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Anjos D, Donato A, Goldenberg-Barbosa R, Carvalho EFDE, Amaral CRL. Molecular identification of whales remains from the Keller Peninsula, Admiralty Bay, King George Island, Antarctica. AN ACAD BRAS CIENC 2024; 96:e20240502. [PMID: 39319852 DOI: 10.1590/0001-3765202420240502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/02/2024] [Indexed: 09/26/2024] Open
Abstract
At the beginning of the 20th century, intense whaling activity took place in the South Shetland Islands, which is represented today in the form of ruins and numerous whale bones scattered along several Antarctic beaches. Despite being exposed to a harsh environment throughout the last decades, the present manuscript tried to answer if these bone remains still have viable DNA to allow species' identification using molecular methods. Several individuals were collected from the shores of Keller Peninsula, Admiralty Bay, Antarctica, and submitted to DNA extraction, amplification and Sanger sequencing. The challenging identification of these bone fragments proved to be still feasible. Mitochondrial DNA was successfully extracted, amplified and sequenced. A database with 43 sequences including previously published and newly determined sequences were built and enabled the precise identification to species level for some of the collected samples, therefore shedding light on the whales species that inhabited the region and how their overexploitation seems to have affected modern day presence of these species within the study area.
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Affiliation(s)
- Dafne Anjos
- Universidade do Estado do Rio de Janeiro, Departamento de Biofísica e Biometria, Núcleo de Genética Molecular Ambiental e Astrobiologia. PHLC, Subsolo, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Anna Donato
- Universidade do Estado do Rio de Janeiro, Departamento de Biofísica e Biometria, Núcleo de Genética Molecular Ambiental e Astrobiologia. PHLC, Subsolo, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
- Universidade do Estado do Rio de Janeiro, Departamento de Ecologia, Programa de Pós-Graduação em Ecologia e Evolução, PHLC, 2º Andar, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Rodrigo Goldenberg-Barbosa
- Universidade do Estado do Rio de Janeiro, Departamento de Biofísica e Biometria, Núcleo de Genética Molecular Ambiental e Astrobiologia. PHLC, Subsolo, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - Elizeu Fagundes DE Carvalho
- Universidade do Estado do Rio de Janeiro, Departamento de Ecologia, Laboratório de Diagnósticos por DNA, PHLC, Térreo, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
- Universidade do Estado do Rio de Janeiro, Mestrado Profissional em Saúde, Medicina Laboratorial e Tecnologia Forense, Pavilhão José Roberto Feresin Moraes, Policlínica Universitária Piquet Carneiro. Av. Marechal Rondon, 381, São Francisco Xavier, Maracanã, 20950-003 Rio de Janeiro, RJ, Brazil
| | - Cesar R L Amaral
- Universidade do Estado do Rio de Janeiro, Departamento de Biofísica e Biometria, Núcleo de Genética Molecular Ambiental e Astrobiologia. PHLC, Subsolo, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
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Bertolini E, Grignani P, Bertoglio B, Marrubini G, Mazzarelli D, Lucheschi S, Bosetti A, Fattorini P, Cattaneo C, Previderé C. Dead migrants in the Mediterranean: genetic analysis of bone samples exposed to seawater. Forensic Sci Int 2022; 340:111421. [PMID: 36029719 DOI: 10.1016/j.forsciint.2022.111421] [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: 04/29/2022] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 11/04/2022]
Abstract
In April 2015, a fishing boat that departed from Libya with about 1,000 migrants on board sank in the Mediterranean Sea. Most of the migrants were packed in the hull of the boat and drowned in the shipwreck. After fifteen months, the ship was recovered from the seabed and brought to a Sicilian naval area for forensic investigations. Skeletal remains belonging to more than 700 people were retrieved. A selected sample composed of 80 victims was considered in order to evaluate the possibility of achieving genetic profiles useful for a positive identification from these challenging specimens. The molecular features of the DNA recovered from a significant number of real casework samples exposed to seawater for long periods of time were described for the first time. Three different DNA extraction protocols and three different commercial kits were employed in order to generate genetic profiles based on the characterization of 21 autosomal STR loci. The combination of multiple DNA extractions and the cross-checking of multiple PCR amplifications with different kits allowed to obtain reliable genetic profiles characterized by at least 16 STR markers in more than 70% of the samples. The factors that could have affected the different quality of the genetic profiles were investigated and the bone preservation was examined through microscopic and macroscopic analyses. The approach presented in this study could be useful in the management of the genetic analysis of bone samples collected in other similar DVI scenarios. The genetic profiles recovered from the bone samples will be compared in kinship analysis to putative relatives of the victims collected in Africa in order to obtain positive identifications.
