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Kirchner CL, Conlan XA, Durdle A. The impact of infrared radiation, solar radiation, and burial exposure on the efficacy of forensic immunoassay testing for blood, semen, and saliva. Forensic Sci Int 2024; 361:112106. [PMID: 38924941 DOI: 10.1016/j.forsciint.2024.112106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/03/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Determining the biological source of a stain can be important information for both investigators and the judiciary in criminal cases. Immunochromatographic assays are commonly used in forensic science for the identification of human biological material. It has previously been demonstrated that various environmental, thermal and chemical insults can affect the efficacy of ABAcard® HemaTrace® in the detection of human blood. In this study, the efficacy of three tests - ABAcard® HemaTrace®, ABAcard® p30, and RSID™-Saliva - was determined for the detection of blood, semen, and saliva respectively, after the fluids had been exposed to adverse environmental conditions. Each biological fluid was deposited on cotton swatches and exposed to infrared (IR) light using a 100 W heat lamp emitting IR light between 620 and 750 nm and heat of 32° for 24, 36 and 48 h. Cotton swatches bearing biological fluids were also buried in outdoor soil for 3, 4 and 5 weeks. To test common forensic scenarios where biological material may be exposed to solar light, samples were placed on a car bonnet and left for 24, 36 and 48 h. ABAcard® HemaTrace® was able to detect haemoglobin in blood that had been exposed to IR and solar light up to 48 h. False negative ABAcard® HemaTrace® results were obtained from 60 % of blood samples buried for 3 and 4 weeks, and 80 % of blood samples buried for 5 weeks. ABAcard® p30 was able to detect p30 in semen that had been exposed to IR and solar light up to 48 h, except for one false negative after 48 h of IR exposure. False negative ABAcard® p30 results were obtained from all semen samples buried for 3, 4 and 5 weeks. RSID™-Saliva was able to detect α-amylase in saliva in all instances, with no false negative results observed. The findings from this study highlight the need to consider the context in which human blood, semen and saliva are found when reporting on negative immunoassay results.
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Affiliation(s)
- C L Kirchner
- Deakin University, Centre for Sustainable Bioproducts, School of Life and Environmental Sciences, Waurn Ponds, VIC 3216, Australia
| | - X A Conlan
- Deakin University, Centre for Sustainable Bioproducts, School of Life and Environmental Sciences, Waurn Ponds, VIC 3216, Australia
| | - A Durdle
- Deakin University, Centre for Sustainable Bioproducts, School of Life and Environmental Sciences, Waurn Ponds, VIC 3216, Australia.
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2
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Chapman B, Cameron C, Keatley D, Coumbaros J, Maker G. A controlled method for the identification of forensic traces from clandestine grave fill. Forensic Sci Int 2024; 357:111985. [PMID: 38522322 DOI: 10.1016/j.forsciint.2024.111985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Deceased human remains are often buried as a forensic countermeasure or method of disposal by homicide perpetrators. Owing to this, the excavation of clandestine grave sites is a task that forensic crime scene teams may only encounter a few times a year. Not all crime scene units have specialised teams for this task, and even those that do, may not have specific protocols for the optimal recovery of forensic traces retained within grave fill as procedures such as sieving require optimisation for the specific soil conditions of the jurisdiction. This study aimed to define the optimal sieving conditions for a sandy environment when searching for minute traces of paint, glass, hair and fibres. Furthermore, this study justifies the practice of retaining grave fill and examining it under controlled laboratory conditions, rather than in-situ adjacent to the grave site. The results demonstrate that using sieve mesh sizes as fine as 0.1 mm can recover up to 82% of the deposited traces and almost all paint, hair and glass traces. The processing of grave fill in the laboratory lead to increased yield of forensic evidence, which on a case-basis may warrant the increased time needed. These findings merit consideration for clandestine grave crime scenes where evidence is scarce or the case is likely to become cold.
