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Haarkötter C, Saiz M, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Álvarez JC, Lorente JA. Evaluation of the usefulness of insertion-null markers in critical skeletal remains. Int J Legal Med 2024:10.1007/s00414-024-03205-3. [PMID: 38509248 DOI: 10.1007/s00414-024-03205-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Forensic DNA analysis in compromised skeletal remains may pose challenges due to DNA degradation, often resulting in partial or negative autosomal STRs profiles. To address this issue, alternative approaches such as mitochondrial DNA or SNPs typing may be employed; however, they are labour-intensive and costly. Insertion-null alleles (INNULs), short interspersed nuclear elements, have been suggested as a valuable tool for human identification in challenging samples due to their small amplicon size. A commercial kit including 20 INNULs markers along with amelogenin (InnoTyper® 21) has been developed. This study assesses its utility using degraded skeletal remains, comparing the results obtained (the number of detected alleles, RFU values, PHR, and the number of reportable markers) to those obtained using GlobalFiler™. Subsequently, the random match probability of the two profiles for each sample was determined using Familias version 3 to evaluate the power of discrimination of the results obtained from each kit. In every sample, InnoTyper® 21 yielded more alleles, higher RFU values, and a greater number of reportable loci. However, in most cases, both profiles were similarly informative. In conclusion, InnoTyper® 21 serves as a valuable complement to the analysis of challenging samples in cases where a poor or negative profile was obtained.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain.
| | - Jose Antonio Lorente
- Laboratory of Genetic Identification & Human Rights (LABIGEN-UGR), Department of Legal Medicine, Faculty of Medicine, University of Granada, Av. Investigación 11 - PTS - 18016, Granada, Spain
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2
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Haarkötter C, Saiz M, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Lorente JA, Álvarez JC. Performance comparison of four qPCR and three autosomal STR commercial kits from degraded skeletal remains. Forensic Sci Int 2023; 353:111856. [PMID: 37863006 DOI: 10.1016/j.forsciint.2023.111856] [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: 05/22/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
This research evaluates the current DNA quantification (Quantifiler™ Trio, PowerQuant®, Investigator® Quantiplex® Pro and InnoQuant® HY Fast) and autosomal STRs amplification kits (GlobalFiler™, PowerPlex® Fusion 6 C, Investigator® 24Plex QS) using 62 degraded skeletal remains from armed conflicts (petrous bone, femur, tibia, and tooth) with several parameters (autosomal small, large, and male target, degradation index, probability of degradation, number of alleles above analytical threshold, number of alleles above stochastic threshold, RFU, peak height ratio, number of reportable loci). The best qPCR/autosomal STRs amplification tandem was determined by comparing quantification results by a DNA quantity estimation based on sample average RFU. InnoQuant® HY Fast was the most sensitive kit, and no significative differences were observed among amplification kits; however, Investigator® 24 Plex QS was found to be the most sensitive in our samples. That is why InnoQuant™ and Investigator® 24Plex QS were determined to be the best tandem.
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Affiliation(s)
- Christian Haarkötter
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Saiz
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain.
| | - Xiomara Gálvez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Diana C Vinueza-Espinosa
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Isabel Medina-Lozano
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - José Antonio Lorente
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Juan Carlos Álvarez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
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Tretmanis JM, Jay F, Avila-Árcos MC, Huerta-Sanchez E. Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560049. [PMID: 37808674 PMCID: PMC10557694 DOI: 10.1101/2023.09.28.560049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (~ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.
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Affiliation(s)
| | - Flora Jay
- Interdisciplinary Laboratory of Numerical Sciences, Université Paris-Saclay
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Haarkötter C, Vinueza-Espinosa DC, Gálvez X, Saiz M, Medina-Lozano MI, Lorente JA, Álvarez JC. A comparison between petrous bone and tooth, femur and tibia DNA analysis from degraded skeletal remains. Electrophoresis 2023; 44:1559-1568. [PMID: 37469183 DOI: 10.1002/elps.202300097] [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: 05/08/2023] [Revised: 06/07/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Skeletal remains are the only biological material that remains after long periods; however, environmental conditions such as temperature, humidity, and pH affect DNA preservation, turning skeletal remains into a challenging sample for DNA laboratories. Sample selection is a key factor, and femur and tooth have been traditionally recommended as the best substrate of genetic material. Recently, petrous bone (cochlear area) has been suggested as a better option due to its DNA yield. This research aims to evaluate the efficiency of petrous bone compared to other cranium samples (tooth) and postcranial long bones (femur and tibia). A total amount of 88 samples were selected from 38 different individuals. The samples were extracted by using an organic extraction protocol, DNA quantification by Quantifiler Trio kit and amplified with GlobalFiler kit. Results show that petrous bone outperforms other bone remains in quantification data, yielding 15-30 times more DNA than the others. DNA profile data presented likeness between petrous bone and tooth regarding detected alleles; however, the amount of DNA extracted in petrous bones allowed us to obtain more informative DNA profiles with superior quality. In conclusion, petrous bone or teeth sampling is recommended if DNA typing is going to be performed with environmentally degraded skeletal remains.
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Affiliation(s)
- Christian Haarkötter
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Diana C Vinueza-Espinosa
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Xiomara Gálvez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - María Saiz
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - María Isabel Medina-Lozano
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - José Antonio Lorente
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
| | - Juan Carlos Álvarez
- Laboratory of Genetic Identification, Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, University of Granada, Granada, Spain
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5
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Żarczyńska M, Żarczyński P, Tomsia M. Nucleic Acids Persistence-Benefits and Limitations in Forensic Genetics. Genes (Basel) 2023; 14:1643. [PMID: 37628694 PMCID: PMC10454188 DOI: 10.3390/genes14081643] [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: 07/13/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The analysis of genetic material may be the only way to identify an unknown person or solve a criminal case. Often, the conditions in which the genetic material was found determine the choice of the analytical method. Hence, it is extremely important to understand the influence of various factors, both external and internal, on genetic material. The review presents information on DNA and RNA persistence, depending on the chemical and physical factors affecting the genetic material integrity. One of the factors taken into account is the time elapsing to genetic material recovery. Temperature can both preserve the genetic material or lead to its rapid degradation. Radiation, aquatic environments, and various types of chemical and physical factors also affect the genetic material quality. The substances used during the forensic process, i.e., for biological trace visualization or maceration, are also discussed. Proper analysis of genetic material degradation can help determine the post-mortem interval (PMI) or time since deposition (TsD), which may play a key role in criminal cases.
