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Corradini B, Gianfreda D, Ferri G, Ferrari F, Borciani I, Santunione AL, Cecchi R. Forensic species identification: practical guide for animal and plant DNA analysis. Int J Legal Med 2024:10.1007/s00414-024-03284-2. [PMID: 38985195 DOI: 10.1007/s00414-024-03284-2] [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: 04/09/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
The importance of non-human DNA in the forensic field has increased greatly in recent years, together with the type of applications. The molecular species identification of animal and botanical material may be crucial both for wildlife trafficking and crime scene investigation. However, especially for forensic botany, several challenges slow down the implementation of the discipline in the routine.Although the importance of molecular analysis of animal origin samples is widely recognized and the same value is acknowledged to the botanical counterpart, the latter does not find the same degree of application.The availability of molecular methods, especially useful in cases where the material is fragmented, scarce or spoiled preventing the morphological identification, is not well known. This work is intended to reaffirm the relevance of non-human forensic genetics (NHFG), highlighting differences, benefits and pitfalls of the current most common molecular analysis workflow for animal and botanical samples, giving a practical guide. A flowchart describing the analysis paths, divided in three major working areas (inspection and sampling, molecular analysis, data processing and interpretation), is provided. More real casework examples of the utility of non-human evidence in forensic investigations should be shared by the scientific community, especially for plants. Moreover, concrete efforts to encourage initiatives in order to promote quality and standardization in the NHFG field are also needed.
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Affiliation(s)
- Beatrice Corradini
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy.
| | - Denise Gianfreda
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Gianmarco Ferri
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Ilaria Borciani
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna Laura Santunione
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Rossana Cecchi
- Department of Biomedical, Metabolic and Neural Sciences, Institute of Legal Medicine, University of Modena and Reggio Emilia, Modena, Italy
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Abdollah S, Reza ZH, Abbas AS, Jafar A. Investigating DNA barcodes of plants growing in some areas of Iran with high crime rate: Quercus brantii, Curpressus arizonica, Crataegus pentagyna, Ziziphus Spina-chtista, and Buxus hyrcana. Sci Justice 2023; 63:624-634. [PMID: 37718009 DOI: 10.1016/j.scijus.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 05/23/2023] [Accepted: 07/23/2023] [Indexed: 09/19/2023]
Abstract
According to criminal botany, the offender unknowingly carries plant samples from the crime scene. Therefore, studying the genetic data of plants native to the crime scene can solve many ambiguities in the criminal files. In this regard, the aim of this study was to investigate the genome of 5 endemic plants in some areas of Iran with high crime rate. Quercus brantii, Curpressus arizonica, Crataegus pentagyna, Ziziphus Spina-chtista, and Buxus hyrcana were assessed using 1 genetic fragment on plastid regions (trnH-psbA) as well as 1 gene on nuclear chromosome called ITS. The alignment of DNA sequences of trnH-psbA and ITS genes was done using BioEdit, Clustal X, and Muscle v4.0 software programs. The phylogenetic analysis was performed on aligned data using Maximum Parsimony (MP) and the Bayesian methods. The Splits Tree v.4.14.4 software program was used for phylogenetic network analysis. Finally, the data combinability test was conducted using the Incongruence Length Difference (ILD) test by PAUP* software program. All data from nrDNA ITS and trnH-psbA sequences were consistent with Information Compatibility Test (ICT) results. Moreover, the nrDNA ITS indicated more resolved relationship than trnH-psbA. The results from MP and Bayesian analyses did not differ significantly between singular and combined forms, except for a slight variance in confidence interval of branches. As the phylogenetic trees provide more thorough and deeper conception of species relations, it is hoped that they would be useful to illuminate some forensic gaps in regions with high crime rates enriched by these plants, not only in Iran, but also in all areas over the world with this vegetation.
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Affiliation(s)
- Sajadian Abdollah
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zamanizadeh Hamid Reza
- Department of Plant Protection, College of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran Iran.
| | - Akhavan Sepahi Abbas
- Department of Microbiology, Faculty of biological Sciences, Islamic Azad University, North Tehran Branch, Tehran Iran
| | - Amani Jafar
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Srivastava A, Harshey A, Das T, Kumar A, Yadav MM, Shrivastava P. Impact of DNA evidence in criminal justice system: Indian legislative perspectives. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2022. [DOI: 10.1186/s41935-022-00309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Abstract
Background
The scientific and technological advances along with the changing socio-economical standards of society have posed new challenges to the criminal justice system. With the changes in society and technology, there is also an increase in crime rate. Forensics provides the scientific proofs beyond the shadow of reasonable doubt and thus significantly contributes in criminal as well as civil investigations and legal matters.
