple to apply, stable, temperature tolerant and cost effective. The addition of a chelating agent, ethylenediaminetetraacetic acid increases the selectivity of this presumptive test for blood. This is a method validation for the hemoglobin chemical reagent test strip with EDTA. A range of substances, metal compounds, chemical solutions, blood and mixtures were tested in this method validation. The chelation with EDTA successfully prevented non-blood (false) positive results from all the substances tested and consistently produced a positive result for blood on a variety of surfaces. This study has shown that this method is capable of discriminating a blood stain on copper metal surfaces and eliminate the positive results generated by clean-up solutions such as hydrogen peroxide, which usually produce a positive result for most other presumptive tests for blood. This modified method is a simple, effective and reliable test for blood stains. A variety of variations were evaluated in this study. The simplest method of application was spraying the surface of the stain with a 0.5 M EDTA solution and testing the surface of the stain, and only requires a spray bottle of 0.5 M EDTA and the chemical reagent test strip. This spray approach is rugged and can be applied to horizontal, vertical and underside surfaces and requires little additional training. Overall, this study provides the forensic science community with an improved method more easily used, stored, transported and selective for blood, than luminol and safer than TMB.

Evolutionary changes in the genome of Mycobacterium tuberculosis and the human genome from 9000 years BP until modern times.

The demonstration of Mycobacterium tuberculosis DNA in ancient skeletons gives researchers an insight into its evolution. Findings of the last two decades sketched the biological relationships between the various species of tubercle bacilli, the time scale involved, their possible origin and dispersal. This paper includes the available evidence and on-going research. In the submerged Eastern Mediterranean Neolithic village of Atlit Yam (9000 BP), a human lineage of M. tuberculosis, defined by the TbD1 deletion in its genome, was demonstrated. An infected infant at the site provides an example of active tuberculosis in a human with a naïve immune system. Over 4000 years later tuberculosis was found in Jericho. Urbanization increases population density encouraging M. tuberculosis/human co-evolution. As susceptible humans die of tuberculosis, survivors develop genetic resistance to disease. Thus in 18th century Hungarian mummies from Vác, 65% were positive for tuberculosis yet a 95-year-old woman had clearly survived a childhood Ghon lesion. Whole genome studies are in progress, to detect changes over the millennia both in bacterial virulence and also host susceptibility/resistance genes that determine the NRAMP protein and Killer Cell Immunoglobulin-like Receptors (KIRs). This paper surveys present evidence and includes initial findings.

Spina bifida in a pre-Columbian Cuban population: A paleoepidemiological study of genetic and dietary risk factors.

A holistic approach is necessary to investigate health in archeological populations. Molecular techniques, particularly multiplex PCR and SNaPshot minisequencing, can be combined with paleopathology and dietary analysis (stable isotope, starch, zooarchaeological analyses) to understand aspects of population health. This article demonstrates how spina bifida, a multi-factorial disease characterized by the midline failure to complete vertebral neural arch formation, can be investigated holistically. Based on skeletal evidence, this disease was prevalent in a pre-Columbian Cuban population from the archeological site of Canimar Abajo (3000-1250 BP). Molecular paleopathological techniques were employed to examine disease potential in this preliminary study, examining 18 individuals (including two individuals with evidence of mild spina bifida, and 16 without such evidence) for four single nucleotide polymorphisms and one insertion sequence associated with spina bifida. The combined effect of these polymorphisms, as well as dietary factors, determines the risk of the population for spina bifida, and these factors united to create the observed high disease prevalence. We demonstrate how molecular paleopathology, corroborated by dietary analyses, can be used within a paleoepidemiological framework to understand population health and disease.

Hominin dispersal into the Nefud Desert and Middle palaeolithic settlement along the Jubbah Palaeolake, Northern Arabia.