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Affiliation(s)
- Małgorzata Żarczyńska
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Piotr Żarczyński
- School of Medicine in Katowice, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland; (M.Ż.); (P.Ż.)
| | - Marcin Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, 18 Medyków Street, 40-752 Katowice, Poland
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6
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Xu C, Ma B, Dong X, Lei L, Hao Q, Zhao C, Liu H. Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing. ACS APPLIED MATERIALS & INTERFACES 2023; 15:24097-24108. [PMID: 37184884 DOI: 10.1021/acsami.3c01860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Due to its high coding density and longevity, DNA is a compelling data storage alternative. However, current DNA data storage systems rely on the de novo synthesis of enormous DNA molecules, resulting in low data editability, high synthesis costs, and restrictions on further applications. Here, we demonstrate the programmable assembly of reusable DNA blocks for versatile data storage using the ancient movable type printing principle. Digital data are first encoded into nucleotide sequences in DNA hairpins, which are then synthesized and immobilized on solid beads as modular DNA blocks. Using DNA polymerase-catalyzed primer exchange reaction, data can be continuously replicated from hairpins on DNA blocks and attached to a primer in tandem to produce new information. The assembly of DNA blocks is highly programmable, producing various data by reusing a finite number of DNA blocks and reducing synthesis costs (∼1718 versus 3000 to 30,000 US$ per megabyte using conventional methods). We demonstrate the flexible assembly of texts, images, and random numbers using DNA blocks and the integration with DNA logic circuits to manipulate data synthesis. This work suggests a flexible paradigm by recombining already synthesized DNA to build cost-effective and intelligent DNA data storage systems.
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Affiliation(s)
- Chengtao Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Biao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Xing Dong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Lanjie Lei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Qing Hao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
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7
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Watherston J, McNevin D. Skull and long bones – Forensic DNA techniques for historic shipwreck human remains. AUST J FORENSIC SCI 2023. [DOI: 10.1080/00450618.2023.2181395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- J. Watherston
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
- Biology Unit, Forensic Science Branch, Nt Police, Fire and Emergency Services, Berrimah, NT, Australia
- College of Health & Human Sciences, Faculty of Science, Charles Darwin University, Casuarina, NT, Australia
| | - D. McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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8
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Senst A, Caliebe A, Scheurer E, Schulz I. Validation and beyond: Next generation sequencing of forensic casework samples including challenging tissue samples from altered human corpses using the MiSeq FGx system. J Forensic Sci 2022; 67:1382-1398. [PMID: 35318655 PMCID: PMC9313618 DOI: 10.1111/1556-4029.15028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023]
Abstract
The proceeding developments in next generation sequencing (NGS) technologies enable increasing discrimination power for short tandem repeat (STR) analyses and provide new possibilities for human identification. Therefore, the growing relevance and demand in forensic casework display the need for reliable validation studies and experiences with challenging DNA samples. The presented validation of the MiSeq FGx system and the ForenSeq™ DNA Signature Prep Kit (1) investigated sensitivity, repeatability, reproducibility, concordance, pooling variations, DNA extraction method variances, DNA mixtures, degraded, and casework samples and (2) optimized the sequencing workflow for challenging samples from human corpses by testing additional PCR purification, pooling adjustments, and adapter volume reductions. Overall results indicate the system's reliability in concordance to traditional capillary electrophoresis (CE)‐based genotyping and reproducibility of sequencing data. Genotyping success rates of 100% were obtained down to 62.5 pg DNA input concentrations. Autosomal STR (aSTR) profiles of artificially degraded samples revealed significantly lower numbers of locus and allelic dropouts than CE. However, it was observed that the system still exposed drawbacks when sequencing highly degraded and inhibited samples from human remains. Due to the lack of studies evaluating the sequencing success of samples from decomposed or skeletonised corpses, the presented optimisation studies provide valuable recommendations such as an additional PCR purification, an increase in library pooling volumes, and a reduction of adapter volumes for samples with concentrations ≥31.2 pg. Thus, this research highlights the importance of all‐encompassing validation studies for implementing novel technologies in forensic casework and presents recommendations for challenging samples.
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Affiliation(s)
- Alina Senst
- Institute of Forensic Medicine, Basel, Switzerland
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University and University-Hospital Schleswig-Holstein, Kiel, Germany
| | - Eva Scheurer
- Institute of Forensic Medicine, Basel, Switzerland
| | - Iris Schulz
- Institute of Forensic Medicine, Basel, Switzerland
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9
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Ravi MS, Manju R. Use of pulp tissue of deciduous teeth for gender determination - A comparative molecular analysis study. Indian J Dent Res 2022; 33:158-163. [DOI: 10.4103/ijdr.ijdr_507_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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10
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Rahmat RA, Humphries MA, Linacre AMT, Malik A, Saedon NA, Austin JJ. Freeze-drying improves DNA yield from teeth. Forensic Sci Int 2021; 326:110938. [PMID: 34343942 DOI: 10.1016/j.forsciint.2021.110938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022]
Abstract
The common method of preparing teeth prior to DNA extraction involves cleaning, decontamination, drying and pulverisation. Moisture in post-mortem teeth can promote bacterial growth and hydrolytic damage that could contribute to DNA degradation, whilst also possibly reducing the efficiency of sample pulverisation and DNA release. Here we compared DNA extraction from pig teeth, with- and without freeze-drying, to examine the impact of removing moisture on DNA yield. Quantitative real-time polymerase chain reaction (qPCR) was used to quantify an 83 bp mitochondrial DNA fragment and two nuclear DNA fragments of 82 bp and 150 bp. The comparative results showed that sample preparation with freeze-drying resulted in a higher DNA yield without compromising the DNA quality. This study highlights the advantage of incorporating a freeze-drying to improve the DNA yield and minimising the loss of DNA during sample preparation of teeth.