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Affiliation(s)
- Brendan Chapman
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia; Cold Case Review, Murdoch, Western Australia 6150, Australia.
| | - Courtney Cameron
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia; Forensic Biology Laboratory, PathWest Laboratory Medicine WA, Nedlands, Western Australia 6009, Australia
| | - David Keatley
- School of Law, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - John Coumbaros
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Garth Maker
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia; Centre for Computational and Systems Medicine, Murdoch University, Perth, Western Australia 6150, Australia
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3
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Dey MK, Iftesum M, Devireddy R, Gartia MR. New technologies and reagents in lateral flow assay (LFA) designs for enhancing accuracy and sensitivity. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4351-4376. [PMID: 37615701 DOI: 10.1039/d3ay00844d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Lateral flow assays (LFAs) are a popular method for quick and affordable diagnostic testing because they are easy to use, portable, and user-friendly. However, LFA design has always faced challenges regarding sensitivity, accuracy, and complexity of the operation. By integrating new technologies and reagents, the sensitivity and accuracy of LFAs can be improved while minimizing the complexity and potential for false positives. Surface enhanced Raman spectroscopy (SERS), photoacoustic techniques, fluorescence resonance energy transfer (FRET), and the integration of smartphones and thermal readers can improve LFA accuracy and sensitivity. To ensure reliable and accurate results, careful assay design and validation, appropriate controls, and optimization of assay conditions are necessary. Continued innovation in LFA technology is crucial to improving the reliability and accuracy of rapid diagnostic testing and expanding its applications to various areas, such as food testing, water quality monitoring, and environmental testing.
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Affiliation(s)
- Mohan Kumar Dey
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Maria Iftesum
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Ram Devireddy
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
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4
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Dawnay N, Sheppard K. From crime scene to courtroom: A review of the current bioanalytical evidence workflows used in rape and sexual assault investigations in the United Kingdom. Sci Justice 2023; 63:206-228. [PMID: 36870701 DOI: 10.1016/j.scijus.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Sexual assault casework requires the collaboration of multiple agency staff to formalise an investigative pipeline running from crime scene to court. While the same could be said of many other forensic investigations, few require the additional support of health care staff and the combined forensic involvement of body-fluid examiners, DNA experts and analytical chemists. The sheer amount of collaborative effort between agencies is laid out through a detailed examination of the investigative workflow from crime scene to courtroom with each step in the pipelines detailed and discussed. Beginning with a review of sexual assault legislation in the United Kingdom this article details how sexual assault investigations are initiated by police and supported by sexual assault referral centre (SARC) staff who are often the first responders providing primary healthcare and patient support to victims while simultaneously collecting and assessing forensic evidence. Detailing the myriad of evidential material that can be documented and collected at the SARC, the review identifies and categorises key forensic tests to first detect and identify body-fluids recovered from evidence through to the secondary analysis of DNA to help identify the suspect. This review also focusses on the collection and analysis of biological material used to support the allegation that the sexual activity was non-consensual and provides a breakdown of common marks and trauma as well as a review of common analytical methods used to infer Drug Facilitated Sexual Assault (DFSA). The culmination of the investigative pipeline is discussed by reviewing the Rape and Serious Sexual Assault (RASSO) workflow used by the Crown Prosecution Service before providing our thoughts on the future of forensic analysis and possible changes to the described workflows.
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Affiliation(s)
- Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom.
| | - Kayleigh Sheppard
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
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5
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A recombinase polymerase amplification (RPA) combined with strip visualization method for RNA-based presumptive tests of saliva and vaginal secretion. Forensic Sci Int Genet 2023; 62:102788. [PMID: 36265335 DOI: 10.1016/j.fsigen.2022.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
Abstract
Identifying the origin of body fluids is a critical step in a forensic investigation. One widely used method to identify human body fluids is based on the color visualization of immune antigen detection strips for detecting hemoglobin in blood and prostate-specific antigen in semen. It is highly imperative to construct an easy-to-perform, mRNA-based method for the point-of-care identification of other human body fluids, such as saliva and vaginal secretion. Here, we established specific strips with the mRNA markers STATH (for saliva) and SPINK5 (for vaginal secretion) via reverse transcription recombinase polymerase amplification (RT-RPA) and lateral flow dipstick (LFD) assays (RT-RPA-LFD). RT-RPA could be accomplished in a single tube at a wide temperature range of 30-42 ℃ within 10-25 min if we do not count time for RNA extraction. The diluted RPA products were added onto the LFD strip pad to visually observe the color change of the Control/Test line. The tissue specificity and detection limit of the assays were evaluated using the optimized reaction conditions of RPA at 37 ℃ for 15 min. The positive signals of STATH were observed both in saliva and nasal secretions. SPINK5 was positive in a template-dependent manner in 4 out of 30 female urine samples in addition to vaginal secretion and menstrual blood samples. Cross-reactions were not detected in semen, skin swabs, sweat, or male urine. Both assays were capable of detecting aged samples, which were stored for 180 days (saliva) or 300 days (vaginal secretion) at room temperature. Moreover, saliva or vaginal secretion was successfully detected in all kinds of mixtures made from various body fluids. Overall, the rapid strip test method by the RT-RPA-LFD assay is simple, time-saving and highly sensitive for estimating the tissue origin of saliva and vaginal secretion. This method for the rapid RNA-based presumptive tests of the tissue type of body fluids is easy to perform prior to a multiplex mRNA analysis, which can demonstrate more reliable saliva or vaginal secretion identification.