Main body of the abstract
Discovery of DNA has opened new avenues and the advancement of DNA technology and its introduction into the court of law has provided extensive aid in the resolution of civil and criminal disputes. In India, the DNA technology was first introduced in a paternity dispute in 1989. However, the need for legislation and guidelines to support grounds for the use of DNA profiling for forensic purposes in India has been recognized for some time now. In July 2019, the DNA Technology (Use and Application) Bill 2019 was introduced in the Indian parliament.
Short conclusion
Herein, this article is focused on the current aspects of DNA based evidence in the Indian Criminal Justice system along with the associated issues, highlighting the need for specific DNA based legislation.
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Dash HR, Arora M. CRISPR-CasB technology in forensic DNA analysis: challenges and solutions. Appl Microbiol Biotechnol 2022; 106:4367-4374. [PMID: 35704073 DOI: 10.1007/s00253-022-12016-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 01/23/2023]
Abstract
CRISPR-Cas technology has revolutionized the field of biotechnology with its precise therapeutic use from genetic as well as infectious diseases point of view. This technology is rapidly evolving to single tool enabling site-directed cut in the genome and highly specific activation or inhibition of gene expression or the exchange of single bases. Besides clinical applications, CRISPR-Cas technology has also shown promising use in the field of forensic DNA analysis. Enrichment of targeted genetic marker for identification followed by sequencing and non-PCR-dependent technique ensures the use of CRISPR-Cas technology in challenging forensic biological samples. The use of this advanced technology is also deemed helpful in mixed profile attribution, mostly in LCN contributors and the generation of a useful DNA profile in degraded samples. Besides its useful applications in forensic DNA analysis, CRISPR-Cas technology poses a huge threat from the generation of ghost DNA profiles by modification/alteration of target genetic markers. Forensic DNA analysts should carry out analysis of additional markers such as non-CODIS markers, Y-, X-chromosome markers, and mitochondrial DNA sequencing in a suspected ghost DNA profile case. KEY POINTS: • CRISPR-Cas9 technique is useful in analyzing LCN, mixed and degraded samples • Alteration of DNA using this technique can lead to generation of ghost DNA profiles • Alternative genetic markers and methylation pattern may detect a ghost DNA profile.
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Affiliation(s)
- Hirak Ranjan Dash
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India.
| | - Mansi Arora
- School of Forensic Sciences, National Forensic Sciences University, Delhi Campus, Sector-3, Rohini, New Delhi, 110085, India
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Ghemrawi M, Fischinger F, Duncan G, Dukes MJ, Guilliano M, McCord B. Developmental validation of SpeID: A pyrosequencing-based assay for species identification. Forensic Sci Int Genet 2021; 55:102560. [PMID: 34507077 DOI: 10.1016/j.fsigen.2021.102560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
In crime scenes, biological exhibits are often human in origin, yet biological stains from other fauna may also be present at a crime scene, creating confusion during an investigation. Furthermore, identifying the source of a biological sample can be critical during an investigation. To identify the presence of biological material from non-human sources, it is common to use genetic markers within mitochondrial DNA such as cytochrome b, 16S rRNA, and 12S rRNA genes. This process usually requires DNA sequencing, a process that is neither quick nor easy. In general, a faster, more standardized method for species identification from tissue and body fluids is desirable.For this reason, we have developed a vertebrate specific real-time quantitation method that is followed by an automated pyrosequencing-based procedure that sequences a short fragment within the 12S rRNA gene. Using no more than 35 bases, the assay can distinguish between 32 different species commonly found in and around a household with a turnaround time of 6 h from extraction to sequencing. -Using this procedure, up to 48 samples can be run at a time without the need for expensive reagents or bioinformatic skills.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | | | - George Duncan
- Nova Southeastern University, Dania Beach, Fl 33004, United State
| | | | | | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States.
