Kafka's beautiful eyes: Forensic intelligence utilisation of phenotypic information.

Franz Kafka had beautiful eyes. So striking, that many of the famous author's friends and peers commented on them - but quite variously ('dark', 'brown', 'grey' & 'blue'). Eye colour as perceived by an observer is subjective, being influenced by physiological, environmental, and even sociocultural factors. In a policing context, this does not mean that trait information such as eye colour is not valuable (far from it), but that it must be managed carefully. The Australian Federal Police has recently implemented a forensic DNA phenotyping (FDP, aka. physical trait prediction or PTP) capability, utilising massively parallel sequencing DNA technology to predict an individual's eye colour, biogeographical ancestry and sex from a crime scene sample. This information alone is not itself 'intelligence', but can be used to generate intelligence through holistic analyses undertaken within a transdisciplinary, all-source forensic intelligence (FORINT) framework. FORINT outputs posit abductive propositions typically at the activity/offence level, to provide insight and influence decision making. However, the use of predicted traits requires that they are compared to something; all Australian police databases include fields for physical traits, but no uniform standard is applied across all agencies. Moreover, collection is inconsistent and no automated systems are in place to capture such data systematically. Consider the 'Kafka problem': his peers gave multiply divergent descriptions of his eyes. If a Biology unit had predicted the eye colour of an 'unidentified author' using DNA - how would Kafka be confidently nominated as the contributor? We posit three maxims for law enforcement: (1) To expand the operational utility of forensic science in line with police demands, forensic science should operationalise FDP (e.g. operationally to rank a list of persons of interest, focus lines of enquiry in serious & organised crime, or assist with human remains identification). (2) Such advanced biological techniques are best delivered through an all-source FORINT framework, to maximise opportunities and minimise risk. (3) One cannot pursue techno-scientific advancements in isolation; it is also necessary to influence the operational posture for their implementation. In this paper we explore these issues and provide recommendations relating to (a) police practices, (b) image capture systems, and (c) research opportunities. Phenotypic trait prediction has great potential and can be operationalised effectively through a rigorous FORINT framework. However, there is (continual) work to be done to enhance the operational capabilities that are complementary to - but necessary for - effective forensic science contribution to investigations.

The secret hidden in dust: Assessing the potential to use biological and chemical properties of the airborne fraction of soil for provenance assignment and forensic casework.

The airborne fraction of soil (dust) is both ubiquitous in nature and contains localised biological and chemical signatures, making it a potential medium for forensic intelligence. Metabarcoding of dust can yield biological communities unique to the site of interest, similarly, geochemical analyses can uncover elements and minerals within dust that can be matched to a geographic location. Combining these analyses presents multiple lines of evidence as to the origin of dust collected from items of interest. In this work, we investigated whether bacterial and fungal communities in dust change through time and whether they are comparable to soil samples of the same site. We integrated dust metabarcoding into a framework amenable to forensic casework, (i.e., using calibrated log-likelihood ratios) to predict the origin of dust samples using models constructed from both dust samples and soil samples from the same site. Furthermore, we tested whether both metabarcoding and geochemical/mineralogical analyses could be conducted on a single swabbed sample, for situations where sampling is limited. We found both analyses could generate results from a single swabbed sample and found biological and chemical signatures unique to sites. However, we did find significant variation within sites, where this did not always correlate with time but was a random effect of sampling. This variation within sites was not greater than between sites and so did not influence site discrimination. When modelling bacterial and fungal diversity using calibrated log-likelihood ratios, we found samples were correctly predicted using dust 67% and 56% of the time and using soil 56% and 22% of the time for bacteria and fungi communities respectively. Incorrect predictions were related to within site variability, highlighting limitations to assigning dust provenance using metabarcoding of soil.

The utility of dust for forensic intelligence: Exploring collection methods and detection limits for environmental DNA, elemental and mineralogical analyses of dust samples.