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6
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One-click device for rapid visualization and extraction of latent evidence through multi-moding light source integration and light-guiding technology. Sci Rep 2022; 12:16966. [PMID: 36216836 PMCID: PMC9551045 DOI: 10.1038/s41598-022-21136-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/22/2022] [Indexed: 12/29/2022] Open
Abstract
Visualizing latent evidence at a crime scene has gained popularity in the field of forensic science during the past few years. Thus, this study designs and develops a one-click device for the rapid visualization and extraction of latent evidence through multimodal light source integration and light-guiding technology. Our device exhibits multispectral and angle timing functions for storing the captured evidence images. Furthermore, the geometric registration, feature extraction, feature optimization, and feature integration of the evidence images are processed by a backend system, and the images are then presented. Overall, this study enhances the standard and the technical content of evidence extraction and simplifies the evidence extraction process. In addition to the rapid handling of the scenes captured at a crime scene, the one-click device has other notable advantages, such as fast imaging, portability, being independent of the environmental conditions and the operator's technical capabilities, and zero pollution to ensure the repeatability of material evidence extraction. Compared with the original optical forensics equipment, the spectrum and angle of our system are more extensive.
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7
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Doménech-Carbó MT, Doménech-Carbó A. Spot tests: past and present. CHEMTEXTS 2022; 8:4. [PMID: 34976574 PMCID: PMC8710564 DOI: 10.1007/s40828-021-00152-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/11/2021] [Indexed: 11/21/2022]
Abstract
Microchemistry, i.e., the chemistry performed at the scale of a microgram or less, has its roots in the late eighteenth and early nineteenth centuries. In the first half of the twentieth century a wide range of spot tests have been developed. For didactic reasons, they are still part of the curriculum of chemistry students. However, they are even highly important for applied analyses in conservation of cultural heritage, food science, forensic science, clinical and pharmacological sciences, geochemistry, and environmental sciences. Modern pregnancy tests, virus tests, etc. are the most recent examples of sophisticated spot tests. The present ChemTexts contribution aims to provide an overview of the past and present of this analytical methodology.
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Affiliation(s)
- María Teresa Doménech-Carbó
- Institut de Restauració del Patrimoni, Universitat Politècnica de València, Camí de Vera 14, 46022 Valencia, Spain
| | - Antonio Doménech-Carbó
- Departament de Química Analítica, Universitat de València. Dr. Moliner, 50, Burjassot, 46100 Valencia, Spain
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8
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Ren ZL, Zhang JR, Zhang XM, Liu X, Lin YF, Bai H, Wang MC, Cheng F, Liu JD, Li P, Kong L, Bo XC, Wang SQ, Ni M, Yan JW. Forensic nanopore sequencing of STRs and SNPs using Verogen's ForenSeq DNA Signature Prep Kit and MinION. Int J Legal Med 2021; 135:1685-1693. [PMID: 33950286 PMCID: PMC8098014 DOI: 10.1007/s00414-021-02604-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/14/2021] [Indexed: 11/17/2022]
Abstract
The MinION nanopore sequencing device (Oxford Nanopore Technologies, Oxford, UK) is the smallest commercially available sequencer and can be used outside of conventional laboratories. The use of the MinION for forensic applications, however, is hindered by the high error rate of nanopore sequencing. One approach to solving this problem is to identify forensic genetic markers that can consistently be typed correctly based on nanopore sequencing. In this pilot study, we explored the use of nanopore sequencing for single nucleotide polymorphism (SNP) and short tandem repeat (STR) profiling using Verogen’s (San Diego, CA, USA) ForenSeq DNA Signature Prep Kit. Thirty single-contributor samples and DNA standard material 2800 M were genotyped using the Illumina (San Diego, CA, USA) MiSeq FGx and MinION (with R9.4.1 flow cells) devices. With an optimized cutoff for allelic imbalance, all 94 identity-informative SNP loci could be genotyped reliably using the MinION device, with an overall accuracy of 99.958% (1 error among 2926 genotypes). STR typing was notably error prone, and its accuracy was locus dependent. We developed a custom-made bioinformatics workflow, and finally selected 13 autosomal STRs, 14 Y-STRs, and 4 X-STRs showing high consistency between nanopore and Illumina sequencing among the tested samples. These SNP and STR loci could be candidates for panel design for forensic analysis based on nanopore sequencing.
