ORCID Profile
0000-0002-4854-6278
Current Organisation
Murdoch University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Microbial Ecology | Genomics | Archaeology | Quality Assurance, Chemometrics, Traceability and Metrological Chemistry | Other Biological Sciences | Access to Justice | Archaeological Science | Forensic Biology |
ANZSRC Socio-Economic Objective (SEO)
Understanding Australia's Past | Conserving Aboriginal and Torres Strait Islander Heritage | Criminal Justice | Flora, Fauna and Biodiversity at Regional or Larger Scales | Expanding Knowledge in History and Archaeology | Trade and Environment
Related Links
Publications
Cytochrome b or cytochrome c oxidase subunit I for mammalian species identification-An answer to the debate
Publisher: Elsevier BV
Date: 12-2009
Southern South Australian groundwater microbe diversity
Publisher: Oxford University Press (OUP)
Date: 10-08-2018
Abstract: Groundwater is increasingly used globally for domestic, industrial and agricultural production. While many studies have focused on groundwater as a resource, the erse ecosystems within are often ignored. Here, we assess 54 Southern South Australian groundwater microbial communities from the populated part of the state to assess their status and dynamics in isolated groundwater systems. We observed a strong site-to-site in iduality in groundwater bacterial communities, likely due to the isolated nature of groundwater bodies leading to unique ecosystems. Rank abundance analysis indicates bacterial ersity is maintained even at low abundances and that the distribution fits classical ecological models for strong competition in resource-limited environments. Combined, our data indicates that despite overrepresentation of pollutant-associated bacterial orders in and around the Adelaide metropolitan area, microbial communities remain erse and show little evidence of converging on a common pollutant-effected community.
The use of mitochondrial DNA genes to identify closely related avian species
Publisher: Elsevier BV
Date: 12-2009
Quantification of trace amounts of human and non-human mitochondrial DNA (mtDNA) using SYBR Green and real time PCR
Publisher: Elsevier BV
Date: 08-2008
A method to identify a large number of mammalian species in the UK from trace samples and mixtures without the use of sequencing
Publisher: Elsevier BV
Date: 08-2008
Identifying endangered species from degraded mixtures at low levels
Publisher: Elsevier BV
Date: 12-2009
Foraminifera-A new find in the microtaphonomical characterization of bones from marine archaeological excavations
Publisher: Wiley
Date: 24-06-2021
DOI: 10.1002/OA.3013
Abstract: Foraminifera are marine single‐celled organisms, ubiquitous in marine environments, present in brackish waters and absent in terrestrial locations. Their presence has been associated with archaeological and forensic studies only rarely and just once and superficially with bones of terrestrial mammals. In this study, a new association is presented between foraminifera enclosed in the dissolving trabecular spaces of terrestrial mammalian bones, recovered in underwater archaeological excavations between 1968 and 1980. Research on the new association aims to detail the micro‐characterization of bone in underwater environments, leading to a better understanding of bone taphonomic trajectories, the chronological sequences of changes occurring between death and the incorporation of the remains of an organism within the depositional environment. The analysis of taphonomic trajectories is known to hold relevance in distinct disciplines, such as archaeology, paleontology, and forensic sciences. Different foraminiferal taxa are linked to different marine environments, characterized by specific ranges of water depth, amount of light and oxygen, temperature, and composition of sediment. The association between foraminifera and terrestrial mammalian bones indicates deposition in a marine or brackish environment thus, the analysis of the specific ecology of the identified foraminiferal taxa can point to a specific environment, adding information to paleontological, archaeological, or forensics casework.
Effect of nucleic acid binding dyes on DNA extraction, amplification, and STR typing
Publisher: Wiley
Date: 10-2015
Abstract: We report on the effects of six dyes used in the detection of DNA on the process of DNA extraction, lification, and detection of STR loci. While dyes can be used to detect the presence of DNA, their use is restricted if they adversely affect subsequent DNA typing processes. Diamond™ Nucleic Acid Dye, GelGreen™, GelRed™, RedSafe™, SYBR(®) Green I, and EvaGreen™ were evaluated in this study. The percentage of dye removed during the extraction process was determined to be: 70.3% for SYBR(®) Green I 99.6% for RedSafe™ 99.4% for EvaGreen™ 52.7% for Diamond™ Dye 50.6% for GelRed™, and could not be determined for GelGreen™. It was then assumed that the amount of dye in the fluorescent quantification assay had no effect on the DNA signal. The presence of all six dyes was then reviewed for their effect on DNA extraction. The t-test showed no significant difference between the dyes and the control. These extracts were then STR profiled and all dyes and control produced full DNA profiles. STR loci in the presence of GelGreen(TM) at 1X concentration showed increased lification products in comparison to the control s les. Full STR profiles were detected in the presence of EvaGreen™ (1X), although with reduced lification products. RedSafe™ (1X), Diamond™ Dye (1X), and SYBR(®) Green I (1X) all exhibited varying degrees of locus drop-out with GelRed™ generating no loci at all. We provide recommendations for the best dye to visualize the presence of DNA profile as a biological stain and its subsequent lification and detection.