Environmental DNA (eDNA), elemental and mineralogical analyses of soil have been shown to be specific to their source material, prompting consideration of using the airborne fraction of soil (dust) for forensic intelligence work. Dust is ubiquitous in the environment and is easily transferred to items belonging to a person of interest, making dust analysis an ideal tool in forensic casework. The advent of Massive Parallel Sequencing technologies means metabarcoding of eDNA can uncover bacterial, fungal, and even plant genetic fingerprints in dust particles. Combining this with elemental and mineralogical compositions offers multiple, complementary lines of evidence for tracing the origin of an unknown dust sample. This is particularly pertinent when recovering dust from a person of interest to ascertain where they may have travelled. Prior to proposing dust as a forensic trace material, however, the optimum sampling protocols and detection limits need to be established to place parameters around its utility in this context. We tested several approaches to collecting dust from different materials and determined the lowest quantity of dust that could be analysed for eDNA, elemental composition and mineralogy, whilst still yielding results capable of distinguishing between sites. We found that fungal eDNA profiles could be obtained from multiple sample types and that tape lifts were the optimum collection method for discriminating between sites. We successfully recovered both fungal and bacterial eDNA profiles down to 3 mg of dust (the lowest tested quantity) and recovered elemental and mineralogical compositions for all tested sample quantities. We show that dust can be reliably recovered from different sample types, using different sampling techniques, and that fungi and bacteria, as well as elemental and mineralogical profiles, can be generated from small sample quantities, highlighting the utility of dust for forensic intelligence.

Evaluation of commercial forensic DNA extraction kits for decontamination and extraction of DNA from biological samples contaminated with radionuclides.

In preparing to respond to security incidents involving radioactive material, States should consider how they might address the unique challenge of analysing forensic evidence contaminated with these materials. In the case of DNA evidence, previous research has suggested that commercial forensic DNA extraction kits may be able to remove radioactive contamination from biological samples. If viable, this would allow the extraction and decontamination of biological samples to be undertaken in a laboratory equipped to handle radioactive material, with the subsequent quantification and profiling of extracted DNA performed in a conventional forensics laboratory. In order to inform the development of an operational capability, this study sought to expand upon previous work to provide a more comprehensive quantitative assessment of the efficacy of commercial DNA extraction kits for the removal of radionuclide contamination from biological samples and the quality of the resultant DNA profiles. Three commercial DNA extraction kits were tested for their ability to remove contaminating radionuclides. Two of these kits proved more effective at removing radionuclide contamination and produced DNA extracts of higher quality. Under all conditions tested in this study, decontamination efficiency was sufficient to allow the release of samples to a forensic laboratory. However, consistent with a prudent approach to radiation safety it is recommended that all samples be screened by gamma spectrometry prior to their release to a forensic laboratory in order to verify decontamination.

Comparison between magnetic bead and qPCR library normalisation methods for forensic MPS genotyping.

Massively parallel sequencing (MPS) is fast approaching operational use in forensic science, with the capability to analyse hundreds of DNA identity and DNA intelligence markers in multiple samples simultaneously. The ForenSeq™ DNA Signature Kit on MiSeq FGx™ (Illumina) workflow can provide profiles for autosomal short tandem repeats (STRs), X chromosome and Y chromosome STRs, identity single nucleotide polymorphisms (SNPs), biogeographical ancestry SNPs and phenotype (eye and hair colour) SNPs from a sample. The library preparation procedure involves a series of steps including target amplification, library purification and library normalisation. This study highlights the comparison between the manufacturer recommended magnetic bead normalisation and quantitative polymerase chain reaction (qPCR) methods. Furthermore, two qPCR chemistries, KAPA® (KAPA Biosystems) and NEBNext® (New England Bio Inc.), have also been compared. The qPCR outperformed the bead normalisation method, while the NEBNext® kit obtained higher genotype concordance than KAPA®. The study also established an MPS workflow that can be utilised in any operational forensic laboratory.

Characterization of Yersinia species by protein profiling using automated microfluidic capillary electrophoresis.

