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Sanchis-Gimeno JA, Iglesias-Bexiga J, Schwab ME, López-García G, Ariza E, Calpe A, Mezquida M, Nalla S, Ercan I. Identification success rates in the post-Spanish Civil War mass graves located in the cemetery of Paterna, Spain: Meta-research on 15 mass graves with 933 subjects. Forensic Sci Int 2024; 361:112122. [PMID: 38936203 DOI: 10.1016/j.forsciint.2024.112122] [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: 05/31/2023] [Revised: 03/21/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Spain suffered a Civil War between 1936 and 1939 that ended with the victory of the National Forces led by General Franco. Once the Spanish Civil War ended, 2238 subjects were executed and buried in several mass graves in the Cemetery of Paterna, one of Spain's largest mass grave sites. Efforts to locate and identify all the victims of the mass graves of the Paterna cemetery are ongoing, but the actual data of the percentage of DNA identifications remains uncertain. Following this, we conducted a meta-research study including 15 mass graves and 933 subjects to determine the DNA identification rates in the mass graves of the Paterna cemetery. We found that the total proportion of identified subjects in the mass graves was 15.9 % (95 % CI: 10.0-22.9). Moreover, we found that the model between the identification success rate (ISR) and the number of relatives that donated DNA (NRTDD) in the mass graves of the cemetery of Paterna was ISR = NRTDD-0.424. Results obtained about the proportion of identified subjects and the model between the ISR and the NRTDD imply the need for a scientific reflection between all the research groups involved in the identification tasks to modify deficiencies and update identification protocols to obtain better future results.
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Affiliation(s)
- Juan A Sanchis-Gimeno
- GIAVAL Research Group, Department of Anatomy and Human Embryology, University of Valencia, Faculty of Medicine, Valencia, Spain.
| | - Javier Iglesias-Bexiga
- GIAVAL Research Group, Department of Anatomy and Human Embryology, University of Valencia, Faculty of Medicine, Valencia, Spain; ArqueoAntro Scientific Association, Spain
| | - Marisol E Schwab
- GIAVAL Research Group, Department of Anatomy and Human Embryology, University of Valencia, Faculty of Medicine, Valencia, Spain; ArqueoAntro Scientific Association, Spain
| | | | - Eloy Ariza
- ArqueoAntro Scientific Association, Spain
| | | | | | - Shahed Nalla
- GIAVAL Research Group, Department of Anatomy and Human Embryology, University of Valencia, Faculty of Medicine, Valencia, Spain; Department of Human Anatomy and Physiology, Faculty of Health Sciences, University of Johannesburg, Johannesburg, South Africa
| | - Ilker Ercan
- Department of Biostatistics, Faculty of Medicine, Bursa Uludag University, Bursa, Turkiye
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2
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Miura Y, Hashimoto M, Nakamura Y, Ishikawa N. Investigation of a DNA Profiling Method Using Only Cementum More Than 70 Years After Death. Cureus 2024; 16:e56998. [PMID: 38681342 PMCID: PMC11045671 DOI: 10.7759/cureus.56998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
Short tandem repeat (STR) typing is widely used not only for blood relationship identification but also for the personal identification of unidentified bodies. However, DNA is susceptible to the effects of environmental factors, consequently leading to reduced DNA yields. Therefore, to maximize the DNA yield required for identification, teeth are generally completely pulverized during DNA extraction. However, this renders subsequent testing after DNA profiling impossible. In this study, we investigated the utility of DNA profiling using only the cementum from teeth that had been left outdoors for long postmortem intervals. We analyzed 90 molars (fresh teeth) that were extracted within six months at a dental clinic and 90 molars (stale teeth) exposed outdoors for over 70 years, and following cementum extraction, the accuracy of STR profiling, optimal site for cementum collection, and minimum amount of cementum required for STR profiling were determined. The results demonstrated that the profiling accuracy of DNA extracted from cementum was comparable to that of DNA from dental pulp and dentin. Furthermore, the collection of cementum from either near the cervical line or from the root apex areas did not show significant differences in DNA profiling accuracy, indicating that securing at least 5 mg of cementum was sufficient to ensure precise DNA profiling. These findings suggest that DNA profiling using only cementum is viable even in teeth that have been subjected to a long postmortem interval.
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Affiliation(s)
- Yuna Miura
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, Chiyoda-ku, JPN
| | - Masatsugu Hashimoto
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, Chiyoda-ku, JPN
| | - Yasutaka Nakamura
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, Chiyoda-ku, JPN
| | - Noboru Ishikawa
- Department of Forensic Odontology and Anthropology, Tokyo Dental College, Chiyoda-ku, JPN
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3
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Obal M, Zupanc T, Zupanič Pajnič I. Measure quantity of mitochondrial DNA in aged bones or calculate it from nuclear DNA quantitative PCR results? Int J Legal Med 2023; 137:1653-1659. [PMID: 37558822 PMCID: PMC10567894 DOI: 10.1007/s00414-023-03074-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/03/2023] [Indexed: 08/11/2023]
Abstract
Mitochondrial DNA (mtDNA) is of great value in forensics to procure information about a person when a next of kin, personal belongings, or other sources of nuclear DNA (nDNA) are unavailable, or nDNA is lacking in quality and quantity. The quality and reliability of the results depend greatly on ensuring optimal conditions for the given method, for instance, the optimal input of the copy number (CN) in next-generation sequencing (NGS) methods. The unavailability of commercial quantitative PCR (qPCR) methods to determine mtDNA CN creates the necessity to rely on recommendations to infer mtDNA CN from nDNA yield. Because nDNA yield varies between individuals, tissues, parts of the same tissue, and because mtDNA CN varies between tissues, such assumptions must be examined for a specific context, rather than be generalized. This study compares mtDNA CN calculated from nDNA yield and qPCR measured mtDNA CN. Seventy-five femurs from the Second World War victims were used as samples; they were cut below the greater trochanter, surface contaminants were removed by mechanical and chemical cleaning, samples were fully demineralized, and DNA was isolated. PowerQuant® Kit (Promega) was used to analyze DNA yield. An in-house method was used to determine mtDNA CN. Comparison of mtDNA CN from nDNA derived calculations and measured mtDNA CN highlighted vast differences. The results emphasize the need to perform qPCR to assess mtDNA CN before NGS analyses of aged bones' mitogenomes rather than estimating mtDNA CN from nDNA yield to ensure the quality and reliability of the results of NGS analysis.
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Affiliation(s)
- Marcel Obal
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
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4
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Chávez-Briones MDL, Jaramillo-Rangel G, Ancer-Arellano A, Ancer-Rodríguez J, Ortega-Martínez M. Identification of the Remains of an Adult Using DNA from Their Deciduous Teeth as a Reference Sample. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1702. [PMID: 37893420 PMCID: PMC10608540 DOI: 10.3390/medicina59101702] [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: 07/29/2023] [Revised: 08/30/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023]
Abstract
In many forensic cases, the identification of human remains is performed by comparing their genetic profile with profiles from reference samples of relatives, usually the parents. Here, we report, for the first time, the identification of the remains of an adult using DNA from the person's deciduous teeth as a reference sample. Fragments of a skeletonized and burned body were found, and a short tandem repeat (STR) profile was obtained. A woman looking for her missing son went to the authorities. When the DNA profile of the woman was compared to a database, a positive match suggested a first-degree kinship with the person to whom the remains belonged. The woman had kept three deciduous molars from her son for more than thirty years. DNA typing of dental pulp was performed. The genetic profiles obtained from the molars and those from the remains coincided in all alleles. The random match probability was 1 in 2.70 × 1021. Thus, the remains were fully identified. In the routine identification of human remains, ambiguous STR results may occur due to the presence of null alleles or other mutational events. In addition, erroneous results can be produced by false matches with close family members or even with people who are completely unrelated to the victim, such that, in some cases, a probability of paternity greater than 99.99% does not necessarily indicate biological paternity. Whenever possible, it is preferable to use reference samples from the putative victim as a source of DNA for identification.
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Affiliation(s)
| | | | | | | | - Marta Ortega-Martínez
- Department of Pathology, School of Medicine, Autonomous University of Nuevo Leon, Monterrey 64460, Mexico; (M.-d.-L.C.-B.); (G.J.-R.); (A.A.-A.); (J.A.-R.)
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5
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Rahmat RA, Humphries MA, Saedon NA, Self PG, Linacre AMT. Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth. Int J Legal Med 2023; 137:1353-1360. [PMID: 37306739 DOI: 10.1007/s00414-023-03017-x] [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: 08/19/2022] [Accepted: 05/09/2023] [Indexed: 06/13/2023]
Abstract
Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).