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Affiliation(s)
- Rabiah A Rahmat
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur 50603, Malaysia; School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia.
| | - Melissa A Humphries
- School of Mathematical Sciences, Faculty of Engineering, Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia; ARC Centre of Excellence for Mathematical and Statistical Frontiers, University of Adelaide, Adelaide, South Australia, Australia.
| | - Adrian M T Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia 5042, Australia.
| | - Arif Malik
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia.
| | - Nor A Saedon
- Forensic DNA Division, Forensic Science Analysis Centre, Department of Chemistry, Selangor 46661, Malaysia.
| | - Jeremy J Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5006, Australia.
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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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12
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Tan X, Ge L, Zhang T, Lu Z. Preservation of DNA for data storage. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The preservation of DNA has attracted significant interest of scientists in diverse research fields from ancient biological remains to the information field. In light of the different DNA safekeeping requirements (e.g., storage time, storage conditions) in these disparate fields, scientists have proposed distinct methods to maintain the DNA integrity. Specifically, DNA data storage is an emerging research, which means that the binary digital information is converted to the sequences of nucleotides leading to dense and durable data storage in the form of synthesized DNA. The intact preservation of DNA plays a significant role because it is closely related to data integrity. This review discusses DNA preservation methods, aiming to confirm an appropriate one for synthetic oligonucleotides in DNA data storage. First, we analyze the impact factors of the DNA long-term storage, including the intrinsic stability of DNA, environmental factors, and storage methods. Then, the benefits and disadvantages of diverse conservation approaches (e.g., encapsulation-free, chemical encapsulation) are discussed. Finally, we provide advice for storing non-genetic information in DNA in vitro. We expect these preservation suggestions to promote further research that may extend the DNA storage time.
The bibliography includes 99 references.
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13
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The Effectiveness of Mini Primer STR CODIS in DNA Degradation as the Effect of High-Temperature Exposure. ACTA ACUST UNITED AC 2020; 2020:2417693. [PMID: 33425665 PMCID: PMC7775127 DOI: 10.1155/2020/2417693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/10/2020] [Indexed: 11/18/2022]
Abstract
Background More and more today, forensic identification through deoxyribonucleic acid (DNA) examination has achieved greater recognition in supporting Indonesia's law enforcement. Such examination is to determine the origin of a child, paternity cases, genealogical relation, or identifying unknown crime victims. However, along with the development of this DNA material examination, problems arise. DNA undergoes a degradation, commonly known as degraded DNA, which is one of the serious issues frequently encountered by forensic and DNA experts. Some forensic DNA experts take one of the alternatives to overcome this issue by implementing a mini primer set that is through a method to reduce the size of STR assays on DNA core locus examination. Methods In this study, the writers conduct research using the mini primers of CSF1PO, FGA, and D21S11 of the molar teeth exposed to 500°C temperature for 20 and 30 minutes and 750°C for the same amount of time. Result The findings show the DNA contents of molar teeth significantly (p < 0.05) decreased as the effect of high-temperature exposure. PCR result visualization shows CSF1PO is the only locus detected with mini primer exposed to 750°C temperature for 30 minutes (the highest exposure during this research). Conclusions This finding suggests that this locus is potential in examining identification through DNA analysis, especially on a degraded condition as the effect of high-temperature exposure. Besides, this could accelerate the identification process especially on mass disaster events or criminal cases.
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14
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Emmons AL, Mundorff AZ, Keenan SW, Davoren J, Andronowski J, Carter DO, DeBruyn JM. Characterizing the postmortem human bone microbiome from surface-decomposed remains. PLoS One 2020; 15:e0218636. [PMID: 32639969 PMCID: PMC7343130 DOI: 10.1371/journal.pone.0218636] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 05/19/2020] [Indexed: 01/19/2023] Open
Abstract
Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.
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Affiliation(s)
- Alexandra L. Emmons
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Amy Z. Mundorff
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Sarah W. Keenan
- Department of Geology and Geological Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota, United States of America
| | - Jonathan Davoren
- Bode Cellmark Forensics, Lorton, Virginia, United States of America
| | - Janna Andronowski
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - David O. Carter
- Division of Natural Sciences and Mathematics, Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, Hawaii, United States of America
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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15
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Kontopoulos I, Penkman K, Mullin VE, Winkelbach L, Unterländer M, Scheu A, Kreutzer S, Hansen HB, Margaryan A, Teasdale MD, Gehlen B, Street M, Lynnerup N, Liritzis I, Sampson A, Papageorgopoulou C, Allentoft ME, Burger J, Bradley DG, Collins MJ. Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PLoS One 2020; 15:e0235146. [PMID: 32584871 PMCID: PMC7316274 DOI: 10.1371/journal.pone.0235146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals’ size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.