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Affiliation(s)
- Zi-Lin Ren
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Jia-Rong Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Xiao-Meng Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Xu Liu
- Beijing Center for Physical and Chemical Analysis, Beijing, 100089, People's Republic of China
| | - Yan-Feng Lin
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Hua Bai
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Meng-Chun Wang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Jin-Ding Liu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Peng Li
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Lei Kong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Xiao-Chen Bo
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Sheng-Qi Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Ming Ni
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China.
| | - Jiang-Wei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, 030001, People's Republic of China.
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9
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Analytical validation of an RI sample cartridge with the RapidHIT® ID system. Int J Legal Med 2021; 135:1257-1265. [PMID: 33754178 DOI: 10.1007/s00414-021-02553-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/24/2021] [Indexed: 10/21/2022]
Abstract
Evaluating the short tandem repeat (STR) in the field is important for the timely identification of a suspect. Several lines showed that the RapidHIT® ID system is reliable for DNA genotyping with buccal swabs and naked DNA. However, the application of this approach with blood samples has been poorly investigated. Because blood samples are among the most common forensic samples in our laboratory, further studies should be conducted. Here, we assessed the analytical performance of 19 STR loci with a newly developed RapidINTEL (RI) Sample Cartridge Kit by using the blood samples with known genotypes. Several commonly used substrates were included in the sensitivity study, and FTA cards proved to be the most promising sample carrier for blood storage and later identification. There was superior sensitivity and specificity with a 100% concordance rate for 0.5 μL of blood or 7 ng of genomic DNA. The performance for blood samples was comparable with that for the standard protocol. High success rate (90.57%) and high-concordance (100%) genotyping were automatically achieved over a wide range of operating conditions except for TH01. No contamination was observed throughout the study. Hematin, indigo, and humic acid had limited influence on the instrument system, while urea and melanin dramatically affected the genotyping results. Generally, the newly developed RI sample cartridge provided an alternative method for the STR genotyping of single-source blood samples over a wide range of operating conditions.
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Chen W, Yao Y, Chen T, Shen W, Tang S, Lee HK. Application of smartphone-based spectroscopy to biosample analysis: A review. Biosens Bioelectron 2020; 172:112788. [PMID: 33157407 DOI: 10.1016/j.bios.2020.112788] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
The emergence of the smartphones has brought extensive changes to our lifestyles, from communicating with one another, to shopping and enjoyment of entertainment, and from studying to functioning at the workplace (and in the field). At the same time, this portable device has also provided new possibilities in scientific research and applications. Based on the growing awareness of good health management, researchers have coupled health monitoring to smartphone sensing technologies. Along the way, there have been developed a variety of smartphone-based optical detection platforms for analyzing biological samples, including standalone smartphone units and integrated smartphone sensing systems. In this review, we outline the applications of smartphone-based optical sensors for biosamples. These applications focus mainly on three aspects: Microscopic imaging sensing, colorimetric sensing and luminescence sensing. We also discuss briefly some limitations of the current state of smartphone-based spectroscopy and present prospects of the future applicability of smartphone sensors.