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Affiliation(s)
- Rabiah A Rahmat
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Melissa A Humphries
- School and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, 5006, Australia
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, the University of Adelaide, Adelaide, South Australia, Australia
| | - Nor A Saedon
- Forensic DNA Division, Forensic Science Analysis Centre, Department of Chemistry, Selangor, 46661, Malaysia
| | - Peter G Self
- CSIRO, Land and Water, Locked Bag 2, Glen Osmond, South Australia, 5064, Australia
| | - Adrian M T Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, 5042, Australia
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6
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Kupsco A, Bloomquist TR, Hu H, Reddam A, Tang D, Goldsmith J, Rundle AG, Baccarelli AA, Herbstman JB. Mitochondrial DNA copy number dynamics and associations with the prenatal environment from birth through adolescence in a population of Dominican and African American children. Mitochondrion 2023; 69:140-146. [PMID: 36804466 PMCID: PMC10006332 DOI: 10.1016/j.mito.2023.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/17/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Mitochondrial DNA copy number (mtDNAcn) dynamics throughout childhood are poorly understood. We profiled mtDNAcn from birth through adolescence and evaluated how the prenatal environment influences mtDNAcn across childhood. Data were collected from children from New York City followed through 18 years. Using duplexed qRT-PCR, we quantified mtDNAcn relative to nuclear DNA in blood collected from the umbilical cord (n = 450), children aged 5-7 (n = 510), and adolescents aged 15-18 (n = 278). We examined mtDNAcn across childhood with linear mixed-effects models (LMM). Relative mtDNAcn was lowest at birth (mean ± SD: 0.67 ± 0.35) and increased in childhood (1.24 ± 0.50) then slightly declined in adolescence (1.13 ± 0.44). We observed no differences in mtDNAcn by sex or race/ethnicity. mtDNAcn was positively associated with prenatal environmental tobacco smoke exposure (0.077 [ 0.01, 0.14] change in relative mtDNAcn) but negatively associated with maternal completion of high school (-0.066 [-0.13, 0.00]), with the receipt of public assistance at birth (-0.074 [-0.14, -0.01]), and when mother born outside the U.S (-0.061 [-0.13, 0.003]). Infant birth outcomes were not associated with mtDNAcn. MtDNAcn levels were dynamic through childhood and associated with some prenatal factors, underscoring the need for the investigation of longitudinal mtDNAcn for human health research.
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Affiliation(s)
- Allison Kupsco
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States.
| | - Tessa R Bloomquist
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Heng Hu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Aalekhya Reddam
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Deliang Tang
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeff Goldsmith
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Andrew G Rundle
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Julie B Herbstman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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7
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Finaughty C, Heathfield LJ, Kemp V, Márquez-Grant N. Forensic DNA extraction methods for human hard tissue: A systematic literature review and meta-analysis of technologies and sample type. Forensic Sci Int Genet 2023; 63:102818. [PMID: 36502616 DOI: 10.1016/j.fsigen.2022.102818] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
DNA identification of human remains has a valuable role in the field of forensic science and wider. Although DNA is vital in identification of unknown human remains, post-mortem environmental factors can lead to poor molecular preservation. In this respect, focus has been placed on DNA extraction methodologies for hard tissue samples, as these are the longest surviving. Despite decades of research being conducted on DNA extraction methods for bone and teeth, little consensus has been reached as to the best performing. Therefore, the aim of this study was to conduct a thorough systematic literature review to identify potential DNA extraction technique(s) which perform optimally for forensic DNA profiling from hard tissue samples. PRISMA guidelines were used, by which a search strategy was developed. This included identifying databases and discipline specific journals, keywords, and exclusion and inclusion criteria. In total, 175 articles were identified that detailed over 50 different DNA extraction methodologies. Results of the meta-analysis conducted on 41 articles - meeting further inclusion criteria - showed that statistically significant higher DNA profiling success was associated with solid-phase magnetic bead/resin methods. In addition, incorporating a demineralisation pre-step resulted in significantly higher profiling successes. For hard tissue type, bone outperformed teeth, and even though dense cortical femur samples were more frequently used across the studies, profiling success was comparable, and in some cases, higher in cancellous bone samples. Notably, incomplete data sharing resulted in many studies being excluded, thus an emphasis for minimum reporting standards is made. In conclusion, this study identifies strategies that may improve success rates of forensic DNA profiling from hard tissue samples. Finally, continued improvements to current methods can ensure faster times to resolution and restoring the identity of those who died in obscurity.
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Affiliation(s)
- Chandra Finaughty
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, Bedfordshire, United Kingdom.
| | - Laura Jane Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Victoria Kemp
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, Bedfordshire, United Kingdom.
| | - Nicholas Márquez-Grant
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, Bedfordshire, United Kingdom.
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8
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Schmidt VM, Zelger P, Woess C, Pallua AK, Arora R, Degenhart G, Brunner A, Zelger B, Schirmer M, Rabl W, Pallua JD. Application of Micro-Computed Tomography for the Estimation of the Post-Mortem Interval of Human Skeletal Remains. BIOLOGY 2022; 11:biology11081105. [PMID: 35892961 PMCID: PMC9331256 DOI: 10.3390/biology11081105] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022]
Abstract
It is challenging to estimate the post-mortem interval (PMI) of skeletal remains within a forensic context. As a result of their interactions with the environment, bones undergo several chemical and physical changes after death. So far, multiple methods have been used to follow up on post-mortem changes. There is, however, no definitive way to estimate the PMI of skeletal remains. This research aimed to propose a methodology capable of estimating the PMI using micro-computed tomography measurements of 104 human skeletal remains with PMIs between one day and 2000 years. The present study indicates that micro-computed tomography could be considered an objective and precise method of PMI evaluation in forensic medicine. The measured parameters show a significant difference regarding the PMI for Cort Porosity p < 0.001, BV/TV p > 0.001, Mean1 p > 0.001 and Mean2 p > 0.005. Using a machine learning approach, the neural network showed an accuracy of 99% for distinguishing between samples with a PMI of less than 100 years and archaeological samples.
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Affiliation(s)
- Verena-Maria Schmidt
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria; (V.-M.S.); (C.W.); (W.R.)
| | - Philipp Zelger
- University Clinic for Hearing, Voice and Speech Disorders, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria;
| | - Claudia Woess
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria; (V.-M.S.); (C.W.); (W.R.)
| | - Anton K. Pallua
- Former Institute for Computed Tomography-Neuro CT, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
| | - Rohit Arora
- University Hospital for Orthopaedics and Traumatology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
| | - Gerald Degenhart
- Department of Radiology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
| | - Andrea Brunner
- Institute of Pathology, Neuropathology, Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria; (A.B.); (B.Z.)
| | - Bettina Zelger
- Institute of Pathology, Neuropathology, Molecular Pathology, Medical University of Innsbruck, Muellerstrasse 44, 6020 Innsbruck, Austria; (A.B.); (B.Z.)
| | - Michael Schirmer
- Department of Internal Medicine, Clinic II, Medical University of Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria;
| | - Walter Rabl
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstraße 44, 6020 Innsbruck, Austria; (V.-M.S.); (C.W.); (W.R.)
| | - Johannes D. Pallua
- University Hospital for Orthopaedics and Traumatology, Medical University of Innsbruck, Anichstraße 35, 6020 Innsbruck, Austria;
- Correspondence:
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9
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Abstract
Abstract
The prospects for application of metagenomic technologies in environmental studies are discussed. The advantages in investigating the taxonomic composition of aquatic and terrestrial ecosystems, as well as examples of trophic and phoric relationships found in ecosystems using the metagenomic approach, are described. The capabilities of metagenomics to study prokaryotic communities in complicated environments such as soils or animal intestines are shown. The role of relic DNA in the metagenome and the possibilities to study ancient organisms are highlighted. Particular attention is paid to the criticism of metagenomic technologies related to the low reproducibility of the sequencing data. Common methodological mistakes in bioinformatics processing of metagenomic data leading to misleading results are considered.
