Microbial Analysis of Bite Marks by Sequence Comparison of Streptococcal DNA

Bite mark injuries often feature in violent crimes. Conventional morphometric methods for the forensic analysis of bite marks involve elements of subjective interpretation that threaten the credibility of this field. Human DNA recovered from bite marks has the highest evidentiary value, however recovery can be compromised by salivary components. This study assessed the feasibility of matching bacterial DNA sequences amplified from experimental bite marks to those obtained from the teeth responsible, with the aim of evaluating the capability of three genomic regions of streptococcal DNA to discriminate between participant samples. Bite mark and teeth swabs were collected from 16 participants. Bacterial DNA was extracted to provide the template for PCR primers specific for streptococcal 16S ribosomal RNA (16S rRNA) gene, 16S–23S intergenic spacer (ITS) and RNA polymerase beta subunit (rpoB). High throughput sequencing (GS FLX 454), followed by stringent quality filtering, generated reads from bite marks for comparison to those generated from teeth samples. For all three regions, the greatest overlaps of identical reads were between bite mark samples and the corresponding teeth samples. The average proportions of reads identical between bite mark and corresponding teeth samples were 0.31, 0.41 and 0.31, and for non-corresponding samples were 0.11, 0.20 and 0.016, for 16S rRNA, ITS and rpoB, respectively. The probabilities of correctly distinguishing matching and non-matching teeth samples were 0.92 for ITS, 0.99 for 16S rRNA and 1.0 for rpoB. These findings strongly support the tenet that bacterial DNA amplified from bite marks and teeth can provide corroborating information in the identification of assailants.     

Genotypic comparison of bacteria recovered from human bite marks and teeth using arbitrarily primed PCR

AIMS: This study assessed, for forensic purposes, the feasibility of genotypically matching oral streptococci recovered from recent human bite marks with those from the teeth of the biter. METHODS AND RESULTS: Streptococci were isolated from the incisors of eight volunteers. Arbitrarily primed PCR (AP-PCR) distinguished 106 streptococcal genotypes among the participants, each harbouring at least eight distinct strains. In a crime simulation, a sample from an experimental bite mark was analysed by an experimenter unaware of its origin. The bacteria were unambiguously matched to the biter by comparing the amplicon profiles with those from the eight participants. In contrast, bacteria from an additional bite mark (not generated by one of the original participants) could not be matched to any of the eight participants. Between 20 and 78% of catalogued bacterial genotypes were recovered 12 months later from each participant. Throughout the study period, none of the bacterial genotypes were shared between participants. CONCLUSIONS: Streptococci isolated from recent bite marks can be catalogued by AP-PCR and matched to the teeth responsible for the bite. SIGNIFICANCE AND IMPACT OF THE STUDY: The study provides 'proof of concept' that genotypic analysis of streptococci from bite marks may provide valuable forensic evidence in situations where the perpetrator's DNA cannot be recovered.     

Whole genome amplification strategy for forensic genetic analysis using single or few cell equivalents of genomic DNA

Evidentiary items sometimes contain an insufficient quantity of DNA for routine forensic genetic analysis. These so-called low copy number DNA samples (< 100 pg of genomic DNA) often fall below the sensitivity limitations of routine DNA analysis methods. Theoretically, one way of making such intractable samples amenable to analysis would be to increase the number of starting genomes available for subsequent STR (short tandem repeat) analysis by a whole genome amplification strategy (WGA). Although numerous studies employing WGA have focused primarily on clinical applications, few in-depth studies have been conducted to evaluate the potential usefulness of these methods in forensic casework. After an initial evaluation of existing methods, a modified WGA strategy was developed that appears to have utility for low copy number forensic casework specimens. The method employs a slight, but important, modification of the "improved primer extension preamplification PCR" method (I-PEP-PCR), which we term mIPEP (modified-I-PEP-PCR). Complete autosomal STR and Y-STR (Y chromosome short tandem repeat) profiles were routinely obtained with 5 pg of template DNA, which is equivalent to 1-2 diploid cells. Remarkably, partial Y- and autosomal STR profiles were obtained from mIPEP-treated DNA recovered from bloodstains exposed to the outside environment for 1 year whereas non-mIPEP-treated samples did not produce profiles. STR profiles were obtained from contact DNA from single dermal ridge fingerprints when the DNA was subjected to prior mIPEP amplification but not when the mIPEP step was omitted.     