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Bisker C, Taylor G, Carney H, Ralebitso-Senior TK. A Combined Application of Molecular Microbial Ecology and Elemental Analyses Can Advance the Understanding of Decomposition Dynamics. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.605817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introducing animal carbon-source to soil initiates biochemical and microbial processes that lead to its decomposition and recycling, which subsequently cause successional shifts in soil microbial community. To investigate the use of soil microbial community to inform criminal investigation, this study was designed to mimic clandestine graves. It compared the decomposition of stillborn piglets (Sus scrofa domesticus), as human analogues, to oak (Quercus robur) leaf litter and soil-only controls outdoors for 720 days. Environmental and edaphic parameters were monitored and showed soil microbial community alignment with temperature seasonality, which highlighted the importance of this abiotic factor. Denaturing gradient gel electrophoresis (DGGE) data were used to calculate Hill numbers and diversity indices of the bacterial 16S rRNA community did not distinguish mammalian- from plant-based decomposition consistently during the first or second year of the study. In contrast, the fungal 18S rRNA community allowed clear differentiation between different treatments (beta diversity) throughout the 720-day experiment and suggested the moment of the decomposing mammalian skin rupture. 16S rRNA-based NGS facilitated the identification of e.g., Pirellulaceae, Acidobacteria ii1-15_order and Candidatus xiphinematobacter as Year 2 bacterial markers of gravesoil at family, order and species taxonomic levels, respectively, and confirmed the similarity of the calculated Hill diversity metrics with those derived from DGGE profiling. Parallel soil elemental composition was measured by portable X-ray Fluorescence where calcium profiles for the piglet-associated soils were distinct from those without carrion. Also, soil calcium content and PMI correlated positively during the first year then negatively during the second. This study is one of the first to apply a multidisciplinary approach based on molecular and physicochemical analytical techniques to assess decomposition. It highlights the recognised potential of using soil microbial community in forensic investigations and provides a proof-of-concept for the application of a combined molecular and elemental approach to further understand the dynamics of decomposition. In addition, it sets the scene for further research in different conditions based on Hill numbers metrics instead of the classic ecological indices for soil necrobiome richness, diversity and evenness.
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Giampaoli S, De Vittori E, Barni F, Anselmo A, Rinaldi T, Baldi M, Miranda KC, Liao A, Brami D, Frajese GV, Berti A. DNA metabarcoding of forensic mycological samples. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2021. [DOI: 10.1186/s41935-021-00221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
DNA metabarcoding and massive parallel sequencing are valuable molecular tools for the characterization of environmental samples. In forensic sciences, the analysis of the sample’s fungal population can be highly informative for the estimation of post-mortem interval, the ascertainment of deposition time, the identification of the cause of death, or the location of buried corpses. Unfortunately, metabarcoding data analysis often requires strong bioinformatic capabilities that are not widely available in forensic laboratories.
Results
The present paper describes the adoption of a user-friendly cloud-based application for the identification of fungi in typical forensic samples. The samples have also been analyzed through the QIIME pipeline, obtaining a relevant data concordance on top genus classification results (88%).
Conclusions
The availability of a user-friendly application that can be run without command line activities will increase the popularity of metabarcoding fungal analysis in forensic samples.
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Nonhuman forensic genetics. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Parry NMA, Stoll A. The rise of veterinary forensics. Forensic Sci Int 2019; 306:110069. [PMID: 31830618 DOI: 10.1016/j.forsciint.2019.110069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/08/2019] [Accepted: 11/15/2019] [Indexed: 01/26/2023]
Abstract
Veterinary forensics is rapidly emerging as a distinct branch of veterinary medicine, especially because of increasing mindfulness about animal cruelty, and of the link between acts of cruelty to animals and violence toward humans. Nevertheless, the application of forensic sciences in veterinary cases lags behind its application in medical cases. Although gaps persist in veterinarians' knowledge of forensics and in how to apply this field to medicolegal cases involving animals, continued research and publication in veterinary forensics are rapidly developing the evidence base in this area. Additionally, educational opportunities in veterinary forensics are also increasing at both undergraduate and postgraduate levels. Together, these changes will continue to improve veterinarians' abilities to investigate cases involving animals. To further strengthen these investigations, veterinarians should also collaborate with the appropriate experts in different disciplines of forensic science.
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Affiliation(s)
| | - Alexander Stoll
- Veterinary Pathology Centre, School of Veterinary Medicine, University of Surrey, Francis Crick Road, GU2 7YW, United Kingdom
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Zenke P, Egyed B, Kovács G, Pádár Z. Implementation of genetic based individualization of White stork (Ciconia ciconia) in forensic casework. Forensic Sci Int Genet 2019; 40:e245-e247. [PMID: 30744983 DOI: 10.1016/j.fsigen.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Petra Zenke
- Department of Animal Breeding and Genetics, University of Veterinary Medicine Budapest, Hungary
| | - Balázs Egyed
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Kovács
- Research Centre for Forensic Sciences and Criminology, University Széchenyi István, Győr, Hungary
| | - Zsolt Pádár
- Department of Forensic Medicine, Medical School, University of Pécs, 7624 Szigeti út 12. Hungary.