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10
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Benedik Bevc T, Božič L, Podovšovnik E, Zupanc T, Zupanič Pajnič I. Intra-bone nuclear DNA variability and STR typing success in Second World War 12th thoracic vertebrae. Forensic Sci Int Genet 2021; 55:102587. [PMID: 34479116 DOI: 10.1016/j.fsigen.2021.102587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 08/12/2021] [Accepted: 08/25/2021] [Indexed: 11/29/2022]
Abstract
Bones are an important source of DNA for identification in forensic medicine, especially when the remains are skeletonized, which is the case when dealing with victims of the Second World War. Often the amount of bone available for sampling is limited, and therefore it is crucial to sample the bone segment with the highest adequate DNA quantity for identification. Studies performed on all representative skeletal element types of the human body showed that the amount of DNA obtained from different skeletal elements of different body regions varies greatly. When bones from torso were analyzed, thoracic vertebrae outperformed other vertebrae (cervical and lumbar) and, alongside the first ribs, were among the most appropriate bone elements for identification purposes. It was also shown that the quantity of DNA varies significantly within a single bone type. This study focused on exploring intra-bone DNA variability between five parts of 12th thoracic vertebrae (laminae + spinous process, pedicles + transverse processes, and corpus right, left, and middle). The research was based on the theory that the distribution of body weight and consequently bone remodeling, as well as the ratio between cancellous and cortical bone, contribute to different quantities of DNA in different parts of vertebra sampled. The vertebrae were cleaned and cut into five parts, and each part was completely ground to obtain homogenous bone powder. Half a gram of powder from each part was decalcified using a full demineralization extraction method. The DNA was purified in a Biorobot EZ1 machine (Qiagen). DNA quantity and quality were determined using the PowerQuant System (Promega) and autosomal STR typing success using the GlobalFiler Amplification Kit (Applied Biosystems). Thirty-five 12th thoracic vertebrae were sampled from a single Second World War mass grave. The best results with the highest DNA quantity were found in laminae and the spinous process, and among them all vertebrae analyzed yielded full STR profiles except three, where only a few dropouts occurred. The second-ranked bone part was the pedicles and transverse processes. The comparison of DNA degradation in the vertebral segments analyzed does not show statistically significant differences. Considering our research, when only the torso is available for identification, the 12th thoracic vertebra should be collected and the vertebral arch should be sampled for genetic analyses.
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Affiliation(s)
- Tajda Benedik Bevc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Laura Božič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Eva Podovšovnik
- Faculty of Tourism Studies - Turistica, University of Primorska, Portorož, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
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11
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Zupanič Pajnič I, Inkret J, Zupanc T, Podovšovnik E. Comparison of nuclear DNA yield and STR typing success in Second World War petrous bones and metacarpals III. Forensic Sci Int Genet 2021; 55:102578. [PMID: 34425360 DOI: 10.1016/j.fsigen.2021.102578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/12/2021] [Accepted: 08/15/2021] [Indexed: 11/17/2022]
Abstract
DNA yield and STR typing success differ among skeletal element types and within individual bones. Consequently, it is necessary to identify the skeletal elements and their intra-skeletal parts that will most likely yield utilizable and informative endogenous DNA for human identification of skeletal remains. The petrous portion of the temporal bone has been shown to be the most suitable skeletal part for sampling archaeological skeletons, and it has also been used successfully in some forensic cases. When all representative bone types were analyzed for three complete Second World War skeletons, metatarsals and metacarpals yielded more DNA than petrous bones (which generated full profiles even if the DNA yield was lower) and, among almost 200 Second World War metatarsals and metacarpals analyzed, metacarpals III were found to be the highest-yielding bones. To further improve the sampling strategy in DNA analysis of aged skeletal remains, a comparison between 26 petrous bones and 30 metacarpals III from Second World War skeletons was made considering intra-bone DNA yield variability. In metacarpals III only epiphyses were sampled, and in petrous bones only the dense part within the otic capsule was used. To exclude the influence of taphonomic issues as much as possible, petrous bones and metacarpals III from a single Second World War mass grave were examined. The difference between petrous bones and metacarpals III was explored by measuring nuclear DNA yield and success of STR typing. After cleaning the samples, full demineralization extraction was used to decalcify 0.5 g of powdered bone. PowerQuant (Promega) was used to determine DNA content and DNA degradation rates, and STR typing was performed using the PowerPlex ESI 17 Fast System (Promega). Metacarpals III produced the same DNA yields and STR typing success as petrous bones with no intra-individual difference observed in concentration of DNA, degradation rate, percentage of successfully amplified alleles, and intensity of electrophoretic signals. Sampling and processing of metacarpal III epiphyses is consequently recommended for genetic identification of highly degraded skeletal remains in routine forensic casework and in buried non-commingled aged skeletal remains whenever metacarpals III are preserved. Metacarpals III are easy to sample and less prone to contamination with modern DNA because no saw is needed for sampling in comparison to the petrous portion of the temporal bone. The data obtained in this study further improve the sampling strategy for genetic identification of Second World War skeletal remains in Slovenia.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
| | - Eva Podovšovnik
- Faculty of Tourism Studies - Turistica, University of Primorska, Portorož, Slovenia.
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12
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Intra-bone nuclear DNA variability and STR typing success in Second World War first ribs. Int J Legal Med 2021; 135:2199-2208. [PMID: 34396484 DOI: 10.1007/s00414-021-02681-1] [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: 01/15/2021] [Accepted: 08/06/2021] [Indexed: 10/20/2022]
Abstract
DNA sampling and typing are used for identifying missing persons or war victims. In recent forensic studies, little focus has been placed on determining intra-bone variability within a single skeletal element. When dealing with aged human bones, complete skeletal remains are rarely present. In cases in which only the torso is available, studies have shown that ribs are one of the most appropriate samples, but intra-bone variability has not yet been studied. A higher degree of remodeling was found to contribute to higher DNA yield in the parts of the skeletal element where the most strain is concentrated. This study explores intra-bone variability in proximal, middle, and distal parts of the first human rib by determining the quantity and quality of DNA using the PowerQuant System (Promega) and autosomal STR typing success using the PowerPlex ESI 17 Fast System (Promega). Thirty first ribs from a single Second World War mass grave were sampled. No variation in DNA degradation was observed across the individual rib. The highest quantity of DNA was measured in the proximal part of the first rib, and in all ribs except three, full or almost full genetic profiles were obtained. Thus, when only the torso is present in archaeological or medico-legal cases, first ribs are recommended to be collected if possible, and the proximal or vertebral ends should be sampled for genetic analysis.
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Rohrlach AB, Papac L, Childebayeva A, Rivollat M, Villalba-Mouco V, Neumann GU, Penske S, Skourtanioti E, van de Loosdrecht M, Akar M, Boyadzhiev K, Boyadzhiev Y, Deguilloux MF, Dobeš M, Erdal YS, Ernée M, Frangipane M, Furmanek M, Friederich S, Ghesquière E, Hałuszko A, Hansen S, Küßner M, Mannino M, Özbal R, Reinhold S, Rottier S, Salazar-García DC, Diaz JS, Stockhammer PW, de Togores Muñoz CR, Yener KA, Posth C, Krause J, Herbig A, Haak W. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe. Sci Rep 2021; 11:15005. [PMID: 34294811 PMCID: PMC8298398 DOI: 10.1038/s41598-021-94491-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
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Affiliation(s)
- Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Marieke van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, 31060, Alahan-Antakya, Hatay, Turkey
| | - Kamen Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | - Yavor Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | | | - Miroslav Dobeš
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, 06800, Ankara, Turkey
| | - Michal Ernée
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | | | | | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
| | - Emmanuel Ghesquière
- Inrap Grand Ouest, Bourguébus, France.,Université de Rennes 1, CNRS, CReAAH-UMR, 6566, Rennes, France
| | - Agata Hałuszko
- Institute of Archaeology, University of Wrocław, Wrocław, Poland.,Archeolodzy.org Foundation, Wrocław, Poland
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archeology, Weimar, Germany
| | - Marcello Mannino
- Department of Archaeology, School of Culture and Society, Aarhus University, 8270, Højbjerg, Denmark
| | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450, Istanbul, Turkey
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Stéphane Rottier
- Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Ludwig Maximilian University Munich, 80799, Munich, Germany
| | | | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, 10028, USA
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences Eberhard Karls University Tübingen, 72070, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
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14
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Chierto E, Cena G, Mann RW, Mattutino G, Nuzzolese E, Robino C. Sweet tooth: DNA profiling of a cranium from an isolated retained root fragment. J Forensic Sci 2021; 66:1973-1979. [PMID: 34106477 PMCID: PMC8453871 DOI: 10.1111/1556-4029.14748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/21/2021] [Indexed: 11/29/2022]
Abstract
Sampling of healthy multi‐rooted teeth is recommended for the genetic identification of human skeletal remains. However, this may not always be possible, as in the reported case consisting of an isolated human cranium found in an aggregate crushing and processing plant in Piedmont, Northwest Italy. The cranium displayed significant weathering, suggesting a post‐mortem interval of several years, and was edentulous with the exception of the apical root fragment of the upper left canine, consequence of an antemortem horizontal fracture. Prolonged decalcification of the root fragment followed by powder‐free DNA extraction from ~10 mg of root tip tissue led to the recovery of >10 ng of high molecular weight human DNA, in comparison with ~0.01 ng of DNA per mg of bone powder obtained from the petrous portion of the temporal bone. Quantity and quality of DNA isolated from apical tooth tissue enabled multiple genotyping, including a reportable female STR profile, mitochondrial DNA analysis, and ancestry‐informative insertion/deletion polymorphisms. Although the cranium remained unidentified after DNA comparisons, our findings confirm that apical tooth tissue is a promising source of DNA, easily obtained through a powder‐free extraction protocol. Results also indicate that root tips should not be overlooked in challenging identification cases, even in the presence of compromised tooth specimens.