The Arabian Peninsula is a key region for understanding hominin dispersals and the effect of climate change on prehistoric demography, although little information on these topics is presently available owing to the poor preservation of archaeological sites in this desert environment. Here, we describe the discovery of three stratified and buried archaeological sites in the Nefud Desert, which includes the oldest dated occupation for the region. The stone tool assemblages are identified as a Middle Palaeolithic industry that includes Levallois manufacturing methods and the production of tools on flakes. Hominin occupations correspond with humid periods, particularly Marine Isotope Stages 7 and 5 of the Late Pleistocene. The Middle Palaeolithic occupations were situated along the Jubbah palaeolake-shores, in a grassland setting with some trees. Populations procured different raw materials across the lake region to manufacture stone tools, using the implements to process plants and animals. To reach the Jubbah palaeolake, Middle Palaeolithic populations travelled into the ameliorated Nefud Desert interior, possibly gaining access from multiple directions, either using routes from the north and west (the Levant and the Sinai), the north (the Mesopotamian plains and the Euphrates basin), or the east (the Persian Gulf). The Jubbah stone tool assemblages have their own suite of technological characters, but have types reminiscent of both African Middle Stone Age and Levantine Middle Palaeolithic industries. Comparative inter-regional analysis of core technology indicates morphological similarities with the Levantine Tabun C assemblage, associated with human fossils controversially identified as either Neanderthals or Homo sapiens.

Titanic's unknown child: the critical role of the mitochondrial DNA coding region in a re-identification effort.

This report describes a re-examination of the remains of a young male child recovered in the Northwest Atlantic following the loss of the Royal Mail Ship Titanic in 1912 and buried as an unknown in Halifax, Nova Scotia shortly thereafter. Following exhumation of the grave in 2001, mitochondrial DNA (mtDNA) hypervariable region 1 sequencing and odontological examination of the extremely limited skeletal remains resulted in the identification of the child as Eino Viljami Panula, a 13-month-old Finnish boy. This paper details recent and more extensive mitochondrial genome analyses that indicate the remains are instead most likely those of an English child, Sidney Leslie Goodwin. The case demonstrates the benefit of targeted mtDNA coding region typing in difficult forensic cases, and highlights the need for entire mtDNA sequence databases appropriate for forensic use.

Molecular exploration of the first-century Tomb of the Shroud in Akeldama, Jerusalem.

The Tomb of the Shroud is a first-century C.E. tomb discovered in Akeldama, Jerusalem, Israel that had been illegally entered and looted. The investigation of this tomb by an interdisciplinary team of researchers began in 2000. More than twenty stone ossuaries for collecting human bones were found, along with textiles from a burial shroud, hair and skeletal remains. The research presented here focuses on genetic analysis of the bioarchaeological remains from the tomb using mitochondrial DNA to examine familial relationships of the individuals within the tomb and molecular screening for the presence of disease. There are three mitochondrial haplotypes shared between a number of the remains analyzed suggesting a possible family tomb. There were two pathogens genetically detected within the collection of osteological samples, these were Mycobacterium tuberculosis and Mycobacterium leprae. The Tomb of the Shroud is one of very few examples of a preserved shrouded human burial and the only example of a plaster sealed loculus with remains genetically confirmed to have belonged to a shrouded male individual that suffered from tuberculosis and leprosy dating to the first-century C.E. This is the earliest case of leprosy with a confirmed date in which M. leprae DNA was detected.

Ancient Leishmaniasis in a highland desert of Northern Chile.

BACKGROUND: Leishmaniasis is an infectious disease endemic today in many areas of South America. METHODOLOGY: We discovered morphologic and molecular evidence of ancient infections in 4 female skulls in the archaeological cemetery of Coyo Oriente, in the desert of San Pedro de Atacama, Northern Chile. The boney facial lesions visible in the skulls could have been caused by a number of chronic infections including chronic Leishmaniasis. This diagnosis was confirmed using PCR-sequenced analyses of bone fragments from the skulls of the affected individuals.Leishmaniasis is not normally found in the high-altitude desert of Northern Chile; where the harsh climate does not allow the parasite to complete its life cycle. The presence of Leishmaniasis in ancient skulls from the region implies infection by the protozoan in an endemic area-likely, in our subjects, to have been the lowlands of North-Eastern Argentina or in Southern Bolivia. CONCLUSIONS: We propose that the presence of the disease in ancient times in the high altitude desert of San Pedro de Atacama is the result of an exogamic system of patrilocal marriages, where women from different cultures followed their husbands to their ancestral homes, allowing immigrant women, infected early in life, to be incorporated in the Atacama desert society before they became disfigured by the disease. The present globalization of goods and services and the extraordinary facile movement of people across borders and continents have lead to a resurgence of infectious diseases and re-emergence of infections such as Leishmaniasis. We show here that such factors were already present millennia ago, shaping demographic trends and the epidemiology of infections just as they do today.

Technical note: removal of metal ion inhibition encountered during DNA extraction and amplification of copper-preserved archaeological bone using size exclusion chromatography.