Finding DNA: Using fluorescent in situ detection
Publisher: Elsevier BV
Date: 12-2015
Piles of scats for piles of DNA: deriving DNA of lizards from their faeces
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/ZO14059
Abstract: Non-invasive genetic s ling using scats has a well established role in conservation biology, but has rarely been applied to reptiles. Using scats from captive and wild Egernia stokesii (Squamata, Scincidae) we evaluated two storage and six DNA-extraction methods and the reliability of subsequent genotype and sequence data. Accurate genotype and sequence data were obtained from frozen and dried captive lizard scat DNA extracted using a QIA ® DNA Stool Mini Kit and a modified Gentra® Puregene® method, but success rates were reduced for wild lizard scats. Wild E. stokesii eat more plants than their captive counterparts, possibly resulting in scat DNA extracts containing plant compounds that inhibit PCR- lifications. Notably, reliable genotypes and sequences were obtained from wild E. stokesii scat DNA extracted using a Qiagen DNeasy® Plant Mini Kit, a method designed to remove plant inhibitory compounds. Results highlight the opportunity for using scat-derived DNA in lizard studies, particularly for species that deposit scats in piles.
Host-specific associations affect the microbiome of Philornis downsi, an introduced parasite to the Galápagos Islands.
Publisher: Wiley
Date: 02-08-2017
DOI: 10.1111/MEC.14219
Abstract: The composition and ersity of bacteria forming the microbiome of parasitic organisms have implications for differential host pathogenicity and host-parasite co-evolutionary interactions. The microbiome of pathogens can therefore have consequences that are relevant for managing disease prevalence and impact on affected hosts. Here, we investigate the microbiome of an invasive parasitic fly Philornis downsi, recently introduced to the Galápagos Islands, where it poses extinction threat to Darwin's finches and other land birds. Larvae infest nests of Darwin's finches and consume blood and tissue of developing nestlings, and have severe mortality impacts. Using 16s rRNA sequencing data, we characterize the bacterial microbiota associated with P. downsi adults and larvae sourced from four finch host species, inhabiting two islands and representing two ecologically distinct groups. We show that larval and adult microbiomes are dominated by the phyla Proteobacteria and Firmicutes, which significantly differ between life stages in their distributions. Additionally, bacterial community structure significantly differed between larvae retrieved from strictly insectivorous warbler finches (Certhidea olivacea) and those parasitizing hosts with broader dietary preferences (ground and tree finches, Geospiza and Camarhynchus spp., respectively). Finally, we found no spatial effects on the larval microbiome, as larvae feeding on the same host (ground finches) harboured similar microbiomes across islands. Our results suggest that the microbiome of P. downsi changes during its development, according to dietary composition or nutritional needs, and is significantly affected by host-related factors during the larval stage. Unravelling the ecological significance of bacteria for this parasite will contribute to the development of novel, effective control strategies.
ELEquant: a developmental framework and validation of forensic and conservation real-time PCR assays
Publisher: Springer Science and Business Media LLC
Date: 05-02-2019
DOI: 10.1007/S11033-019-04660-7
Abstract: A framework for the development and validation of a qPCR assay for species identification and DNA quantification for conservation and forensic purposes is presented. Elephants are commonly poached for their ivory tusks, which is the primary driving force behind their endangered status. In addition to poaching and trade, habitat loss due to logging and mining has also resulted in loss of elephants. Crimes against animals can be deterred and/or further prosecution sought through testing with forensic genetic techniques. The creation of novel genetic assays can greatly impact wildlife forensic science investigations in identifying the species. Molecular genetic techniques can help enforce conservation efforts however, they must be properly developed and validated to be of evidentiary quality for court systems. African and Asian elephant buccal cells were used as model in this work. The assay provides a method to differentiate biological fluids of both genera of elephants simultaneously. It can be used for identification of elephant derived products and presents valuable quantification for optimized further testing, such as microsatellite detection.