A Diagnosis of Alligator mississippiensis Bite Marks with Comparisons to Existing Crocodylian Datasets

Crocodylians are known to consume and modify bones, but actualistic observations of their bite marks have been limited to forensic case studies and surveys of two taxa: Crocodylus niloticus and Crocodylus porosus. To further explore patterns of crocodylian bite mark expression, we conducted a survey of traces left by Alligator mississippiensis. We compared the results to pre-existing crocodylian datasets regarding the potentially diagnostic traits of bisected marks, hook scores, and a lack of furrows. Mark type did not correlate with vital statistics of the sampled animals or collections protocol. Bisected marks were found in rates similar to those seen in one previous survey of C. niloticus, and rates of hook scoring and bone breakage were higher. These traces were all present in higher rates than those reported in C. porosus. Unlike results seen in Crocodylus, furrows were identified in the A. mississippiensis samples. Hook scores were also identified, but recent surveys of non-crocodylian taxa have shown that these features are not unique to crocodylians and instead are related to inertial feeding strategies. The presence and rate of bisected marks found in this study bolster the interpretation that these traces are a clade-wide phenomenon and a useful diagnostic indicator for Crocodylia.     

Seed-breaking forces exerted by orang-utans with their teeth in captivity and a new technique for estimating forces produced in the Wild

Orang-utans (Pongo pygmaeus) at the Singapore Zoological Gardens were presented with two thick-shelled edible seeds, Mezzettia parviflora (Annonaceae) and Macadamia ternifolia (Proteaceae) in order to estimate their maximum bite forces. The orang-utans could break the Macadamia seeds in one bite, while those of Mezzettia required repeated attempts. Examination of shell fragments showed that many had scratches and some had clear, but small (ca. 1–2 mm diameter), impressions on them. Building upon this information, semi-imitative tests were performed on the seeds in a universal testing machine by loading them in compression with either flat plates or metal casts of orang-utan cheek teeth. The maximum forces required to break the seeds were similar with both the flat plates and the metal teeth; the average for the Macadamia seeds being about 2,000 N (which forms a minimum estimate for the maximum bite forces in orang-utans) and for the Mezzettia seeds, 6,000 N. The work done with the metal teeth was much greater than with the plates. A mechanical analysis showed that this extra work went into producing permanent impressions (“bite marks”) in the shell with the tooth cusps. These impressions were larger than those found on the shells of seeds bitten by the orang-utans. Nevertheless, it is shown theoretically that the size of these indentations can give an estimate of the bite forces used. The maximum force developed in the machine tests with the metal teeth was correlated with the force calculated from analysis of the bite marks. The method is suitable for use in field studies where the marks left on remnants of hard foods eaten by primates may be used to estimate, very roughly, the forces used to produce them. © 1994 Wiley-Liss, Inc.     

Exposing the grey seal as a major predator of harbour porpoises

Harbour porpoises (Phocoena phocoena) stranding in large numbers around the southern North Sea with fatal, sharp-edged mutilations have spurred controversy among scientists, the fishing industry and conservationists, whose views about the likely cause differ. The recent detection of grey seal (Halichoerus grypus) DNA in bite marks on three mutilated harbour porpoises, as well as direct observations of grey seal attacks on porpoises, have identified this seal species as a probable cause. Bite mark characteristics were assessed in a retrospective analysis of photographs of dead harbour porpoises that stranded between 2003 and 2013 (n = 1081) on the Dutch coastline. There were 271 animals that were sufficiently fresh to allow macroscopic assessment of grey seal-associated wounds with certainty. In 25% of these, bite and claw marks were identified that were consistent with the marks found on animals that had tested positive for grey seal DNA. Affected animals were mostly healthy juveniles that had a thick blubber layer and had recently fed. We conclude that the majority of the mutilated harbour porpoises were victims of grey seal attacks and that predation by this species is one of the main causes of death in harbour porpoises in The Netherlands. We provide a decision tree that will help in the identification of future cases of grey seal predation on porpoises.     

Random Whole Metagenomic Sequencing for Forensic Discrimination of Soils

Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.     

Evaluation of reliability on STR typing at leukemic patients used for forensic purposes

