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Graham K, Houston R. Evaluation of chloroplast DNA barcoding markers to individualize Papaver somniferum for forensic intelligence purposes. Int J Legal Med 2024; 138:267-275. [PMID: 35788906 DOI: 10.1007/s00414-022-02862-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
Abstract
The opium poppy, Papaver somniferum L., is a forensically important plant due to the medicinal and illegal uses for the milky latex stored in the pods. This latex contains the alkaloids morphine, codeine, and thebaine that are used for their analgesic properties and/or for synthesizing other opioids. However, these compounds are highly addictive and have caused a national opioid epidemic. Two other Papaver species, P. setigerum DC. and P. bracteatum Lindl., are also of forensic interest because they pose both forensic and legal issues. They are largely uncontrolled under the Controlled Substances Act, making these species a common defense strategy. Current morphological and chemical identification methods have been moderately successful but have drawbacks. There is also a lack of sequencing data available. Therefore, exploiting the genome using chloroplast DNA barcoding markers could help to accurately identify these species of interest when plant material is taken. This study screened and assessed the genetic variation both between species and within populations of P. somniferum in nine cpDNA barcode regions (ndhF-rpl32, petA-psbJ, rpl32-trnL, rps16-trnQ, trnE-trnT, trnH-psbA, trnL-trnF, rpl16 intron, and psbE-petL). Published reference genomes from the NCBI GenBank database were aligned and compared for an initial in silico screening. Additionally, ten P. somniferum seed samples from various vendors were sequenced and compared across samples and to published reference data at the various barcode regions of interest. This study showed that the regions trnH-psbA and petA-psbJ have promise for utility in individualization for both inter- and intra-species individualization of P. somniferum.
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Affiliation(s)
- Kari Graham
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA.
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Guillardín L, MacKay JJ. Comparing DNA isolation methods for forest trees: quality, plastic footprint, and time-efficiency. PLANT METHODS 2023; 19:111. [PMID: 37858169 PMCID: PMC10588216 DOI: 10.1186/s13007-023-01086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Genetic and genomic studies are seeing an increase in sample sizes together with a wider range of species investigated in response to environmental change concerns. In turn, these changes may come with challenges including the time and difficulty to isolate nucleic acids (DNA or RNA), the sequencing cost and environmental impacts of the growing amount of plastic waste generated in the process. Pseudotsuga menziesii var. menziesii (Mirbel) Franco (PM), Tsuga heterophylla (Raf.) Sarg. (TH) and Thuja plicata Donn ex D.Don (TP) are conifer species found in diverse woodlands both as natives and naturalized exotics. Our study was carried out whilst investigating their genetics to understand their population structure and potential for adaptation. RESULTS In the present study, we compared two different DNA isolation methods, i.e., spin-column DNeasy plant mini kit (QIAGEN), and temperature-driven enzymatic cocktail Plant DNA Extraction (MicroGEM). The quantity of recovered DNA and the quality of DNA were assessed along with the plastic footprint and time needed for three tree species. Both methods were optimised and proven to provide enough DNA for each studied species. The yield of DNA for each method depended on the species: QIAGEN showed higher yield in P. menziesii and T. heterophylla, while T. plicata recovered similar amount of DNA for both methods. The DNA quality was investigated using DNA barcoding techniques by confirming species identity and species discrimination. No difference was detected in the PCR amplification of the two barcoding loci, (rbcL and trnH-psbA), and the recovered sequences between DNA isolation methods. Measurement of the plastic use and the processing time per sample indicated that MicroGEM had a 52.64% lower plastic footprint and was 51.8% faster than QIAGEN. CONCLUSIONS QIAGEN gave higher yields in two of the species although both methods showed similar quality results across all species. However, MicroGEM was clearly advantageous to decrease the plastic footprint and improve the time efficiency. Overall, MicroGEM recovers sufficient and reliable DNA to perform common downstream analyses such as PCR and sequencing. Our findings illustrate the benefits of research and efforts towards developing more sustainable methods and techniques to reduce the environmental footprint of molecular analyses.
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Affiliation(s)
- Laura Guillardín
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom.
| | - John J MacKay
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom
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Affiliation(s)
- David Love
- United States Drug Enforcement Administration, Special Testing and Research Laboratory, USA
| | - Nicole S. Jones
- RTI International, Applied Justice Research Division, Center for Forensic Sciences, 3040 E. Cornwallis Road, Research Triangle Park, NC, 22709-2194, USA,70113th Street, N.W., Suite 750, Washington, DC, 20005-3967, USA,Corresponding author. RTI International, Applied Justice Research Division, Center for Forensic Sciences, 3040 E. Cornwallis Road, Research Triangle Park, NC, 22709-2194, USA.
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Haniffa MACM, Munawar K, Chee CY, Pramanik S, Halilu A, Illias HA, Rizwan M, Senthilnithy R, Mahanama KRR, Tripathy A, Azman MF. Cellulose supported magnetic nanohybrids: Synthesis, physicomagnetic properties and biomedical applications-A review. Carbohydr Polym 2021; 267:118136. [PMID: 34119125 DOI: 10.1016/j.carbpol.2021.118136] [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: 11/30/2020] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/27/2022]
Abstract
Cellulose and its forms are widely used in biomedical applications due to their biocompatibility, biodegradability and lack of cytotoxicity. It provides ample opportunities for the functionalization of supported magnetic nanohybrids (CSMNs). Because of the abundance of surface hydroxyl groups, they are surface tunable in either homogeneous or heterogeneous solvents and thus act as a substrate or template for the CSMNs' development. The present review emphasizes on the synthesis of various CSMNs, their physicomagnetic properties, and potential applications such as stimuli-responsive drug delivery systems, MRI, enzyme encapsulation, nucleic acid extraction, wound healing and tissue engineering. The impact of CSMNs on cytotoxicity, magnetic hyperthermia, and folate-conjugates is highlighted in particular, based on their structures, cell viability, and stability. Finally, the review also discussed the challenges and prospects of CSMNs' development. This review is expected to provide CSMNs' development roadmap in the context of 21st-century demands for biomedical therapeutics.
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Affiliation(s)
| | - Khadija Munawar
- Centre of Advanced Manufacturing and Material Processing, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Ching Yern Chee
- Centre of Advanced Manufacturing and Material Processing, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Sumit Pramanik
- Functional and Biomaterials Engineering Lab, Department of Mechanical Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Kancheepuram, 603203, Chennai, Tamil Nadu, India.
| | - Ahmed Halilu
- Department of Chemical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hazlee Azil Illias
- Centre of Advanced Manufacturing and Material Processing, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Electrical Engineering, Faculty of Engineering, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Muhammad Rizwan
- Department of Chemistry, The University of Lahore, Lahore, Pakistan
| | - Rajendram Senthilnithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, 10250 Nawala, Nugegoda, Sri Lanka
| | | | - Ashis Tripathy
- Center for MicroElectroMechanics Systems (CMEMS), University of Minho, Campus de Azurém, 4800-058 Guimarães, Portugal
| | - Mohd Fahmi Azman
- Physics Division, Centre for foundation studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
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