Microbial micropatches within microbial hotspots
Publisher: Public Library of Science (PLoS)
Date: 22-05-2018
DNA typing in wildlife crime: recent developments in species identification
Publisher: Springer Science and Business Media LLC
Date: 05-06-2010
DOI: 10.1007/S12024-010-9168-7
Abstract: Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can in idual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown s le to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the in idual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of s les being tested in alleged wildlife crimes.
A new assay for identifying endangered species in Traditional East Asian Medicine
Publisher: Elsevier BV
Date: 12-2011
Identification multiplex assay of 19 terrestrial mammal species present in New Zealand
Publisher: Wiley
Date: 13-11-2013
Abstract: An identification assay has been developed that allows accurate detection of 19 of the most common terrestrial mammals present in New Zealand (cow, red deer, goat, dog, horse, hedgehog, cat, tammar wallaby, mouse, weasel, ferret, stoat, sheep, rabbit, Pacific rat, Norway rat, ship rat, pig, and brushtail possum). This technique utilizes species-specific primers that, combined in a multiplex PCR, target small fragments of the mitochondrial cytochrome b gene. Each species, except hedgehog, produces two distinctive species-specific fragments, making the assay self-confirmatory and enabling the identification of multiple species simultaneously in DNA mixtures. The multiplex assay detects as little as 100 copies of mitochondrial DNA, which makes it a very reliable tool for degraded and trace s les. Reliability, accuracy, reproducibility, and sensitivity tests to validate the technique were performed. The technique featured here enabled a prompt response in a predation specific event, but can also be useful for wildlife management and conservation, pest incursions detection, forensic, and industrial purposes in a very simple and cost-effective manner.
Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome B and cytochrome oxidase subunit I mitochondrial genes.
Publisher: Public Library of Science (PLoS)
Date: 30-11-2010
Duration of in situ fluorescent signals within hairs follicles
Publisher: Elsevier BV
Date: 12-2015
Erratum to: The complete mitochondrial genome analysis of the tiger (Panthera tigris)
Publisher: Springer Science and Business Media LLC
Date: 08-2012
Species identification of human and deer from mixed biological material
Publisher: Elsevier BV
Date: 07-2007
A multiplex assay to identify 18 European mammal species from mixtures using the mitochondrial cytochromeb gene
Publisher: Wiley
Date: 2008
Abstract: A novel species-specific multiplex to identify 18 common European mammalian species (badger, cat, cow, dog, donkey, fox, goat, guinea pig, harvest mouse, hedgehog, horse, house mouse, human, pig, rabbit, rat, red deer and sheep), many of which are often associated with forensic investigations, has been developed. The assay is based on the mitochondrial cytochrome b gene, which is commonly used in species identification and phylogeny studies. Areas of homology and variation were identified and were used to create universal and species-specific primers. The species-specific primers were designed such that they will only react with the species for which they were designed. Two primer sets were designed for each species making the test self-confirmatory. All primer sets produced the expected results. The multiplex was balanced at template concentration of 40 000 copies (approximately 1.36 pg). Validation was accomplished by analysing the same s le ten times to determine run variation and several s les for each species to determine between-s le variation. Twenty-eight additional mammalian species were reacted with the multiplex. The multiplex provides, for the first time, a definitive method for identification of species in a forensic context.
Where does this tiger come from?-A robust molecular technique for simultaneous identification of endangered species and subspecies
Publisher: Elsevier BV
Date: 12-2011
Complete Genome Sequences of the Endophytic Streptomyces Strains EN16, EN23, and EN27, Isolated from Wheat Plants
Publisher: American Society for Microbiology
Date: 29-12-2016
Abstract: The complete genome sequences of three endophytic Streptomyces species were compared. Strains EN16, EN23, and EN27 were isolated from surface-sterilized roots of wheat plants from South Australia. In field trials, these strains are effective in suppressing fungal root diseases of wheat when added as spore coatings to wheat seed.