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Affiliation(s)
- Emilie Bertolini
- LABANOF, Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale, Università degli Studi di Milano, Italy; Laboratorio di Genetica Forense, Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Pavia, Italy
| | - Pierangela Grignani
- Laboratorio di Genetica Forense, Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Pavia, Italy
| | - Barbara Bertoglio
- LABANOF, Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale, Università degli Studi di Milano, Italy; Laboratorio di Genetica Forense, Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Pavia, Italy
| | - Giorgio Marrubini
- Dipartimento di Scienze del Farmaco, Università di Pavia, Pavia, Italy
| | - Debora Mazzarelli
- LABANOF, Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale, Università degli Studi di Milano, Italy
| | - Stanilla Lucheschi
- LABANOF, Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale, Università degli Studi di Milano, Italy
| | | | - Paolo Fattorini
- Dipartimento Clinico di Scienze Mediche, Chirurgiche e della Salute, Università di Trieste, Trieste, Italy
| | - Cristina Cattaneo
- LABANOF, Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale, Università degli Studi di Milano, Italy
| | - Carlo Previderé
- Laboratorio di Genetica Forense, Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Pavia, Italy.
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Evaluation of Parameters for Estimating the Postmortem Interval of Skeletal Remains Using Bovine Femurs: A Pilot Study. Diagnostics (Basel) 2020; 10:diagnostics10121066. [PMID: 33317185 PMCID: PMC7764391 DOI: 10.3390/diagnostics10121066] [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: 11/13/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/21/2022] Open
Abstract
The postmortem interval (PMI) of victims is a key parameter in criminal investigations. However, effective methods for estimating the PMI of skeletal remains have not been established because it is determined by various factors, including environmental conditions. To identify effective parameters for estimating the PMI of skeletal remains, we investigated the change in bone focusing on the amount of DNA, element concentrations, and bone density that occurred in the bone samples of bovine femurs, each maintained under one of five simulated environmental conditions (seawater, freshwater, underground, outdoors, and indoors) for 1 year. The amount of extracted mitochondrial DNA (mtDNA; 404 bp fragment) decreased over time, and significant DNA degradation (p < 0.01), as estimated by a comparison with amplification results for a shorter fragment (128 bp), was detected between 1 month and 3 months. Eleven of 30 elements were detected in samples by inductively coupled plasma optical emission spectrometry, and Na and Ba showed significant quantitative differences in terms of environmental conditions and time (p < 0.01). This preliminary study suggests that the level of DNA degradation determined by real-time polymerase chain reaction and element concentrations determined by inductively coupled plasma optical emission may be useful indices for estimating the PMI of victims under a wide range of environmental conditions. However, this study is a limited experimental research and not applicable to forensic cases as it is. Further studies of human bone with longer observation periods are required to verify these findings and to establish effective methods for PMI estimation.
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Thornton I, Cartozzo C, Mays D, Singh B, Simmons T. Development of a quantitative PCR-based method for studying temporal DNA degradation in waterlogged bone. J Forensic Sci 2020; 66:1114-1123. [PMID: 33275292 DOI: 10.1111/1556-4029.14641] [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: 08/04/2020] [Revised: 10/31/2020] [Accepted: 11/10/2020] [Indexed: 11/27/2022]
Abstract
While several studies have examined temporal DNA degradation in bones collected from terrestrial environments, studies on temporal DNA degradation in bones collected from aquatic environments are limited and mostly based on case studies. The objective of this study was to assess the impact of long-term submersion, aquatic environment, bone type and DNA extraction method on DNA quality and quantity. Bone samples (scapulae and ribs), collected every ~1000 ADD from a freshwater lake and river, underwent DNA extraction via ChargeSwitch® gDNA Plant Kit and organic phenol-chloroform methods, and DNA quantitation using both TaqMan and SYBR Green-based quantitative PCR (qPCR) methods. Results suggest that in both bone types, quality of recovered DNA (i.e., degradation index) declined significantly with increase in submersion time. Among two bone types, quality of recovered DNA from scapulae declined faster than rib samples. There was no significant difference in recovered DNA quantity between bone types, DNA extraction methods, or locations but various interactions between these variables showed significant difference. Overall, it can be concluded that DNA can be extracted from waterlogged bone in sufficient quantity to generate an STR profile up to 4000 ADD.
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Affiliation(s)
- Isis Thornton
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Claire Cartozzo
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - D'Arcy Mays
- Department of Statistics, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Tal Simmons
- Department of Forensic Science, Virginia Commonwealth University, Richmond, Virginia, USA
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Caputo M, Corach D. Reply to comment “A DNA extraction method of small quantities of bone for high-quality genotyping”. Forensic Sci Int Genet 2019; 41:e18-e19. [DOI: 10.1016/j.fsigen.2019.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/26/2022]
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