Yersinia pestis is a biological agent of high risk to national security due to its ability to be easily disseminated and transmitted among humans. If Y. pestis was to be utilized in a deliberate disease outbreak it would be essential to rapidly and accurately identify the agent. Current identification methods for Yersinia species are limited by their reliance on cultivation, the time taken to achieve results and/or the use of protocols that are not amenable for field use. Faster identification methods are urgently required. Microfluidic capillary electrophoresis was used to identify seven Yersinia species based on their protein profiles. Further objectives included determining if Yersinia species could be detected in mixtures of milk products and Escherichia coli, determining if Yersinia could be detected in a blinded identification and reproducibility across two platforms. Two characteristic protein bands were detected at 50 kilodaltons (kDa) and between 50 and 75 kDa for the Yersinia species. Individual Yersinia species could be differentiated from one another and distinguished from E. coli, Bacillus anthracis Sterne strain and Dipel (containing Bacillus thuringiensis). Due to the high protein content of milk products Yersinia could not be detected when mixed with these but was detected when mixed with E. coli. Species were correctly identified with 96% success in blinded procedures using 12 individuals. Whilst protein profile patterns were reproducible across platforms there was some discrepancy in protein sizing. This study demonstrates that protein profiling using microfluidic capillary electrophoresis is able to rapidly and reproducibly identify and characterize Yersinia species. Results show this technique is a powerful front-line, rapid and broad range screening method capable of identifying and differentiating biological agents, hoax agents and environmental bacterial species.

Background frequency of Bacillus species at the Canberra Airport: A 12 month study.

Anthrax, caused by Bacillus anthracis, is a naturally occurring disease in Australia. Whilst mainly limited to livestock in grazing regions of Victoria and New South Wales, movement of people, stock and vehicles means B. anthracis could be present outside this region. Of particular interest is the "background" prevalence of B. anthracis at transport hubs including airports. The aim of this study was to determine the background frequency of B. anthracis and the commonly used hoax agent Bacillus thuringiensis at the Canberra Airport over a 12 month period. Samples were collected daily for seven days each month from August 2011-July 2012 and analyzed using species specific real-time polymerase chain reaction. Fourteen samples (of a total of 575) were positive for the B. anthracis PL3 genomic marker, 24 for the cya (pXO1) plasmid marker and five for the capB (pXO2) plasmid marker. Whilst five samples were positive for both PL3 and cya, no samples were positive for all three markers hence there is no evidence to suggest the presence of pathogenic B. anthracis strains. B. anthracis targets were detected primarily in February 2012 and B. thuringiensis peaked in October and November 2011 and again in April and May 2012. This study provides a rapid method to screen for, and differentiate, Bacillus species. Armed with this information investigators will be able to discriminate a "threat" from "background" frequencies should the need arise.

Characterization of Bacillus strains and hoax agents by protein profiling using automated microfluidic capillary electrophoresis.

PURPOSE: In recent times, but especially since 2001, bioterrorism has been of increasing concern. In addition to the use of biological agents, including Bacillus anthracis (anthrax), there have been numerous hoax white powder "scares." It is imperative to rapidly and accurately identify any suspicious powder as hazardous or hoax. Classical methods for identification typically rely on time-consuming cultivation or highly specific molecular tests which are limited if the agent is unknown. Faster and field portable methods for analysis of suspicious powders are urgently required. METHODS: Potential hoax agents, including Bacillus species and household powders, were analyzed using automated microfluidic capillary electrophoresis to determine if protein profiling can distinguish between, and identify, samples. RESULTS: Distinctive protein profiles were produced for Bacillus species, with the presence and/or absence of certain bands, aiding identification. In particular B. anthracis Sterne strain contained a distinctive doublet band above 100 kDa which was not present in any other Bacillus species or hoax agents examined. The majority of powders produced distinctive banding that could enable the identification of the sample while simultaneously ruling out B. anthracis with a high degree of confidence. CONCLUSIONS: Results show automated microfluidic capillary electrophoresis can rapidly and reproducibly characterize Bacillus species and hoax agents based on protein profiles without the need for culture. Results were reproducible and there was enhanced resolution and rapidity compared to traditional protein profiling methods. Results show this technique is amenable to field use at a bioterrorism incident, thereby providing essential information to investigators regarding containment and treatment strategies.

Recovery and identification of bacterial DNA from illicit drugs.