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Affiliation(s)
- Ioannis Kontopoulos
- Department of Archaeology, BioArCh, University of York, York, United Kingdom
- * E-mail:
| | - Kirsty Penkman
- Department of Chemistry, BioArCh, University of York, York, United Kingdom
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martina Unterländer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
- German Federal Criminal Police Office, Wiesbaden, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Henrik B. Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Birgit Gehlen
- Collaborative Research Centre, project D4, Cologne University, Cologne, Germany
| | - Martin Street
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM Leibniz Research Institute for Archaeology, Neuwied, Germany
| | - Niels Lynnerup
- Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ioannis Liritzis
- Laboratory of Archaeometry, Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
- Center on Yellow River Civilization of Henan Province, Key Research Institute of Yellow River Civilization and Sustainable Development and Collaborative Innovation, Henan University, Kaifeng, China
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
| | - Morten E. Allentoft
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Matthew J. Collins
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- Centre for Evogenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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16
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Meixner E, Kallupurackal V, Kratzer A, Voegeli P, Thali MJ, Bolliger SA. Persistence and detection of touch DNA and blood stain DNA on pig skin exposed to water. Forensic Sci Med Pathol 2020; 16:243-251. [DOI: 10.1007/s12024-020-00234-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2020] [Indexed: 01/15/2023]
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17
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Agostini V. DNA analysis of the last Brazilian unknown soldier's remains buried in Pistoia (Italy). Forensic Sci Res 2020; 5:336-340. [PMID: 33457052 PMCID: PMC7782302 DOI: 10.1080/20961790.2020.1713453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
During World War II, many nations took part in the war. Among the supporters of the Alliance there was also Brazil. In August 1944, under the leadership of President Getúlio Vargas, Brazil declared war on Nazi Germany and took part in the Italian campaign by sending many troops to support the Allies in the Central Italy. Once the conflict was over, the deceased Brazilian soldiers were buried in Pistoia, a few kilometers from Florence. But only in 1960 the Brazilian government authorized the transfer of the dead soldiers to their homeland. Five years later, during the building of the Brazilian Military Votive Monument, still in the Pistoia cemetery, a last body was found but could not be identified: so he was buried as an "unknown soldier". In December 2012, the Brazilian Embassy in Italy asked for performing forensic genetics analysis for identification purposes on the remains of this last unknown Brazilian soldier. After almost 70 years a complete short tandem repeats (STR) profile was obtained, useful for any relatives searching. Key points: Identification of the last Brazilian Unknown Soldier buried in Italy.DNA analysis on 70 years old skeletal remains.Brazilian soldier's history during World War II.
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Affiliation(s)
- Vincenzo Agostini
- Università Degli Studi Del Piemonte Orientale "A. Avogadro", Alessandria, Italy
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18
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Schmidt N, Schücker K, Krause I, Dörk T, Klintschar M, Hummel S. Genome‐wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:99-109. [DOI: 10.1002/ajpa.23996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/21/2019] [Accepted: 12/13/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Nicole Schmidt
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
| | - Katharina Schücker
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
- Max‐Planck‐Institute for Biophysical Chemistry Göttingen Germany
| | - Ina Krause
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
| | - Thilo Dörk
- Gynaecological Research UnitHannover Medical School Hannover Germany
| | | | - Susanne Hummel
- Department of Historical Anthropology and Human EcologyUniversity of Göttingen Göttingen Germany
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19
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Inter and intra-individual variation in skeletal DNA preservation in buried remains. Forensic Sci Int Genet 2020; 44:102193. [DOI: 10.1016/j.fsigen.2019.102193] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/28/2019] [Accepted: 10/22/2019] [Indexed: 11/23/2022]
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20
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Agostini V, Bailo P, Chiti E, Linarello P, Gentile G, Primignani P, Giriodi M, Piccinini A. Ocular swabs on exhumed bodies: An alternative to the collection of “classical” tissue samples in forensic genetics. Forensic Sci Int Genet 2020; 44:102206. [DOI: 10.1016/j.fsigen.2019.102206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 10/16/2019] [Accepted: 11/15/2019] [Indexed: 10/25/2022]
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21
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Finaughty C, Gibbon VE, Speed B, Heathfield LJ. Lost at sea: A pilot study investigating DNA recovery from teeth in a South African natural marine environment. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Generality of Post-Antimicrobial Treatment Persistence of Borrelia burgdorferi Strains N40 and B31 in Genetically Susceptible and Resistant Mouse Strains. Infect Immun 2019; 87:IAI.00442-19. [PMID: 31308087 DOI: 10.1128/iai.00442-19] [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: 06/04/2019] [Accepted: 07/11/2019] [Indexed: 01/22/2023] Open
Abstract
A basic feature of infection caused by Borrelia burgdorferi, the etiological agent of Lyme borreliosis, is that persistent infection is the rule in its many hosts. The ability to persist and evade host immune clearance poses a challenge to effective antimicrobial treatment. A link between therapy failure and the presence of persister cells has started to emerge. There is growing experimental evidence that viable but noncultivable spirochetes persist following treatment with several different antimicrobial agents. The current study utilized the mouse model to evaluate if persistence occurs following antimicrobial treatment in disease-susceptible (C3H/HeJ [C3H]) and disease-resistant (C57BL/6 [B6]) mouse strains infected with B. burgdorferi strains N40 and B31 and to confirm the generality of this phenomenon, as well as to assess the persisters' clinical relevance. The status of infection was evaluated at 12 and 18 months after treatment. The results demonstrated that persistent spirochetes remain viable for up to 18 months following treatment, as well as being noncultivable. The phenomenon of persistence in disease-susceptible C3H mice is equally evident in disease-resistant B6 mice and not unique to any particular B. burgdorferi strain. The results also demonstrate that, following antimicrobial treatment, both strains of B. burgdorferi, N40 and B31, lose one or more plasmids. The study demonstrated that noncultivable spirochetes can persist in a host following antimicrobial treatment for a long time but did not demonstrate their clinical relevance in a mouse model of chronic infection. The clinical relevance of persistent spirochetes beyond 18 months following antimicrobial treatment requires further studies in other animal models.