A novel technique for the removal of metal ions inhibiting DNA extraction and PCR of archaeological bone extracts is presented using size exclusion chromatography. Two case studies, involving copper inhibition, demonstrate the effective removal of metal ion inhibition. Light microscopy, SEM, elemental analysis, and genetic analysis were used to demonstrate the effective removal of metal ions from samples that previously exhibited molecular inhibition. This research identifies that copper can cause inhibition of DNA polymerase during DNA amplification. The use of size exclusion chromatography as an additional purification step before DNA amplification from degraded bone samples successfully removes metal ions and other inhibitors, for the analysis of archaeological bone. The biochemistry of inhibition is explored through chemical and enzymatic extraction methodology on archaeological material. We demonstrate a simple purification technique that provides a high yield of purified DNA (>95%) that can be used to address most types of inhibition commonly associated with the analysis of degraded archaeological and forensic samples. We present a new opportunity for the molecular analysis of archaeological samples preserved in the presence of metal ions, such as copper, which have previously yielded no DNA results.

Postmortem miscoding lesions in sequence analysis of human ancient mitochondrial DNA.

Genetic miscoding lesions can cause inaccuracies during the interpretation of ancient DNA sequence data. In this study, genetic miscoding lesions were identified and assessed by cloning and direct sequencing of degraded, amplified mitochondrial DNA (mtDNA) extracted from human remains. Forty-two individuals, comprising nine collections from five geographic locations, were analyzed for the presence of DNA damage that can affect the generation of a correct mtDNA profile. In agreement with previous studies, high levels (56.5% of all damage sites) of proposed hydrolytic damage products were observed. Among these, type 2 transitions (cytosine --> thymine or guanine --> adenine), which are highly indicative of hydrolytic deamination, were observed in 50% of all misincorporations that occurred. In addition to hydrolytic damage products, oxidative damage products were also observed in this study and were responsible for approximately 43.5% of all misincorporations. This level of misincorporation is in contrast to previous studies characterizing miscoding lesions from the analysis of bone and teeth, where few to no oxidative damage products were observed. Of all the oxidative damage products found in this study, type 2 transversions (cytosine --> adenine/guanine --> thymine or cytosine --> guanine/guanine --> cytosine), which are commonly formed through the generation of 8-hydroxyguanine, accounted for 30.3% of all genetic miscoding lesions observed. This study identifies the previously unreported presence of oxidative DNA damage and proposes that damage to degraded DNA templates is highly specific in type, correlating with the geographic location and the taphonomic conditions of the depositional environment from which the remains are recovered.

Co-infection of Mycobacterium tuberculosis and Mycobacterium leprae in human archaeological samples: a possible explanation for the historical decline of leprosy.

Both leprosy and tuberculosis were prevalent in Europe during the first millennium but thereafter leprosy declined. It is not known why this occurred, but one suggestion is that cross-immunity protected tuberculosis patients from leprosy. To investigate any relationship between the two diseases, selected archaeological samples, dating from the Roman period to the thirteenth century, were examined for both Mycobacterium leprae and Mycobacterium tuberculosis DNA, using PCR. The work was carried out and verified in geographically separate and independent laboratories. Several specimens with palaeopathological signs of leprosy were found to contain DNA from both pathogens, indicating that these diseases coexisted in the past. We suggest that the immunological changes found in multi-bacillary leprosy, in association with the socio-economic impact on those suffering from the disease, led to increased mortality from tuberculosis and therefore to the historical decline in leprosy.

Detection of a single nucleotide polymorphism in the IL-6 promoter region of ancient nuclear DNA.

In the current study a method was developed to examine the G/C single nucleotide polymorphism (SNP) at position -174 in the IL-6 promoter from nuclear DNA samples isolated from human skeletal remains from Manitoba, Canada, dating to as early as 3500 years ago. The IL-6 (-174) SNP was detected in three ancient samples and determined, as expected, in three out of three to be homozygous G/G. The analysis of cytokine SNPs of ancient nuclear DNA may provide novel insights into the genetic basis of autoimmune diseases and the susceptibility/resistance to infectious agents.

Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA.

During the past 10 years palaeomicrobiology, a new scientific discipline, has developed. The study of ancient pathogens by direct detection of their DNA has answered several historical questions and shown changes to pathogens over time. However, ancient DNA (aDNA) continues to be controversial and great care is needed to provide valid data. Here we review the most successful application of the technology, which is the study of tuberculosis. This has provided direct support for the current theory of Mycobacterium tuberculosis evolution, and suggests areas of investigation for the interaction of M tuberculosis with its host.