1
|
Hughes DA, Szkuta B, van Oorschot RAH, Conlan XA. "Technical Note:" Optimisation of Diamond™ Nucleic Acid Dye preparation, application, and visualisation, for latent DNA detection. Forensic Sci Int 2021; 330:111096. [PMID: 34794062 DOI: 10.1016/j.forsciint.2021.111096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022]
Abstract
A targeted sampling approach of latent DNA, deposited when a person makes contact with a surface, can prove challenging during crime scene or evidence processing, with the sampling of latent DNA often relying on the expert judgement from crime scene officers and forensic examiners. As such, the ability to use the quick and robust screening tool Diamond™ Nucleic Acid Dye (DD) was explored, with a focus on the visualisation of latent DNA on non-porous substrates, namely polypropylene, acrylic, aluminium, PVC composite material, glass, and crystalline silicon. The application of DD was performed according to methods reported in literature, where 10 µL of the dye solution (20-fold dilution of DD in 75% EtOH) was applied onto a variety of non-porous substrates via a micropipette and then subsequently visualised using a portable fluorescence microscope. It was discovered that there was scope for improvement in the reported methods due to the observation of crystal formations on all test substrates upon drying of the DD, resulting in the impaired visualisation of latent DNA and fingerprint detail. Thus, changes to the EtOH water ratio of the dye solution, and changes to the mode of dye application from a micropipette to a spray application, were explored to improve the drying time of the dye and mitigate the formation of crystals. While changes to the EtOH water ratio did not improve the overall drying time, the mode of dye application enhanced visualisation, with a spray application eliminating the formation of crystals no matter the EtOH water ratio. Visualisation with a portable Dino-Lite and Zeiss Widefield fluorescence microscope were also explored, with the Zeiss Widefield fluorescence microscope proving to be useful in whole print imaging and a more efficient imaging tool in a laboratory setting.
Collapse
Affiliation(s)
- Deborah A Hughes
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia
| | - Bianca Szkuta
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Victoria, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Centre, Macleod, Victoria, Australia; School of Molecular Sciences, La Trobe University, Bundoora, Victoria, Australia
| | - Xavier A Conlan
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia.
| |
Collapse
|
2
|
Champion J, Kanokwongnuwut P, van Oorschot RAH, Taylor D, Linacre A. Evaluation of a fluorescent dye to visualize touch DNA on various substrates. J Forensic Sci 2021; 66:1435-1442. [PMID: 33629435 DOI: 10.1111/1556-4029.14695] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
A wide variety of items are submitted as evidence in a forensic investigation. Identifying the location of DNA on such items is central to maximizing DNA profiling success and thus the ability to link a person of interest to a particular item or crime. Recent publications describe a fluorescent staining method using Diamond™ Dye (DD) to visualize cellular material on the surface of non-porous items (e.g., glass, plastic). However, substrates of varying porosity and background color have not yet been examined. Varying porous substrates (i.e., paper bank note, stamp, cigarette, wooden matchstick, and fabric) and non-porous substrates (i.e., enamel tooth and plastic bank note) were examined for their suitability with the use of DD. To improve the visualization of cellular material on the porous substrates, we also explored two DD diluents and adjusting image contrast. The results suggest the optimal diluent depends on the absorbent nature of the substrate. For example, ethanol was sufficient for visualization on the non-porous substrates, whereas water was better for the porous substrates. While cellular material was detected on the paper bank note, tooth, and stamp, background fluorescence or autofluorescence and surface type of matchstick prevented clear visualization on this substrate. It was also determined that by adjusting the contrast of images for tooth, paper bank note and matchstick aided in the detection of cellular material. Overall, this study extends the use of DD for latent DNA detection to absorbent substrates, highlights the limitations associated with these substrate types, and suggests modifications to improve visualization on these challenging substrates.
Collapse
Affiliation(s)
- Jessica Champion
- College of Science & Engineering, Flinders University, Adelaide, SA, Australia
| | | | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Vic., Australia.,School of Molecular Sciences, La Trobe University, Bundoora, Vic., Australia
| | - Duncan Taylor
- College of Science & Engineering, Flinders University, Adelaide, SA, Australia.,Forensic Science South Australia, Adelaide, SA, Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, SA, Australia
| |
Collapse
|
3
|
Kanokwongnuwut P, Paul Kirkbride K, Linacre A. An assessment of tape-lifts. Forensic Sci Int Genet 2020; 47:102292. [DOI: 10.1016/j.fsigen.2020.102292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 01/30/2023]
|
4
|
Burrill J, Daniel B, Frascione N. Illuminating touch deposits through cellular characterization of hand rinses and body fluids with nucleic acid fluorescence. Forensic Sci Int Genet 2020; 46:102269. [PMID: 32155589 DOI: 10.1016/j.fsigen.2020.102269] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 02/20/2020] [Accepted: 02/29/2020] [Indexed: 12/23/2022]
Abstract
Forensic DNA typing from touched or handled items in routine casework is increasing as the sensitivity of detection techniques improves. Our understanding of the cellular/acellular content of touch deposits and the origins of the DNA therein is still limited. This work explores the cellular content of rinses from washed and unwashed hands, as well as saliva, nasal and eye washes which could be sources of transferred DNA onto hands. Flow cytometry and microscopic examination were used to detect granularity, size and nucleic acid fluorescence data. Cellular content did not vary significantly within an individual, although some differences were observed between donors. Saliva contained populations of nucleated epithelia as well as smaller cells and debris, all positive for DNA. Hand rinses consisted almost entirely of anucleate corneocytes, many of which also stained positive for nucleic acids. These data raise questions about shed corneocyte DNA content previously assumed to be negligible.