Marine sponge bioerosion in the forensic taphonomy of terrestrial bone
Publisher: Elsevier BV
Date: 06-2023
On the trial of tigers–tracking tiger in Traditional East Asian Medicine
Publisher: Elsevier BV
Date: 08-2008
An assessment of the genetic diversity of the founders of the European captive population of Asian lion (Panthera leo leo), using microsatellite markers and studbook analysis
Publisher: Springer Science and Business Media LLC
Date: 2018
Singleplex quantitative real-time PCR for the assessment of human mitochondrial DNA quantity and quality
Publisher: Springer Science and Business Media LLC
Date: 20-01-2018
DOI: 10.1007/S12024-017-9944-8
Abstract: Mitochondrial DNA (mtDNA) can provide a means for forensic identity testing when genotyping of nuclear DNA (nuDNA) targets is not possible due to degradation or lack of template. For degraded s les, an indication of the quantity and quality of mtDNA is essential to allow selection of appropriately sized targets for hypervariable region (HVR) analysis, which may conserve s le and resources. Three human-specific mtDNA targets of increasing length (86, 190 and 452 base pairs) were lified by singleplex quantitative real-time PCR (qPCR), capable of providing an index of mtDNA degradation from fragment length information. Quantification was achieved by preparation of a standard curve for each target, using a purified mtDNA standard containing all three targets of interest, which produced a linear, accurate and precise result from 1×10
Recovery of human DNA profiles from poached deer remains part 2: Improved recovery protocol without the need for LCN analysis
Publisher: Elsevier BV
Date: 03-2013
DOI: 10.1016/J.SCIJUS.2012.03.002
Abstract: Although poaching is a common wildlife crime, the high and prohibitive cost of specialised animal testing means that many cases are left un-investigated. We previously described a novel approach to wildlife crime investigation that looked at the identification of human DNA on poached animal remains (Tobe, Govan and Welch, 2011). Human DNA was successfully isolated and lified from simulated poaching incidents, however a low template protocol was required which made this method unsuitable for use in many laboratories. We now report on an optimised recovery and lification protocol which removes the need for low template analysis. S les from 10 deer (40 s les total - one from each leg) analysed in the original study were re-analysed in the current study with an additional 11 deer s les. Four s les analysed using Chelex did not show any results and a new method was devised whereby the available DNA was concentrated. By combining the DNA extracts from all tapings of the same deer remains followed by concentration, the recovered quantity of human DNA was found to be 29.5pg±43.2pg, 31× greater than the previous study. The use of the Investigator Decaplex SE (QIAGEN) STR kit provided better results in the form of more complete profiles than did the AmpFℓSTR® SGM Plus® kit at 30cycles (Applied Biosystems). Re-analysis of the s les from the initial study using the new, optimised protocol resulted in an average increase of 18% of recovered alleles. Over 17 s les, 71% of the s les analysed using the optimised protocol showed sufficient lification for comparison to a reference profile and gave match probabilities ranging from 7.7690×10(-05) to 2.2706×10(-14). The removal of low template analysis means this optimised method provides evidence of high probative value and is suitable for immediate use in forensic laboratories. All methods and techniques used are standard and are compatible with current SOPs. As no high cost non-human DNA analysis is required the overall process is no more expensive than the investigation of other volume crime s les. The technique is suitable for immediate use in poaching incidents.
The complete mitochondrial genome analysis of the tiger (Panthera tigris)
Publisher: Springer Science and Business Media LLC
Date: 30-12-2011
DOI: 10.1007/S11033-011-1384-Z
Abstract: The complete mitochondrial genomes of five tiger s les from three subspecies (P. t. sumatrae, P. t. altica, and P. t. tigris) were successfully obtained by using 26 specifically designed Panthera-specific primer sets. The genome organization and gene arrangement of the five tiger s les were similar to each other however polymorphic tandem repeat sequences were observed in the control region (CR). This led to a difference in the genome lengths obtained from these five s les with an average size of 16,994 bp for the five tiger mitochondrial genomes. The nucleotide base composition was on average as follows: A, 31.8% T, 27.0% C, 26.6% G, 14.6% and exhibited compositional asymmetry. Most of tiger mitochondrial genome characteristics are similar to those of other common vertebrate species however, some distinctive features were observed in the CR. First, the repetitive sequence 2 (RS 2) contained two repeat units of 80 bp and the first 15 bp of what would be the third repeat motif. The repetitive sequence 3 (RS 3) contained 47-50 repeat motifs of a shorter 8 bp (ACGTAYAC)(n). Second, length heteroplasmy polycystosine (poly-C) stretches was observed at the end of the HV I locus in all tiger s les.
Assigning confidence to sequence comparisons for species identification: A detailed comparison of the cytochrome b and cytochrome oxidase subunit I mitochondrial genes
Publisher: Elsevier BV
Date: 12-2011
Properties of nucleic acid staining dyes used in gel electrophoresis
Publisher: Wiley
Date: 23-02-2015
Abstract: Nucleic acid staining dyes are used for detecting nucleic acids in electrophoresis gels. Historically, the most common dye used for gel staining is ethidium bromide, however due to its toxicity and mutagenicity other dyes that are safer to the user and the environment are preferred. This Short Communication details the properties of dyes now available and their sensitivity for detection of DNA and their ability to permeate the cell membrane. It was found that GelRed™ was the most sensitive and safest dye to use with UV light excitation, and both GelGreen™ and Diamond™ Nucleic Acid Dye were sensitive and the safer dyes using blue light excitation.
