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Aldeias V, Stahlschmidt MC. Sediment DNA can revolutionize archaeology-if it is used the right way. Proc Natl Acad Sci U S A 2024; 121:e2317042121. [PMID: 38900796 DOI: 10.1073/pnas.2317042121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Affiliation(s)
- Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour, Universidade do Algarve, Faro 8005-139, Portugal
| | - Mareike C Stahlschmidt
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1010, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna 1010, Austria
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2
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de Groot NF. A contextual integrity approach to genomic information: what bioethics can learn from big data ethics. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2024:10.1007/s11019-024-10211-0. [PMID: 38865053 DOI: 10.1007/s11019-024-10211-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/27/2024] [Indexed: 06/13/2024]
Abstract
Genomic data is generated, processed and analysed at an increasingly rapid pace. This data is not limited to the medical context, but plays an important role in other contexts in society, such as commercial DNA testing, the forensic setting, archaeological research, and genetic surveillance. Genomic information also crosses the borders of these domains, e.g. forensic use of medical genetic information, insurance use of medical genomic information, or research use of commercial genomic data. This paper (1) argues that an informed consent approach for genomic information has limitations in many societal contexts, and (2) seeks to broaden the bioethical debate on genomic information by suggesting an approach that is applicable across multiple societal contexts. I argue that the contextual integrity framework, a theory rooted in information technology and big data ethics, is an effective tool to explore ethical challenges that arise from genomic information within a variety of different contexts. Rather than focusing on individual control over information, the contextual integrity approach holds that information should be shared and protected according to the norms that govern certain distinct social contexts. Several advantages of this contextual integrity approach will be discussed. The paper concludes that the contextual integrity framework helps to articulate and address a broad spectrum of ethical, social, and political factors in a variety of different societal contexts, while giving consideration to the interests of individuals, groups, and society at large.
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Affiliation(s)
- Nina F de Groot
- Department of Philosophy, Faculty of Humanities, VU University Amsterdam, Amsterdam, the Netherlands.
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3
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Dass MA, Sherman CDH, van Oorschot RAH, Tuohey K, Hartman D, Carter G, Durdle A. Assessing eDNA capture method from aquatic environment to optimise recovery of human mt-eDNA. Forensic Sci Int 2024; 361:112085. [PMID: 38850619 DOI: 10.1016/j.forsciint.2024.112085] [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: 02/20/2024] [Revised: 05/05/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Previous studies have shown that environmental DNA (eDNA) from human sources can be recovered from natural bodies of water, and the generation of DNA profiles from such environmental samples may assist in forensic investigations. However, fundamental knowledge gaps exist around the factors influencing the probability of detecting human eDNA and the design of optimal sampling protocols. One of these is understanding the particle sizes eDNA signals are most strongly associated with and the most appropriate filter size needed for efficiently capturing eDNA particles. This study assessed the amount of mitochondrial eDNA associated with different particle sizes from human blood and skin cells recovered from freshwater samples. Samples (300 mL) were taken from experimental 10 L tanks of freshwater spiked with 50 µL of human blood or skin cells deposited by vigorously rubbing hands together for two minutes in freshwater. Subsamples were collected by passing 250 mL of experimental water sample through six different filter pore sizes (from 0.1 to 8 µm). This process was repeated at four time intervals after spiking over 72 hours to assess if the particle size of the amount of eDNA recovered changes as the eDNA degrades. Using a human-specific quantitative polymerase chain reaction (qPCR) assay targeting the HV1 mitochondrial gene region, the total amount of mitochondrial eDNA associated with different particle size fractions was determined. In the case of human blood, at 0 h, the 0.45 µm filter pore size captured the greatest amount of mitochondrial eDNA, capturing 42 % of the eDNA detected. The pattern then changed after 48 h, with the 5 µm filter pore size capturing the greatest amount of eDNA (67 %), and 81 % of eDNA at 72 h. Notably, a ten-fold dilution proved to be a valuable strategy for enhancing eDNA recovery from the 8 µm filter at all time points, primarily due to the PCR inhibition observed in hemoglobin. For human skin cells, the greatest amounts of eDNA were recovered from the 8 µm filter pore size and were consistent through time (capturing 37 %, 56 %, and 88 % of eDNA at 0 hours, 48 hours, and 72 hours respectively). There is a clear variation in the amount of eDNA recovered between different cell types, and in some forensic scenarios, there is likely to be a mix of cell types present. These results suggest it would be best to use a 5 µm filter pore size to capture human blood and an 8 µm filter pore size to capture human skin cells to maximize DNA recovery from freshwater samples. Depending on the cell type contributing to the eDNA, a combination of different filter pore sizes may be employed to optimize the recovery of human DNA from water samples. This study provides the groundwork for optimizing a strategy for the efficient recovery of human eDNA from aquatic environments, paving the way for its broader application in forensic and environmental sciences.