Collapse
Affiliation(s)
- Julia Burrill
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, Franklin-Wilkins Building, 4.122, 150 Stamford Street, London SE1 9NH, United Kingdom.
| | - Barbara Daniel
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, Franklin-Wilkins Building, 4.122, 150 Stamford Street, London SE1 9NH, United Kingdom.
| | - Nunzianda Frascione
- King's Forensics, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, King's College London, Franklin-Wilkins Building, 4.122, 150 Stamford Street, London SE1 9NH, United Kingdom.
| |
Collapse
|
5
|
Employing DNA binding dye to improve detection of Enterocytozoon hepatopenaei in real-time LAMP. Sci Rep 2019; 9:15860. [PMID: 31676806 PMCID: PMC6825238 DOI: 10.1038/s41598-019-52459-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/16/2019] [Indexed: 01/25/2023] Open
Abstract
Enterocytozoon hepatopenaei (EHP) is a pathogen in the pancreatic tissue of prawn, as reported in recent years. Enterosporidiosis caused by EHP in Penaeus genus is spreading widely, which seriously threatens the sustainable development of shrimp aquaculture in the world. Empolying the DNA binding dye of SYTO-16, a real-time quantitative loop-mediated isothermal amplification (LAMP) method has been established herein to detect EHP. The primer sequences used in the LAMP reaction were according to the SSU rRNA gene. The LAMP assay has reached a sensitivity of 101 copies/µL and no cross-reaction with other aquatic pathogens. Compared with normal PCR, the efficiency of the LAMP technique is more sensitive, which has a shorter detection time. The use of fluorescent nucleic acid dye (SYTO-16) reveals a more satisfactory performance relative to calcein. The quantitative LAMP assay can be considered as a valid tool for rapid detection of microsporidian in prawns. Our study provides a scientific basis to follow the effect of the pathogen infection on growth of cultured penaeid shrimp.
Collapse
|
6
|
Banerjee I, Aralaguppe SG, Lapins N, Zhang W, Kazemzadeh A, Sönnerborg A, Neogi U, Russom A. Microfluidic centrifugation assisted precipitation based DNA quantification. LAB ON A CHIP 2019; 19:1657-1664. [PMID: 30931470 DOI: 10.1039/c9lc00196d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleic acid amplification methods are increasingly being used to detect trace quantities of DNA in samples for various diagnostic applications. However, quantifying the amount of DNA from such methods often requires time consuming purification, washing or labeling steps. Here, we report a novel microfluidic centrifugation assisted precipitation (μCAP) method for single-step DNA quantification. The method is based on formation of a visible precipitate, which can be quantified, when an intercalating dye (GelRed) is added to the DNA sample and centrifuged for a few seconds. We describe the mechanism leading to the precipitation phenomenon. We utilize centrifugal microfluidics to precisely control the formation of the visible and quantifiable mass. Using a standard CMOS sensor for imaging, we report a detection limit of 45 ng μl-1. Furthermore, using an integrated lab-on-DVD platform we recently developed, the detection limit is lowered to 10 ng μl-1, which is comparable to those of current commercially available instruments for DNA quantification. As a proof of principle, we demonstrate the quantification of LAMP products for a HIV-1B type genome containing plasmid on the lab-on-DVD platform. The simple DNA quantification system could facilitate advanced point of care molecular diagnostics.
Collapse
Affiliation(s)
- I Banerjee
- Division of Nanobiotechnology, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Sweden.
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Affiliation(s)
- P. Kanokwongnuwut
- College of Science and Engineering, Flinders University, Adelaide, Australia
| | - P. Kirkbride
- College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, Adelaide, Australia
| |
Collapse
|
8
|
Kanokwongnuwut P, Kirkbride P, Linacre A. Visualising latent DNA on swabs. Forensic Sci Int 2018; 291:115-123. [DOI: 10.1016/j.forsciint.2018.08.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/20/2018] [Accepted: 08/17/2018] [Indexed: 01/23/2023]
|