Determining the Geographic Origin of Animal Samples
Publisher: CRC Press
Date: 12-03-2009
Molecular analysis of botanical evidence by DNA thermal dissociation temperature
Publisher: Elsevier BV
Date: 12-2011
Species Identification Using DNA Loci
Publisher: CRC Press
Date: 12-03-2009
Tackling poaching: Recovery of human DNA profiles from deer remains
Publisher: Elsevier BV
Date: 12-2011
Evaluation of Six Presumptive Tests for Blood, Their Specificity, Sensitivity, and Effect on High Molecular-Weight DNA
Publisher: Wiley
Date: 07-12-2007
DOI: 10.1111/J.1556-4029.2006.00324.X
Abstract: Luminol, leuchomalachite green, phenolphthalein, Hemastix, Hemident, and Bluestar are all used as presumptive tests for blood. In this study, the tests were subjected to dilute blood (from 1:10,000 to 1:10,000,000), many common household substance, and chemicals. S les were tested for DNA to determine whether the presumptive tests damaged or destroyed DNA. The DNA loci tested were D2S1338 and D19S433. Leuchomalachite green had a sensitivity of 1:10,000, while the remaining tests were able to detect blood to a dilution of 1:100,000. Substances tested include saliva, semen, potato, tomato, tomato sauce, tomato sauce with meat, red onion, red kidney bean, horseradish, 0.1 M ascorbic acid, 5% bleach, 10% cupric sulfate, 10% ferric sulfate, and 10% nickel chloride. Of all the substances tested, not one of the household items reacted with every test however, the chemicals did. DNA was recovered and lified from luminol, phenolphthalein, Hemastix, and Bluestar, but not from leuchomalachite green or Hemident.
Recovery of human DNA profiles from poached deer remains: A feasibility study
Publisher: Elsevier BV
Date: 12-2011
DOI: 10.1016/J.SCIJUS.2011.06.002
Abstract: Poaching is a crime that occurs worldwide and can be extremely difficult to investigate and prosecute due to the nature of the evidence available. If a species is protected by international legislation such as the Convention on International Trade in Endangered Species of Wild Fauna and Flora then simply possessing any part of that species is illegal. Previous studies have focused on the identification of endangered species in cases of potential poaching. Difficulties arise if the poached animal is not endangered. Species such as deer have hunting seasons whereby they can legally be hunted however poaching is the illegal take of deer, irrespective of season. Therefore, identification of deer alone has little probative value as s les could have originated from legal hunting activities in season. After a deer is hunted it is usual to remove the innards, head and lower limbs. The limbs are removed through manual force and represent a potential source of human touch DNA. We investigate the potential to recover and profile human autosomal DNA from poached deer remains. S les from the legs of ten culled deer were obtained (40 in total) using minitapes. DNA from s les was extracted, quantified and lified to determine if it would be possible to recover human STR profiles. Low quantification data led to the use of an extended PCR cycling protocol of 34 cycles. S les from seven deer lified, however some s les were excluded from further analysis due to 'drop in' alleles or the low level of successfully lified loci. S les from five deer could be further analysed and gave match probabilities ranging from 6.37×10(-3) to 9.53×10(-11). This study demonstrates the potential of recovering human touch DNA from poached animal remains. There is the potential for this test to be used in relation to other species of poached remains or other types of wildlife crimes. This is the first time, to our knowledge, that human STR profiling has been successfully applied to touch DNA in regards to simulated wildlife crime.
