Isriya Bunyasiri

A novel forensic DNA profiling technique for protected species

Publisher: Elsevier BV

Date: 12-2015

DOI: 10.1016/J.FSIGSS.2015.09.103

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.

A novel approach for rapid cell assessment to estimate DNA recovery from human bone tissue

Publisher: Springer Science and Business Media LLC

Date: 11-10-2021

DOI: 10.1007/S12024-021-00428-3

Abstract: We report on the use of a DNA staining dye to locate and record nucleated osteocytes and other bone-related cells within sections of archived formalin-fixed and paraffin-embedded human tibia from which informative DNA profiles were obtained. Eleven of these archived tibia s les were sectioned at a thickness of 5 µm. Diamond™ Nucleic Acid Dye was applied to the sections and cells within the matrix of the bone fluoresced so that their location and number of cells could be photographed. DNA was isolated from these 11 s les using a standard extraction process and the yields were quantified by real-time PCR. Complete STR profiles were generated from ten bone extracts where low-level inhibition was recorded with an incomplete STR profile obtained from one s le with higher inhibition. The stained image of this s le showed that few cells were present. There was a significant relationship between the number of DD-stained cells and the number of alleles obtained (p < 0.05). Staining cells to determine the prevalence of bone cell nuclei allows a triage of s les prior to any subsequent DNA profiling.

Perceptions, Problems and Prospects of Contract Farming: Insights from Rice Production in Vietnam

Publisher: MDPI AG

Date: 30-09-2022

DOI: 10.3390/SU141912472

Abstract: Contract farming (CF) is considered a relevant measure to tackle the challenges to sustainable development from the serious effects of climate change and the COVID-19 pandemic. Despite the positive effects of CF, low participation and frequent breaching of contracts remain challenges. Several studies have mentioned the advantages and disadvantages of CF but little is known about their rankings and perceptions of CF from the involved stakeholders. To address these evidence gaps, this study surveys stakeholders, ranks the perceived advantages and disadvantages of CF, and investigates the problems and prospects of CF. The study utilizes data triangulation from three stakeholders: farmers, contractors, and government policymakers. Data include twenty-seven key informant interviews (KIIs), seven focus group discussions (FGDs), and two participant observations (POs). Data are analyzed by a mixed method approach with methods of constant comparison, content analysis, and Rank Based Quotient (RBQ). The results indicate that while the main perceived advantage of CF relates to the outputs, the top three disadvantages of CF relate to issues likely to cause a breach of contract. The results also reveal that there seems to be a difference in the perception of CF’s advantages and disadvantages among the stakeholders. Despite the problems such as breaching several contract terms, mistrust, or market manipulation from the local collectors, CF in Vietnam is overall promising.

A complementary forensic ‘proteo-genomic’ approach for the direct identification of biological fluid traces under fingernails

Publisher: Springer Science and Business Media LLC

Date: 12-07-2018

DOI: 10.1007/S00216-018-1223-3

Abstract: Violent contact between in iduals during a crime can result in body fluids becoming trapped under the fingernails of the in iduals involved. The traces under fingernails represent valuable forensic evidence because DNA profiling can indicate from whom the trace originated and proteomic methods can be used to determine the type of fluid in the trace, thus providing evidence as to the circumstances surrounding the crime. Here, we present an initial study of an analytical strategy that involves two complementary techniques, direct PCR DNA profiling and direct mass spectrometry-based protein biomarker detection, for the comprehensive examination of traces of biological fluids gathered from underneath fingernails. With regard to protein biomarker detection, direct MALDI-ToF MS/MS is very sensitive, allowing results to be obtained from biological material present on only a few fibres plucked from a microswab used to collect the traces. Human cornulin, a protein biomarker for vaginal fluid, could be detected up to 5 h after it had been deposited under fingernails whereas haemoglobin, a biomarker for blood, is somewhat more persistent under fingernails and could be detected up to 18 h post-deposition. Bottom-up tandem mass spectrometry techniques were used to provide a high level of confidence in assigning the identity of protein biomarkers. nLC-ESI-qToF MS/MS offered higher levels of confidence and the ability to detect traces that had been present under fingernails for longer periods of time, but this performance came with the cost of longer analysis time and a more laborious s ling approach. Graphical abstract ᅟ.