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Affiliation(s)
- Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Greta Cena
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Robert W Mann
- John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Grazia Mattutino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Emilio Nuzzolese
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
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15
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Raffone C, Baeta M, Lambacher N, Granizo-Rodríguez E, Etxeberria F, de Pancorbo MM. Intrinsic and extrinsic factors that may influence DNA preservation in skeletal remains: A review. Forensic Sci Int 2021; 325:110859. [PMID: 34098475 DOI: 10.1016/j.forsciint.2021.110859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/11/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The identification of skeletal human remains, severely compromised by putrefaction, or highly deteriorated, is important for legal and humanitarian reasons. There are different tools that can help in the identification process such as anthropological and genetic studies. The success observed during the last decade in genetic analysis of skeletal remains has been possible especially due to the refinements of DNA extraction and posterior analysis techniques. However, despite these progresses, many challenges keep influencing the results of such analysis, mainly the limited amount and the degradation of the DNA recovered from badly preserved samples. By now, there is still no wide-range knowledge about post-mortem kinetics of DNA degradation. Therefore, taphonomy studies can play a key role in the reconstruction of post-mortem transformations that skeletal remains, and consequently DNA, have undergone. Thus, the goal of the present review focuses on the assessment of the literature regarding the possible effect of intrinsic (characteristics of the bone) and extrinsic (environmental) factors on the state of preservation of skeletal remains recovered in a terrestrial environment and their genetic material. The establishment of useful indicators describing the state of the remains is a key factor in order to determine their suitability for posterior biomolecular analysis.
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Affiliation(s)
- Caterina Raffone
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Department of Physical Anthropology, Society of Sciences Aranzadi, Donostia-San Sebastian, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Nicole Lambacher
- Department of Physical Anthropology, Society of Sciences Aranzadi, Donostia-San Sebastian, Spain
| | - Eva Granizo-Rodríguez
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francisco Etxeberria
- Department of Legal Medicine, University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
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16
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Akbulut N, Çetin S, Bilecenoğlu B, Altan A, Ocak M, Şen E, Atakan C, Orhan K. Evaluation of the detectability of early mandible fracture healing findings in terms of vitality aspect by using micro-CT technology in postmortem interval. Leg Med (Tokyo) 2021; 52:101914. [PMID: 34091405 DOI: 10.1016/j.legalmed.2021.101914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/03/2021] [Accepted: 05/26/2021] [Indexed: 11/26/2022]
Abstract
The purpose of the present study was to investigate the vitality aspect of mandibular fractures using micro-CT in the analysis of bone mineral density and other bone microstructure trabecular parameters in the postmortem interval. This study included 72 female Wistar rats. In the study groups, the rats' mandibles were first fractured and after three days of living, the rats were sacrificed. In the control groups, the rats were sacrificed first and then the mandibles were fractured. All rats were left for a natural putrefaction period according to their group's time as week-0, week-1, week-2, week-4, week-8, and week-12. All fractured hemi-mandibles were scanned by micro-CT and analyzed in terms of BMD and other bone trabecular microstructures. BMD and the other bone trabecular microstructures, such as bone volume, percent bone volume, trabecular separation, and trabecular pattern factor, showed statistically significant differences in both the study and control groups (p ≤ 0.05). There were statistically significant differences between the study and control groups in comparisons of BMD in groups 1, 2, 3, 4 and 5, bone volume and percent bone volume in groups 1 and 3, bone surface and bone surface density in group 6, trabecular separation in group 1, and trabecular number, trabecular pattern factor, and structural model index in group 6. Micro-CT scanning and analysis of BMD and other bone trabecular microstructure parameters for evaluation of vitality aspects of mandible fractures in the PMI has various valuable results that should provide guidance for possible studies in the future.
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Affiliation(s)
- Nihat Akbulut
- Tokat Gaziosmanpaşa University, Faculty of Dentistry, Oral and Maxillofacial Surgery Department, Tokat, Turkey
| | - Selçuk Çetin
- Tokat Gaziosmanpaşa University, Faculty of Medicine, Forensic Medicine Department, Tokat, Turkey
| | - Burak Bilecenoğlu
- Ankara Medipol University, Faculty of Medicine, Anatomy Department, Ankara, Turkey
| | - Ahmet Altan
- Tokat Gaziosmanpaşa University, Faculty of Dentistry, Oral and Maxillofacial Surgery Department, Tokat, Turkey.
| | - Mert Ocak
- Ankara University, Faculty of Dentistry, Anatomy Department, Ankara, Turkey
| | - Esengül Şen
- Tokat Gaziosmanpaşa University, Faculty of Dentistry, Oral and Maxillofacial Surgery Department, Tokat, Turkey
| | - Cemal Atakan
- Ankara University, Faculty of Sciences, Statistics Department, Ankara, Turkey
| | - Kaan Orhan
- Ankara University, Faculty of Dentistry, Department of DentoMaxillofacial Radiology, Ankara, Turkey
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17
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Keighley X, Bro‐Jørgensen MH, Ahlgren H, Szpak P, Ciucani MM, Sánchez Barreiro F, Howse L, Gotfredsen AB, Glykou A, Jordan P, Lidén K, Olsen MT. Predicting sample success for large-scale ancient DNA studies on marine mammals. Mol Ecol Resour 2021; 21:1149-1166. [PMID: 33463014 PMCID: PMC8248401 DOI: 10.1111/1755-0998.13331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.
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Affiliation(s)
- Xénia Keighley
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Arctic Centre/Groningen Institute of ArchaeologyFaculty of ArtsUniversity of GroningenAS GroningenThe Netherlands
| | - Maiken Hemme Bro‐Jørgensen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Hans Ahlgren
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Paul Szpak
- Department of AnthropologyTrent UniversityPeterboroughOntarioCanada
| | - Marta Maria Ciucani
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
| | | | - Lesley Howse
- Archaeology CentreUniversity of TorontoTorontoOntarioCanada
| | | | - Aikaterini Glykou
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Peter Jordan
- Department of Archaeology and Ancient HistoryLund UniversityLundSweden
| | - Kerstin Lidén
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Morten Tange Olsen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
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18
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Mckinnon M, Henneberg M, Higgins D. A review of the current understanding of burned bone as a source of DNA for human identification. Sci Justice 2021; 61:332-338. [PMID: 34172121 DOI: 10.1016/j.scijus.2021.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/16/2021] [Accepted: 03/13/2021] [Indexed: 10/21/2022]
Abstract
Identification of incinerated human remains may rely on genetic analysis of burned bone which can prove far more challenging than fresh tissues. Severe thermal insult results in the destruction or denaturation of DNA in soft tissues, however genetic material may be preserved in the skeletal tissues. Considerations for DNA retrieval from these samples include low levels of exogenous DNA, the dense, mineralised nature of bone, and the presence of contamination, and qPCR inhibitors. This review collates current knowledge in three areas relating to optimising DNA recovery from burned bone: 1) impact of burning on bone and subsequent effects on sample collection, 2) difficulties of preparing burned samples for DNA extraction, and 3) protocols for bone decalcification and DNA extraction. Bone decalcification and various DNA extraction protocols have been tested and optimised for ancient bone, suggesting that prolonged EDTA (Ethylenediaminetetraacetic acid) demineralisation followed by solid-phased silica-based extraction techniques provide the greatest DNA yield. However, there is significantly less literature exploring the optimal protocol for incinerated bones. Although burned bone, like ancient and diagenetic bone, can be considered "low-copy", the taphonomic processes occurring are likely different. As techniques developed for ancient samples are tailored to deal with bone that has been altered in a particular way, it is important to understand if burned bone undergoes similar or different changes. Currently the effects of burning on bone and the DNA within it is not fully understood. Future research should focus on increasing our understanding of the effects of heat on bone and on comparing the outcome of various DNA extraction protocols for these tissues.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia.