Taphonomy and Diagenesis of Human Bone in Underwater Archaeology: A Review of the Current Status and the Proposal of Post-Mortem Submersion Interval (PMSI) as a Potential Forensic Application
Publisher: Springer Science and Business Media LLC
Date: 02-01-2021
Bone diagenesis in the marine environment-I: Characterization and distribution of trace elements in terrestrial mammalian bones recovered from historic shipwrecks
Publisher: Wiley
Date: 25-01-2022
DOI: 10.1002/OA.3072
Abstract: Unlike the chemical composition and diagenetic modification of buried bones, subaqueous archaeological bone diagenesis has not been studied in detail. This observational work presents a macroscopic and microscopic characterization of 11 variably preserved archaeological terrestrial mammalian bones submerged in seawater and/or surrounded by marine sediment for 169–347 years. In situ trace element analysis was undertaken to identify geochemical fingerprints of diagenesis. The analyzed bones belong to a collection of underwater archaeological faunal materials excavated from four shipwreck sites. With one exception, all archaeological bones were fragmented, some were also heavily stained, and in two s les, the damage to the cortical layer was extensive. Bioerosion was assessed by scanning electron microscopy (SEM), and bone trace element chemistry (by laser ablation inductively coupled mass spectrometry—LA‐ICP‐MS) was compared with that of an unsubmerged modern sheep bone control. In the control, several trace elements were low in concentration (weighted mean concentration ppm Cr, Co, Ni, Cu, Y, rare earth elements, Th, U). In the submerged archaeological bones, the weighted mean concentration of Li, Cr, Cu, and U was enriched relative to the modern sheep bone, whereas Rb and Ba were depleted. The best‐preserved bone, recovered from Batavia, showed less variation in trace element patterns compared with the more poorly preserved bones. The only archaeological bone with preserved macroscopic structure and cortex showed a gradual decrease in trace element concentration from the outer surface towards the medullary cavity, whereas in s les where more cortical damage was noted, the distribution of these elements is more irregular. With the exception of Cu and Cr, the elements focused on in this work (Li, U, Rb, and Ba) are nonessential to life, supported by their low concentration in the modern sheep bone (with the exception of Ba). The results suggest that early macroscopic and microscopic diagenetic alteration influences the concentration and distribution of chemical elements in submerged bones and that in situ trace element analysis provides clues for the reconstruction of taphonomic trajectories.
Complete Genome Sequences of the Endophytic Streptomyces sp. Strains LUP30 and LUP47B, Isolated from Lucerne Plants
Publisher: American Society for Microbiology
Date: 15-06-2017
Abstract: The complete genome sequences of two endophytic Streptomyces sp. strains, LUP30 and LUP47B, were analyzed. These strains were isolated from surface-sterilized roots of lucerne plants from South Australia and were found to promote the growth of the rhizobial partner in vitro and significantly increased nodulation and nitrogen fixation in lucerne plants.
The development and validation of a single SNaPshot multiplex for tiger species and subspecies identification - Implications for forensic purposes
Publisher: Elsevier BV
Date: 03-2012
Sensitivity and specificity of presumptive tests for blood, saliva and semen
Publisher: Springer Science and Business Media LLC
Date: 18-01-2014
DOI: 10.1007/S12024-013-9515-6
Abstract: Despite their wide use, the limits of presumptive tests can be poorly understood. The aim of this study was to investigate the specificity and sensitivity of conventional, as well as innovative, presumptive tests for blood, semen and saliva. We investigated Kastle-Meyer (KM) and leucomalachite green (LMG) tests for blood with regard to their sensitivity and specificity in the presence of oxidizing (hypochlorite) and anti-oxidizing (ascorbic acid) agents. The suitability and specificity of the red starch paper (RSP) test for saliva was assessed. Finally, the inhibitory effect of detergent on the acid phosphatase (AP) test for semen was investigated along with possible cross reactions to tea stains. Our results confirm previous findings of higher sensitivity and specificity of the KM test compared to LMG test for blood. Contrary to previous studies, no statistically significant difference was observed in the sensitivity of the tests between dry and wet stains. The novel RSP test was found to successfully detect saliva. We demonstrated that acid phosphatase (AP) testing for semen is possible on used RSP. A common multipurpose detergent had an inhibitory effect on AP tests. False positive results were obtained from tea stains. Testing different sorts of tea (black, green and herbal teas) revealed that only Camellia varieties produce positive result with the AP test, due to AP being present in the plants. From our results we conclude that specific knowledge of each test, including substances that may affect the test outcome, is imperative to ensure correct interpretation of presumptive test results.
Optimization of Diamond Nucleic Acid Dye for quantitative PCR
Publisher: Future Science Ltd
Date: 10-2016
DOI: 10.2144/000114458
Abstract: Here, we evaluate Diamond Nucleic Acid Dye (DD) for use in quantitative PCR (qPCR) applications. Although DD is a commercially available stain for detection of DNA separated by gel electrophoresis, its use as a detection dye in qPCR has yet to be described. To determine if DD can be used in qPCR, we investigated its inhibitory effects on qPCR at concentrations ranging 0.1–2.5×. Serial dilution of DNA was used to determine the efficiency, sensitivity, and linearity of DD-generated qPCR data in comparison to other commonly used fluorescent dyes such as SYBR Green (SG), EvaGreen (EG), and BRYT Green (BG). DD was found to be comparable with other dyes for qPCR applications, with an R2 value .9 and an efficiency of 0.83. Mitochondrial DNA (mtDNA) target signals were successfully produced by DD over a DNA dilution range of ∼28 ng— 0.28 pg, demonstrating comparable sensitivity to the other dyes investigated. C q values obtained using DD were lower than those using EG by almost 7 cycles. We conclude that Diamond Nucleic Acid Dye is a cheaper, less toxic alternative for qPCR applications.