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Affiliation(s)
- Marie Antony Dass
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia.
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia; School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, VIC 3086, Australia
| | - Kate Tuohey
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia
| | - Dadna Hartman
- Victorian Institute of Forensic Medicine, Southbank, VIC 3006, Australia; Department of Forensic Medicine, Monash University, Southbank, VIC 3006, Australia
| | - Gemma Carter
- Victorian Institute of Forensic Medicine, Southbank, VIC 3006, Australia
| | - Annalisa Durdle
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3220, Australia; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC 3085, Australia
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4
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Goray M, Taylor D, Bibbo E, Fantinato C, Fonneløp AE, Gill P, van Oorschot RAH. Emerging use of air eDNA and its application to forensic investigations - A review. Electrophoresis 2024; 45:916-932. [PMID: 38419135 DOI: 10.1002/elps.202300228] [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: 10/11/2023] [Revised: 12/17/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024]
Abstract
Biological material is routinely collected at crime scenes and from exhibits and is a key type of evidence during criminal investigations. Improvements in DNA technologies allow collection and profiling of trace samples, comprised of few cells, significantly expanding the types of exhibits targeted for DNA analysis to include touched surfaces. However, success rates from trace and touch DNA samples tend to be poorer compared to other biological materials such as blood. Simultaneously, there have been recent advances in the utility of environmental DNA collection (eDNA) in identification and tracking of different biological organisms and species from bacteria to naked mole rats in different environments, including, soil, ice, snow, air and aquatic. This paper examines the emerging methods and research into eDNA collection, with a special emphasis on the potential forensic applications of human DNA collection from air including challenges and further studies required to progress implementation.
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Affiliation(s)
- Mariya Goray
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Duncan Taylor
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
- Forensic Science SA, Adelaide, South Australia, Australia
| | - Emily Bibbo
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Chiara Fantinato
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ane Elida Fonneløp
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Peter Gill
- Forensic Genetics Research Group, Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Roland A H van Oorschot
- Victoria Police Forensic Services Department, Office of Chief Forensic Scientist, Macleod, Victoria, Australia
- School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
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5
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Van Haeften S, Campbell BC, Milic A, Addison-Smith E, Al Kouba J, Huete A, Beggs PJ, Davies JM. Environmental DNA analysis of airborne poaceae (grass) pollen reveals taxonomic diversity across seasons and climate zones. ENVIRONMENTAL RESEARCH 2024; 247:117983. [PMID: 38163541 DOI: 10.1016/j.envres.2023.117983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Grasses populate most biogeographical zones, and their diversity influences allergic sensitisation to pollen. Previously, the contribution of different Poaceae subfamilies to airborne pollen has mostly been inferred from historical herbarium records. We recently applied environmental (e)DNA metabarcoding at one subtropical site revealing that successive airborne grass pollen peaks were derived from repeated flowering of Chloridoid and Panicoid grasses over a season. This study aimed to compare spatiotemporal patterns in grass pollen exposure across seasons and climate zones. METHODS Airborne pollen concentrations across two austral pollen seasons spanning 2017-2019 at subtropical (Mutdapilly and Rocklea, Queensland) and temperate (Macquarie Park and Richmond, New South Wales) sites, were determined with a routine volumetric impaction sampler and counting by light microscopy. Poaceae rbcL metabarcode sequences amplified from daily pollen samples collected once per week were assigned to subfamily and genus using a ribosomal classifier and compared with Atlas of Living Australia sighting records. RESULTS eDNA analysis revealed distinct dominance patterns of grass pollen at various sites: Panicoid grasses prevailed in both subtropical Mutdapilly and temperate Macquarie Park, whilst Chloridoid grasses dominated the subtropical Rocklea site. Overall, subtropical sites showed significantly higher proportion of pollen from Chloridoid grasses than temperate sites, whereas the temperate sites showed a significantly higher proportion of pollen from Pooideae grasses than subtropical sites. Timing of airborne Pooid (spring), Panicoid and Chloridoid (late spring to autumn), and Arundinoid (autumn) pollen were significantly related to number of days from mid-winter. Proportions of eDNA for subfamilies correlated with distributions grass sighting records between climate zones. CONCLUSIONS eDNA analysis enabled finer taxonomic discernment of Poaceae pollen records across seasons and climate zones with implications for understanding adaptation of grasslands to climate change, and the complexity of pollen exposure for patients with allergic respiratory diseases.