| | - Maciej Henneberg
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia
| | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, the University of Adelaide, Adelaide, Australia
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19
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Inkret J, Podovšovnik E, Zupanc T, Haring G, Pajnič IZ. Intra-bone nuclear DNA variability in Second World War metatarsal and metacarpal bones. Int J Legal Med 2021; 135:1245-1256. [PMID: 33624158 DOI: 10.1007/s00414-021-02528-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/03/2021] [Indexed: 11/30/2022]
Abstract
DNA analysis of Second World War skeletal remains is challenging because of the limited yield of DNA that is usually recovered. Recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA, and little focus has been placed on measuring intra-bone variability. Metatarsals and metacarpals outperformed all the other bones in DNA yield when analyzing all representative skeletal elements of three Second World War victims, and intra-bone variability was not studied. Soft-tissue remnants were found to contribute to higher DNA yield in trabecular bone tissue. Because metatarsals and metacarpals are composed of trabecular epiphyses and a dense diaphysis, the goal of this study was to explore intra-bone variability in DNA content by measuring nuclear DNA quantity and quality using the PowerQuant System (Promega). A total of 193 bones from a single Second World War mass grave were examined. From each bone, DNA was extracted from the compact diaphysis and from both spongy epiphyses combined. This study confirms higher DNA quantity in epiphyses than diaphyses among all the bones analyzed, and more DNA was obtained from metacarpal epiphyses than from metatarsal epiphyses. Therefore, whenever the possibility for sampling both metacarpals and metatarsals from skeletal remains exists, collecting metacarpals is recommended. In cases in which the hands are missing, metatarsals should be sampled. In any case, epiphyses are a richer source of DNA than diaphyses.
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Affiliation(s)
- Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Eva Podovšovnik
- Faculty of Tourism Studies - Turistica, University of Primorska, Portorož, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Gregor Haring
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
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20
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Ugrappa S, Jain A. An emergence of dental tissues in the forensic medicine for the postmortem interval estimation: A scoping review. JOURNAL OF FORENSIC SCIENCE AND MEDICINE 2021. [DOI: 10.4103/jfsm.jfsm_20_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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21
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Mckinnon M, Higgins D. Comparison of bone demineralisation procedures for DNA recovery from burned remains. Forensic Sci Int Genet 2020; 51:102448. [PMID: 33373911 DOI: 10.1016/j.fsigen.2020.102448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 11/26/2022]
Abstract
Recovering DNA from modern incinerated bones can be challenging and may require alteration of routine DNA extraction protocols. It has been postulated that incinerated bones share some similarities with ancient bones, including fragmented DNA, surface contamination and highly mineralised structure, all of which can inhibit the successful recovery of genetic material. For this reason, ancient DNA extraction protocols are often used for incinerated modern samples; however, their effectiveness is still somewhat unclear. Much of this uncertainty exists around the demineralisation step of extraction, specifically the length of incubation and retention or removal of supernatant. As obtaining human samples for forensic research can be challenging, porcine models (Sus scrofa domesticus) are often used as substitutes. This study developed real time PCR assays for porcine nuclear DNA in order to investigate the effects of modified demineralisation protocols on DNA yield from femurs exposed to either short (60 min) or prolonged (120 min) burning. Gradient PCR results indicated 56 °C was the ideal amplification temperature for targeted amplicons, with melt curve analysis showing short and long amplicons corresponded to 80.3 °C and 83 °C peaks respectively. Results of altered extraction protocol showed a trend towards higher DNA yields from longer demineralisation periods however this was not significant. By comparison, retaining supernatant post-demineralisation resulted in significantly greater DNA yields compared to discarding it (P < 0.009). Although DNA content yield decreased with burn duration, the demineralisation treatment variations appeared to have the same effect for all burn lengths. These results suggest that for incinerated modern bone retaining the supernatant following demineralisation can dramatically increase DNA yield.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.
| | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, The University of Adelaide, Adelaide, Australia
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22
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Parker C, Rohrlach AB, Friederich S, Nagel S, Meyer M, Krause J, Bos KI, Haak W. A systematic investigation of human DNA preservation in medieval skeletons. Sci Rep 2020; 10:18225. [PMID: 33106554 PMCID: PMC7588426 DOI: 10.1038/s41598-020-75163-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.
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Affiliation(s)
- Cody Parker
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Adam B Rohrlach
- Max Planck Institute for the Science of Human History, Jena, Germany
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA, Australia
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.
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23
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Peyrégne S, Peter BM. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination. Genome Biol 2020; 21:246. [PMID: 32933569 PMCID: PMC7490890 DOI: 10.1186/s13059-020-02123-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/27/2020] [Indexed: 12/31/2022] Open
Abstract
Contamination from present-day DNA is a fundamental issue when studying ancient DNA from historical or archaeological material, and quantifying the amount of contamination is essential for downstream analyses. We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded DNA libraries. The prediction is based solely on the patterns of post-mortem damage observed on ancient DNA sequences. The method has the power to quantify contamination from as few as 10,000 mapped sequences, making it particularly useful for analysing specimens that are poorly preserved or for which little data is available.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Benjamin M Peter
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
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24
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Ferreira S, Ashby R, Jeunen GJ, Rutherford K, Collins C, Todd EV, Gemmell NJ. DNA from mollusc shell: a valuable and underutilised substrate for genetic analyses. PeerJ 2020; 8:e9420. [PMID: 32821530 PMCID: PMC7396136 DOI: 10.7717/peerj.9420] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
Mollusc shells are an abundant resource that have been long used to predict the structures of ancient ecological communities, examine evolutionary processes, reconstruct paleoenvironmental conditions, track and predict responses to climatic change, and explore the movement of hominids across the globe. Despite the ubiquity of mollusc shell in many environments, it remains relatively unexplored as a substrate for molecular genetic analysis. Here we undertook a series of experiments using the New Zealand endemic greenshell mussel, Perna canaliculus, to explore the utility of fresh, aged, beach-cast and cooked mollusc shell for molecular genetic analyses. We find that reasonable quantities of DNA (0.002-21.48 ng/mg shell) can be derived from aged, beach-cast and cooked mussel shell and that this can routinely provide enough material to undertake PCR analyses of mitochondrial and nuclear gene fragments. Mitochondrial PCR amplification had an average success rate of 96.5% from shell tissue extracted thirteen months after the animal's death. A success rate of 93.75% was obtained for cooked shells. Amplification of nuclear DNA (chitin synthase gene) was less successful (80% success from fresh shells, decreasing to 10% with time, and 75% from cooked shells). Our results demonstrate the promise of mollusc shell as a substrate for genetic analyses targeting both mitochondrial and nuclear genes.
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Affiliation(s)
- Sara Ferreira
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Rachael Ashby
- Invermay Agricultural Centre, AgResearch, Dunedin, New Zealand
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Erica V. Todd
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Neil J. Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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25
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Peyrégne S, Prüfer K. Present-Day DNA Contamination in Ancient DNA Datasets. Bioessays 2020; 42:e2000081. [PMID: 32648350 DOI: 10.1002/bies.202000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/20/2020] [Indexed: 01/06/2023]
Abstract
Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.
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Affiliation(s)
- Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, 07745, Germany
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26
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Toppinen M, Pratas D, Väisänen E, Söderlund-Venermo M, Hedman K, Perdomo MF, Sajantila A. The landscape of persistent human DNA viruses in femoral bone. Forensic Sci Int Genet 2020; 48:102353. [PMID: 32668397 DOI: 10.1016/j.fsigen.2020.102353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
The imprints left by persistent DNA viruses in the tissues can testify to the changes driving virus evolution as well as provide clues on the provenance of modern and ancient humans. However, the history hidden in skeletal remains is practically unknown, as only parvovirus B19 and hepatitis B virus DNA have been detected in hard tissues so far. Here, we investigated the DNA prevalences of 38 viruses in femoral bone of recently deceased individuals. To this end, we used quantitative PCRs and a custom viral targeted enrichment followed by next-generation sequencing. The data was analyzed with a tailor-made bioinformatics pipeline. Our findings revealed bone to be a much richer source of persistent DNA viruses than earlier perceived, discovering ten additional ones, including several members of the herpes- and polyomavirus families, as well as human papillomavirus 31 and torque teno virus. Remarkably, many of the viruses found have oncogenic potential and/or may reactivate in the elderly and immunosuppressed individuals. Thus, their persistence warrants careful evaluation of their clinical significance and impact on bone biology. Our findings open new frontiers for the study of virus evolution from ancient relics as well as provide new tools for the investigation of human skeletal remains in forensic and archaeological contexts.