Microbial composition analyses by 16S rRNA sequencing: A proof of concept approach to provenance determination of archaeological ochre
Publisher: Public Library of Science (PLoS)
Date: 18-10-2017
Stygofauna enhance prokaryotic transport in groundwater ecosystems
Publisher: Springer Science and Business Media LLC
Date: 06-09-2016
DOI: 10.1038/SREP32738
Abstract: More than 97% of the world’s freshwater reserves are found in aquifers, making groundwater one of the most important resources on the planet. Prokaryotic communities in groundwater underpin the turnover of energy and matter while also maintaining groundwater purity. Thus, knowledge of microbial transport in the subsurface is crucial for maintaining groundwater health. Here, we describe for the first time the importance of stygofauna as vectors for prokaryotes. The “hitch-hiking” prokaryotes associated with stygofauna may be up to 5 orders of magnitude higher in abundance and transported up to 34× faster than bulk groundwater flow. We also demonstrate that prokaryotic ersity associated with stygofauna may be higher than that of the surrounding groundwater. Stygofauna are a newly recognized prokaryotic niche in groundwater ecosystems that have the potential to transport remediating, water purifying and pathogenic prokaryotes. Therefore, stygofauna may influence ecosystem dynamics and health at a microbial level, and at a larger scale could be a new source of prokaryotic ersity in groundwater ecosystems.
Successful DNA typing of a drug positive urine sample from a race horse
Publisher: Elsevier BV
Date: 11-2007
Forensic validation of a SNP and INDEL panel for individualisation of timber from bigleaf maple (Acer macrophyllum Pursch)
Publisher: Elsevier BV
Date: 05-2020
Commentary on: Comparison of presumptive blood test kits including Hexagon OBTI
Publisher: Wiley
Date: 29-12-2009
Detection of DNA within fingermarks
Publisher: Elsevier BV
Date: 2013
A technique for the quantification of human and non-human mammalian mitochondrial DNA copy number in forensic and other mixtures
Publisher: Elsevier BV
Date: 09-2008
DOI: 10.1016/J.FSIGEN.2008.03.002
Abstract: The number of mitochondria per cell varies by cell type and the number of mitochondrial DNA (mtDNA) genomes varies per mitochondrion. Biological s les from unknown species are encountered frequently in forensic science investigations and are often contaminated with human mtDNA making analysis difficult. Currently, no techniques to quantify non-human mtDNA are available. We report on a method to accurately quantify, sensitive to 100 copies (1.7fg), mtDNA from human and non-human sources when present as a mixture. The test developed uses the cytochrome b (cytb) and the ribosomal 12S genes on the mitochondrial genome. Universal and human specific fragments of similar size are lified and quantified using SYBR Green. We validate the test with 24 human s les and 27 non-human mammalian s les. The human fraction of a s le can then be subtracted from the universal fraction for an accurate estimation of non-human mtDNA copy number.
Development of a multiplex, PCR-based genotyping assay for African and Asian elephants for forensic purposes
Publisher: Springer Science and Business Media LLC
Date: 12-06-2020
DOI: 10.1007/S00414-019-02097-Y
Abstract: Wildlife crimes and the threats they present to elephant populations raise the need to develop and implement DNA-based methodology as an aid for wildlife forensic investigations and conservation efforts. This study describes the development of a tetra-nucleotide repeat STR multiplex, genotyping assay that will identify Asian elephant (Elephas maximus) and African elephant (Loxodonta africana) DNA. The assay targets six tetra-nucleotide STRs and two sex-typing markers simultaneously in both genera of elephants, a first for elephant genotyping assays. The developed assay has potential application in wildlife investigations to associate a biological s le to a particular in idual elephant and additionally in conservation science for population management.
Successful direct STR amplification of hair follicles after nuclear staining
Publisher: Elsevier BV
Date: 12-2015
A novel forensic DNA profiling technique for protected species
Publisher: Elsevier BV
Date: 12-2015
Molecular identification of python species: Development and validation of a novel assay for forensic investigations
Publisher: Elsevier BV
Date: 05-2015
DOI: 10.1016/J.FSIGEN.2014.12.002
Abstract: Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that lifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species lification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product lification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question.