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Affiliation(s)
- Wenhui Chen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, China
| | - Yao Yao
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, China
| | - Tianyu Chen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu Province, China.
| | - Hian Kee Lee
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore; National University of Singapore Environmental Research Institute, T-Lab Building #02-01, 5A Engineering Drive 1, Singapore, 117411, Singapore; Tropical Marine Science Institute, National University of Singapore, S2S Building, 18 Kent Ridge Road, Singapore, 119227, Singapore.
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Krishna R, Anil EM. A comparative analytical study on reagent-fused silica gel plate and wax painted paper-based microfluidic device for serological testing. Forensic Sci Int 2020; 317:110517. [PMID: 32979844 DOI: 10.1016/j.forsciint.2020.110517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/22/2020] [Accepted: 09/13/2020] [Indexed: 11/30/2022]
Abstract
The detection and identification of body fluids at a crime scene shed light on the events which might have occurred and the people involved in the crime; the techniques used being lengthy, makes the on-scene detection a tough process to carry out and handle. This study aims to develop an on-spot detection method for serological testing using silica gel encapsulation technique and a modified microfluidic paper-based analytical device (μPADs). Kastle-Meyer reagent was incorporated into the μPAD and Silica Gel plate and was subsequently validated for the detection of blood. This study revealed that the μPAD was a better option. The emerging technique of μPADs allows a cost-effective and simple method of detection for body fluids. The fibrous network of the paper is manipulated to fabricate a guided channel for the fluid flow. The guided channels in the modified μPADs were fabricated by patterning a hydrophobic barrier out of wax. The analyte of interest for this study is blood but the principle can be modified to include other biological fluids.
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Affiliation(s)
- Rohith Krishna
- Forensic Science Department, Jain (Deemed-to-be) University, JC Road, 560002, India.
| | - Esha Maria Anil
- Forensic Science Department, Jain (Deemed-To-Be) University, JC Road, 560002, India.
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12
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Abstract
Mobile devices for on-field DNA analysis have been used for medical diagnostics
at the point-of-care, forensic investigations and environmental surveys, but
still have to be validated for ancient DNA studies. We report here on a mobile
laboratory that we setup using commercially available devices, including a
compact real-time PCR machine, and describe procedures to perform DNA extraction
and analysis from a variety of archeological samples within 4 hours. The process
is carried out on 50 mg samples that are identified at the species level using
custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated
the potential of this approach in museums lacking facilities for DNA studies by
analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3
deposits), and also performed experiments during an excavation campaign at the
Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples
only yielded DNA for the extinct steppe bison (Bison priscus),
whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta
crocuta spelaea) DNA together, for some of them, with DNA for the
European bison sister species/subspecies (Bison
schoetensacki/Bb1-X), thus highlighting the cave hyena diet.
Roc-en-Pail Bovinae bone and tooth samples also contained DNA
for the Bison schoetensacki/Bb1-X clade, and
Cervidae bone samples only yielded reindeer
(Rangifer tarandus) DNA. Subsequent DNA sequencing analyses
confirmed that correct species identification had been achieved using our TaqMan
assays, hence validating these assays for future studies. We conclude that our
approach enables the rapid genetic characterization of tens of millennia-old
archeological samples and is expected to be useful for the on-site screening of
museums and freshly excavated samples for DNA content. Because our mobile
laboratory is made up of commercially available instruments, this approach is
easily accessible to other investigators.
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13
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Masters A, Ogden R, Wetton JH, Dawnay N. Defining end user requirements for a field-based molecular detection system for wildlife forensic investigations. Forensic Sci Int 2019; 301:231-239. [PMID: 31181408 DOI: 10.1016/j.forsciint.2019.05.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/17/2019] [Indexed: 11/29/2022]
Abstract
The increasing use of non-laboratory-based DNA and protein detection methods promise to provide rapid investigative intelligence and support sample prioritisation. Primarily developed for human forensic or medical applications, current systems may also show utility in the field of wildlife forensic science. However, it is currently unknown whether the requirements of the wildlife forensic community can be met by current non-laboratory based tools. Given the diverse array of stakeholders and sample types commonly encountered, it is necessary to first identify the needs of the community and then try and map their needs to current instrumentation. By using a market research style questionnaire, this study identified key requirements for a non-laboratory-based system following feedback from the wildlife forensic community. Data showed that there is strong support for field-based detection methods while highlighting concerns including contamination risks and reduced quality assurance associated with non-laboratory testing. Key species and applications were identified alongside hurdles to implementation and adoption. Broadly, the requirements align with many of the developmental drivers that have led to the rise of in-field portable detection instrumentation, specifically rapid detection within one hour, ease-of-use, and ≥95% accuracy. Several existing platforms exist that met some of the identified requirements but not all. With further collaboration between industry partners and the wildlife forensic community it is possible that new field-based systems can be developed and applied routinely.