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Affiliation(s)
- Mari Toppinen
- Department of Virology, University of Helsinki, Finland
| | - Diogo Pratas
- Department of Virology, University of Helsinki, Finland; Department of Electronics, Telecommunications and Informatics, University of Aveiro, Portugal; Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Portugal
| | | | | | - Klaus Hedman
- Department of Virology, University of Helsinki, Finland; HUSLAB, Helsinki University Hospital, Finland
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Finland; Forensic Medicine Unit, Finnish Institute of Health and Welfare, Finland.
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27
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Simoes Dutra Correa H, Cortellini V, Brescia G, Verzeletti A. Human identification through DNA analysis of restored postmortem teeth. Forensic Sci Int Genet 2020; 47:102302. [DOI: 10.1016/j.fsigen.2020.102302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/30/2022]
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28
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Mckinnon M, Henneberg M, Simpson E, Higgins D. A comparison of crystal structure in fresh, burned and archaic bone - Implications for forensic sampling. Forensic Sci Int 2020; 313:110328. [PMID: 32502739 DOI: 10.1016/j.forsciint.2020.110328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
Abstract
Standard protocols for extracting DNA from bone are variable and are largely dependent on the state of preservation. In archaic samples, endogenous DNA is believed to be tightly bound to crystal aggregates in the Hydroxyapatite (HAp) matrix requiring prolonged demineralisation to allow its release. By comparison, fresh bone contains abundant cellular material, discounting the need for demineralisation. Recommendations for incinerated bone, specifically how viable sampling sites should be selected and the ideal techniques for DNA recovery are unclear, and the protocol used is often selected based on macroscopic sample appearance. It has been postulated that like archaic bone, burned bone is 'highly degraded' and therefore aDNA techniques may present better results for DNA recovery than using fresh protocols. However, little research has been undertaken comparing the crystal structure of burnt, fresh and archaic bone. This study uses a combination of XRPD and SEM analysis to compare the crystalline profile and microscopic appearance of burned bone subjected to temperatures ranging from 100-1000°C, with archaic and fresh samples. Although macroscopically visually different, fresh samples and samples heated up to 500°C showed no microscopic differences or significant changes in crystallinity. By comparison, samples heated above 500°C became significantly more crystalline, with HAp crystal size increasing dramatically. Archaic samples were different again, more closely resembling the amorphous fresh samples than the highly crystalline incinerated samples. These results suggests that, potentially, samples burned at 500°C or lower can be treated as fresh samples, whilst samples exposed to higher temperatures may require adapted protocols. Whether or not these highly burned samples require demineralisation needs to be investigated.
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Affiliation(s)
- Meghan Mckinnon
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Adelaide, Australia.
| | - Maciej Henneberg
- Discipline of Anatomy and Pathology, Adelaide Medical School, the University of Adelaide, Frome Road, Adelaide, SA 5000, Australia
| | | | - Denice Higgins
- Forensic Odontology Unit, Adelaide Dental School, the University of Adelaide, Adelaide, Australia
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29
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Gonzalez A, Cannet C, Zvénigorosky V, Geraut A, Koch G, Delabarde T, Ludes B, Raul JS, Keyser C. The petrous bone: Ideal substrate in legal medicine? Forensic Sci Int Genet 2020; 47:102305. [PMID: 32446165 DOI: 10.1016/j.fsigen.2020.102305] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022]
Abstract
Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.
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Affiliation(s)
- Angéla Gonzalez
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Catherine Cannet
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Vincent Zvénigorosky
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France; CNRS, FRE2029-BABEL, Université Paris Descartes, France.
| | - Annie Geraut
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Guillaume Koch
- Institut d'Anatomie Normale, Hôpitaux Universitaires de Strasbourg, Faculté de médecine de Strasbourg, France.
| | | | - Bertrand Ludes
- CNRS, FRE2029-BABEL, Université Paris Descartes, France; Institut Médico-Légal de Paris, France; Institut National de la Transfusion Sanguine, Paris, France.
| | - Jean-Sébastien Raul
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France.
| | - Christine Keyser
- Institut de Médecine Légale, Université de Strasbourg, Faculté de médecine de Strasbourg, France; CNRS, FRE2029-BABEL, Université Paris Descartes, France; Institut National de la Transfusion Sanguine, Paris, France.
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30
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Mai BHA, Drancourt M, Aboudharam G. Ancient dental pulp: Masterpiece tissue for paleomicrobiology. Mol Genet Genomic Med 2020; 8:e1202. [PMID: 32233019 PMCID: PMC7284042 DOI: 10.1002/mgg3.1202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/21/2020] [Indexed: 12/19/2022] Open
Abstract
Introduction Dental pulp with special structure has become a good reference sample in paleomicrobiology‐related blood‐borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins. Objectives This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe. Methods The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: “ancient,” “dental pulp,” “teeth,” “anatomy,” “structure,” “collection,” “preservation,” “selection,” “photography,” “radiography,” “contamination,” “decontamination,” “DNA,” “protein,” “extraction,” “bone,” “paleomicrobiology,” “bacteria,” “virus,” “pathogen,” “molecular biology,” “proteomics,” “PCR,” “MALDI‐TOF,” “LC/MS,” “ELISA,” “immunology,” “immunochromatography,” “genome,” “microbiome,” “metagenomics.” Results The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty‐seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species. Conclusions Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.
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Affiliation(s)
- Ba Hoang Anh Mai
- Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Hue University of Medicine and Pharmacy, Thua Thien Hue, Vietnam
| | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,UFR Odontologie, Aix-Marseille Université, Marseille, France
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31
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Ewart KM, Lightson AL, Sitam FT, Rovie-Ryan JJ, Mather N, McEwing R. Expediting the sampling, decalcification, and forensic DNA analysis of large elephant ivory seizures to aid investigations and prosecutions. Forensic Sci Int Genet 2019; 44:102187. [PMID: 31670244 DOI: 10.1016/j.fsigen.2019.102187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/27/2019] [Accepted: 10/12/2019] [Indexed: 02/02/2023]
Abstract
The illegal ivory trade continues to drive elephant poaching. Large ivory seizures in Africa and Asia are still commonplace. Wildlife forensics is recognised as a key enforcement tool to combat this trade. However, the time and resources required to effectively test large ivory seizures is often prohibitive. This limits or delays testing, which may impede investigations and/or prosecutions. Typically, DNA analysis of an ivory seizure involves pairing and sorting the tusks, sampling the tusks, powdering the sample, decalcification, then DNA extraction. Here, we optimize the most time-consuming components of this process: sampling and decalcification. Firstly, using simulations, we demonstrate that tusks do not need to be paired to ensure an adequate number of unique elephants are sampled in a large seizure. Secondly, we determined that directly powdering the ivory using a Dremel drill with a high-speed cutter bit, instead of cutting the ivory with a circular saw and subsequently powdering the sample in liquid nitrogen with a freezer mill, produces comparable results. Finally, we optimized a rapid 2 -h decalcification protocol that produces comparable results to a standard 3-day protocol. We tested/optimised the protocols on 33 raw and worked ivory samples, and demonstrated their utility on a case study, successfully identifying 94% of samples taken from 123 tusks. Using these new rapid protocols, the entire sampling and DNA extraction process takes less than one day and requires less-expensive equipment. We expect that the implementation of these rapid protocols will promote more consistent and timely testing of ivory seizures suitable for enforcement action.