Tiger species identification based on molecular approach
Publisher: Elsevier BV
Date: 12-2009
An assessment of the subjectivity of sperm scoring
Publisher: Elsevier BV
Date: 06-2015
DOI: 10.1016/J.FORSCIINT.2015.03.014
Abstract: Current histological investigation of vaginal swabs after alleged sexual assault includes the scoring of spermatozoa (0, + to ++++) and the recording of visible tails. It is a method that is universally employed. Despite this method being used for 40 years, there has never been a study investigating its suitability for forensic science. Here, we investigate the reproducibility and subjectivity of sperm scoring among different investigators. Dilutions of seminal fluid were randomly distributed onto 20 slides, stained with haematoxylin/eosin and assessed by 37 investigators, over 2 years. Slides were assessed for levels of spermatozoa and the presence of tails. Each slide was scored by a minimum of 25 investigators. On no slide was there a consensus between all scores. Standard deviation remained below 1, but relative standard deviation (RSD) ranged from 6 to 105% in a positive correlation as the average score decreased. Spermatozoa were not observed 56 times (9.6%) and 27 investigators (73%) did not observe spermatozoa on at least one slide. Spermatozoa with tails were observed on every slide by at least 10 examiners, but as the average score of the slide decreased, so did the observation of tails. The current sperm scoring method is highly subjective with a particularly high %RSD in slides with low overall sperm counts. Moreover, the recording of tails does not add value to the current technique of sperm scoring. Further research might improve the objectivity of sperm scoring and the reliability of recording of tails.
A proof of principal study on the use of direct PCR of semen and spermatozoa and development of a differential isolation protocol for use in cases of alleged sexual assault
Publisher: Springer Science and Business Media LLC
Date: 10-11-2016
DOI: 10.1007/S00414-016-1461-X
Abstract: Sexual assault s les are some of the most common s les encountered in forensic analysis. These s les can require a significant time investment due to differential extraction processes. We report on the first record of successful direct lification of semen for STR analysis. Neat seminal fluid, dilutions ranging from 1:5 to 1:160 and GEDNAP s les were successfully lified using a direct method. A mild differential isolation technique to enrich spermatozoa was developed and successfully implemented to separate and directly lify a mixture of semen and female epithelial cells. Aliquots of s les subjected to the differential isolation protocol were stained with Haemotoxylin and Eosin for sperm scoring. S les stained after PCR showed a complete lack of intact spermatozoa demonstrating that the cells are lysed during the PCR process. This paper demonstrates the potential to incorporate direct PCR in cases of sexual assault to more rapidly obtain results and achieve a higher sensitivity.
Using synthetic oligonucleotides as standards in probe-based qPCR
Publisher: Future Science Ltd
Date: 04-2018
Abstract: Real-time PCR (qPCR) is widely used in the life sciences. For quantifying DNA, a standard curve is required. Common methods for standard development are time consuming, costly, necessitate a specific skill set, and pose a contamination risk. Using a targeted synthetic oligonucleotide, such as a gBlocks ® Gene Fragment, overcomes these drawbacks and provides researchers an accurate and quick solution to standard development. Here, we demonstrate that using a gBlocks fragment as a standard provides comparable sensitivity, reliability, and assay performance to a purified licon standard.
Generation of DNA profiles from fabrics without DNA extraction
Publisher: Elsevier BV
Date: 02-2010
DOI: 10.1016/J.FSIGEN.2009.07.006
Abstract: DNA profiles can be obtained from fabrics where a person has made direct contact with clothing. A standard approach is to cut out a section of the fabric and then use a commercially available method to extract and isolate the DNA. Alternative methods to isolate DNA include the use of adhesive tape to remove traces of cellular material from the fabric prior to extraction. We report on a process to obtain full DNA profiles using direct lification from a range of fabrics. The absence of an extraction step both reduces the opportunity for contamination and reduces the loss of DNA during the extraction process, increasing the sensitivity of the process of generating a DNA profile. The process does not require the use of commercially available extraction kits thus reducing the cost of generating a DNA profile from trace amounts of starting material. The results are in part dependent upon the nature of the fabric used to which the DNA has been transferred.
An overview to the investigative approach to species testing in wildlife forensic science
Publisher: Springer Science and Business Media LLC
Date: 2011
Microscale distributions of freshwater planktonic viruses and prokaryotes are patchy and taxonomically distinct
Publisher: Inter-Research Science Center
Date: 12-08-2016
DOI: 10.3354/AME01788
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