Bacterial infections, including Bacillus anthracis (anthrax), are a common risk associated with illicit drug use, particularly among injecting drug users. There is, therefore, an urgent need to survey illicit drugs used for injection for the presence of bacteria and provide valuable information to health and forensic authorities. The objectives of this study were to develop a method for the extraction of bacterial DNA from illicit drugs and conduct a metagenomic survey of heroin and methamphetamine seized in the Australian Capital Territory during 2002-2011 for the presence of pathogens. Trends or patterns in drug contamination and their health implications for injecting drug users were also investigated. Methods based on the ChargeSwitch(®)gDNA mini kit (Invitrogen), QIAamp DNA extraction mini kit (QIAGEN) with and without bead-beating, and an organic phenol/chloroform extraction with ethanol precipitation were assessed for the recovery efficiency of both free and cellular bacterial DNA. Bacteria were identified using polymerase chain reaction and electrospray ionization-mass spectrometry (PCR/ESI-MS). An isopropanol pre-wash to remove traces of the drug and diluents, followed by a modified ChargeSwitch(®) method, was found to efficiently lyse cells and extract free and cellular DNA from Gram-positive and Gram-negative bacteria in heroin and methamphetamine which could then be identified by PCR/ESI-MS. Analysis of 12 heroin samples revealed the presence of DNA from species of Comamonas, Weissella, Bacillus, Streptococcus and Arthrobacter. No organisms were detected in the nine methamphetamine samples analysed. This study develops a method to extract and identify Gram-positive and Gram-negative bacteria from illicit drugs and demonstrates the presence of a range of bacterial pathogens in seized drug samples. These results will prove valuable for future work investigating trends or patterns in drug contamination and their health implications for injecting drug users as well as enabling forensic links between seizures to be examined.

Diagnosis of Queensland tick typhus and African tick bite fever by PCR of lesion swabs.

We report 3 cases of Queensland tick typhus (QTT) and 1 case of African tick bite fever in which the causative rickettsiae were detected by PCR of eschar and skin lesions in all cases. An oral mucosal lesion in 1 QTT case was also positive.

Diagnosing Smith-Magenis syndrome and duplication 17p11.2 syndrome by RAI1 gene copy number variation using quantitative real-time PCR.

Smith-Magenis syndrome (SMS) and duplication 17p11.2 (dup17p11.2) syndrome are multiple congenital anomalies/mental retardation disorders resulting from either a deletion or duplication of the 17p11.2 region, respectively. The retinoic acid induced 1 (RAI1) gene is the causative gene for SMS and is included in the 17p11.2 region of dup17p11.2 syndrome. Currently SMS and dup17p11.2 syndrome are diagnosed using a combination of clinically recognized phenotypes and molecular cytogenetic analyses such as fluorescent in situ hybridization (FISH). However, these methods have proven to be highly expensive, time consuming, and dependent upon the low resolving capabilities of the assay. To address the need for improved diagnostic methods for SMS and dup17p11.2 syndrome, we designed a quantitative real-time PCR (Q-PCR) assay that measures RAI1 copy number using the comparative C(t) method, DeltaDeltaC(t). We tested our assay with samples blinded to their previous SMS or dup17p11.2 syndrome status. In all cases, we were able to determine RAI1 copy number status and render a correct diagnosis accordingly. We validated these results by both FISH and multiplex ligation-dependent probe amplification (MLPA). We conclude that Q-PCR is an accurate, reproducible, low-cost, and reliable assay that can be employed for routine use in SMS and dup17p11.2 diagnosis.

The detection of Chlamydia pneumoniae in atherosclerotic plaques of Australian subjects.

AIM: To determine whether the common respiratory pathogen, Chlamydia pneumoniae, was associated with atherosclerotic plaques in Australian subjects. METHODS: A total of 29 coronary atherosclerotic lesions and 18 normal coronary arterial samples were tested for the presence of C. pneumoniae by PCR and immunofluorescence methods. RESULTS: Chlamydia pneumoniae was detected in 15 of the atheromatous lesions as well as in three of the normal tissues; the immunofluorescence assay was more sensitive (P=0.028) than PCR (P=0.26). CONCLUSIONS: These findings contradict previous Australian studies which did not detect C. pneumoniae in atherosclerotic plaques, thereby discounting the speculation that its absence was likely due to geographical variation. The detection of the bacterium in some of the normal tissues suggests that C. pneumoniae infection might be an initial trigger of atherosclerotic development.