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Affiliation(s)
- Alice Masters
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Rob Ogden
- Royal School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK; TRACE Wildlife Forensics Network, Edinburgh, EH12 6LE, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.
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14
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Senn HV, Ghazali M, Kaden J, Barclay D, Harrower B, Campbell RD, Macdonald DW, Kitchener AC. Distinguishing the victim from the threat: SNP-based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration. Evol Appl 2019; 12:399-414. [PMID: 30828363 PMCID: PMC6383845 DOI: 10.1111/eva.12720] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/15/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023] Open
Abstract
The degree of introgressive hybridization between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here, we use a 35-SNP-marker test, designed to assess hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild-living and captive cat samples, and test the assumptions of the test using 3,097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild-living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridized, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective.
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Affiliation(s)
- Helen V. Senn
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Muhammad Ghazali
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Jennifer Kaden
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - David Barclay
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Ben Harrower
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | | | - David W. Macdonald
- Wildlife Conservation Research Unit, Zoology, Recanati Kaplan Centre, Zoology DepartmentOxford UniversityOxfordUK
| | - Andrew C. Kitchener
- Department Natural SciencesNational Museums ScotlandEdinburghUK
- Institute of Geography, School of GeosciencesUniversity of EdinburghEdinburghUK
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15
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Jiao L, Xueli L, Xiujuan S, Song J, Jie X, Lixia L, Wenzhuo Y, Lei X. A Designed Experiment: Polymorphism Analysis of Angiotensin-Converting Enzyme Gene from Human Buccal Epithelial Cells. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:168-174. [PMID: 30694603 DOI: 10.1002/bmb.21215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/08/2018] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
For medical students, we combine the laboratory practice with clinical applications by developing biochemical and molecular biology experiments. In this experiment, students first collect their own buccal epithelial cells by a noninvasive mouthwash method. Then, they extract genomic DNA and perform polymerase chain reaction (PCR) to amplify angiotensin-converting enzyme (ACE) gene using genomic DNA as a template. Finally, the polymorphism of ACE gene is observed by electrophoresis. Students not only learn the techniques but also acquire knowledge of the ACE gene polymorphism. By establishing the relationship among ACE polymorphism and high blood pressure and myocardial hypertrophy, students should be able to understand the gene polymorphism and its association with susceptibility to disease. This laboratory practice teaching can also stimulate desire to do scientific research. Experimental results from many individuals can help us determine and analyze the fractions of ACE gene types in Chinese cohorts. Such an experiment strongly activates students and provides a solid foundation for the medical students' future research and clinical application. © 2019 International Union of Biochemistry and Molecular Biology, 47(2): 168-174, 2019.
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Affiliation(s)
- Li Jiao
- Department of Biochemistry and Molecular Biology Laboratory, Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, China
| | - Li Xueli
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Shi Xiujuan
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Jia Song
- Department of Biochemistry and Molecular Biology Laboratory, Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, China
| | - Xu Jie
- Department of Biochemistry and Molecular Biology Laboratory, Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, China
| | - Lv Lixia
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Yang Wenzhuo
- Educational Administration, Tongji University School of Medicine, Shanghai, China
| | - Xu Lei
- Department of Biochemistry and Molecular Biology Laboratory, Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, China
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16
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Plesivkova D, Richards R, Harbison S. A review of the potential of the MinION™ single‐molecule sequencing system for forensic applications. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/wfs2.1323] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Diana Plesivkova
- Forensic Science Programme, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rebecca Richards
- Forensic Science Programme, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Ltd Auckland New Zealand
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17
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Dawnay N, Flamson R, Hall MJ, Steadman DW. Impact of sample degradation and inhibition on field-based DNA identification of human remains. Forensic Sci Int Genet 2018; 37:46-53. [DOI: 10.1016/j.fsigen.2018.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 11/30/2022]
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