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Affiliation(s)
- Kyle M Ewart
- TRACE Wildlife Forensics Network, Edinburgh, Scotland, United Kingdom.
| | - Amanda L Lightson
- TRACE Wildlife Forensics Network, Edinburgh, Scotland, United Kingdom
| | - Frankie T Sitam
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | | | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, Scotland, United Kingdom
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32
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Mansour H, Krebs O, Pinnschmidt HO, Griem N, Hammann-Ehrt I, Püschel K. Factors affecting dental DNA in various real post-mortem conditions. Int J Legal Med 2019; 133:1751-1759. [DOI: 10.1007/s00414-019-02151-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/20/2019] [Indexed: 11/24/2022]
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33
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Akbulut N, Çetin S, Bilecenoğlu B, Altan A, Akbulut S, Ocak M, Orhan K. The micro-CT evaluation of enamel-cement thickness, abrasion, and mineral density in teeth in the postmortem interval (PMI): new parameters for the determination of PMI. Int J Legal Med 2019; 134:645-653. [DOI: 10.1007/s00414-019-02104-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/13/2019] [Indexed: 11/29/2022]
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34
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Vitoševic K, Todorovic D, Slovic Z, Zivkovic-Zaric R, Todorovic M. Forensic Genetics and Genotyping. SERBIAN JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2019. [DOI: 10.1515/sjecr-2016-0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractForensic genetics represents a combination of molecular and population genetics. Personal identification and kinship analysis (e.g. paternity testing) are the two main subjects of forensic DNA analysis. Biological specimens from which DNA is isolated are blood, semen, saliva, tissues, bones, teeth, hairs. Genotyping has become a basis in the characterization of forensic biological evidence. It is performed using a variety of genetic markers, which are divided into two large groups: bi-allelic (single-nucleotide polymorphisms, SNP) and multi-allelic polymorphisms (variable number of tandem repeats, VNTR and short tandem repeats, STR). This review describes the purpose of genetic markers in forensic investigation and their limitations. The STR loci are currently the most informative genetic markers for identity testing, but in cases without a suspect SNP can predict offender’s ancestry and phenotype traits such as skin, eyes and hair color. Nowadays, many countries worldwide have established forensic DNA databases based on autosomal short tandem repeats and other markers. In order for DNA profile database to be useful at a national or international level, it is essential to standardize genetic markers used in laboratories.
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Affiliation(s)
- Katarina Vitoševic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Danijela Todorovic
- Department of Human Genetics, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Zivana Slovic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Radica Zivkovic-Zaric
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
| | - Milos Todorovic
- Department of Anatomy and Forensic Medicine, Faculty of Medical Sciences , University of Kragujevac , Kragujevac , Serbia
- Department of Forensic Medicine and Toxicology , Clinical Centre Kragujevac , Kragujevac , Serbia
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35
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Sigwart JD, Garbett A. Biodiversity Assessment, DNA Barcoding, and the Minority Majority. Integr Comp Biol 2019; 58:1146-1156. [PMID: 30053016 DOI: 10.1093/icb/icy076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The majority of species on Earth are in "under-studied" groups, and indeed probably the majority of species remain undiscovered and undescribed. Species are natural units of evolution, and they are formed from branching phylogenetic processes that have a mathematical structure. So it follows that we should be able to develop a set of general principles that describe global patterns of species groups, like genera. Understanding such patterns would lend considerable power to the approach of "taxonomic surrogacy." In environmental assessments, ecology, and paleontology, it is common to substitute genus-level or family-level identification where definitive species identification is impractical. Clarity and confidence in fundamental patterns, based on a robust null model for species and genus level diversity, can accelerate species discovery: there are more species in the tropics, species-poor genera are very common, large genera are rare. Much hope has been placed in DNA barcoding as an effective tool to increase the pace of species discovery, but it is abundantly clear that certain mitochondrial DNA (mtDNA) markers are more or less variable in different clades and universal threshold values are impractical to delimit species. This study further examines the patterns of divergence in one common mtDNA barcode fragment, cytochrome c oxidase subunit 1at the genus level. We compared pairwise divergence in this fragment between two animal clades that have similar species richness but different evolutionary histories: birds and bivalves. We analyzed quality controlled alignments of over 39,000 published sequences in 1223 genera. Median pairwise differences at the genus level are positively correlated with the species richness of a genus, and this is not dependent of the number of sequences sampled. Unsurprisingly, sequence divergence in vertebrates was far more constrained than in evolutionarily more ancient non-vertebrate clades. Differences among the groups examined highlight the need for DNA barcode approaches to be considered in the context of specific biological groups. Vertebrates are better studied, but not necessarily representative of the majority of biodiversity. A technique that provides powerful insights for vertebrate species may be ineffective for the majority of organisms.
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Affiliation(s)
- Julia D Sigwart
- Queen's University Marine Laboratory, 12-13 The Strand, Portaferry BT22 1PF, Northern Ireland
| | - Amy Garbett
- Queen's University Marine Laboratory, 12-13 The Strand, Portaferry BT22 1PF, Northern Ireland
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36
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Decorte R, Polet C, Boudin M, Tilquin F, Matroule JY, Dieu M, Charles C, Carlier A, Lebecque F, Deparis O. An interdisciplinary study around the reliquary of the late cardinal Jacques de Vitry. PLoS One 2019; 14:e0201424. [PMID: 30794540 PMCID: PMC6386372 DOI: 10.1371/journal.pone.0201424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 01/18/2019] [Indexed: 11/24/2022] Open
Abstract
The reliquary of Jacques de Vitry, a prominent clergyman and theologian in the early 13th century, has experienced several transfers over the last centuries, which seriously question the attribution of the remains to the late Cardinal. Uncertainty about the year of his birth poses an additional question regarding his age at death in 1240. The reliquary, located in the Saint Marie d'Oigines church, Belgium, was reopened in 2015 for an interdisciplinary study around his relics as well as the Treasure of Oignies, a remarkable cultural heritage notably built from Jacques de Vitry's donation. Anthropological, isotopic and genetic analyses were performed independently on the remains found in the reliquary. Results of the analyses provided evidence that the likelihood that these remains are those of Jacques de Vitry is very high: the remains belong to the same human male individual and the historical tradition about his age is confirmed. In addition, a separate relic (left tibia) was analysed and found to match with the remains of the reliquary (right tibia). The unique Jacques de Vitry's mitre, made of parchment, was sampled non-destructively and the extracted parchment collagen was analysed by a proteomic method in order to determine the animal species. The results showed that, surprisingly, not all parts of the mitre were made from the same species. All together, these findings are expected to fertilize knowledge carried by historical tradition around the relics of Jacques de Vitry and his related cultural heritage.
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Affiliation(s)
- Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven (KUL), Leuven, Belgium
- Laboratory of Forensic Genetics and Molecular Archaeology, Department of Forensic Medicine, UZ Leuven (UZL), Leuven, Belgium
| | - Caroline Polet
- Department of Palaeontology, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Mathieu Boudin
- Radiocarbon Dating Laboratory, Royal Institute for Cultural Heritage (KIK-IRPA), Brussels, Belgium
| | - Françoise Tilquin
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, ILEE Institute, University of Namur, Namur, Belgium
| | - Jean-Yves Matroule
- Research Unit in Microorganisms Biology (URBM), Narilis Institute, ILEE Institute, University of Namur, Namur, Belgium
| | - Marc Dieu
- Mass Spectrometry Facility (MaSUN), University of Namur, Namur, Belgium
| | - Catherine Charles
- Moretus Plantin University Library, University of Namur, Namur, Belgium
| | | | | | - Olivier Deparis
- Heritages, Transmissions, Inheritances (PaTHs) Institute & Department of Physics, University of Namur, Namur, Belgium
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Furtwängler A, Reiter E, Neumann GU, Siebke I, Steuri N, Hafner A, Lösch S, Anthes N, Schuenemann VJ, Krause J. Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis. Sci Rep 2018; 8:14075. [PMID: 30232341 PMCID: PMC6145933 DOI: 10.1038/s41598-018-32083-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022] Open
Abstract
In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.
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Affiliation(s)
- Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.
| | - Ella Reiter
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Gunnar U Neumann
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Inga Siebke
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Noah Steuri
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Albert Hafner
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Nils Anthes
- Institute of Ecology and Evolution, Animal Evolutionary Ecology group University of Tübingen, Tübingen, Germany
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Jena, Germany.