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23
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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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24
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Klein RG. Population structure and the evolution of
Homo sapiens
in Africa. Evol Anthropol 2019; 28:179-188. [DOI: 10.1002/evan.21788] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 01/01/2023]
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25
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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26
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Thomas AE, Holben B, Dueño K, Snow M. Mitochondrial DNA Extraction from Burial Soil Samples at Incremental Distances: A Preliminary Study. J Forensic Sci 2018; 64:845-851. [PMID: 30332495 DOI: 10.1111/1556-4029.13931] [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: 05/22/2018] [Revised: 09/23/2018] [Accepted: 09/28/2018] [Indexed: 11/28/2022]
Abstract
Preservation variance of soil DNA is neglected in the literature, and exceptional cases exaggerate amplification capabilities. This study sought to amplify a short mitochondrial fragment (212 bp) specific to Sus scrofa domesticus from the soil surrounding decomposing pig remains from an open-air locale. Samples collected above the body at incremental distances after 145 days of initial placement yielded pig DNA. A secondary sampling was collected in 2017, approximately 768 days after burial. Inhibition tests corroborated that pig DNA was no longer present in the soil resulting in a loss of original DNA between 145 and 768 days. The results provide evidence that genetic material leaches out radially from the source and DNA fragments longer than 200 bp do not persist in soil for a relatively short timeframe in western Montana. The conclusions support the collection of soil in crime scene investigation procedures within the first few months of decomposition.
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Affiliation(s)
- Ariane E Thomas
- Anthropology Department, University of Montana, Missoula, MT
| | - Bill Holben
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Kora Dueño
- Anthropology Department, University of Montana, Missoula, MT.,Division of Biological Sciences, University of Montana, Missoula, MT
| | - Meradeth Snow
- Anthropology Department, University of Montana, Missoula, MT
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27
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Otte JM, Blackwell N, Soos V, Rughöft S, Maisch M, Kappler A, Kleindienst S, Schmidt C. Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples? FEMS Microbiol Ecol 2018; 94:5104375. [DOI: 10.1093/femsec/fiy189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Julia M Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Viktoria Soos
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Saskia Rughöft
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Markus Maisch
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
- Geomicrobiology, Center for Geomicrobiology, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
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28
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Antinick TC, Foran DR. Intra- and Inter-Element Variability in Mitochondrial and Nuclear DNA from Fresh and Environmentally Exposed Skeletal Remains. J Forensic Sci 2018; 64:88-97. [PMID: 29940697 DOI: 10.1111/1556-4029.13843] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 05/16/2018] [Accepted: 06/05/2018] [Indexed: 11/30/2022]
Abstract
Successful identification of skeletonized remains often relies upon DNA analyses, frequently focusing on the mid-diaphysis of weight-bearing long bones. This study explored intra-bone DNA variability using bovine and porcine femora, along with calcanei and tali. DNA from fresh and short-term environmentally exposed bone was extracted utilizing demineralization and standard lysis buffer protocols, and DNA quantity and quality were measured. Overall, femoral epiphyses, metaphyses, and the tarsals had more nuclear and mitochondrial DNA than did the femoral diaphyses. DNA loss was much more rapid in buried bones than in surface exposed bones, while DNA quality differed based on environment, but not bone region/element. The demineralization protocol generated more DNA in some bone regions, while the standard lysis was more effective in others, and neither significantly affected DNA quality. Taken together, these findings reinforce the importance of considering inter- and intra-bone heterogeneity when sampling skeletal material for forensic DNA-based identifications.
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Affiliation(s)
- Timothy C Antinick
- Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
| | - David R Foran
- Forensic Science Program, School of Criminal Justice and Department of Integrative Biology, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
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29
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Koczur LM, Williford D, DeYoung RW, Ballard BM. Bringing back the dead: Genetic data from avian carcasses. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lianne M. Koczur
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Bart M. Ballard
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
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30
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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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31
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Brown H, Thompson R, Murphy G, Peters D, La Rue B, King J, Montgomery AH, Carroll M, Baus J, Sinha S, Wendt FR, Song B, Chakraborty R, Budowle B, Sinha SK. Development and validation of a novel multiplexed DNA analysis system, InnoTyper® 21. Forensic Sci Int Genet 2017; 29:80-99. [DOI: 10.1016/j.fsigen.2017.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/08/2017] [Accepted: 03/15/2017] [Indexed: 01/21/2023]
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32
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Pfeifer CM, Gass A, Klein-Unseld R, Wiegand P. DNA persistence of bite marks on food and its relevance for STR typing. Int J Legal Med 2017; 131:1221-1228. [PMID: 28653154 DOI: 10.1007/s00414-017-1627-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/13/2017] [Indexed: 01/20/2023]
Abstract
In forensic DNA analysis, salivary traces at crime scenes are a promising way to identify a person. However, crime scenes are oftentimes investigated a while after the crime and recovered samples might have been degraded leading to poor PCR amplification. Probably due to decomposition and negative visual impression of spoiled food, bite mark samples make up only a small part of our casework routine. In this study, bite marks on apples and chocolate bars as well as on an inert surface (microscope slide) were stored up to 3 weeks indoors and outdoors during different seasons and analyzed for amylase activity and DNA quantity and quality. The results underlined the stability of human nuclear DNA not only on inert but also on biological surfaces and their forensic usefulness even when bite marks are stored 21 days under adverse but realistic conditions at a crime scene. Overall, amylase activity as well as DNA quantity decreased over time depending on storage environment with a certain inter- and intrapersonal variation. But amylase activity testing was not found to be an appropriate screening tool for further analysis. Apple bite marks resulted in generally higher DNA amounts than chocolate bars and microscope slides. Although mold reduced the DNA quantity, complete STR profiles could be analyzed. High air humidity and cold temperatures were found to act preservative on raw food with high water content but caused loss of information over time for smooth inert surfaces and hygroscopic foods like sweets. Many factors are involved in the stability of DNA in bite marks and its resulting quality and quantity available for an STR analysis. However, since there was a substantial proportion of informative STR profiles even from bite marks stored for 21 days, the results encourage the analysis of those even if their visual appearance seems unfavorable.