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Affiliation(s)
- Shanice Van Haeften
- School of Biomedical Sciences, Centre Immunology and Infection Control and Centre for Environment, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Bradley C Campbell
- School of Biomedical Sciences, Centre Immunology and Infection Control and Centre for Environment, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Andelija Milic
- School of Biomedical Sciences, Centre Immunology and Infection Control and Centre for Environment, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Elizabeth Addison-Smith
- School of Biomedical Sciences, Centre Immunology and Infection Control and Centre for Environment, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jane Al Kouba
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Alfredo Huete
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Paul J Beggs
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Janet M Davies
- School of Biomedical Sciences, Centre Immunology and Infection Control and Centre for Environment, Queensland University of Technology, Brisbane, Queensland, Australia.
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6
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DiEuliis D, Giordano JJ. Safely balancing a double-edged blade: identifying and mitigating emerging biosecurity risks in precision medicine. Front Med (Lausanne) 2024; 11:1364703. [PMID: 38572161 PMCID: PMC10987748 DOI: 10.3389/fmed.2024.1364703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/14/2024] [Indexed: 04/05/2024] Open
Abstract
Tools and methods of precision medicine are developing rapidly, through both iterative discoveries enabled by innovations in biomedical research (e.g., genome editing, synthetic biology, bioengineered devices). These are strengthened by advancements in information technology and the increasing body of data-as assimilated, analyzed, and made accessible-and affectable-through current and emerging cyber-and systems- technologies. Taken together, these approaches afford ever greater volume and availability of individual and collective human data. Machine learning and/or artificial intelligence approaches are broadening this dual use risk; and in the aftermath of COVID-19, there is growing incentive and impetus to gather more biological data from individuals and their environments on a routine basis. By engaging these data-and the interventions that are based upon them, precision medicine offer promise of highly individualized treatments for disease and injury, optimization of structure and function, and concomitantly, the potential for (mis) using data to incur harm. This double-edged blade of benefit and risk obligates the need to safeguard human data from purloinment, through systems, guidelines and policies of a novel discipline, cyberbiosecurity, which, as coupled to ethical precepts, aims to protect human privacy, agency, and safety in ways that remain apace with scientific and technological advances in biomedicine. Herein, current capabilities and trajectories precision medicine are described as relevant to their dual use potential, and approaches to biodata security (viz.- cyberbiosecurity) are proposed and discussed.
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Affiliation(s)
- Diane DiEuliis
- Center for the Study of Weapons of Mass Destruction, National Defense University, Washington, DC, United States
| | - James J Giordano
- Departments of Neurology and Biochemistry, Georgetown University Medical Center, Washington, DC, United States
- Defense Medical Ethics Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Simon Center for the Professional Military Ethic, United States Military Academy, West Point, NY, United States
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7
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Bernatchez L, Ferchaud AL, Berger CS, Venney CJ, Xuereb A. Genomics for monitoring and understanding species responses to global climate change. Nat Rev Genet 2024; 25:165-183. [PMID: 37863940 DOI: 10.1038/s41576-023-00657-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2023] [Indexed: 10/22/2023]
Abstract
All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species' evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
- Parks Canada, Office of the Chief Ecosystem Scientist, Protected Areas Establishment, Quebec City, Quebec, Canada.
| | - Chloé Suzanne Berger
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Amanda Xuereb
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
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8
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Wilkinson SP, Gault AA, Welsh SA, Smith JP, David BO, Hicks AS, Fake DR, Suren AM, Shaffer MR, Jarman SN, Bunce M. TICI: a taxon-independent community index for eDNA-based ecological health assessment. PeerJ 2024; 12:e16963. [PMID: 38426140 PMCID: PMC10903356 DOI: 10.7717/peerj.16963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.
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Affiliation(s)
- Shaun P. Wilkinson
- Wilderlab NZ Ltd., Wellington, New Zealand
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | | | | | - Joshua P. Smith
- School of Science, The University of Waikato, Hamilton, Waikato, New Zealand
- Waikato Regional Council, Hamilton, Waikato, New Zealand
| | - Bruno O. David
- Waikato Regional Council, Hamilton, Waikato, New Zealand
| | - Andy S. Hicks
- Ministry for the Environment, Wellington, New Zealand
- Hawke’s Bay Regional Council, Napier, Hawke’s Bay, New Zealand
| | - Daniel R. Fake
- Hawke’s Bay Regional Council, Napier, Hawke’s Bay, New Zealand
| | - Alastair M. Suren
- Bay of Plenty Regional Council, Tauranga, Bay of Plenty, New Zealand
| | - Megan R. Shaffer
- School of Marine and Environmental Affairs, University of Washington, Seattle, WA, United States of America
| | - Simon N. Jarman
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Michael Bunce
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Department of Conservation, Wellington, New Zealand
- School of Biomedical Sciences, University of Otago, Dunedin, Otago, New Zealand
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9
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McCauley M, Koda SA, Loesgen S, Duffy DJ. Multicellular species environmental DNA (eDNA) research constrained by overfocus on mitochondrial DNA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169550. [PMID: 38142009 DOI: 10.1016/j.scitotenv.2023.169550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Environmental DNA (eDNA) is becoming an established tool across the biological and medical sciences. Despite the evident successes and wide adoption of eDNA approaches, some fundamental questions remain. For instance, there is almost a dogma in the field around the superiority of mitochondrial DNA for use in eDNA studies, however robust comparison with nuclear eDNA is widely lacking. The dominance of mitochondrial-based eDNA for animal and plant studies appears to be largely settled, despite a widespread lack of rigorous nuclear eDNA testing. Outside of the source organism the protections conferred on eDNA by the cell, mitochondrial and nuclear membranes are poorly understood, including the contribution of each to eDNA persistence and degradation. Utilizing shotgun sequencing to unbiasedly assess the level of nuclear and mitochondrial eDNA across samples, we reveal stark differences in nuclear versus mitochondrial eDNA persistence and abundance. By focusing too heavily on mitochondrial DNA alone the field is underutilizing eDNA's full potential.