Bottom‐up in situ proteomic differentiation of human and non‐human haemoglobins for forensic purposes by matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry

Publisher: Wiley

Date: 11-10-2017

DOI: 10.1002/RCM.7986

Abstract: The detection and identification of human blood on crime-related items are of particular relevance to many investigations because shed blood can provide evidence of violent contact between in iduals. However, for any detection and identification technique, specificity is a critical performance characteristic to assess that is, whether the technique has the capability to differentiate between human blood (which usually is of relevance to a criminal investigation) and non-human blood (which usually would not be associated with a crime but may be detected incidentally). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) approaches using "top-down" (detection of intact proteins) and "bottom-up" (detection of tryptic peptide markers) were used to detect and identify haemoglobin in blood from humans and from a range of Australian native mammals the technique could be carried out directly on blood stains without the need to extract proteins (i.e., in situ measurement). Imaging of haemoglobin was achieved in bloodied fingermarks, including those that had been enhanced using two "industry standard" fingermark enhancement processes. Differentiation of intact haemoglobin proteins in human and non-human blood using "top-down" MALDI-TOF-MS was difficult. However, in situ "bottom-up" approaches using tandem mass spectrometry (MS/MS) and de novo sequencing of tryptic digest peptides allowed unambiguous differentiation. Imaging mass spectrometry of human haemoglobin, even when it was mixed with animal blood, was achieved in bloodied fingermarks that had been enhanced using two common processes (staining with Amido Black or dusted with magnetic powder) and "lifted" using adhesive tape. The MALDI-TOF-MS-based in situ "bottom-up" proteomic methodology described here shows great promise for the detection of human blood and even imaging of blood in bloodied fingermarks. The approach is sensitive, can differentiate between human blood and that from many animals (including several Australian native animals), and can be implemented after traditional crime scene fingermark enhancement techniques have been carried out.

Stakeholders’ Preferences towards Contract Attributes: Evidence from Rice Production in Vietnam

Publisher: MDPI AG

Date: 16-03-2022

DOI: 10.3390/SU14063478

Abstract: Contract farming is typically considered an appropriate measure for small-scale farmers to solve their constraints and problems. However, despite positive effects, low participation in and high dropout rates from contract farming schemes remain challenges. Therefore, this study objects to evaluate preferences for contract attributes and attribute levels among contracting buyers, farmers, and government officials through data triangulation from key informant interviews, focus group discussions, and participant observations. Based on Henry Garrett Ranking, Rank Based Quotient, and Rank Based Sum methods, results indicate that the most important attributes were price options, payment, delivery arrangement, input provision, input-use requirements, and product quality standards. Despite a consensus on the ranking of the contract attributes, the preferences for the attribute levels among the stakeholders were heterogeneous. It is recommended that attributes and their levels should be pertinent in contract agreements. Thus, contract design with an adjusted or premium price, 50% of estimated payment before harvesting and the rest after delivery three to five days or lump-sum immediate payment, delivery after harvesting, inputs provision by the contractors through the representative branches or stores located at the local areas or cooperatives, banning active-ingredients or flexible use of inputs from the contractors to produce Good Agricultural Practices or organic products are considerable options.

The benefits and limitations of expanded Y-chromosome short tandem repeat (Y-STR) loci

Publisher: Elsevier BV

Date: 12-2015

DOI: 10.1016/J.FSIGSS.2015.09.012

DNA profiling from human bone cells in the absence of decalcification and DNA extraction

Publisher: Wiley

Date: 24-03-2022

DOI: 10.1111/1556-4029.15033

Abstract: Bone cells are a suitable substrate for DNA analysis if required to identify the person from whom a s le was taken. Osteocytes, the most abundant cell type in bone, are embedded within mineralized bone matrix. To release DNA from osteocytes for subsequent analyses, either demineralization of the mineral matrix or an overnight incubation is routinely carried out. In this study, we report on a simplified and rapid approach to analyze preserved bone s les that omits this lengthy decalcification process. Nine tibial bone s les were processed to release matrix‐free bone cells after fragmentation without the use of liquid nitrogen. Cell morphology was assessed by microscopy at 220× magnification following staining with Diamond ™ Nucleic Acid Dye. Based on the presence of stained nuclei, s les were processed either using a DNA extraction process or by a semi‐direct PCR process. The analysis of the quantity and quality of DNA isolated by both methods was carried out by real‐time PCR and STR profiling to assess inhibition of PCR and DNA degradation. All s les resulted in informative STR profiles with minimal indication of inhibitors. These results demonstrate a potential approach of STR profiling from matrix‐free bone cells within 8 hours without decalcification and DNA extraction.