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Affiliation(s)
- Céline M Pfeifer
- Institute of Legal Medicine, Albert-Einstein-Allee 23, 89081, Ulm, Germany.
| | - Anja Gass
- Institute of Legal Medicine, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | | | - Peter Wiegand
- Institute of Legal Medicine, Albert-Einstein-Allee 23, 89081, Ulm, Germany
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33
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Microsatellite Analysis for Identification of Individuals Using Bone from the Extinct Steller's Sea Cow (Hydrodamalis gigas). Methods Mol Biol 2017. [PMID: 28502003 DOI: 10.1007/978-1-4939-6990-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Microsatellite DNA can provide more detailed population genetic information than mitochondrial DNA which is normally used to research ancient bone. The methods detailed in this chapter can be utilized for any type of bone. However, for this example, four microsatellite loci were isolated from Steller's sea cow (Hydrodamalis gigas) using published primers for manatee and dugong microsatellites. The primers DduC05 (Broderick et al., Mol Ecol Notes 6:1275-1277, 2007), Tmakb60, TmaSC5 (Pause et al., Mol Ecol Notes 6: 1073-1076, 2007), and TmaE11 (Garcia-Rodriguez et al., Mol Ecol 12:2161-2163, 2000) all successfully amplified microsatellites from H. gigas. The DNA samples were from bone collected on Bering or St. Lawrence Islands. DNA was analyzed using primers with the fluorescent label FAM-6. Sequenced alleles were then used to indicate a difference in the number of repeats and thus a difference in individuals. This is the first time that H. gigas microsatellite loci have been isolated. These techniques for ancient bone microsatellite analysis allow an estimate of population size for a newly discovered St. Lawrence Island sea cow population.
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34
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Alghafri R, Zupanič Pajnič I, Zupanc T, Balažic J, Shrivastava P. Rapidly mutating Y-STR analyses of compromised forensic samples. Int J Legal Med 2017; 132:397-403. [PMID: 28466124 DOI: 10.1007/s00414-017-1600-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/24/2017] [Indexed: 11/25/2022]
Abstract
Rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) were identified to improve differentiation of unrelated males and also to enable separating closely and distantly related males in human identity testing in forensic and other applications. RM-Yplex assay was developed as a single multiplex that is capable of simultaneously amplifying all currently known RM Y-STRs, and reproducibility and sensitivity testing were performed on reference samples. Additional analyses are necessary to test its suitability for analysing compromised forensic samples. For this purpose, we applied the RM-Yplex assay to approximately 70-year-old skeletons that were used as a model for poorly preserved, challenging forensic samples. We analysed 57 male skeletal remains (bones and teeth) from 55 skeletons excavated from the Second World War (WWII) mass graves in Slovenia. The RM-Yplex typing was successful in all 57 samples; there were 56% full profiles obtained, and in partial profiles, up to 7 locus drop-outs were observed and they appeared correlated with low DNA quantities and degradation of DNA obtained from WWII bone and tooth samples. The longest loci, DYS403S1b, DYS547, DYS627 and DYS526b, were the most often dropped-out RM Y-STRs. In spite of high frequency of drop-out events, the RM-Yplex typing was successful in all WWII samples, showing the possibility of successful amplification of at least half of the RM Y-STRs even from the most compromised samples analysed.
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Affiliation(s)
- Rashed Alghafri
- General Department of Forensic Sciences and Criminology, Dubai Police General Head Quarters, Al Tawar 1, Dubai, United Arab Emirates
| | - Irena Zupanič Pajnič
- 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
| | - Jože Balažic
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Pankaj Shrivastava
- DNA Fingerprinting Unit, State Forensic Science Laboratory, Govt. of Madhya Pradesh, Sagar, 470001, India
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Wadsworth C, Procopio N, Anderung C, Carretero JM, Iriarte E, Valdiosera C, Elburg R, Penkman K, Buckley M. Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites. J Proteomics 2017; 158:1-8. [DOI: 10.1016/j.jprot.2017.01.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/21/2016] [Accepted: 01/06/2017] [Indexed: 12/23/2022]
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Chaitanya L, Pajnič IZ, Walsh S, Balažic J, Zupanc T, Kayser M. Bringing colour back after 70 years: Predicting eye and hair colour from skeletal remains of World War II victims using the HIrisPlex system. Forensic Sci Int Genet 2016; 26:48-57. [PMID: 27780108 DOI: 10.1016/j.fsigen.2016.10.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 09/26/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
Abstract
Retrieving information about externally visible characteristics from DNA can provide investigative leads to find unknown perpetrators, and can also help in disaster victim and other missing person identification cases. Aiming for the application to both types of forensic casework, we previously developed and forensically validated the HIrisPlex test system enabling parallel DNA prediction of eye and hair colour. Although a recent proof-of-principle study demonstrated the general suitability of the HIrisPlex system for successfully analysing DNA from bones and teeth of various storage times and conditions, practical case applications to human remains are scarce. In this study, we applied the HIrisPlex system to 49 DNA samples obtained from bones or teeth of World War II victims excavated at six sites, mostly mass graves, in Slovenia. PCR-based DNA quantification ranged from 4pg/μl to 313pg/μl and on an average was 41pg/μl across all samples. All 49 samples generated complete HIrisPlex profiles with the exception of one MC1R DNA marker (N29insA) missing in 83.7% of the samples. In 44 of the 49 samples (89.8%) complete 15-loci autosomal STR (plus amelogenin) profiles were obtained. Of 5 pairs of skeletal remains for which STR profiling suggested an origin in the same individuals, respectively, 4 showed the same HIrisPlex profiles and predicted eye and hair colours, respectively, while discrepancies in one pair (sample 26 and 43) are likely to be explained by DNA quantity and quality issues observed in sample 43. Sample 43 had the lowest DNA concentration of only 4pg/μl, producing least reliable STR results and could be misleading in concluding that samples 43 and 26 originate from the same individual. The HIrisPlex-predicted eye and hair colours from two skeletal samples, suggested to derive from two brothers via STR profiling together with a living sister, were confirmed by the living sister's report. Overall, we demonstrate that after more than 70 years, HIrisPlex-based eye and hair colour prediction from skeletal remains is feasible with high success rate. Our results further encourage the use of the HIrisPlex system in missing person/disaster victim identification to aid the identification process in cases where ante-mortem samples or putative relatives are not directly available, and DNA predicted eye and hair colour information provides leads for locating them, allowing STRbased individual identification.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jože Balažic
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Lech T. A Discovered Ducal Seal Does Not Belong to the Incorporation Charter for the City of Krakow Solving the Mystery Using Genetic Methods. PLoS One 2016; 11:e0161591. [PMID: 27560131 PMCID: PMC4999217 DOI: 10.1371/journal.pone.0161591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 08/04/2016] [Indexed: 11/18/2022] Open
Abstract
The Incorporation Charter for the city of Krakow, the former capital of Poland, is one of the most valuable documents stored in the National Archives in Krakow. The document, which was written in 1257 on parchment, grants Krakow the Magdeburg rights and regulates its legal, statutory, economic and settlement-related aspects. The Charter was placed in the National Register of the Memory of the World UNESCO programme in 2014. A ducal seal, considered to be the lost seal detached from the Incorporation Charter, was found in the sphragistic collection after nearly 500 years. Unfortunately, it was uncertain whether the seal in question was indeed the missing part of the document. The aim of the study presented below was to solve this mystery. For this purpose, the parchment on which the Incorporation Charter was written was compared with the fragment of the parchment attached to the discovered seal. The study involved the analysis of selected mitochondrial DNA sequences and additional analysis at the level of nuclear DNA using microsatellite markers in the form of 11 STR (Short Tandem Repeat) loci, to identify the species and individual whose skin had been used to make the parchment. This analysis revealed that seal and parchment was from different individuals and thereby discovered that the seal was never a part of the Incorporation Charter. The study is further an example of informative DNA preservation in cultural heritage objects.