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Affiliation(s)
- Mark McCauley
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
| | - Samantha A Koda
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA
| | - Sandra Loesgen
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - David J Duffy
- The Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL 32080, USA; Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL 32611, USA
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10
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Knight T, Sureka S. A New Paradigm for Threat Agnostic Biodetection: Biological Intelligence (BIOINT). Health Secur 2024; 22:31-38. [PMID: 38054947 PMCID: PMC10902261 DOI: 10.1089/hs.2023.0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Affiliation(s)
- Thomas Knight
- Thomas Knight, PhD, is Co-Founder and Ginkgo Fellow, Ginkgo Bioworks, Boston, MA
| | - Swati Sureka
- Swati Sureka, MSc (Oxon, Edin), is Business Operations Manager; Ginkgo Bioworks, Boston, MA
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11
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Fantinato C, Fonneløp AE, Bleka Ø, Vigeland MD, Gill P. The invisible witness: air and dust as DNA evidence of human occupancy in indoor premises. Sci Rep 2023; 13:19059. [PMID: 37925517 PMCID: PMC10625553 DOI: 10.1038/s41598-023-46151-7] [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: 07/24/2023] [Accepted: 10/28/2023] [Indexed: 11/06/2023] Open
Abstract
Humans constantly shed deoxyribonucleic acid (DNA) into the surrounding environment. This DNA may either remain suspended in the air or it settles onto surfaces as indoor dust. In this study, we explored the potential use of human DNA recovered from air and dust to investigate crimes where there are no visible traces available-for example, from a recently vacated drugs factory where multiple workers had been present. Samples were collected from three indoor locations (offices, meeting rooms and laboratories) characterized by different occupancy types and cleaning regimes. The resultant DNA profiles were compared with the reference profiles of 55 occupants of the premises. Our findings showed that indoor dust samples are rich sources of DNA and provide an historical record of occupants within the specific locality of collection. Detectable levels of DNA were also observed in air and dust samples from ultra-clean forensic laboratories which can potentially contaminate casework samples. We provide a Bayesian statistical model to estimate the minimum number of dust samples needed to detect all inhabitants of a location. The results of this study suggest that air and dust could become novel sources of DNA evidence to identify current and past occupants of a crime scene.
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Affiliation(s)
- Chiara Fantinato
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.
- Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Ane Elida Fonneløp
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Øyvind Bleka
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
| | | | - Peter Gill
- Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway
- Department of Forensic Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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12
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Jordan B. [DNA everywhere]. Med Sci (Paris) 2023; 39:777-779. [PMID: 37943139 DOI: 10.1051/medsci/2023111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
Advanced analysis of environmental DNA for diversity monitoring using deep sequencing reveals the presence of human DNA in many samples connected to human activity.Moreover, this DNA is in relatively good condition and can be used for genetic survey of populations and even individuals. This opens many interesting scientific opportunities but also raises serious privacy issues.
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Affiliation(s)
- Bertrand Jordan
- Biologiste, généticien et immunologiste, Président d'Aprogène (Association pour la promotion de la Génomique), 13007 Marseille, France
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13
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Doi H, Kelly RP. Ethical considerations for human sequences in environmental DNA. Nat Ecol Evol 2023; 7:1334-1335. [PMID: 37414951 DOI: 10.1038/s41559-023-02124-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Affiliation(s)
- Hideyuki Doi
- Graduate School of Informatics, Kyoto University, Kyoto, Japan.
| | - Ryan P Kelly
- School of Marine & Environmental Affairs, University of Washington, Seattle, WA, USA.
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14
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Ram N. The ethics of human sequences in environmental samples. Nat Ecol Evol 2023:10.1038/s41559-023-02072-2. [PMID: 37188964 DOI: 10.1038/s41559-023-02072-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Natalie Ram
- University of Maryland Francis King Carey School of Law, Baltimore, MD, USA.
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