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38
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Winters M, Torkelson A, Booth R, Mailand C, Hoareau Y, Tucker S, Wasser S. Isolation of DNA from small amounts of elephant ivory: Sampling the cementum with total demineralization extraction. Forensic Sci Int 2018; 288:131-139. [DOI: 10.1016/j.forsciint.2018.04.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 12/11/2022]
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39
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Bardan F, Higgins D, Austin JJ. A mini-multiplex SNaPshot assay for the triage of degraded human DNA. Forensic Sci Int Genet 2018; 34:62-70. [DOI: 10.1016/j.fsigen.2018.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/03/2018] [Accepted: 02/05/2018] [Indexed: 12/01/2022]
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40
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Cementum as a source of DNA in challenging forensic cases. J Forensic Leg Med 2018; 54:76-81. [DOI: 10.1016/j.jflm.2017.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/23/2017] [Accepted: 12/30/2017] [Indexed: 11/20/2022]
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41
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Crime investigation through DNA methylation analysis: methods and applications in forensics. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0042-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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42
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A comparative analysis of preservation techniques for the optimal molecular detection of hookworm DNA in a human fecal specimen. PLoS Negl Trop Dis 2018; 12:e0006130. [PMID: 29346412 PMCID: PMC5773002 DOI: 10.1371/journal.pntd.0006130] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/22/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Proper collection and storage of fecal samples is necessary to guarantee the subsequent reliability of DNA-based soil-transmitted helminth diagnostic procedures. Previous research has examined various methods to preserve fecal samples for subsequent microscopic analysis or for subsequent determination of overall DNA yields obtained following DNA extraction. However, only limited research has focused on the preservation of soil-transmitted helminth DNA in stool samples stored at ambient temperature or maintained in a cold chain for extended periods of time. METHODOLOGY Quantitative real-time PCR was used in this study as a measure of the effectiveness of seven commercially available products to preserve hookworm DNA over time and at different temperatures. Results were compared against "no preservative" controls and the "gold standard" of rapidly freezing samples at -20°C. The preservation methods were compared at both 4°C and at simulated tropical ambient temperature (32°C) over a period of 60 days. Evaluation of the effectiveness of each preservative was based on quantitative real-time PCR detection of target hookworm DNA. CONCLUSIONS At 4°C there were no significant differences in DNA amplification efficiency (as measured by Cq values) regardless of the preservation method utilized over the 60-day period. At 32°C, preservation with FTA cards, potassium dichromate, and a silica bead two-step desiccation process proved most advantageous for minimizing Cq value increases, while RNA later, 95% ethanol and Paxgene also demonstrate some protective effect. These results suggest that fecal samples spiked with known concentrations of hookworm-derived egg material can remain at 4°C for 60 days in the absence of preservative, without significant degradation of the DNA target. Likewise, a variety of preservation methods can provide a measure of protection in the absence of a cold chain. As a result, other factors, such as preservative toxicity, inhibitor resistance, preservative cost, shipping requirements, sample infectivity, and labor costs should be considered when deciding upon an appropriate method for the storage of fecal specimens for subsequent PCR analysis. Balancing logistical factors and the need to preserve the target DNA, we believe that under most circumstances 95% ethanol provides the most pragmatic choice for preserving stool samples in the field.
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43
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Methodological evaluation of DNA-based molecular keys to identify categories of mislabelling in commercial products from genus Merluccius spp. Food Chem 2018; 239:640-648. [DOI: 10.1016/j.foodchem.2017.06.138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/06/2017] [Accepted: 06/26/2017] [Indexed: 11/19/2022]
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44
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Liu Q, Liu L, Zhang M, Zhang Q, Wang Q, Ding X, Shao L, Zhou Z, Wang S. A Simple and Efficient Method of Extracting DNA from Aged Bones and Teeth. J Forensic Sci 2017; 63:824-828. [PMID: 29240980 DOI: 10.1111/1556-4029.13603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/27/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
DNA is often difficult to extract from old bones and teeth due to low levels of DNA and high levels of degradation. This study established a simple yet efficient method for extracting DNA from 20 aged bones and teeth (approximately 60 years old). Based on the concentration and STR typing results, the new method of DNA extraction (OM) developed in this study was compared with the PrepFiler™ BTA Forensic DNA Extraction Kit (BM). The total amount of DNA extracted using the OM method was not significantly different from that extracted using the commercial kit (p > 0.05). However, the number of STR loci detected was significantly higher in the samples processed using the OM method than using the BM method (p < 0.05). This study aimed to establish a DNA extraction method for aged bones and teeth to improve the detection rate of STR typing and reduce costs compared to the BM technique.
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Affiliation(s)
- Qiqi Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liyan Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Minli Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qingzhen Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qiong Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiaoran Ding
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liting Shao
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhe Zhou
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
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Corrêa HSD, Pedro FLM, Volpato LER, Pereira TM, Siebert Filho G, Borges ÁH. Forensic DNA typing from teeth using demineralized root tips. Forensic Sci Int 2017; 280:164-168. [DOI: 10.1016/j.forsciint.2017.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/28/2017] [Accepted: 10/04/2017] [Indexed: 10/18/2022]
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46
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Dos Santos Rocha A, de Amorim ISS, Simão TDA, da Fonseca ADS, Garrido RG, Mencalha AL. High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science. J Forensic Sci 2017; 63:536-540. [PMID: 28834547 DOI: 10.1111/1556-4029.13552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Abstract
Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics.
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Affiliation(s)
- Alípio Dos Santos Rocha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil.,Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Isis Salviano Soares de Amorim
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Tatiana de Almeida Simão
- Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
| | - Adenilson de Souza da Fonseca
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Rodrigo Grazinoli Garrido
- Polícia Civil do Estado do Rio de Janeiro, Instituto de Pesquisas e Perícias em Genética Forense-IPPGF, Rio de Janeiro, RJ, 20230-240, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ, 20551-030, Brazil
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47
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Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum. PLoS One 2017; 12:e0170940. [PMID: 28129388 PMCID: PMC5271384 DOI: 10.1371/journal.pone.0170940] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/12/2017] [Indexed: 01/08/2023] Open
Abstract
Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA). In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad) applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements.
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48
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Therkildsen NO, Palumbi SR. Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Mol Ecol Resour 2016; 17:194-208. [DOI: 10.1111/1755-0998.12593] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/27/2016] [Accepted: 07/02/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Nina Overgaard Therkildsen
- Hopkins Marine Station; Department of Biology; Stanford University; 120 Oceanview Blvd. Pacific Grove CA 93950 USA
| | - Stephen R. Palumbi
- Hopkins Marine Station; Department of Biology; Stanford University; 120 Oceanview Blvd. Pacific Grove CA 93950 USA
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49
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Analysis of Short Tandem Repeat and Single Nucleotide Polymorphism Loci From Single-Source Samples Using a Custom HaloPlex Target Enrichment System Panel. Am J Forensic Med Pathol 2016; 37:99-107. [DOI: 10.1097/paf.0000000000000228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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50
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Giuliani C, Cilli E, Bacalini MG, Pirazzini C, Sazzini M, Gruppioni G, Franceschi C, Garagnani P, Luiselli D. Inferring chronological age from DNA methylation patterns of human teeth. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:585-95. [PMID: 26667772 DOI: 10.1002/ajpa.22921] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Current methods to determine chronological age from modern and ancient remains rely on both morphological and molecular approaches. However, low accuracy and the lack of standardized protocols make the development of alternative methods for the estimation of individual's age even more urgent for several research fields, such as biological anthropology, biodemography, forensics, evolutionary genetics, and ancient DNA studies. Therefore, the aim of this study is to identify genomic regions whose DNA methylation level correlates with age in modern teeth. METHODS We used MALDI-TOF mass spectrometry to analyze DNA methylation levels of specific CpGs located in the ELOVL2, FHL2, and PENK genes. We considered methylation data from cementum, dentin and pulp of 21 modern teeth (from 17 to 77 years old) to construct a mathematical model able to exploit DNA methylation values to predict age of the individuals. RESULTS The median difference between the real age and that estimated using DNA methylation values is 1.20 years (SD = 1.9) if DNA is recovered from both cementum and pulp of the same modern teeth, 2.25 years (SD = 2.5) if DNA is recovered from dental pulp, 2.45 years (SD = 3.3) if DNA is extracted from cementum and 7.07 years (SD = 7.0) when DNA is recovered from dentin only. DISCUSSION We propose for the first time the evaluation of DNA methylation at ELOVL2, FHL2, and PENK genes as a powerful tool to predict age in modern teeth for anthropological applications. Future studies are needed to apply this method also to historical and relatively ancient human teeth.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy
| | - Marco Sazzini
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
| | - Giorgio Gruppioni
- Department of Cultural Heritage (DBC), Laboratories of Physical Anthropology and Ancient DNA, University of Bologna, Ravenna, 48121, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,IRCCS Institute of Neurological Sciences, Bologna, 40139, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, 40126, Italy.,Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Bologna, 40126, Italy.,Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Bologna, 40126, Italy
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