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Affiliation(s)
- Tomasz Lech
- Department of Microbiology, Faculty of Commodity Science, Cracow University of Economics, Krakow, Poland
- * E-mail:
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Kyselicová K, Šebest L, Bognár C, Šarkan M, Baldovič M, Beňuš R, Kádaši Ľ. Molecular detection of Mycobacterium tuberculosis complex in the 8th century skeletal remains from the territory of Slovakia. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study. Mob DNA 2016; 7:7. [PMID: 27096009 PMCID: PMC4836192 DOI: 10.1186/s13100-016-0063-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/31/2016] [Indexed: 01/21/2023] Open
Abstract
Background As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter. Results For 26 of the 30 Alu loci investigated, definite results were obtained. We were able to demonstrate that presence/absence analyses of Alu elements can be conducted on individuals who lived 3,000 years ago. The preservation of the ancient DNA (aDNA) is good enough in two out of three ancient individuals to routinely allow the amplification of 500 bp fragments. The third individual revealed less well-preserved DNA, which results in allelic dropout or complete amplification failures. We here present an alternative molecular approach to deal with these degradation phenomena by using internal Alu subfamily specific primers producing short fragments of approximately 150 bp. Conclusions Our data clearly show the possibility of presence/absence analyses of Alu elements in individuals from the Lichtenstein cave. Thus, we demonstrate that our method is reliably applicable for aDNA samples with good or moderate DNA preservation. This method will be very useful for further investigations with more Alu loci and larger datasets. Human population genetic studies and other large-scale investigations would provide insight into Alu SINE-based microevolutionary processes in humans during the last few thousand years and help us comprehend the evolutionary dynamics of our genome. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0063-y) contains supplementary material, which is available to authorized users.
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Rannamäe E, Lõugas L, Niemi M, Kantanen J, Maldre L, Kadõrova N, Saarma U. Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia. Anim Genet 2016; 47:208-18. [PMID: 26805771 DOI: 10.1111/age.12407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2015] [Indexed: 12/01/2022]
Abstract
Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations.
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Affiliation(s)
- E Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Jakobi 2, 51014, Tartu, Estonia
| | - L Lõugas
- Department of Archaeobiology, Institute of History, Tallinn University, Rüütli 6, 10130, Tallinn, Estonia
| | - M Niemi
- Department of Forensic Medicine, University of Helsinki, FI-00014, Helsinki, Finland.,Green Technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland.,Department of Biology, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - L Maldre
- Department of Archaeobiology, Institute of History, Tallinn University, Rüütli 6, 10130, Tallinn, Estonia
| | - N Kadõrova
- Department of Natural Sciences, Institute of Mathematics and Natural Sciences, Tallinn University, Narva Rd 25, 10120, Tallinn, Estonia
| | - U Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
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Abstract
In recent years the recovery and analysis of DNA from skeletal remains has been applied to several contexts ranging from disaster victim identification to the identification of the victims of conflict. Here are described procedures for processing the bone and tooth samples including mechanical and chemical cleaning, cutting and powdering in the presence of liquid nitrogen, complete demineralization of bone and tooth powder, DNA extraction, DNA purification using magnetic beads, and the precautions and strategies implemented to avoid and detect contamination. It has proven highly successful in the analysis of bones and teeth from Second World War victims' skeletal remains that have been excavated from mass graves in Slovenia and is also suitable for genetic identification of relatively fresh human remains.
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Affiliation(s)
- Irena Zupanič Pajnič
- Laboratory of Molecular Genetics, Institute of Forensic Medicine, Vrazov trg 2, 1104, Ljubljana, Slovenia.