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de Groot M, van Haeringen WA. An evaluation of the International Society for Animal Genetics recommended parentage and identification panel for the domestic pigeon (Columba livia domestica
). Anim Genet 2017; 48:431-435. [DOI: 10.1111/age.12555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2017] [Indexed: 11/29/2022]
Affiliation(s)
- M. de Groot
- VHLGenetics; Agro Business Park 100 NL 6708 PW Wageningen The Netherlands
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Elkins KM, Perez ACU, Quinn AA. Simultaneous Identification of Four "Legal High" Plant Species in a Multiplex PCR High-Resolution Melt Assay . J Forensic Sci 2016; 62:593-601. [PMID: 27957736 DOI: 10.1111/1556-4029.13321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/26/2016] [Accepted: 07/31/2016] [Indexed: 11/26/2022]
Abstract
The international prevalence of "legal high" drugs necessitates the development of a method for their detection and identification. Herein, we describe the development and validation of a tetraplex multiplex real-time polymerase chain reaction (PCR) assay used to simultaneously identify morning glory, jimson weed, Hawaiian woodrose, and marijuana detected by high-resolution melt using LCGreen Plus® . The PCR assay was evaluated based on the following: (i) specificity and selectivity-primers were tested on DNA extracted from 30 species and simulated forensic samples, (ii) sensitivity-serial dilutions of the target DNA were prepared, and (iii) reproducibility and reliability-sample replicates were tested and remelted on different days. The assay is ideal for cases in which inexpensive assays are needed to quickly detect and identify trace biological material present on drug paraphernalia that is too compromised for botanical microscopic identification and for which analysts are unfamiliar with the morphology of the emerging "legal high" species.
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Affiliation(s)
- Kelly M Elkins
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
| | - Anjelica C U Perez
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
| | - Alicia A Quinn
- Chemistry Department, Forensic Science Program, Towson University, 8000 York Road, Towson, MD, 21252
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Barrientos LS, Crespi JA, Fameli A, Posik DM, Morales H, Peral García P, Giovambattista G. DNA profile of dog feces as evidence to solve a homicide. Leg Med (Tokyo) 2016; 22:54-7. [PMID: 27591540 DOI: 10.1016/j.legalmed.2016.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/20/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022]
Abstract
Dog fecal samples were collected at the crime scene and from the shoes of the suspect to see whether they could be linked. DNA was genotyped using a 145bp fragment containing a 60bp hotspot region of the mitochondrial DNA (mtDNA) control region. Once the species origin was identified, sequences were aligned with the 23 canine haplotypes defined, showing that evidence and reference had 100% identity with haplotype 5. The frequency of haplotype 5 and the exclusion power of the reference population were 0.056 and 0.89, respectively. The forensic index showed that it was 20 times more likely that the evidence belonged to the reference dog than to some other unknown animal. The results support that the mtDNA hypervariable region 1 (HV1) is a good alternative for typing in trace or degraded casework samples when the STR panel fails, and demonstrate the utility of domestic animal samples to give additional information to solve human legal cases.
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Affiliation(s)
- L S Barrientos
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, La Plata, Buenos Aires, Argentina
| | - J A Crespi
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, La Plata, Buenos Aires, Argentina
| | - A Fameli
- GECOBI - Grupo de Genética y Ecología en Conservación y Biodiversidad, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Av. Angel Gallardo 470, C1405DJR Buenos Aires, Argentina
| | - D M Posik
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, La Plata, Buenos Aires, Argentina
| | - H Morales
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, La Plata, Buenos Aires, Argentina
| | - P Peral García
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, La Plata, Buenos Aires, Argentina
| | - G Giovambattista
- IGEVET - Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), Facultad de Ciencias Veterinarias, UNLP, La Plata, Buenos Aires, Argentina.
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Kanthaswamy S. Review: domestic animal forensic genetics - biological evidence, genetic markers, analytical approaches and challenges. Anim Genet 2015; 46:473-84. [DOI: 10.1111/age.12335] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2015] [Indexed: 01/09/2023]
Affiliation(s)
- S. Kanthaswamy
- School of Mathematical and Natural Sciences; Arizona State University (ASU) at the West Campus; 4701 W Thunderbird Road Glendale AZ 85306-4908 USA
- California National Primate Research Center; University of California; Davis CA 95616 USA
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