Over the past decades, main advances in the field of molecular biology, coupled with benefits in genomic technologies, have led to detailed molecular investigations in the genetic diversity generated by researchers. Short tandem repeat (STR) loci are polymorphic loci found throughout all eukaryotic genome. DNA profiling identification, parental testing and kinship analysis by analysis of STR loci have been widely used in forensic sciences since 1993. Malignant tissues may sometimes be the source of biological material for forensic analysis, including identification of individuals or paternity testing. There are a number of studies on microsatellite instability in different types of tumors by comparing the STR profiles of malignant and healthy tissues on the same individuals. Defects in DNA repair pathways (non-repair or mis-repair) and metabolism lead to an accumulation of microsatellite alterations in genomic DNA of various cancer types that result genomic instabilities on forensic analyses. Common forms of genomic instability are loss of heterozygosity (LOH) and microsatellite instability (MSI). In this study, the applicability of autosomal STR markers, which are routinely used in forensic analysis, were investigated in order to detect genotypes in blood samples collected from leukemic patients to estimate the reliability of the results when malignant tissues are used as a source of forensic individual identification. Specimens were collected from 90 acute and 10 chronic leukemia volunteers with oral swabs as well as their paired peripheral blood samples from the Oncology Centre of the Department of Hematology at Istanbul University, during the years 2010–2011. Specimens were tested and compared with 16 somatic STR loci (CSFIPO, THO1, TPOX, vWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11 and FGA) widely used in forensic identification and kinship. Only two STR instabilities were encountered among 100 specimens. An MSI in the FGA loci and a LOH in the D2S1338 loci were determined in two individuals separately. Our results demonstrate that the use of the biological samples from leukemia patients in forensic identification and kinship testing is questionable, especially if known microsatellite instability is available. Genetic instabilities may alter the STR polymorphism, leading to potential errors on forensic identification of individuals. Therefore, typing of autosomal STRs from leukemia patients should be performed with both healthy and malignant tissue samples of individual as references.     

大熊猫气味标记DNA的制备和序列分析

大熊猫气味标记在其个体间的通讯中具有重要意义。用不同方法收集了７只大熊猫个体的９个气味标记样品,运用Ｉｎｓｔａｇｅｎｅ Ｋｉｔ制备出了ＤＮＡ。采用ＰＣＲ扩增线粒体Ｄ－环区和细胞色素ｂ基因、Ｔｈｒ－ｔＲＮＡ基因片段并作序列分析。结果提示,不同收集方式所得气味标记样品均有ＤＮＡ,但用干棉花收集样品的方法最佳。该方法为大熊猫的遗传多样性研究提供了新的简捷有效的ＤＮＡ来源。     

Tooth wear and compensatory modification of the anterior dentoalveolar complex in humans

In populations living in environments where teeth wear severely, some compensatory modification of the dentoalveolar complex is thought to occur during life whereby functional occlusion is maintained as tooth substance is lost by wear. This study investigates one aspect of this modification process: Changes in the anterior dentoalveolar complex that are accompanied with wear were examined in a series of Japanese skeletal samples. In the prehistoric Japanese hunter-gatherer population heavy wear occurs over the entire dentition. The following changes were demonstrated to have occurred in the anterior segment of the dentition accompanied by wear on the anterior teeth: The anterior teeth tip lingually with wear up to a nearly upright position to fill in interproximal spaces that would have been generated by wear, and to maintain contact relations between adjacent teeth. At the same time, the anterior surface of the maxillary alveolar process also inclines lingually to a certain extent. The amount of lingual tipping is greater in the maxillary anterior teeth than in their mandibular antagonists. It is because of this discrepancy that, with age, the horizontal component of the overlap between maxillary and mandibular anterior teeth decreases, and their bite form changes from scissor bite to edge-to-edge bite. Lesser degrees of lingual tipping of the anterior teeth were also detected in the prehistoric agriculturists and historic Japanese populations. The variation in the degree of lingual tipping observed among the samples is explained by inter-population variation in severity and pattern of tooth wear. This and other evidence suggests that mechanisms that compensate for wear in the anterior dentition may be characteristic of all living human populations, independently of the degree of wear severity endured in their environments.     

Social Exclusion Changes Histone Modifications H3K4me3 and H3K27ac in Liver Tissue of Wild House Mice

Wild house mice form social hierarchies with aggressive males defending territories, in which females, young mice and submissive adult males share nests. In contrast, socially excluded males are barred from breeding groups, have numerous bite wounds and patches of thinning fur. Since their feeding times are often disrupted, we investigated whether social exclusion leads to changes in epigenetic marks of metabolic genes in liver tissue. We used chromatin immunoprecipitation and quantitative PCR to measure enrichment of two activating histone marks at 15 candidate loci. The epigenetic profiles of healthy males sampled from nest boxes differed significantly from the profiles of ostracized males caught outside of nests and showing bite wounds indicative of social exclusion. Enrichment of histone-3 lysine-4 trimethylation (H3K4me3) changed significantly at genes Cyp4a14, Gapdh, Nr3c1, Pck1, Ppara, and Sqle. Changes at histone-3 lysine-27 acetylation (H3K27ac) marks were detected at genes Fasn, Nr3c1, and Plin5. A principal components analysis separated the socialized from the ostracized mice. This was independent of body weight for the H3K4me3 mark, and partially dependent for H3K27ac. There was no separation, however, between healthy males that had been sampled from two different nests. A hierarchical cluster analysis also separated the two phenotypes, which was independent of body weight for both markers. Our study shows that a period of social exclusion during adult life leads to quantitative changes in histone modification patterns in mouse liver tissue. Similar epigenetic changes might occur during the development of stress-induced metabolic disorders in humans.     