Identification multiplex assay of 19 terrestrial mammal species present in New Zealand

Publisher: Wiley

Date: 13-11-2013

DOI: 10.1002/ELPS.201300324

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.

Direct identification of forensic body fluids using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Publisher: Elsevier BV

Date: 03-2016

DOI: 10.1016/J.IJMS.2016.01.002

Rice Contract Farming in Vietnam: Insights from a Qualitative Study

Publisher: MDPI

Date: 19-11-2021

DOI: 10.3390/ENGPROC2021009006

Characterisation of novel and rare Y-chromosome short tandem repeat alleles in self-declared South Australian Aboriginal database

Publisher: Springer Science and Business Media LLC

Date: 19-09-2013

DOI: 10.1007/S00414-013-0911-Y

Abstract: Y-chromosome short tandem repeats (Y-STRs) are used in forensic science laboratories all over the world, as their application is wide and often vital in solving casework. Analysis of an in-house database of South Australian self-declared Aboriginal males held by Forensic Science South Australia (FSSA) using the Applied Biosystem's AmpFℓSTR® Yfiler™ PCR Amplification Kit revealed 43 variant Y-STR alleles at 6 of the 17 loci. All variant alleles were sequenced to determine the exact repeat structure for each. As a high level of admixture has previously been found within the SA Aboriginal database, s les were haplogrouped using Y-SNPs to determine their likely geographical origin. Although a number of variant alleles were associated with non-Aboriginal Y-haplogroups, a high frequency was observed within the Australian K-M9 lineage. Detailed knowledge of these variant alleles may have further application in the development of new DNA markers for identification purposes, and in population and evolutionary studies of Australian Aborigines.

A mass spectrometry-based forensic toolbox for imaging and detecting biological fluid evidence in finger marks and fingernail scrapings

Publisher: Springer Science and Business Media LLC

Date: 27-04-2017

DOI: 10.1007/S00414-017-1587-5

Abstract: During a crime, biological material such as blood or vaginal fluid may become smeared on the fingers of the victim or suspect or trapped under their fingernails. The type of trapped fluid is extremely valuable forensic information. Furthermore, if either person touches an object at the crime scene with their 'contaminated' finger then a 'contaminated' finger mark may be deposited. Such marks have great value as they could identify not only who deposited the mark but also who they touched and which part of the body they touched. Here, we describe preliminary work towards a 'toolbox' of techniques based on mass spectrometry (MS) for the identification of biological fluid traces under fingernails or the imaging of them in finger marks. Liquid chromatography-multidimensional MS was effective for the detection of protein biomarkers characteristic of vaginal fluid and blood trapped under fingernails, even after hands had been washed. In regard to examination of finger marks for the presence of biological fluids, the most practical implementation of any technique is to integrate it with, but after, routine crime scene finger mark enhancement has been applied. Here, we demonstrate the usage of matrix-assisted laser desorption ionization-time of flight-MS for the detection and mapping of proteins and peptides from body fluids in finger marks, including marks enhanced using aluminium-containing magnetic powder and then 'lifted' with adhesive tape. Hitherto, only small molecules have been detected in enhanced, lifted marks. In a novel development, aluminium in the enhancement powder assisted ionization of small molecules in finger marks to the extent that conventional matrix was not required for MS.

Profiling pythons to combat common illegal wildlife activities

Publisher: Elsevier BV

Date: 2013

DOI: 10.1016/J.FSIGSS.2013.10.015

University Of Sussex

Location: United Kingdom of Great Britain and Northern Ireland

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University Of Strathclyde

Location: United Kingdom of Great Britain and Northern Ireland

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Linkage Infrastructure, Equipment And Facilities - Grant ID: LE160100154

Start Date: 05-2016

End Date: 12-2017

Amount: $250,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE130100115

Start Date: 2013

End Date: 12-2013

Amount: $180,000.00

Funder: Australian Research Council