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Zupanič Pajnič I, Debska M, Gornjak Pogorelc B, Vodopivec Mohorčič K, Balažic J, Zupanc T, Štefanič B, Geršak K. Highly efficient automated extraction of DNA from old and contemporary skeletal remains. J Forensic Leg Med 2016; 37:78-86. [DOI: 10.1016/j.jflm.2015.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/03/2015] [Indexed: 10/22/2022]
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Jakovski Z, Ajanovska RJ, Stankov A, Pavlovski G, Poposka V, Marjanovic D. Comparative study of two dna extraction methods in different tissues and conditions of degradation. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Restored teeth can be used as samples for genotyping? FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Alia-García E, Parra-Pecharromán D, Sánchez-Díaz A, Mendez S, Royuela A, Gil-Alberdi L, López-Palafox J, del Campo R. Forensic identification in teeth with caries. Forensic Sci Int 2015; 257:236-241. [DOI: 10.1016/j.forsciint.2015.08.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 08/05/2015] [Accepted: 08/24/2015] [Indexed: 11/24/2022]
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46
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Zaiko A, Martinez JL, Ardura A, Clusa L, Borrell YJ, Samuiloviene A, Roca A, Garcia-Vazquez E. Detecting nuisance species using NGST: Methodology shortcomings and possible application in ballast water monitoring. MARINE ENVIRONMENTAL RESEARCH 2015; 112:64-72. [PMID: 26174116 DOI: 10.1016/j.marenvres.2015.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 06/20/2015] [Accepted: 07/01/2015] [Indexed: 06/04/2023]
Abstract
Detecting the presence of potential invasive species in ballast water is a priority for preventing their spread into new environments. Next generation sequencing technologies are being increasingly used for exploring and assessing biodiversity from environmental samples. Here we apply high throughput sequencing from DNA extracted from ballast water (BW) samples employing two different platforms, Ion Torrent and 454, and compare the putative species catalogues from the resulting Operational Taxonomic Units (OTU). Water samples were taken from the RV Polastern ballast tank in five different days between the second and the twentieth navigation day. Pronounced decrease of oxygen concentration and increase of temperature occurred in the BW during this time, coincident with a progressively higher proportion of unassigned OTU and short reads indicating DNA degradation. Discrepancy between platforms for species catalogues was consistent with previously published bias in AT-rich sequences for Ion Torrent platform. Some putative species detected from the two platforms increased in frequency during the Polarstern travel, which suggests they were alive and therefore tolerant to adverse conditions. OTU assigned to the highly invasive red alga Polysiphonia have been detected at low but increasing frequency from the two platforms. Although in this moment NGST could not replace current methods of sampling, sorting and individual taxonomic identification of BW biota, it has potential as an exploratory methodology especially for detecting scarce species.
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Affiliation(s)
- Anastasija Zaiko
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand
| | - Jose L Martinez
- Sequencing Unit, Edificio Severo Ochoa, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Alba Ardura
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Laura Clusa
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Yaisel J Borrell
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Aurelija Samuiloviene
- Marine Science and Technology Center, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania; Department of Ecology and Biology, Klaipeda University, H. Manto 84, 92294 Klaipeda, Lithuania
| | - Agustín Roca
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain
| | - Eva Garcia-Vazquez
- Department of Functional Biology, C/ Julian Claveria s/n, University of Oviedo, Oviedo 33006, Spain.
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Tridico SR, Koch S, Michaud A, Thomson G, Kirkbride KP, Bunce M. Interpreting biological degradative processes acting on mammalian hair in the living and the dead: which ones are taphonomic? Proc Biol Sci 2015; 281:20141755. [PMID: 25339725 DOI: 10.1098/rspb.2014.1755] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the taphonomic (post-mortem) degradation processes relevant to teeth and bones have been well described, those taking place with regards to mammalian hairs have not been characterized to the same extent. This present article describes, in detail, microscopic changes resulting from the actions of biological agents that digest and degrade hairs. The most noteworthy and prevalent agents responsible for the destruction of hair structure are fungi, which use a range of strategies to invade and digest hairs. One of the most important finds to emerge from this study is that taphonomic structures and processes can easily be interpreted by the unwary as 'real', or as class characteristics for a particular animal taxon. Moreover, under certain conditions, 'taphonomic' processes normally associated with the dead are also present on the hairs of the living. This work will improve the reliability of hair examinations in forensic, archaeological and palaeontological applications-in addition, the finding has relevance in the protection of mammalian collections susceptible to infestation. This article also addresses the popular myth that ancient peoples were often red-haired and discusses phenomena responsible for this observation. Insights gained from detailed characterization of taphonomic processes in 95 hairs from a variety of species demonstrate the range and breadth of degradative effects on hair structure and colour. Lastly, the study demonstrates that hairs often tell a story and that there is value of extracting as much morphological data as possible from hairs, prior to destructive sampling for biomolecules.
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Affiliation(s)
- Silvana R Tridico
- Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, Australia School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Sandra Koch
- Department of Anthropology, The Pennsylvania State University, 403C Carpenter Building, University Park, PA 16801, USA
| | - Amy Michaud
- Bureau of Alcohol, Tobacco, Firearms and Explosives, 6000 Ammendale Road, Beltsville, MD 20705, USA
| | - Gordon Thomson
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - K Paul Kirkbride
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6845, Australia School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
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Nori DV, McCord BR. The application of alkaline lysis and pressure cycling technology in the differential extraction of DNA from sperm and epithelial cells recovered from cotton swabs. Anal Bioanal Chem 2015; 407:6975-84. [DOI: 10.1007/s00216-015-8737-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/14/2015] [Accepted: 04/24/2015] [Indexed: 10/23/2022]
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Smith RWA, Monroe C, Bolnick DA. Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing. PLoS One 2015; 10:e0125344. [PMID: 26016479 PMCID: PMC4445908 DOI: 10.1371/journal.pone.0125344] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/14/2015] [Indexed: 12/18/2022] Open
Abstract
While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.
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Affiliation(s)
- Rick W A Smith
- Department of Anthropology, University of Texas at Austin, Austin, Texas, United States of America
| | - Cara Monroe
- Department of Anthropology, Washington State University, Pullman, Washington, United States of America; Department of Anthropology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Deborah A Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas, United States of America; Population Research Center, University of Texas at Austin, Austin, Texas, United States of America
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Differential nuclear and mitochondrial DNA preservation in post-mortem teeth with implications for forensic and ancient DNA studies. PLoS One 2015; 10:e0126935. [PMID: 25992635 PMCID: PMC4438076 DOI: 10.1371/journal.pone.0126935] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/09/2015] [Indexed: 11/29/2022] Open
Abstract
Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Futhermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard extraction methods, without the need for specialised equipment or large-volume demineralisation steps.
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