Ventral bite marks in Mesozoic ammonoids

Reports on the predators of ammonoids are rare, although ammonoids were abundant and diverse invertebrates in many Paleozoic and Mesozoic marine ecosystems. Most previous work on lethal ammonoid predation has focused on (sub)circular tooth marks which resulted from fish and mosasaur attacks. In the present study we discuss a relatively common type of bite mark in ammonoid shells, the ‘ventral bite mark’. This typically occurs in a restricted position on the ventral side of the outer body chamber whorl and does not affect either the aperture or the phragmocone. Ammonoid specimens revealing ventral bite marks used in this study were collected from a wide range of strata which range in age from the Lower Jurassic to the uppermost Cretaceous (close to the Cretaceous–Paleogene boundary). These ventral bite marks are absent in the Paleozoic collections studied. The vast majority of ventral bite marks are situated at the end of the body chamber, close to the phragmocone. This is interpreted as the result of predatory attacks on the back or blind side of ammonoids in their living position. The predators aimed for the vital parts and muscle attachments to obtain the edible soft tissues. The agents for most of the ventral bite marks to ammonoids are probably coleoid cephalopods (especially teuthoids) and predatory fishes to a lesser extent.     

Genetic clues from olfactory cues: brown hyaena scent marks provide a non-invasive source of DNA for genetic profiling

Brown hyaena scent marks were tested for their potential to provide DNA suitable for PCR. Up to 100% of scent marks were successfully amplified. The approach can potentially be adapted to other species with similar pasting behaviour and scent mark morphology, or to samples that are environmentally exposed/degraded/inhibitor-rich or where there are very limited amounts of sample.     

Killing in the Pliocene: shark attack on a dolphin from Italy

Abstract: Shark bite marks, including striae, sulci and abrasions, in a well‐preserved fossil dolphin skeleton referred to Astadelphis gastaldii (Cetacea, Delphinidae) from Pliocene sediments of Piedmont (northern Italy), are described in detail. The exceptional combination of a fossil dolphin having a significant part of the skeleton preserved and a large number of bite marks on the bones represents one of the few detailed documentations of shark attack in the past. Most bite marks have been referred to a shark about 4 m long with unserrated teeth, belonging to Cosmopolitodus hastalis, on the basis of their shape and their general disposition on the dolphin skeleton. According to our hypothesis, the shark attacked the dolphin with an initial mortal bite to the abdomen from the rear and right, in a similar way as observed for the living white shark when attacking pinnipeds. A second, less strong, bite was given on the dorsal area when the dolphin, mortally injured, probably rolled to the left. The shark probably released the prey, dead or dying, and other sharks or fishes probably scavenged the torn body of the dolphin.     

Role of short tandem repeat DNA in forensic casework in the UK--past, present, and future perspectives

The analysis of short tandem repeat (STR) DNA sequences is of fundamental importance to forensic science because they have become the recognized standard in constructing national public databases. Consequently, considerable effort has been expended in developing multiplexed (one tube) reactions that analyze several loci in combination. The implementation of STRs in casework cannot take place without a full understanding of the systems used. The purpose of validation is to characterize multiplexes when one is challenged with forensic samples. For example, mixtures are often encountered that may be particularly difficult to interpret against a background of allelic artifacts. By increasing the number of PCR amplification cycles, it is possible to dramatically boost the sensitivity of the system so that just a handful of cells may be successfully analyzed. However, interpretation is much more complex because the origin of DNA profiles may be less certain and complicated by issues such as contamination, the potential for innocent transfer and a predominance of mixtures. This review provides a brief historical background of the development of STRs in forensic casework that culminated in the creation of national DNA databases. The development of guidelines to interpret complex DNA profiles, such as mixtures, is outlined. Finally, the recent innovation of low copy number DNA profiling is explained along with the special considerations needed to report in court.     

Enhanced Genetic Analysis of Single Human Bioparticles Recovered by Simplified Micromanipulation from Forensic ‘Touch DNA’ Evidence

DNA profiles can be obtained from ‘touch DNA’ evidence, which comprises microscopic traces of human biological material. Current methods for the recovery of trace DNA employ cotton swabs or adhesive tape to sample an area of interest. However, such a ‘blind-swabbing’ approach will co-sample cellular material from the different individuals, even if the individuals’ cells are located in geographically distinct locations on the item. Thus, some of the DNA mixtures encountered in touch DNA samples are artificially created by the swabbing itself. In some instances, a victim’s DNA may be found in significant excess thus masking any potential perpetrator’s DNA.In order to circumvent the challenges with standard recovery and analysis methods, we have developed a lower cost, ‘smart analysis’ method that results in enhanced genetic analysis of touch DNA evidence. We describe an optimized and efficient micromanipulation recovery strategy for the collection of bio-particles present in touch DNA samples, as well as an enhanced amplification strategy involving a one-step 5 µl microvolume lysis/STR amplification to permit the recovery of STR profiles from the bio-particle donor(s). The use of individual or few (i.e., “clumps”) bioparticles results in the ability to obtain single source profiles. These procedures represent alternative enhanced techniques for the isolation and analysis of single bioparticles from forensic touch DNA evidence. While not necessary in every forensic investigation, the method could be highly beneficial for the recovery of a single source perpetrator DNA profile in cases involving physical assault (e.g., strangulation) that may not be possible using standard analysis techniques. Additionally, the strategies developed here offer an opportunity to obtain genetic information at the single cell level from a variety of other non-forensic trace biological material.     

Mammalian DNA demethylation

DNA cytosine methylation is a reversible epigenetic mark regulating gene expression. Aberrant methylation profiles are concomitant with developmental defects and cancer. Numerous studies in the past decade have identified enzymes and pathways responsible for active DNA demethylation both on a genome-wide as well as gene-specific scale. Recent findings have strengthened the idea that 5-methylcytosine oxidation catalyzed by members of the ten-eleven translocation (Tet1–3) oxygenases in conjunction with replication-coupled dilution of the conversion products causes the majority of genome-wide erasure of methylation marks during early development. In contrast, short and long patch DNA excision repair seems to be implicated mainly in gene-specific demethylation. Growth arrest and DNA damage-inducible protein 45 a (Gadd45a) regulates gene-specific demethylation within regulatory sequences of limited lengths raising the question of how such site specificity is achieved. A new study identified the protein inhibitor of growth 1 (Ing1) as a reader of the active chromatin mark histone H3 lysine 4 trimethylation (H3K4me3). Ing1 binds and directs Gadd45a to target sites, thus linking the histone code with DNA demethylation.     

HBV套式PCR技术的建立及HBcAb血清的检测

本文实验设计了套式ＰＣＲ引物进行ＨＢＶＤＮＡ诊断。外引物限定ＨＢＶＣ基因的一个６１３ｂｐ片段,内引物限定其内－５０７ｂｐ的片段,扩增后产物被限制性内切酶图谱证明。该技术的特异性强,重复性好,灵敏性达到１－１０ｆｇ,对ＨＢＶ血清可做出明确诊断。应用这项技术,对４２例ＨＢｃＡｂ血清进行了检测,实验表明仅ＨＢｃＡｂ阳性血清同带ＨＢｓＡｇ的ＨＢｃＡｂ阳性血清一样,体内持续进行着大量ＨＢＶＤＡＮ复制。     

Monitoring DNA Contamination in Handled vs. Directly Excavated Ancient Human Skeletal Remains

Bones, teeth and hair are often the only physical evidence of human or animal presence at an archaeological site; they are also the most widely used sources of samples for ancient DNA (aDNA) analysis. Unfortunately, the DNA extracted from ancient samples, already scarce and highly degraded, is widely susceptible to exogenous contaminations that can affect the reliability of aDNA studies. We evaluated the molecular effects of sample handling on five human skeletons freshly excavated from a cemetery dated between the 11 to the 14^th century. We collected specimens from several skeletal areas (teeth, ribs, femurs and ulnas) from each individual burial. We then divided the samples into two different sets: one labeled as “virgin samples” (i.e. samples that were taken by archaeologists under contamination-controlled conditions and then immediately sent to the laboratory for genetic analyses), and the second called “lab samples”(i.e. samples that were handled without any particular precautions and subject to normal washing, handling and measuring procedures in the osteological lab). Our results show that genetic profiles from “lab samples” are incomplete or ambiguous in the different skeletal areas while a different outcome is observed in the “virgin samples” set. Generally, all specimens from different skeletal areas in the exception of teeth present incongruent results between “lab” and “virgin” samples. Therefore teeth are less prone to contamination than the other skeletal areas we analyzed and may be considered a material of choice for classical aDNA studies. In addition, we showed that bones can also be a good candidate for human aDNA analysis if they come directly from the excavation site and are accompanied by a clear taphonomic history.